diff --git a/LICENSE b/LICENSE index 8dada3e..2b82bc8 100644 --- a/LICENSE +++ b/LICENSE @@ -186,7 +186,7 @@ same "printed page" as the copyright notice for easier identification within third-party archives. - Copyright {yyyy} {name of copyright owner} + Copyright {2016} {hogehoge} Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/build.sh b/build.sh index 9110491..809294f 100755 --- a/build.sh +++ b/build.sh @@ -1,2 +1,17 @@ +#******************************************************************************* +# Copyright 2016 Kaito Ii +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +#******************************************************************************* #!/bin/sh xjc -J-Duser.language=en -d src schema/CellDesigner.xsd schema/sbml-level-2-v4-wo-annotation.xsd schema/sbml-mathml.xsd schema/sbmlCellDesignerExtension_v4_2.xsd diff --git a/src/org/sbml/_2001/ns/celldesigner/AntisenseRNA.java b/src/org/sbml/_2001/ns/celldesigner/AntisenseRNA.java index c1c2fa7..526663b 100644 --- a/src/org/sbml/_2001/ns/celldesigner/AntisenseRNA.java +++ b/src/org/sbml/_2001/ns/celldesigner/AntisenseRNA.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * For antisense RNA. * @@ -62,12 +78,21 @@ }) public class AntisenseRNA { + /** The notes. */ protected Notes notes; + + /** The list of regions. */ protected ListOfRegions listOfRegions; + + /** The id. */ @XmlAttribute(name = "id", required = true) protected String id; + + /** The name. */ @XmlAttribute(name = "name", required = true) protected String name; + + /** The type. */ @XmlAttribute(name = "type", required = true) protected String type; diff --git a/src/org/sbml/_2001/ns/celldesigner/BaseProduct.java b/src/org/sbml/_2001/ns/celldesigner/BaseProduct.java index 274365d..28e9225 100644 --- a/src/org/sbml/_2001/ns/celldesigner/BaseProduct.java +++ b/src/org/sbml/_2001/ns/celldesigner/BaseProduct.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Base product. * @@ -48,9 +64,14 @@ }) public class BaseProduct { + /** The link anchor. */ protected LinkAnchor linkAnchor; + + /** The alias. */ @XmlAttribute(name = "alias", required = true) protected String alias; + + /** The species. */ @XmlAttribute(name = "species", required = true) protected String species; diff --git a/src/org/sbml/_2001/ns/celldesigner/BaseProducts.java b/src/org/sbml/_2001/ns/celldesigner/BaseProducts.java index e3f0f24..1d90ba0 100644 --- a/src/org/sbml/_2001/ns/celldesigner/BaseProducts.java +++ b/src/org/sbml/_2001/ns/celldesigner/BaseProducts.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * List of base products. * @@ -44,6 +60,7 @@ }) public class BaseProducts { + /** The base product. */ @XmlElement(required = true) protected List baseProduct; @@ -66,8 +83,8 @@ public class BaseProducts { *

* Objects of the following type(s) are allowed in the list * {@link BaseProduct } - * - * + * + * @return the base product */ public List getBaseProduct() { if (baseProduct == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/BaseReactant.java b/src/org/sbml/_2001/ns/celldesigner/BaseReactant.java index f759672..50679ec 100644 --- a/src/org/sbml/_2001/ns/celldesigner/BaseReactant.java +++ b/src/org/sbml/_2001/ns/celldesigner/BaseReactant.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Base reactant. * @@ -48,9 +64,14 @@ }) public class BaseReactant { + /** The link anchor. */ protected LinkAnchor linkAnchor; + + /** The alias. */ @XmlAttribute(name = "alias", required = true) protected String alias; + + /** The species. */ @XmlAttribute(name = "species", required = true) protected String species; diff --git a/src/org/sbml/_2001/ns/celldesigner/BaseReactants.java b/src/org/sbml/_2001/ns/celldesigner/BaseReactants.java index 5b0f889..1f49f82 100644 --- a/src/org/sbml/_2001/ns/celldesigner/BaseReactants.java +++ b/src/org/sbml/_2001/ns/celldesigner/BaseReactants.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * List of base reactants. * @@ -44,6 +60,7 @@ }) public class BaseReactants { + /** The base reactant. */ @XmlElement(required = true) protected List baseReactant; @@ -66,8 +83,8 @@ public class BaseReactants { *

* Objects of the following type(s) are allowed in the list * {@link BaseReactant } - * - * + * + * @return the base reactant */ public List getBaseReactant() { if (baseReactant == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/BindingRegion.java b/src/org/sbml/_2001/ns/celldesigner/BindingRegion.java index e469cc1..4d49a6e 100644 --- a/src/org/sbml/_2001/ns/celldesigner/BindingRegion.java +++ b/src/org/sbml/_2001/ns/celldesigner/BindingRegion.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for bindingRegion complex type. * @@ -40,12 +56,19 @@ @XmlType(name = "bindingRegion") public class BindingRegion { + /** The angle. */ @XmlAttribute(name = "angle") protected BigDecimal angle; + + /** The id. */ @XmlAttribute(name = "id") protected String id; + + /** The name. */ @XmlAttribute(name = "name") protected String name; + + /** The size. */ @XmlAttribute(name = "size") protected BigDecimal size; diff --git a/src/org/sbml/_2001/ns/celldesigner/BindingSiteInBlockDiagram.java b/src/org/sbml/_2001/ns/celldesigner/BindingSiteInBlockDiagram.java index 5a61f05..0d4283d 100644 --- a/src/org/sbml/_2001/ns/celldesigner/BindingSiteInBlockDiagram.java +++ b/src/org/sbml/_2001/ns/celldesigner/BindingSiteInBlockDiagram.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Binding site on the left side of a block(protein). * @@ -80,22 +96,34 @@ @XmlType(name = "bindingSiteInBlockDiagram") public class BindingSiteInBlockDiagram { + /** The id. */ @XmlAttribute(name = "id", required = true) protected short id; + + /** The offset Y. */ @XmlAttribute(name = "offsetY", required = true) protected BigDecimal offsetY; + + /** The name. */ @XmlAttribute(name = "name", required = true) protected String name; + + /** The name offset X. */ @XmlAttribute(name = "nameOffsetX", required = true) protected BigDecimal nameOffsetX; + + /** The name offset Y. */ @XmlAttribute(name = "nameOffsetY", required = true) protected BigDecimal nameOffsetY; + + /** The protein. */ @XmlAttribute(name = "protein", required = true) protected String protein; /** * Gets the value of the id property. - * + * + * @return the id */ public short getId() { return id; @@ -103,7 +131,8 @@ public short getId() { /** * Sets the value of the id property. - * + * + * @param value the new id */ public void setId(short value) { this.id = value; diff --git a/src/org/sbml/_2001/ns/celldesigner/Block.java b/src/org/sbml/_2001/ns/celldesigner/Block.java index 7905ba2..5bba179 100644 --- a/src/org/sbml/_2001/ns/celldesigner/Block.java +++ b/src/org/sbml/_2001/ns/celldesigner/Block.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Block(protein) on canvas. * @@ -78,22 +94,34 @@ @XmlType(name = "block") public class Block { + /** The width. */ @XmlAttribute(name = "width", required = true) protected short width; + + /** The height. */ @XmlAttribute(name = "height", required = true) protected short height; + + /** The x. */ @XmlAttribute(name = "x", required = true) protected short x; + + /** The y. */ @XmlAttribute(name = "y", required = true) protected short y; + + /** The name offset X. */ @XmlAttribute(name = "nameOffsetX", required = true) protected BigDecimal nameOffsetX; + + /** The name offset Y. */ @XmlAttribute(name = "nameOffsetY", required = true) protected BigDecimal nameOffsetY; /** * Gets the value of the width property. - * + * + * @return the width */ public short getWidth() { return width; @@ -101,7 +129,8 @@ public short getWidth() { /** * Sets the value of the width property. - * + * + * @param value the new width */ public void setWidth(short value) { this.width = value; @@ -109,7 +138,8 @@ public void setWidth(short value) { /** * Gets the value of the height property. - * + * + * @return the height */ public short getHeight() { return height; @@ -117,7 +147,8 @@ public short getHeight() { /** * Sets the value of the height property. - * + * + * @param value the new height */ public void setHeight(short value) { this.height = value; @@ -125,7 +156,8 @@ public void setHeight(short value) { /** * Gets the value of the x property. - * + * + * @return the x */ public short getX() { return x; @@ -133,7 +165,8 @@ public short getX() { /** * Sets the value of the x property. - * + * + * @param value the new x */ public void setX(short value) { this.x = value; @@ -141,7 +174,8 @@ public void setX(short value) { /** * Gets the value of the y property. - * + * + * @return the y */ public short getY() { return y; @@ -149,7 +183,8 @@ public short getY() { /** * Sets the value of the y property. - * + * + * @param value the new y */ public void setY(short value) { this.y = value; diff --git a/src/org/sbml/_2001/ns/celldesigner/BlockDiagram.java b/src/org/sbml/_2001/ns/celldesigner/BlockDiagram.java index 5a695c8..f70258a 100644 --- a/src/org/sbml/_2001/ns/celldesigner/BlockDiagram.java +++ b/src/org/sbml/_2001/ns/celldesigner/BlockDiagram.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -15,6 +30,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Block diagram for a protein. * @@ -66,25 +82,46 @@ }) public class BlockDiagram { + /** The canvas. */ @XmlElement(required = true) protected Canvas canvas; + + /** The block. */ @XmlElement(required = true) protected Block block; + + /** The halo. */ @XmlElement(required = true) protected Halo halo; + + /** The list of residues in block diagram. */ @XmlElement(required = true) protected ListOfResiduesInBlockDiagram listOfResiduesInBlockDiagram; + + /** The list of external names for residue. */ @XmlElement(required = true) protected ListOfExternalNamesForResidue listOfExternalNamesForResidue; + + /** The list of binding sites in block diagram. */ @XmlElement(required = true) protected ListOfBindingSitesInBlockDiagram listOfBindingSitesInBlockDiagram; + + /** The list of effect sites in block diagram. */ @XmlElement(required = true) protected ListOfEffectSitesInBlockDiagram listOfEffectSitesInBlockDiagram; + + /** The degraded in block diagram. */ protected DegradedInBlockDiagram degradedInBlockDiagram; + + /** The list of internal operators in block diagram. */ @XmlElement(required = true) protected ListOfInternalOperatorsInBlockDiagram listOfInternalOperatorsInBlockDiagram; + + /** The list of internal links in block diagram. */ @XmlElement(required = true) protected ListOfInternalLinksInBlockDiagram listOfInternalLinksInBlockDiagram; + + /** The protein. */ @XmlAttribute(name = "protein", required = true) protected String protein; diff --git a/src/org/sbml/_2001/ns/celldesigner/Bounds.java b/src/org/sbml/_2001/ns/celldesigner/Bounds.java index 9c75138..5617454 100644 --- a/src/org/sbml/_2001/ns/celldesigner/Bounds.java +++ b/src/org/sbml/_2001/ns/celldesigner/Bounds.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Bound of an object on canvas. * @@ -64,12 +80,19 @@ @XmlType(name = "bounds") public class Bounds { + /** The h. */ @XmlAttribute(name = "h", required = true) protected BigDecimal h; + + /** The w. */ @XmlAttribute(name = "w", required = true) protected BigDecimal w; + + /** The x. */ @XmlAttribute(name = "x", required = true) protected BigDecimal x; + + /** The y. */ @XmlAttribute(name = "y", required = true) protected BigDecimal y; diff --git a/src/org/sbml/_2001/ns/celldesigner/BoxSize.java b/src/org/sbml/_2001/ns/celldesigner/BoxSize.java index fe26d4d..06be041 100644 --- a/src/org/sbml/_2001/ns/celldesigner/BoxSize.java +++ b/src/org/sbml/_2001/ns/celldesigner/BoxSize.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Box size. Width and height. * @@ -52,8 +68,11 @@ @XmlType(name = "boxSize") public class BoxSize { + /** The height. */ @XmlAttribute(name = "height", required = true) protected BigDecimal height; + + /** The width. */ @XmlAttribute(name = "width", required = true) protected BigDecimal width; diff --git a/src/org/sbml/_2001/ns/celldesigner/BriefView.java b/src/org/sbml/_2001/ns/celldesigner/BriefView.java index df492a2..6088525 100644 --- a/src/org/sbml/_2001/ns/celldesigner/BriefView.java +++ b/src/org/sbml/_2001/ns/celldesigner/BriefView.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Data for drawing object with brief (compact) view. * @@ -47,12 +63,19 @@ }) public class BriefView { + /** The inner position. */ @XmlElement(required = true) protected InnerPosition innerPosition; + + /** The box size. */ @XmlElement(required = true) protected BoxSize boxSize; + + /** The single line. */ @XmlElement(required = true) protected SingleLine singleLine; + + /** The paint. */ @XmlElement(required = true) protected Paint paint; diff --git a/src/org/sbml/_2001/ns/celldesigner/Canvas.java b/src/org/sbml/_2001/ns/celldesigner/Canvas.java index 4ebf37f..a322dc3 100644 --- a/src/org/sbml/_2001/ns/celldesigner/Canvas.java +++ b/src/org/sbml/_2001/ns/celldesigner/Canvas.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Canvas size of block diagrams. * @@ -50,14 +66,18 @@ @XmlType(name = "canvas") public class Canvas { + /** The height. */ @XmlAttribute(name = "height", required = true) protected short height; + + /** The width. */ @XmlAttribute(name = "width", required = true) protected short width; /** * Gets the value of the height property. - * + * + * @return the height */ public short getHeight() { return height; @@ -65,7 +85,8 @@ public short getHeight() { /** * Sets the value of the height property. - * + * + * @param value the new height */ public void setHeight(short value) { this.height = value; @@ -73,7 +94,8 @@ public void setHeight(short value) { /** * Gets the value of the width property. - * + * + * @return the width */ public short getWidth() { return width; @@ -81,7 +103,8 @@ public short getWidth() { /** * Sets the value of the width property. - * + * + * @param value the new width */ public void setWidth(short value) { this.width = value; diff --git a/src/org/sbml/_2001/ns/celldesigner/Catalyzed.java b/src/org/sbml/_2001/ns/celldesigner/Catalyzed.java index 922d966..807e99f 100644 --- a/src/org/sbml/_2001/ns/celldesigner/Catalyzed.java +++ b/src/org/sbml/_2001/ns/celldesigner/Catalyzed.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Catalyzed reaction. * @@ -37,6 +53,7 @@ @XmlType(name = "catalyzed") public class Catalyzed { + /** The reaction. */ @XmlAttribute(name = "reaction", required = true) protected String reaction; diff --git a/src/org/sbml/_2001/ns/celldesigner/CompartmentAlias.java b/src/org/sbml/_2001/ns/celldesigner/CompartmentAlias.java index 7c625f6..b4f657f 100644 --- a/src/org/sbml/_2001/ns/celldesigner/CompartmentAlias.java +++ b/src/org/sbml/_2001/ns/celldesigner/CompartmentAlias.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -15,6 +30,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * For compartment aliases. * @@ -68,20 +84,37 @@ }) public class CompartmentAlias { + /** The clazz. */ @XmlElement(name = "class", required = true) protected String clazz; + + /** The bounds. */ protected Bounds bounds; + + /** The point. */ protected Point point; + + /** The name point. */ @XmlElement(required = true) protected Point namePoint; + + /** The double line. */ @XmlElement(required = true) protected DoubleLine doubleLine; + + /** The paint. */ @XmlElement(required = true) protected Paint paint; + + /** The info. */ @XmlElement(required = true) protected Info info; + + /** The compartment. */ @XmlAttribute(name = "compartment", required = true) protected String compartment; + + /** The id. */ @XmlAttribute(name = "id", required = true) protected String id; diff --git a/src/org/sbml/_2001/ns/celldesigner/CompartmentAnnotationType.java b/src/org/sbml/_2001/ns/celldesigner/CompartmentAnnotationType.java index 2f72f94..cd5bec5 100644 --- a/src/org/sbml/_2001/ns/celldesigner/CompartmentAnnotationType.java +++ b/src/org/sbml/_2001/ns/celldesigner/CompartmentAnnotationType.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Annotation for compartment. * @@ -51,6 +67,7 @@ }) public class CompartmentAnnotationType { + /** The extension. */ @XmlElement(required = true) protected CompartmentAnnotationType.Extension extension; @@ -104,6 +121,7 @@ public void setExtension(CompartmentAnnotationType.Extension value) { }) public static class Extension { + /** The name. */ @XmlElement(required = true) protected String name; diff --git a/src/org/sbml/_2001/ns/celldesigner/ComplexSpeciesAlias.java b/src/org/sbml/_2001/ns/celldesigner/ComplexSpeciesAlias.java index cba4002..2393e75 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ComplexSpeciesAlias.java +++ b/src/org/sbml/_2001/ns/celldesigner/ComplexSpeciesAlias.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * For species aliases of complex species. * @@ -86,28 +102,53 @@ }) public class ComplexSpeciesAlias { + /** The activity. */ @XmlElement(required = true) protected String activity; + + /** The bounds. */ @XmlElement(required = true) protected Bounds bounds; + + /** The view. */ @XmlElement(required = true) protected View view; + + /** The backup size. */ @XmlElement(required = true) protected ComplexSpeciesAlias.BackupSize backupSize; + + /** The backup view. */ @XmlElement(required = true) protected View backupView; + + /** The structural state. */ protected StructuralStateAngle structuralState; + + /** The usual view. */ @XmlElement(required = true) protected UsualView usualView; + + /** The brief view. */ @XmlElement(required = true) protected BriefView briefView; + + /** The list of species tag. */ protected ListOfSpeciesTag listOfSpeciesTag; + + /** The info. */ @XmlElement(required = true) protected Info info; + + /** The compartment alias. */ @XmlAttribute(name = "compartmentAlias") protected String compartmentAlias; + + /** The id. */ @XmlAttribute(name = "id", required = true) protected String id; + + /** The species. */ @XmlAttribute(name = "species", required = true) protected String species; @@ -446,8 +487,11 @@ public void setSpecies(String value) { @XmlType(name = "") public static class BackupSize { + /** The w. */ @XmlAttribute(name = "w") protected Double w; + + /** The h. */ @XmlAttribute(name = "h") protected Double h; diff --git a/src/org/sbml/_2001/ns/celldesigner/ConnectScheme.java b/src/org/sbml/_2001/ns/celldesigner/ConnectScheme.java index 288f150..52a1d48 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ConnectScheme.java +++ b/src/org/sbml/_2001/ns/celldesigner/ConnectScheme.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Connection scheme. * @@ -52,10 +68,15 @@ }) public class ConnectScheme { + /** The list of line direction. */ @XmlElement(required = true) protected ListOfLineDirection listOfLineDirection; + + /** The connect policy. */ @XmlAttribute(name = "connectPolicy", required = true) protected String connectPolicy; + + /** The rectangle index. */ @XmlAttribute(name = "rectangleIndex") @XmlSchemaType(name = "anySimpleType") protected String rectangleIndex; diff --git a/src/org/sbml/_2001/ns/celldesigner/DegradedInBlockDiagram.java b/src/org/sbml/_2001/ns/celldesigner/DegradedInBlockDiagram.java index 8b2b165..fc3dcfe 100644 --- a/src/org/sbml/_2001/ns/celldesigner/DegradedInBlockDiagram.java +++ b/src/org/sbml/_2001/ns/celldesigner/DegradedInBlockDiagram.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Degradation of a protein represented by the block. * @@ -57,10 +73,15 @@ }) public class DegradedInBlockDiagram { + /** The degraded shape in block diagram. */ @XmlElement(required = true) protected DegradedShapeInBlockDiagram degradedShapeInBlockDiagram; + + /** The id. */ @XmlAttribute(name = "id", required = true) protected short id; + + /** The offset Y. */ @XmlAttribute(name = "offsetY", required = true) protected BigDecimal offsetY; @@ -90,7 +111,8 @@ public void setDegradedShapeInBlockDiagram(DegradedShapeInBlockDiagram value) { /** * Gets the value of the id property. - * + * + * @return the id */ public short getId() { return id; @@ -98,7 +120,8 @@ public short getId() { /** * Sets the value of the id property. - * + * + * @param value the new id */ public void setId(short value) { this.id = value; diff --git a/src/org/sbml/_2001/ns/celldesigner/DegradedShapeInBlockDiagram.java b/src/org/sbml/_2001/ns/celldesigner/DegradedShapeInBlockDiagram.java index d1a8415..0f9b8c7 100644 --- a/src/org/sbml/_2001/ns/celldesigner/DegradedShapeInBlockDiagram.java +++ b/src/org/sbml/_2001/ns/celldesigner/DegradedShapeInBlockDiagram.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Degradation symbol. * @@ -64,18 +80,26 @@ @XmlType(name = "degradedShapeInBlockDiagram") public class DegradedShapeInBlockDiagram { + /** The width. */ @XmlAttribute(name = "width", required = true) protected short width; + + /** The height. */ @XmlAttribute(name = "height", required = true) protected short height; + + /** The offset X. */ @XmlAttribute(name = "offsetX", required = true) protected BigDecimal offsetX; + + /** The offset Y. */ @XmlAttribute(name = "offsetY", required = true) protected BigDecimal offsetY; /** * Gets the value of the width property. - * + * + * @return the width */ public short getWidth() { return width; @@ -83,7 +107,8 @@ public short getWidth() { /** * Sets the value of the width property. - * + * + * @param value the new width */ public void setWidth(short value) { this.width = value; @@ -91,7 +116,8 @@ public void setWidth(short value) { /** * Gets the value of the height property. - * + * + * @return the height */ public short getHeight() { return height; @@ -99,7 +125,8 @@ public short getHeight() { /** * Sets the value of the height property. - * + * + * @param value the new height */ public void setHeight(short value) { this.height = value; diff --git a/src/org/sbml/_2001/ns/celldesigner/DoubleLine.java b/src/org/sbml/_2001/ns/celldesigner/DoubleLine.java index 23cec18..f7f6e4e 100644 --- a/src/org/sbml/_2001/ns/celldesigner/DoubleLine.java +++ b/src/org/sbml/_2001/ns/celldesigner/DoubleLine.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Double line type to draw object. * @@ -59,10 +75,15 @@ @XmlType(name = "doubleLine") public class DoubleLine { + /** The inner width. */ @XmlAttribute(name = "innerWidth", required = true) protected BigDecimal innerWidth; + + /** The outer width. */ @XmlAttribute(name = "outerWidth", required = true) protected BigDecimal outerWidth; + + /** The thickness. */ @XmlAttribute(name = "thickness", required = true) protected BigDecimal thickness; diff --git a/src/org/sbml/_2001/ns/celldesigner/EditPoints.java b/src/org/sbml/_2001/ns/celldesigner/EditPoints.java index 9655520..20479a4 100644 --- a/src/org/sbml/_2001/ns/celldesigner/EditPoints.java +++ b/src/org/sbml/_2001/ns/celldesigner/EditPoints.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -18,6 +33,7 @@ import javax.xml.bind.annotation.XmlValue; +// TODO: Auto-generated Javadoc /** * Edit points. * @@ -77,16 +93,27 @@ }) public class EditPoints { + /** The value. */ @XmlValue protected List value; + + /** The num 0. */ @XmlAttribute(name = "num0") protected Short num0; + + /** The num 1. */ @XmlAttribute(name = "num1") protected Short num1; + + /** The num 2. */ @XmlAttribute(name = "num2") protected Short num2; + + /** The omitted shape index. */ @XmlAttribute(name = "omittedShapeIndex") protected Short omittedShapeIndex; + + /** The t shape index. */ @XmlAttribute(name = "tShapeIndex") protected Short tShapeIndex; @@ -109,8 +136,8 @@ public class EditPoints { *

* Objects of the following type(s) are allowed in the list * {@link String } - * - * + * + * @return the value */ public List getValue() { if (value == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/EffectInBlockDiagram.java b/src/org/sbml/_2001/ns/celldesigner/EffectInBlockDiagram.java index 92d6c0e..9a39bcd 100644 --- a/src/org/sbml/_2001/ns/celldesigner/EffectInBlockDiagram.java +++ b/src/org/sbml/_2001/ns/celldesigner/EffectInBlockDiagram.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -18,6 +33,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Type and targets of an effect. * @@ -53,8 +69,11 @@ }) public class EffectInBlockDiagram { + /** The effect target in block diagram. */ @XmlElement(required = true) protected List effectTargetInBlockDiagram; + + /** The type. */ @XmlAttribute(name = "type", required = true) protected String type; @@ -77,8 +96,8 @@ public class EffectInBlockDiagram { *

* Objects of the following type(s) are allowed in the list * {@link EffectTargetInBlockDiagram } - * - * + * + * @return the effect target in block diagram */ public List getEffectTargetInBlockDiagram() { if (effectTargetInBlockDiagram == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/EffectSiteInBlockDiagram.java b/src/org/sbml/_2001/ns/celldesigner/EffectSiteInBlockDiagram.java index 296639f..dff3a0b 100644 --- a/src/org/sbml/_2001/ns/celldesigner/EffectSiteInBlockDiagram.java +++ b/src/org/sbml/_2001/ns/celldesigner/EffectSiteInBlockDiagram.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Effect site on the lower side of a block(protein). * @@ -82,21 +98,38 @@ }) public class EffectSiteInBlockDiagram { + /** The effect in block diagram. */ protected EffectInBlockDiagram effectInBlockDiagram; + + /** The id. */ @XmlAttribute(name = "id", required = true) protected short id; + + /** The offset X. */ @XmlAttribute(name = "offsetX", required = true) protected BigDecimal offsetX; + + /** The offset Y. */ @XmlAttribute(name = "offsetY", required = true) protected BigDecimal offsetY; + + /** The name. */ @XmlAttribute(name = "name", required = true) protected String name; + + /** The name offset X. */ @XmlAttribute(name = "nameOffsetX", required = true) protected BigDecimal nameOffsetX; + + /** The name offset Y. */ @XmlAttribute(name = "nameOffsetY", required = true) protected BigDecimal nameOffsetY; + + /** The reaction. */ @XmlAttribute(name = "reaction") protected String reaction; + + /** The species. */ @XmlAttribute(name = "species") protected String species; @@ -126,7 +159,8 @@ public void setEffectInBlockDiagram(EffectInBlockDiagram value) { /** * Gets the value of the id property. - * + * + * @return the id */ public short getId() { return id; @@ -134,7 +168,8 @@ public short getId() { /** * Sets the value of the id property. - * + * + * @param value the new id */ public void setId(short value) { this.id = value; diff --git a/src/org/sbml/_2001/ns/celldesigner/EffectTargetInBlockDiagram.java b/src/org/sbml/_2001/ns/celldesigner/EffectTargetInBlockDiagram.java index 4534a8a..89619cf 100644 --- a/src/org/sbml/_2001/ns/celldesigner/EffectTargetInBlockDiagram.java +++ b/src/org/sbml/_2001/ns/celldesigner/EffectTargetInBlockDiagram.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Target protein of an effect. * @@ -42,6 +58,7 @@ @XmlType(name = "effectTargetInBlockDiagram") public class EffectTargetInBlockDiagram { + /** The protein. */ @XmlAttribute(name = "protein", required = true) protected String protein; diff --git a/src/org/sbml/_2001/ns/celldesigner/EndPointInBlockDiagram.java b/src/org/sbml/_2001/ns/celldesigner/EndPointInBlockDiagram.java index b2025f5..d1c9215 100644 --- a/src/org/sbml/_2001/ns/celldesigner/EndPointInBlockDiagram.java +++ b/src/org/sbml/_2001/ns/celldesigner/EndPointInBlockDiagram.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -18,6 +33,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * End point (residue, binding site, effect site, operator, link, degrade) of the link. * @@ -93,20 +109,35 @@ @XmlType(name = "endPointInBlockDiagram") public class EndPointInBlockDiagram { + /** The offset X. */ @XmlAttribute(name = "offsetX", required = true) protected List offsetX; + + /** The offset Y. */ @XmlAttribute(name = "offsetY", required = true) protected BigDecimal offsetY; + + /** The residue. */ @XmlAttribute(name = "residue") protected Short residue; + + /** The binding site. */ @XmlAttribute(name = "bindingSite") protected Short bindingSite; + + /** The effect site. */ @XmlAttribute(name = "effectSite") protected Short effectSite; + + /** The operator. */ @XmlAttribute(name = "operator") protected Short operator; + + /** The link. */ @XmlAttribute(name = "link") protected Short link; + + /** The degrade. */ @XmlAttribute(name = "degrade") protected Short degrade; @@ -129,8 +160,8 @@ public class EndPointInBlockDiagram { *

* Objects of the following type(s) are allowed in the list * {@link BigDecimal } - * - * + * + * @return the offset X */ public List getOffsetX() { if (offsetX == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ExternalConnectionInBlockDiagram.java b/src/org/sbml/_2001/ns/celldesigner/ExternalConnectionInBlockDiagram.java index 341f6c6..970834d 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ExternalConnectionInBlockDiagram.java +++ b/src/org/sbml/_2001/ns/celldesigner/ExternalConnectionInBlockDiagram.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * External connection to a residue. * @@ -58,16 +74,22 @@ @XmlType(name = "externalConnectionInBlockDiagram") public class ExternalConnectionInBlockDiagram { + /** The residue. */ @XmlAttribute(name = "residue", required = true) protected short residue; + + /** The type. */ @XmlAttribute(name = "type", required = true) protected String type; + + /** The predefined. */ @XmlAttribute(name = "predefined") protected Boolean predefined; /** * Gets the value of the residue property. - * + * + * @return the residue */ public short getResidue() { return residue; @@ -75,7 +97,8 @@ public short getResidue() { /** * Sets the value of the residue property. - * + * + * @param value the new residue */ public void setResidue(short value) { this.residue = value; diff --git a/src/org/sbml/_2001/ns/celldesigner/ExternalNameForResidue.java b/src/org/sbml/_2001/ns/celldesigner/ExternalNameForResidue.java index 0ac5e4b..960006b 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ExternalNameForResidue.java +++ b/src/org/sbml/_2001/ns/celldesigner/ExternalNameForResidue.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * External protein name connecting to residues. * @@ -81,18 +97,31 @@ }) public class ExternalNameForResidue { + /** The list of external connections in block diagram. */ @XmlElement(required = true) protected ListOfExternalConnectionsInBlockDiagram listOfExternalConnectionsInBlockDiagram; + + /** The id. */ @XmlAttribute(name = "id", required = true) protected short id; + + /** The offset Y. */ @XmlAttribute(name = "offsetY", required = true) protected BigDecimal offsetY; + + /** The name. */ @XmlAttribute(name = "name", required = true) protected String name; + + /** The name offset X. */ @XmlAttribute(name = "nameOffsetX", required = true) protected BigDecimal nameOffsetX; + + /** The name offset Y. */ @XmlAttribute(name = "nameOffsetY", required = true) protected BigDecimal nameOffsetY; + + /** The protein. */ @XmlAttribute(name = "protein") protected String protein; @@ -122,7 +151,8 @@ public void setListOfExternalConnectionsInBlockDiagram(ListOfExternalConnections /** * Gets the value of the id property. - * + * + * @return the id */ public short getId() { return id; @@ -130,7 +160,8 @@ public short getId() { /** * Sets the value of the id property. - * + * + * @param value the new id */ public void setId(short value) { this.id = value; diff --git a/src/org/sbml/_2001/ns/celldesigner/Gene.java b/src/org/sbml/_2001/ns/celldesigner/Gene.java index 715d399..999b134 100644 --- a/src/org/sbml/_2001/ns/celldesigner/Gene.java +++ b/src/org/sbml/_2001/ns/celldesigner/Gene.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * For gene. * @@ -62,12 +78,21 @@ }) public class Gene { + /** The notes. */ protected Notes notes; + + /** The list of regions. */ protected ListOfRegions listOfRegions; + + /** The id. */ @XmlAttribute(name = "id", required = true) protected String id; + + /** The name. */ @XmlAttribute(name = "name", required = true) protected String name; + + /** The type. */ @XmlAttribute(name = "type", required = true) protected String type; diff --git a/src/org/sbml/_2001/ns/celldesigner/Group.java b/src/org/sbml/_2001/ns/celldesigner/Group.java index 210dcca..ed6cba7 100644 --- a/src/org/sbml/_2001/ns/celldesigner/Group.java +++ b/src/org/sbml/_2001/ns/celldesigner/Group.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Group of speciesAliases. * @@ -49,8 +65,11 @@ @XmlType(name = "group") public class Group { + /** The id. */ @XmlAttribute(name = "id", required = true) protected String id; + + /** The members. */ @XmlAttribute(name = "members", required = true) protected String members; diff --git a/src/org/sbml/_2001/ns/celldesigner/Halo.java b/src/org/sbml/_2001/ns/celldesigner/Halo.java index 56b0eb9..7eb8627 100644 --- a/src/org/sbml/_2001/ns/celldesigner/Halo.java +++ b/src/org/sbml/_2001/ns/celldesigner/Halo.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Halo around a block(protein). * @@ -64,18 +80,26 @@ @XmlType(name = "halo") public class Halo { + /** The width. */ @XmlAttribute(name = "width", required = true) protected short width; + + /** The height. */ @XmlAttribute(name = "height", required = true) protected short height; + + /** The x. */ @XmlAttribute(name = "x", required = true) protected short x; + + /** The y. */ @XmlAttribute(name = "y", required = true) protected short y; /** * Gets the value of the width property. - * + * + * @return the width */ public short getWidth() { return width; @@ -83,7 +107,8 @@ public short getWidth() { /** * Sets the value of the width property. - * + * + * @param value the new width */ public void setWidth(short value) { this.width = value; @@ -91,7 +116,8 @@ public void setWidth(short value) { /** * Gets the value of the height property. - * + * + * @return the height */ public short getHeight() { return height; @@ -99,7 +125,8 @@ public short getHeight() { /** * Sets the value of the height property. - * + * + * @param value the new height */ public void setHeight(short value) { this.height = value; @@ -107,7 +134,8 @@ public void setHeight(short value) { /** * Gets the value of the x property. - * + * + * @return the x */ public short getX() { return x; @@ -115,7 +143,8 @@ public short getX() { /** * Sets the value of the x property. - * + * + * @param value the new x */ public void setX(short value) { this.x = value; @@ -123,7 +152,8 @@ public void setX(short value) { /** * Gets the value of the y property. - * + * + * @return the y */ public short getY() { return y; @@ -131,7 +161,8 @@ public short getY() { /** * Sets the value of the y property. - * + * + * @param value the new y */ public void setY(short value) { this.y = value; diff --git a/src/org/sbml/_2001/ns/celldesigner/Info.java b/src/org/sbml/_2001/ns/celldesigner/Info.java index df195e7..13986f2 100644 --- a/src/org/sbml/_2001/ns/celldesigner/Info.java +++ b/src/org/sbml/_2001/ns/celldesigner/Info.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for info complex type. * @@ -40,12 +56,19 @@ @XmlType(name = "info") public class Info { + /** The state. */ @XmlAttribute(name = "state") protected String state; + + /** The prefix. */ @XmlAttribute(name = "prefix") protected String prefix; + + /** The label. */ @XmlAttribute(name = "label") protected String label; + + /** The angle. */ @XmlAttribute(name = "angle", required = true) protected BigDecimal angle; diff --git a/src/org/sbml/_2001/ns/celldesigner/InnerPosition.java b/src/org/sbml/_2001/ns/celldesigner/InnerPosition.java index 05e3eeb..1816774 100644 --- a/src/org/sbml/_2001/ns/celldesigner/InnerPosition.java +++ b/src/org/sbml/_2001/ns/celldesigner/InnerPosition.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Innerposition relative to a surrounding object. * @@ -50,8 +66,11 @@ @XmlType(name = "innerPosition") public class InnerPosition { + /** The x. */ @XmlAttribute(name = "x", required = true) protected BigDecimal x; + + /** The y. */ @XmlAttribute(name = "y", required = true) protected BigDecimal y; diff --git a/src/org/sbml/_2001/ns/celldesigner/InternalLinkInBlockDiagram.java b/src/org/sbml/_2001/ns/celldesigner/InternalLinkInBlockDiagram.java index 7cdb0d9..c158f09 100644 --- a/src/org/sbml/_2001/ns/celldesigner/InternalLinkInBlockDiagram.java +++ b/src/org/sbml/_2001/ns/celldesigner/InternalLinkInBlockDiagram.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -15,6 +30,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Link between operators, residues, binding sites, effect sites. and degradation. * @@ -61,12 +77,19 @@ }) public class InternalLinkInBlockDiagram { + /** The starting point in block diagram. */ @XmlElement(required = true) protected StartingPointInBlockDiagram startingPointInBlockDiagram; + + /** The end point in block diagram. */ @XmlElement(required = true) protected EndPointInBlockDiagram endPointInBlockDiagram; + + /** The id. */ @XmlAttribute(name = "id", required = true) protected short id; + + /** The type. */ @XmlAttribute(name = "type", required = true) protected String type; @@ -120,7 +143,8 @@ public void setEndPointInBlockDiagram(EndPointInBlockDiagram value) { /** * Gets the value of the id property. - * + * + * @return the id */ public short getId() { return id; @@ -128,7 +152,8 @@ public short getId() { /** * Sets the value of the id property. - * + * + * @param value the new id */ public void setId(short value) { this.id = value; diff --git a/src/org/sbml/_2001/ns/celldesigner/InternalOperatorInBlockDiagram.java b/src/org/sbml/_2001/ns/celldesigner/InternalOperatorInBlockDiagram.java index 08ef85f..491c93e 100644 --- a/src/org/sbml/_2001/ns/celldesigner/InternalOperatorInBlockDiagram.java +++ b/src/org/sbml/_2001/ns/celldesigner/InternalOperatorInBlockDiagram.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Operator inside of a block(protein) describing logic. * @@ -85,15 +101,26 @@ }) public class InternalOperatorInBlockDiagram { + /** The internal operator value in block diagram. */ protected InternalOperatorValueInBlockDiagram internalOperatorValueInBlockDiagram; + + /** The id. */ @XmlAttribute(name = "id", required = true) protected short id; + + /** The type. */ @XmlAttribute(name = "type", required = true) protected String type; + + /** The sub. */ @XmlAttribute(name = "sub") protected String sub; + + /** The offset X. */ @XmlAttribute(name = "offsetX", required = true) protected BigDecimal offsetX; + + /** The offset Y. */ @XmlAttribute(name = "offsetY", required = true) protected BigDecimal offsetY; @@ -123,7 +150,8 @@ public void setInternalOperatorValueInBlockDiagram(InternalOperatorValueInBlockD /** * Gets the value of the id property. - * + * + * @return the id */ public short getId() { return id; @@ -131,7 +159,8 @@ public short getId() { /** * Sets the value of the id property. - * + * + * @param value the new id */ public void setId(short value) { this.id = value; diff --git a/src/org/sbml/_2001/ns/celldesigner/InternalOperatorValueInBlockDiagram.java b/src/org/sbml/_2001/ns/celldesigner/InternalOperatorValueInBlockDiagram.java index 6c25be4..1c51cd4 100644 --- a/src/org/sbml/_2001/ns/celldesigner/InternalOperatorValueInBlockDiagram.java +++ b/src/org/sbml/_2001/ns/celldesigner/InternalOperatorValueInBlockDiagram.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Assigned value to the operator. * @@ -56,10 +72,15 @@ @XmlType(name = "internalOperatorValueInBlockDiagram") public class InternalOperatorValueInBlockDiagram { + /** The value. */ @XmlAttribute(name = "value", required = true) protected BigDecimal value; + + /** The offset X. */ @XmlAttribute(name = "offsetX", required = true) protected BigDecimal offsetX; + + /** The offset Y. */ @XmlAttribute(name = "offsetY", required = true) protected BigDecimal offsetY; diff --git a/src/org/sbml/_2001/ns/celldesigner/KeyInfo.java b/src/org/sbml/_2001/ns/celldesigner/KeyInfo.java index b022b5c..bfc7e6f 100644 --- a/src/org/sbml/_2001/ns/celldesigner/KeyInfo.java +++ b/src/org/sbml/_2001/ns/celldesigner/KeyInfo.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for KeyInfo complex type. * @@ -36,8 +52,11 @@ @XmlType(name = "KeyInfo") public class KeyInfo { + /** The name. */ @XmlAttribute(name = "name") protected String name; + + /** The direct. */ @XmlAttribute(name = "direct") protected String direct; diff --git a/src/org/sbml/_2001/ns/celldesigner/Layer.java b/src/org/sbml/_2001/ns/celldesigner/Layer.java index 884e8c3..03aecbc 100644 --- a/src/org/sbml/_2001/ns/celldesigner/Layer.java +++ b/src/org/sbml/_2001/ns/celldesigner/Layer.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -15,6 +30,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for layer complex type. * @@ -48,17 +64,30 @@ }) public class Layer { + /** The list of texts. */ protected ListOfTexts listOfTexts; + + /** The list of squares. */ protected ListOfSquares listOfSquares; + + /** The list of free lines. */ protected ListOfFreeLines listOfFreeLines; + + /** The id. */ @XmlAttribute(name = "id") @XmlSchemaType(name = "anySimpleType") protected String id; + + /** The name. */ @XmlAttribute(name = "name") @XmlSchemaType(name = "anySimpleType") protected String name; + + /** The locked. */ @XmlAttribute(name = "locked", required = true) protected boolean locked; + + /** The visible. */ @XmlAttribute(name = "visible", required = true) protected boolean visible; @@ -184,7 +213,8 @@ public void setName(String value) { /** * Gets the value of the locked property. - * + * + * @return true, if is locked */ public boolean isLocked() { return locked; @@ -192,7 +222,8 @@ public boolean isLocked() { /** * Sets the value of the locked property. - * + * + * @param value the new locked */ public void setLocked(boolean value) { this.locked = value; @@ -200,7 +231,8 @@ public void setLocked(boolean value) { /** * Gets the value of the visible property. - * + * + * @return true, if is visible */ public boolean isVisible() { return visible; @@ -208,7 +240,8 @@ public boolean isVisible() { /** * Sets the value of the visible property. - * + * + * @param value the new visible */ public void setVisible(boolean value) { this.visible = value; diff --git a/src/org/sbml/_2001/ns/celldesigner/LayerCompartmentAlias.java b/src/org/sbml/_2001/ns/celldesigner/LayerCompartmentAlias.java index 81409c3..37a617a 100644 --- a/src/org/sbml/_2001/ns/celldesigner/LayerCompartmentAlias.java +++ b/src/org/sbml/_2001/ns/celldesigner/LayerCompartmentAlias.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -15,6 +30,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for layerCompartmentAlias complex type. * @@ -50,10 +66,15 @@ }) public class LayerCompartmentAlias { + /** The bounds. */ @XmlElement(required = true) protected Bounds bounds; + + /** The paint. */ @XmlElement(required = true) protected Paint paint; + + /** The type. */ @XmlAttribute(name = "type", required = true) protected String type; diff --git a/src/org/sbml/_2001/ns/celldesigner/LayerFreeLine.java b/src/org/sbml/_2001/ns/celldesigner/LayerFreeLine.java index 735b45a..8412d36 100644 --- a/src/org/sbml/_2001/ns/celldesigner/LayerFreeLine.java +++ b/src/org/sbml/_2001/ns/celldesigner/LayerFreeLine.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -15,6 +30,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for layerFreeLine complex type. * @@ -44,12 +60,19 @@ }) public class LayerFreeLine { + /** The bounds. */ @XmlElement(required = true) protected LayerLineBounds bounds; + + /** The line. */ @XmlElement(required = true) protected Line line; + + /** The is arrow. */ @XmlAttribute(name = "isArrow") protected Boolean isArrow; + + /** The is dotted. */ @XmlAttribute(name = "isDotted") protected Boolean isDotted; diff --git a/src/org/sbml/_2001/ns/celldesigner/LayerLineBounds.java b/src/org/sbml/_2001/ns/celldesigner/LayerLineBounds.java index 92967f0..ef8934a 100644 --- a/src/org/sbml/_2001/ns/celldesigner/LayerLineBounds.java +++ b/src/org/sbml/_2001/ns/celldesigner/LayerLineBounds.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for layerLineBounds complex type. * @@ -40,12 +56,19 @@ @XmlType(name = "layerLineBounds") public class LayerLineBounds { + /** The sx. */ @XmlAttribute(name = "sx") protected BigDecimal sx; + + /** The sy. */ @XmlAttribute(name = "sy") protected BigDecimal sy; + + /** The ex. */ @XmlAttribute(name = "ex") protected BigDecimal ex; + + /** The ey. */ @XmlAttribute(name = "ey") protected BigDecimal ey; diff --git a/src/org/sbml/_2001/ns/celldesigner/LayerSpeciesAlias.java b/src/org/sbml/_2001/ns/celldesigner/LayerSpeciesAlias.java index b792f3e..c97f2a4 100644 --- a/src/org/sbml/_2001/ns/celldesigner/LayerSpeciesAlias.java +++ b/src/org/sbml/_2001/ns/celldesigner/LayerSpeciesAlias.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for layerSpeciesAlias complex type. * @@ -60,20 +76,35 @@ }) public class LayerSpeciesAlias { + /** The layer notes. */ @XmlElement(required = true) protected String layerNotes; + + /** The bounds. */ @XmlElement(required = true) protected Bounds bounds; + + /** The paint. */ @XmlElement(required = true) protected Paint paint; + + /** The font. */ @XmlElement(required = true) protected LayerSpeciesAlias.Font font; + + /** The target. */ @XmlAttribute(name = "target", required = true) protected String target; + + /** The target id. */ @XmlAttribute(name = "targetId", required = true) protected String targetId; + + /** The x. */ @XmlAttribute(name = "x", required = true) protected BigDecimal x; + + /** The y. */ @XmlAttribute(name = "y", required = true) protected BigDecimal y; @@ -291,6 +322,7 @@ public void setY(BigDecimal value) { @XmlType(name = "") public static class Font { + /** The size. */ @XmlAttribute(name = "size") protected Integer size; diff --git a/src/org/sbml/_2001/ns/celldesigner/Line.java b/src/org/sbml/_2001/ns/celldesigner/Line.java index b859476..95e54ca 100644 --- a/src/org/sbml/_2001/ns/celldesigner/Line.java +++ b/src/org/sbml/_2001/ns/celldesigner/Line.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Line color and width. * @@ -52,8 +68,11 @@ @XmlType(name = "line") public class Line { + /** The color. */ @XmlAttribute(name = "color", required = true) protected String color; + + /** The width. */ @XmlAttribute(name = "width", required = true) protected BigDecimal width; diff --git a/src/org/sbml/_2001/ns/celldesigner/LineDirection.java b/src/org/sbml/_2001/ns/celldesigner/LineDirection.java index 991d05a..31dbd38 100644 --- a/src/org/sbml/_2001/ns/celldesigner/LineDirection.java +++ b/src/org/sbml/_2001/ns/celldesigner/LineDirection.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Line direction designator. * @@ -60,16 +76,22 @@ @XmlType(name = "lineDirection") public class LineDirection { + /** The index. */ @XmlAttribute(name = "index", required = true) protected short index; + + /** The value. */ @XmlAttribute(name = "value", required = true) protected String value; + + /** The arm. */ @XmlAttribute(name = "arm") protected Short arm; /** * Gets the value of the index property. - * + * + * @return the index */ public short getIndex() { return index; @@ -77,7 +99,8 @@ public short getIndex() { /** * Sets the value of the index property. - * + * + * @param value the new index */ public void setIndex(short value) { this.index = value; diff --git a/src/org/sbml/_2001/ns/celldesigner/LineType2.java b/src/org/sbml/_2001/ns/celldesigner/LineType2.java index 114dd66..33ffd50 100644 --- a/src/org/sbml/_2001/ns/celldesigner/LineType2.java +++ b/src/org/sbml/_2001/ns/celldesigner/LineType2.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Line color, width and curve style. * @@ -60,10 +76,15 @@ @XmlType(name = "lineType2") public class LineType2 { + /** The color. */ @XmlAttribute(name = "color", required = true) protected String color; + + /** The width. */ @XmlAttribute(name = "width", required = true) protected BigDecimal width; + + /** The type. */ @XmlAttribute(name = "type", required = true) protected String type; diff --git a/src/org/sbml/_2001/ns/celldesigner/LinkAnchor.java b/src/org/sbml/_2001/ns/celldesigner/LinkAnchor.java index a11bc90..d668d2d 100644 --- a/src/org/sbml/_2001/ns/celldesigner/LinkAnchor.java +++ b/src/org/sbml/_2001/ns/celldesigner/LinkAnchor.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Link position designator to species alias. * @@ -58,6 +74,7 @@ @XmlType(name = "linkAnchor") public class LinkAnchor { + /** The position. */ @XmlAttribute(name = "position", required = true) protected String position; diff --git a/src/org/sbml/_2001/ns/celldesigner/LinkTarget.java b/src/org/sbml/_2001/ns/celldesigner/LinkTarget.java index 5ca186f..0c91ad6 100644 --- a/src/org/sbml/_2001/ns/celldesigner/LinkTarget.java +++ b/src/org/sbml/_2001/ns/celldesigner/LinkTarget.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -15,6 +30,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Target of a link. * @@ -49,10 +65,15 @@ }) public class LinkTarget { + /** The link anchor. */ @XmlElement(required = true) protected LinkAnchor linkAnchor; + + /** The alias. */ @XmlAttribute(name = "alias", required = true) protected String alias; + + /** The species. */ @XmlAttribute(name = "species", required = true) protected String species; diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfAntisenseRNAs.java b/src/org/sbml/_2001/ns/celldesigner/ListOfAntisenseRNAs.java index d5ed9be..1a76fb0 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfAntisenseRNAs.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfAntisenseRNAs.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * List of asRNAs. * @@ -44,6 +60,7 @@ }) public class ListOfAntisenseRNAs { + /** The antisense RNA. */ @XmlElement(name = "AntisenseRNA") protected List antisenseRNA; @@ -66,8 +83,8 @@ public class ListOfAntisenseRNAs { *

* Objects of the following type(s) are allowed in the list * {@link AntisenseRNA } - * - * + * + * @return the antisense RNA */ public List getAntisenseRNA() { if (antisenseRNA == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfBindingRegions.java b/src/org/sbml/_2001/ns/celldesigner/ListOfBindingRegions.java index 2a9ae82..d54d5c5 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfBindingRegions.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfBindingRegions.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for listOfBindingRegions complex type. * @@ -42,6 +58,7 @@ }) public class ListOfBindingRegions { + /** The binding region. */ @XmlElement(required = true) protected List bindingRegion; @@ -64,8 +81,8 @@ public class ListOfBindingRegions { *

* Objects of the following type(s) are allowed in the list * {@link BindingRegion } - * - * + * + * @return the binding region */ public List getBindingRegion() { if (bindingRegion == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfBindingSitesInBlockDiagram.java b/src/org/sbml/_2001/ns/celldesigner/ListOfBindingSitesInBlockDiagram.java index 28a5924..b217447 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfBindingSitesInBlockDiagram.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfBindingSitesInBlockDiagram.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * List of binding sites of a block(protein). * @@ -43,6 +59,7 @@ }) public class ListOfBindingSitesInBlockDiagram { + /** The binding site in block diagram. */ protected List bindingSiteInBlockDiagram; /** @@ -64,8 +81,8 @@ public class ListOfBindingSitesInBlockDiagram { *

* Objects of the following type(s) are allowed in the list * {@link BindingSiteInBlockDiagram } - * - * + * + * @return the binding site in block diagram */ public List getBindingSiteInBlockDiagram() { if (bindingSiteInBlockDiagram == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfBlockDiagrams.java b/src/org/sbml/_2001/ns/celldesigner/ListOfBlockDiagrams.java index ee92118..d17e098 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfBlockDiagrams.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfBlockDiagrams.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * List of block diagrams. * @@ -43,6 +59,7 @@ }) public class ListOfBlockDiagrams { + /** The block diagram. */ protected List blockDiagram; /** @@ -64,8 +81,8 @@ public class ListOfBlockDiagrams { *

* Objects of the following type(s) are allowed in the list * {@link BlockDiagram } - * - * + * + * @return the block diagram */ public List getBlockDiagram() { if (blockDiagram == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfCatalyzedReactions.java b/src/org/sbml/_2001/ns/celldesigner/ListOfCatalyzedReactions.java index 5d1de77..6208a3d 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfCatalyzedReactions.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfCatalyzedReactions.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * List of catalyzed reaction. * @@ -44,6 +60,7 @@ }) public class ListOfCatalyzedReactions { + /** The catalyzed. */ @XmlElement(required = true) protected List catalyzed; @@ -66,8 +83,8 @@ public class ListOfCatalyzedReactions { *

* Objects of the following type(s) are allowed in the list * {@link Catalyzed } - * - * + * + * @return the catalyzed */ public List getCatalyzed() { if (catalyzed == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfCompartmentAliases.java b/src/org/sbml/_2001/ns/celldesigner/ListOfCompartmentAliases.java index d32e909..10161fa 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfCompartmentAliases.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfCompartmentAliases.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * List of compartment aliases. * @@ -43,6 +59,7 @@ }) public class ListOfCompartmentAliases { + /** The compartment alias. */ protected List compartmentAlias; /** @@ -64,8 +81,8 @@ public class ListOfCompartmentAliases { *

* Objects of the following type(s) are allowed in the list * {@link CompartmentAlias } - * - * + * + * @return the compartment alias */ public List getCompartmentAlias() { if (compartmentAlias == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfComplexSpeciesAliases.java b/src/org/sbml/_2001/ns/celldesigner/ListOfComplexSpeciesAliases.java index 5ddd377..bc2928e 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfComplexSpeciesAliases.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfComplexSpeciesAliases.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * List of complex species aliases. * @@ -52,6 +68,7 @@ }) public class ListOfComplexSpeciesAliases { + /** The complex species alias. */ protected List complexSpeciesAlias; /** @@ -73,8 +90,8 @@ public class ListOfComplexSpeciesAliases { *

* Objects of the following type(s) are allowed in the list * {@link ListOfComplexSpeciesAliases.ComplexSpeciesAlias } - * - * + * + * @return the complex species alias */ public List getComplexSpeciesAlias() { if (complexSpeciesAlias == null) { @@ -107,6 +124,7 @@ public static class ComplexSpeciesAlias extends org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias { + /** The complex species alias. */ @XmlAttribute(name = "complexSpeciesAlias") protected String complexSpeciesAlias; diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfEffectSitesInBlockDiagram.java b/src/org/sbml/_2001/ns/celldesigner/ListOfEffectSitesInBlockDiagram.java index 5a8eec1..cba52e8 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfEffectSitesInBlockDiagram.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfEffectSitesInBlockDiagram.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * List of effect sites. * @@ -43,6 +59,7 @@ }) public class ListOfEffectSitesInBlockDiagram { + /** The effect site in block diagram. */ protected List effectSiteInBlockDiagram; /** @@ -64,8 +81,8 @@ public class ListOfEffectSitesInBlockDiagram { *

* Objects of the following type(s) are allowed in the list * {@link EffectSiteInBlockDiagram } - * - * + * + * @return the effect site in block diagram */ public List getEffectSiteInBlockDiagram() { if (effectSiteInBlockDiagram == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfExternalConnectionsInBlockDiagram.java b/src/org/sbml/_2001/ns/celldesigner/ListOfExternalConnectionsInBlockDiagram.java index 694be89..a758b9a 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfExternalConnectionsInBlockDiagram.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfExternalConnectionsInBlockDiagram.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * List of external connections to residues. * @@ -44,6 +60,7 @@ }) public class ListOfExternalConnectionsInBlockDiagram { + /** The external connection in block diagram. */ @XmlElement(required = true) protected List externalConnectionInBlockDiagram; @@ -66,8 +83,8 @@ public class ListOfExternalConnectionsInBlockDiagram { *

* Objects of the following type(s) are allowed in the list * {@link ExternalConnectionInBlockDiagram } - * - * + * + * @return the external connection in block diagram */ public List getExternalConnectionInBlockDiagram() { if (externalConnectionInBlockDiagram == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfExternalNamesForResidue.java b/src/org/sbml/_2001/ns/celldesigner/ListOfExternalNamesForResidue.java index 71ec151..2196652 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfExternalNamesForResidue.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfExternalNamesForResidue.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * List of external names. * @@ -43,6 +59,7 @@ }) public class ListOfExternalNamesForResidue { + /** The external name for residue. */ protected List externalNameForResidue; /** @@ -64,8 +81,8 @@ public class ListOfExternalNamesForResidue { *

* Objects of the following type(s) are allowed in the list * {@link ExternalNameForResidue } - * - * + * + * @return the external name for residue */ public List getExternalNameForResidue() { if (externalNameForResidue == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfFreeLines.java b/src/org/sbml/_2001/ns/celldesigner/ListOfFreeLines.java index b41981f..afd47f5 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfFreeLines.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfFreeLines.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for listOfFreeLines complex type. * @@ -42,6 +58,7 @@ }) public class ListOfFreeLines { + /** The layer free line. */ @XmlElement(required = true) protected List layerFreeLine; @@ -64,8 +81,8 @@ public class ListOfFreeLines { *

* Objects of the following type(s) are allowed in the list * {@link LayerFreeLine } - * - * + * + * @return the layer free line */ public List getLayerFreeLine() { if (layerFreeLine == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfGenes.java b/src/org/sbml/_2001/ns/celldesigner/ListOfGenes.java index 715562a..3381fb4 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfGenes.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfGenes.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * List of genes. * @@ -43,6 +59,7 @@ }) public class ListOfGenes { + /** The gene. */ protected List gene; /** @@ -64,8 +81,8 @@ public class ListOfGenes { *

* Objects of the following type(s) are allowed in the list * {@link Gene } - * - * + * + * @return the gene */ public List getGene() { if (gene == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfGroups.java b/src/org/sbml/_2001/ns/celldesigner/ListOfGroups.java index 8da6949..fedc651 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfGroups.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfGroups.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * List of groups. * @@ -43,6 +59,7 @@ }) public class ListOfGroups { + /** The group. */ protected List group; /** @@ -64,8 +81,8 @@ public class ListOfGroups { *

* Objects of the following type(s) are allowed in the list * {@link Group } - * - * + * + * @return the group */ public List getGroup() { if (group == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfIncludedSpecies.java b/src/org/sbml/_2001/ns/celldesigner/ListOfIncludedSpecies.java index 94a0745..e8dda67 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfIncludedSpecies.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfIncludedSpecies.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * List of species included by complexes. * @@ -44,6 +60,7 @@ }) public class ListOfIncludedSpecies { + /** The species. */ @XmlElement(required = true) protected List species; @@ -66,8 +83,8 @@ public class ListOfIncludedSpecies { *

* Objects of the following type(s) are allowed in the list * {@link Species } - * - * + * + * @return the species */ public List getSpecies() { if (species == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfInternalLinksInBlockDiagram.java b/src/org/sbml/_2001/ns/celldesigner/ListOfInternalLinksInBlockDiagram.java index d3868f8..a3105ff 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfInternalLinksInBlockDiagram.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfInternalLinksInBlockDiagram.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * List of links of a block(protein). * @@ -43,6 +59,7 @@ }) public class ListOfInternalLinksInBlockDiagram { + /** The internal link in block diagram. */ protected List internalLinkInBlockDiagram; /** @@ -64,8 +81,8 @@ public class ListOfInternalLinksInBlockDiagram { *

* Objects of the following type(s) are allowed in the list * {@link InternalLinkInBlockDiagram } - * - * + * + * @return the internal link in block diagram */ public List getInternalLinkInBlockDiagram() { if (internalLinkInBlockDiagram == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfInternalOperatorsInBlockDiagram.java b/src/org/sbml/_2001/ns/celldesigner/ListOfInternalOperatorsInBlockDiagram.java index 8eee133..f0dcd30 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfInternalOperatorsInBlockDiagram.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfInternalOperatorsInBlockDiagram.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * List of internal operators. * @@ -43,6 +59,7 @@ }) public class ListOfInternalOperatorsInBlockDiagram { + /** The internal operator in block diagram. */ protected List internalOperatorInBlockDiagram; /** @@ -64,8 +81,8 @@ public class ListOfInternalOperatorsInBlockDiagram { *

* Objects of the following type(s) are allowed in the list * {@link InternalOperatorInBlockDiagram } - * - * + * + * @return the internal operator in block diagram */ public List getInternalOperatorInBlockDiagram() { if (internalOperatorInBlockDiagram == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfLayers.java b/src/org/sbml/_2001/ns/celldesigner/ListOfLayers.java index ee2ad2a..924cee1 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfLayers.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfLayers.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for listOfLayers complex type. * @@ -42,6 +58,7 @@ }) public class ListOfLayers { + /** The layer. */ @XmlElement(required = true) protected List layer; @@ -64,8 +81,8 @@ public class ListOfLayers { *

* Objects of the following type(s) are allowed in the list * {@link Layer } - * - * + * + * @return the layer */ public List getLayer() { if (layer == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfLineDirection.java b/src/org/sbml/_2001/ns/celldesigner/ListOfLineDirection.java index 96f237a..647ed26 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfLineDirection.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfLineDirection.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * List of line direction. * @@ -44,6 +60,7 @@ }) public class ListOfLineDirection { + /** The line direction. */ @XmlElement(required = true) protected List lineDirection; @@ -66,8 +83,8 @@ public class ListOfLineDirection { *

* Objects of the following type(s) are allowed in the list * {@link LineDirection } - * - * + * + * @return the line direction */ public List getLineDirection() { if (lineDirection == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfModification.java b/src/org/sbml/_2001/ns/celldesigner/ListOfModification.java index 8a6cac0..4f0c3fa 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfModification.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfModification.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * List of line modification. * @@ -44,6 +60,7 @@ }) public class ListOfModification { + /** The modification. */ @XmlElement(required = true) protected List modification; @@ -66,8 +83,8 @@ public class ListOfModification { *

* Objects of the following type(s) are allowed in the list * {@link Modification } - * - * + * + * @return the modification */ public List getModification() { if (modification == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfModificationResidues.java b/src/org/sbml/_2001/ns/celldesigner/ListOfModificationResidues.java index ef61235..449f823 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfModificationResidues.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfModificationResidues.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * List of modification residues. * @@ -44,6 +60,7 @@ }) public class ListOfModificationResidues { + /** The modification residue. */ @XmlElement(required = true) protected List modificationResidue; @@ -66,8 +83,8 @@ public class ListOfModificationResidues { *

* Objects of the following type(s) are allowed in the list * {@link ModificationResidue } - * - * + * + * @return the modification residue */ public List getModificationResidue() { if (modificationResidue == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfModifications.java b/src/org/sbml/_2001/ns/celldesigner/ListOfModifications.java index 31dc36f..f587fe4 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfModifications.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfModifications.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -18,6 +33,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * List of residue modification. * @@ -72,6 +88,7 @@ }) public class ListOfModifications { + /** The modification. */ @XmlElement(required = true) protected List modification; @@ -94,8 +111,8 @@ public class ListOfModifications { *

* Objects of the following type(s) are allowed in the list * {@link ListOfModifications.Modification } - * - * + * + * @return the modification */ public List getModification() { if (modification == null) { @@ -145,8 +162,11 @@ public List getModification() { @XmlType(name = "") public static class Modification { + /** The residue. */ @XmlAttribute(name = "residue", required = true) protected String residue; + + /** The state. */ @XmlAttribute(name = "state", required = true) protected String state; diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfProductLinks.java b/src/org/sbml/_2001/ns/celldesigner/ListOfProductLinks.java index ae0d0b9..7e87080 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfProductLinks.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfProductLinks.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * List of product link types. * @@ -44,6 +60,7 @@ }) public class ListOfProductLinks { + /** The product link. */ @XmlElement(required = true) protected List productLink; @@ -66,8 +83,8 @@ public class ListOfProductLinks { *

* Objects of the following type(s) are allowed in the list * {@link ProductLink } - * - * + * + * @return the product link */ public List getProductLink() { if (productLink == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfProteins.java b/src/org/sbml/_2001/ns/celldesigner/ListOfProteins.java index 0398a1a..3d2182f 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfProteins.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfProteins.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * List of proteins. * @@ -43,6 +59,7 @@ }) public class ListOfProteins { + /** The protein. */ protected List protein; /** @@ -64,8 +81,8 @@ public class ListOfProteins { *

* Objects of the following type(s) are allowed in the list * {@link Protein } - * - * + * + * @return the protein */ public List getProtein() { if (protein == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfRNAs.java b/src/org/sbml/_2001/ns/celldesigner/ListOfRNAs.java index 60fab1d..53eef55 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfRNAs.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfRNAs.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * List of RNAs. * @@ -44,6 +60,7 @@ }) public class ListOfRNAs { + /** The rna. */ @XmlElement(name = "RNA") protected List rna; @@ -66,8 +83,8 @@ public class ListOfRNAs { *

* Objects of the following type(s) are allowed in the list * {@link RNA } - * - * + * + * @return the rna */ public List getRNA() { if (rna == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfReactantLinks.java b/src/org/sbml/_2001/ns/celldesigner/ListOfReactantLinks.java index d37a87b..4c522fa 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfReactantLinks.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfReactantLinks.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * List of reactant link types. * @@ -44,6 +60,7 @@ }) public class ListOfReactantLinks { + /** The reactant link. */ @XmlElement(required = true) protected List reactantLink; @@ -66,8 +83,8 @@ public class ListOfReactantLinks { *

* Objects of the following type(s) are allowed in the list * {@link ReactantLink } - * - * + * + * @return the reactant link */ public List getReactantLink() { if (reactantLink == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfRegions.java b/src/org/sbml/_2001/ns/celldesigner/ListOfRegions.java index 06e330c..be5df8c 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfRegions.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfRegions.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * List of regions. * @@ -51,6 +67,7 @@ }) public class ListOfRegions { + /** The region. */ @XmlElement(required = true) protected List region; @@ -73,8 +90,8 @@ public class ListOfRegions { *

* Objects of the following type(s) are allowed in the list * {@link ListOfRegions.Region } - * - * + * + * @return the region */ public List getRegion() { if (region == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfResiduesInBlockDiagram.java b/src/org/sbml/_2001/ns/celldesigner/ListOfResiduesInBlockDiagram.java index 65d2089..4246ec4 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfResiduesInBlockDiagram.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfResiduesInBlockDiagram.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * List of residues on a block(protein). * @@ -43,6 +59,7 @@ }) public class ListOfResiduesInBlockDiagram { + /** The residue in block diagram. */ protected List residueInBlockDiagram; /** @@ -64,8 +81,8 @@ public class ListOfResiduesInBlockDiagram { *

* Objects of the following type(s) are allowed in the list * {@link ResidueInBlockDiagram } - * - * + * + * @return the residue in block diagram */ public List getResidueInBlockDiagram() { if (residueInBlockDiagram == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfSpeciesAliases.java b/src/org/sbml/_2001/ns/celldesigner/ListOfSpeciesAliases.java index ac72c0c..9d16220 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfSpeciesAliases.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfSpeciesAliases.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * List of simple species aliases. * @@ -44,6 +60,7 @@ }) public class ListOfSpeciesAliases { + /** The species alias. */ @XmlElement(required = true) protected List speciesAlias; @@ -66,8 +83,8 @@ public class ListOfSpeciesAliases { *

* Objects of the following type(s) are allowed in the list * {@link SpeciesAlias } - * - * + * + * @return the species alias */ public List getSpeciesAlias() { if (speciesAlias == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfSpeciesTag.java b/src/org/sbml/_2001/ns/celldesigner/ListOfSpeciesTag.java index a94e2b7..e8fe5e2 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfSpeciesTag.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfSpeciesTag.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for listOfSpeciesTag complex type. * @@ -42,6 +58,7 @@ }) public class ListOfSpeciesTag { + /** The species tag. */ @XmlElement(name = "SpeciesTag", required = true) protected List speciesTag; @@ -64,8 +81,8 @@ public class ListOfSpeciesTag { *

* Objects of the following type(s) are allowed in the list * {@link SpeciesTag } - * - * + * + * @return the species tag */ public List getSpeciesTag() { if (speciesTag == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfSquares.java b/src/org/sbml/_2001/ns/celldesigner/ListOfSquares.java index e2b3e61..84d65be 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfSquares.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfSquares.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for listOfSquares complex type. * @@ -42,6 +58,7 @@ }) public class ListOfSquares { + /** The layer compartment alias. */ @XmlElement(required = true) protected List layerCompartmentAlias; @@ -64,8 +81,8 @@ public class ListOfSquares { *

* Objects of the following type(s) are allowed in the list * {@link LayerCompartmentAlias } - * - * + * + * @return the layer compartment alias */ public List getLayerCompartmentAlias() { if (layerCompartmentAlias == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfStructuralStates.java b/src/org/sbml/_2001/ns/celldesigner/ListOfStructuralStates.java index 100a49f..0e32566 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfStructuralStates.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfStructuralStates.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for listOfStructuralStates complex type. * @@ -39,6 +55,7 @@ }) public class ListOfStructuralStates { + /** The structural state. */ @XmlElement(required = true) protected StructuralStates structuralState; diff --git a/src/org/sbml/_2001/ns/celldesigner/ListOfTexts.java b/src/org/sbml/_2001/ns/celldesigner/ListOfTexts.java index 14054d9..4fe0bd8 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ListOfTexts.java +++ b/src/org/sbml/_2001/ns/celldesigner/ListOfTexts.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for listOfTexts complex type. * @@ -42,6 +58,7 @@ }) public class ListOfTexts { + /** The layer species alias. */ @XmlElement(required = true) protected List layerSpeciesAlias; @@ -64,8 +81,8 @@ public class ListOfTexts { *

* Objects of the following type(s) are allowed in the list * {@link LayerSpeciesAlias } - * - * + * + * @return the layer species alias */ public List getLayerSpeciesAlias() { if (layerSpeciesAlias == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ModelAnnotationType.java b/src/org/sbml/_2001/ns/celldesigner/ModelAnnotationType.java index cf0473e..f15c435 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ModelAnnotationType.java +++ b/src/org/sbml/_2001/ns/celldesigner/ModelAnnotationType.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Annotation for model. * @@ -65,6 +81,7 @@ }) public class ModelAnnotationType { + /** The extension. */ @XmlElement(required = true) protected ModelAnnotationType.Extension extension; @@ -142,28 +159,53 @@ public void setExtension(ModelAnnotationType.Extension value) { }) public static class Extension { + /** The model version. */ @XmlElement(required = true) protected BigDecimal modelVersion; + + /** The model display. */ @XmlElement(required = true) protected ModelDisplay modelDisplay; + + /** The list of included species. */ protected ListOfIncludedSpecies listOfIncludedSpecies; + + /** The list of compartment aliases. */ @XmlElement(required = true) protected ListOfCompartmentAliases listOfCompartmentAliases; + + /** The list of complex species aliases. */ @XmlElement(required = true) protected ListOfComplexSpeciesAliases listOfComplexSpeciesAliases; + + /** The list of species aliases. */ @XmlElement(required = true) protected ListOfSpeciesAliases listOfSpeciesAliases; + + /** The list of groups. */ @XmlElement(required = true) protected ListOfGroups listOfGroups; + + /** The list of proteins. */ @XmlElement(required = true) protected ListOfProteins listOfProteins; + + /** The list of genes. */ @XmlElement(required = true) protected ListOfGenes listOfGenes; + + /** The list of RN as. */ @XmlElement(required = true) protected ListOfRNAs listOfRNAs; + + /** The list of antisense RN as. */ @XmlElement(required = true) protected ListOfAntisenseRNAs listOfAntisenseRNAs; + + /** The list of layers. */ protected ListOfLayers listOfLayers; + + /** The list of block diagrams. */ protected ListOfBlockDiagrams listOfBlockDiagrams; /** diff --git a/src/org/sbml/_2001/ns/celldesigner/ModelDisplay.java b/src/org/sbml/_2001/ns/celldesigner/ModelDisplay.java index 71661f2..168d2fa 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ModelDisplay.java +++ b/src/org/sbml/_2001/ns/celldesigner/ModelDisplay.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Model size, width and height. * @@ -50,14 +66,18 @@ @XmlType(name = "modelDisplay") public class ModelDisplay { + /** The size X. */ @XmlAttribute(name = "sizeX", required = true) protected short sizeX; + + /** The size Y. */ @XmlAttribute(name = "sizeY", required = true) protected short sizeY; /** * Gets the value of the sizeX property. - * + * + * @return the size X */ public short getSizeX() { return sizeX; @@ -65,7 +85,8 @@ public short getSizeX() { /** * Sets the value of the sizeX property. - * + * + * @param value the new size X */ public void setSizeX(short value) { this.sizeX = value; @@ -73,7 +94,8 @@ public void setSizeX(short value) { /** * Gets the value of the sizeY property. - * + * + * @return the size Y */ public short getSizeY() { return sizeY; @@ -81,7 +103,8 @@ public short getSizeY() { /** * Sets the value of the sizeY property. - * + * + * @param value the new size Y */ public void setSizeY(short value) { this.sizeY = value; diff --git a/src/org/sbml/_2001/ns/celldesigner/Modification.java b/src/org/sbml/_2001/ns/celldesigner/Modification.java index 1a8bc1e..2b5f74d 100644 --- a/src/org/sbml/_2001/ns/celldesigner/Modification.java +++ b/src/org/sbml/_2001/ns/celldesigner/Modification.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -19,6 +34,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Line modification. * @@ -145,29 +161,56 @@ }) public class Modification { + /** The connect scheme. */ protected ConnectScheme connectScheme; + + /** The link target. */ protected List linkTarget; + + /** The line. */ protected Line line; + + /** The aliases. */ @XmlAttribute(name = "aliases", required = true) protected String aliases; + + /** The modifiers. */ @XmlAttribute(name = "modifiers", required = true) protected String modifiers; + + /** The type. */ @XmlAttribute(name = "type", required = true) protected String type; + + /** The target line index. */ @XmlAttribute(name = "targetLineIndex", required = true) protected String targetLineIndex; + + /** The edit points. */ @XmlAttribute(name = "editPoints") protected List editPoints; + + /** The num 0. */ @XmlAttribute(name = "num0") protected BigInteger num0; + + /** The num 1. */ @XmlAttribute(name = "num1") protected BigInteger num1; + + /** The num 2. */ @XmlAttribute(name = "num2") protected BigInteger num2; + + /** The modification. */ @XmlAttribute(name = "modification") protected String modification; + + /** The offset X. */ @XmlAttribute(name = "offsetX") protected BigDecimal offsetX; + + /** The offset Y. */ @XmlAttribute(name = "offsetY") protected BigDecimal offsetY; @@ -214,8 +257,8 @@ public void setConnectScheme(ConnectScheme value) { *

* Objects of the following type(s) are allowed in the list * {@link LinkTarget } - * - * + * + * @return the link target */ public List getLinkTarget() { if (linkTarget == null) { @@ -363,8 +406,8 @@ public void setTargetLineIndex(String value) { *

* Objects of the following type(s) are allowed in the list * {@link String } - * - * + * + * @return the edits the points */ public List getEditPoints() { if (editPoints == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ModificationResidue.java b/src/org/sbml/_2001/ns/celldesigner/ModificationResidue.java index e3a72af..cb075ab 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ModificationResidue.java +++ b/src/org/sbml/_2001/ns/celldesigner/ModificationResidue.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * For modification residue of proteins. * @@ -60,12 +76,19 @@ @XmlType(name = "modificationResidue") public class ModificationResidue { + /** The id. */ @XmlAttribute(name = "id", required = true) protected String id; + + /** The name. */ @XmlAttribute(name = "name") protected String name; + + /** The angle. */ @XmlAttribute(name = "angle") protected BigDecimal angle; + + /** The side. */ @XmlAttribute(name = "side") @XmlSchemaType(name = "anySimpleType") protected String side; diff --git a/src/org/sbml/_2001/ns/celldesigner/Notes.java b/src/org/sbml/_2001/ns/celldesigner/Notes.java index ec9bc67..c3b1d0e 100644 --- a/src/org/sbml/_2001/ns/celldesigner/Notes.java +++ b/src/org/sbml/_2001/ns/celldesigner/Notes.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -19,6 +34,7 @@ import org.w3c.dom.Element; +// TODO: Auto-generated Javadoc /** * Notes as in sbml. * @@ -46,6 +62,7 @@ }) public class Notes { + /** The any. */ @XmlAnyElement protected List any; @@ -68,8 +85,8 @@ public class Notes { *

* Objects of the following type(s) are allowed in the list * {@link Element } - * - * + * + * @return the any */ public List getAny() { if (any == null) { diff --git a/src/org/sbml/_2001/ns/celldesigner/ObjectFactory.java b/src/org/sbml/_2001/ns/celldesigner/ObjectFactory.java index 61268e7..1fb134a 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ObjectFactory.java +++ b/src/org/sbml/_2001/ns/celldesigner/ObjectFactory.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.namespace.QName; +// TODO: Auto-generated Javadoc /** * This object contains factory methods for each * Java content interface and Java element interface @@ -34,19 +50,46 @@ @XmlRegistry public class ObjectFactory { + /** The Constant _ReactionType_QNAME. */ private final static QName _ReactionType_QNAME = new QName("http://www.sbml.org/2001/ns/celldesigner", "reactionType"); + + /** The Constant _Hypothetical_QNAME. */ private final static QName _Hypothetical_QNAME = new QName("http://www.sbml.org/2001/ns/celldesigner", "hypothetical"); + + /** The Constant _AntisensernaReference_QNAME. */ private final static QName _AntisensernaReference_QNAME = new QName("http://www.sbml.org/2001/ns/celldesigner", "antisensernaReference"); + + /** The Constant _ComplexSpecies_QNAME. */ private final static QName _ComplexSpecies_QNAME = new QName("http://www.sbml.org/2001/ns/celldesigner", "complexSpecies"); + + /** The Constant _Class_QNAME. */ private final static QName _Class_QNAME = new QName("http://www.sbml.org/2001/ns/celldesigner", "class"); + + /** The Constant _Homodimer_QNAME. */ private final static QName _Homodimer_QNAME = new QName("http://www.sbml.org/2001/ns/celldesigner", "homodimer"); + + /** The Constant _Name_QNAME. */ private final static QName _Name_QNAME = new QName("http://www.sbml.org/2001/ns/celldesigner", "name"); + + /** The Constant _Alias_QNAME. */ private final static QName _Alias_QNAME = new QName("http://www.sbml.org/2001/ns/celldesigner", "alias"); + + /** The Constant _Activity_QNAME. */ private final static QName _Activity_QNAME = new QName("http://www.sbml.org/2001/ns/celldesigner", "activity"); + + /** The Constant _ModelVersion_QNAME. */ private final static QName _ModelVersion_QNAME = new QName("http://www.sbml.org/2001/ns/celldesigner", "modelVersion"); + + /** The Constant _ProteinReference_QNAME. */ private final static QName _ProteinReference_QNAME = new QName("http://www.sbml.org/2001/ns/celldesigner", "proteinReference"); + + /** The Constant _RnaReference_QNAME. */ private final static QName _RnaReference_QNAME = new QName("http://www.sbml.org/2001/ns/celldesigner", "rnaReference"); + + /** The Constant _PositionToCompartment_QNAME. */ private final static QName _PositionToCompartment_QNAME = new QName("http://www.sbml.org/2001/ns/celldesigner", "positionToCompartment"); + + /** The Constant _GeneReference_QNAME. */ private final static QName _GeneReference_QNAME = new QName("http://www.sbml.org/2001/ns/celldesigner", "geneReference"); /** @@ -57,40 +100,45 @@ public ObjectFactory() { } /** - * Create an instance of {@link ListOfRegions } - * + * Create an instance of {@link ListOfRegions }. + * + * @return the list of regions */ public ListOfRegions createListOfRegions() { return new ListOfRegions(); } /** - * Create an instance of {@link LayerSpeciesAlias } - * + * Create an instance of {@link LayerSpeciesAlias }. + * + * @return the layer species alias */ public LayerSpeciesAlias createLayerSpeciesAlias() { return new LayerSpeciesAlias(); } /** - * Create an instance of {@link ListOfModifications } - * + * Create an instance of {@link ListOfModifications }. + * + * @return the list of modifications */ public ListOfModifications createListOfModifications() { return new ListOfModifications(); } /** - * Create an instance of {@link Species } - * + * Create an instance of {@link Species }. + * + * @return the species */ public Species createSpecies() { return new Species(); } /** - * Create an instance of {@link ListOfComplexSpeciesAliases } - * + * Create an instance of {@link ListOfComplexSpeciesAliases }. + * + * @return the list of complex species aliases */ public ListOfComplexSpeciesAliases createListOfComplexSpeciesAliases() { return new ListOfComplexSpeciesAliases(); @@ -98,639 +146,719 @@ public ListOfComplexSpeciesAliases createListOfComplexSpeciesAliases() { /** * Create an instance of {@link org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias } - * + * + * @return the complex species alias */ public org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias createComplexSpeciesAlias() { return new org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias(); } /** - * Create an instance of {@link ReactionAnnotationType } - * + * Create an instance of {@link ReactionAnnotationType }. + * + * @return the reaction annotation type */ public ReactionAnnotationType createReactionAnnotationType() { return new ReactionAnnotationType(); } /** - * Create an instance of {@link ModelAnnotationType } - * + * Create an instance of {@link ModelAnnotationType }. + * + * @return the model annotation type */ public ModelAnnotationType createModelAnnotationType() { return new ModelAnnotationType(); } /** - * Create an instance of {@link SpeciesAnnotationType } - * + * Create an instance of {@link SpeciesAnnotationType }. + * + * @return the species annotation type */ public SpeciesAnnotationType createSpeciesAnnotationType() { return new SpeciesAnnotationType(); } /** - * Create an instance of {@link CompartmentAnnotationType } - * + * Create an instance of {@link CompartmentAnnotationType }. + * + * @return the compartment annotation type */ public CompartmentAnnotationType createCompartmentAnnotationType() { return new CompartmentAnnotationType(); } /** - * Create an instance of {@link SpeciesReferenceAnnotationType } - * + * Create an instance of {@link SpeciesReferenceAnnotationType }. + * + * @return the species reference annotation type */ public SpeciesReferenceAnnotationType createSpeciesReferenceAnnotationType() { return new SpeciesReferenceAnnotationType(); } /** - * Create an instance of {@link ModelDisplay } - * + * Create an instance of {@link ModelDisplay }. + * + * @return the model display */ public ModelDisplay createModelDisplay() { return new ModelDisplay(); } /** - * Create an instance of {@link DoubleLine } - * + * Create an instance of {@link DoubleLine }. + * + * @return the double line */ public DoubleLine createDoubleLine() { return new DoubleLine(); } /** - * Create an instance of {@link ReactantLink } - * + * Create an instance of {@link ReactantLink }. + * + * @return the reactant link */ public ReactantLink createReactantLink() { return new ReactantLink(); } /** - * Create an instance of {@link ListOfAntisenseRNAs } - * + * Create an instance of {@link ListOfAntisenseRNAs }. + * + * @return the list of antisense RN as */ public ListOfAntisenseRNAs createListOfAntisenseRNAs() { return new ListOfAntisenseRNAs(); } /** - * Create an instance of {@link Paint } - * + * Create an instance of {@link Paint }. + * + * @return the paint */ public Paint createPaint() { return new Paint(); } /** - * Create an instance of {@link Halo } - * + * Create an instance of {@link Halo }. + * + * @return the halo */ public Halo createHalo() { return new Halo(); } /** - * Create an instance of {@link ListOfProteins } - * + * Create an instance of {@link ListOfProteins }. + * + * @return the list of proteins */ public ListOfProteins createListOfProteins() { return new ListOfProteins(); } /** - * Create an instance of {@link ListOfInternalOperatorsInBlockDiagram } - * + * Create an instance of {@link ListOfInternalOperatorsInBlockDiagram }. + * + * @return the list of internal operators in block diagram */ public ListOfInternalOperatorsInBlockDiagram createListOfInternalOperatorsInBlockDiagram() { return new ListOfInternalOperatorsInBlockDiagram(); } /** - * Create an instance of {@link InternalOperatorValueInBlockDiagram } - * + * Create an instance of {@link InternalOperatorValueInBlockDiagram }. + * + * @return the internal operator value in block diagram */ public InternalOperatorValueInBlockDiagram createInternalOperatorValueInBlockDiagram() { return new InternalOperatorValueInBlockDiagram(); } /** - * Create an instance of {@link StructuralStateAngle } - * + * Create an instance of {@link StructuralStateAngle }. + * + * @return the structural state angle */ public StructuralStateAngle createStructuralStateAngle() { return new StructuralStateAngle(); } /** - * Create an instance of {@link KeyInfo } - * + * Create an instance of {@link KeyInfo }. + * + * @return the key info */ public KeyInfo createKeyInfo() { return new KeyInfo(); } /** - * Create an instance of {@link Protein } - * + * Create an instance of {@link Protein }. + * + * @return the protein */ public Protein createProtein() { return new Protein(); } /** - * Create an instance of {@link Block } - * + * Create an instance of {@link Block }. + * + * @return the block */ public Block createBlock() { return new Block(); } /** - * Create an instance of {@link State } - * + * Create an instance of {@link State }. + * + * @return the state */ public State createState() { return new State(); } /** - * Create an instance of {@link ListOfFreeLines } - * + * Create an instance of {@link ListOfFreeLines }. + * + * @return the list of free lines */ public ListOfFreeLines createListOfFreeLines() { return new ListOfFreeLines(); } /** - * Create an instance of {@link ConnectScheme } - * + * Create an instance of {@link ConnectScheme }. + * + * @return the connect scheme */ public ConnectScheme createConnectScheme() { return new ConnectScheme(); } /** - * Create an instance of {@link BoxSize } - * + * Create an instance of {@link BoxSize }. + * + * @return the box size */ public BoxSize createBoxSize() { return new BoxSize(); } /** - * Create an instance of {@link Canvas } - * + * Create an instance of {@link Canvas }. + * + * @return the canvas */ public Canvas createCanvas() { return new Canvas(); } /** - * Create an instance of {@link ListOfBlockDiagrams } - * + * Create an instance of {@link ListOfBlockDiagrams }. + * + * @return the list of block diagrams */ public ListOfBlockDiagrams createListOfBlockDiagrams() { return new ListOfBlockDiagrams(); } /** - * Create an instance of {@link LayerLineBounds } - * + * Create an instance of {@link LayerLineBounds }. + * + * @return the layer line bounds */ public LayerLineBounds createLayerLineBounds() { return new LayerLineBounds(); } /** - * Create an instance of {@link Gene } - * + * Create an instance of {@link Gene }. + * + * @return the gene */ public Gene createGene() { return new Gene(); } /** - * Create an instance of {@link SingleLine } - * + * Create an instance of {@link SingleLine }. + * + * @return the single line */ public SingleLine createSingleLine() { return new SingleLine(); } /** - * Create an instance of {@link EffectTargetInBlockDiagram } - * + * Create an instance of {@link EffectTargetInBlockDiagram }. + * + * @return the effect target in block diagram */ public EffectTargetInBlockDiagram createEffectTargetInBlockDiagram() { return new EffectTargetInBlockDiagram(); } /** - * Create an instance of {@link InternalOperatorInBlockDiagram } - * + * Create an instance of {@link InternalOperatorInBlockDiagram }. + * + * @return the internal operator in block diagram */ public InternalOperatorInBlockDiagram createInternalOperatorInBlockDiagram() { return new InternalOperatorInBlockDiagram(); } /** - * Create an instance of {@link BaseReactant } - * + * Create an instance of {@link BaseReactant }. + * + * @return the base reactant */ public BaseReactant createBaseReactant() { return new BaseReactant(); } /** - * Create an instance of {@link ListOfIncludedSpecies } - * + * Create an instance of {@link ListOfIncludedSpecies }. + * + * @return the list of included species */ public ListOfIncludedSpecies createListOfIncludedSpecies() { return new ListOfIncludedSpecies(); } /** - * Create an instance of {@link EndPointInBlockDiagram } - * + * Create an instance of {@link EndPointInBlockDiagram }. + * + * @return the end point in block diagram */ public EndPointInBlockDiagram createEndPointInBlockDiagram() { return new EndPointInBlockDiagram(); } /** - * Create an instance of {@link ListOfSquares } - * + * Create an instance of {@link ListOfSquares }. + * + * @return the list of squares */ public ListOfSquares createListOfSquares() { return new ListOfSquares(); } /** - * Create an instance of {@link BaseReactants } - * + * Create an instance of {@link BaseReactants }. + * + * @return the base reactants */ public BaseReactants createBaseReactants() { return new BaseReactants(); } /** - * Create an instance of {@link Bounds } - * + * Create an instance of {@link Bounds }. + * + * @return the bounds */ public Bounds createBounds() { return new Bounds(); } /** - * Create an instance of {@link BriefView } - * + * Create an instance of {@link BriefView }. + * + * @return the brief view */ public BriefView createBriefView() { return new BriefView(); } /** - * Create an instance of {@link ListOfRNAs } - * + * Create an instance of {@link ListOfRNAs }. + * + * @return the list of RN as */ public ListOfRNAs createListOfRNAs() { return new ListOfRNAs(); } /** - * Create an instance of {@link LayerCompartmentAlias } - * + * Create an instance of {@link LayerCompartmentAlias }. + * + * @return the layer compartment alias */ public LayerCompartmentAlias createLayerCompartmentAlias() { return new LayerCompartmentAlias(); } /** - * Create an instance of {@link StructuralStates } - * + * Create an instance of {@link StructuralStates }. + * + * @return the structural states */ public StructuralStates createStructuralStates() { return new StructuralStates(); } /** - * Create an instance of {@link DegradedShapeInBlockDiagram } - * + * Create an instance of {@link DegradedShapeInBlockDiagram }. + * + * @return the degraded shape in block diagram */ public DegradedShapeInBlockDiagram createDegradedShapeInBlockDiagram() { return new DegradedShapeInBlockDiagram(); } /** - * Create an instance of {@link CompartmentAlias } - * + * Create an instance of {@link CompartmentAlias }. + * + * @return the compartment alias */ public CompartmentAlias createCompartmentAlias() { return new CompartmentAlias(); } /** - * Create an instance of {@link BlockDiagram } - * + * Create an instance of {@link BlockDiagram }. + * + * @return the block diagram */ public BlockDiagram createBlockDiagram() { return new BlockDiagram(); } /** - * Create an instance of {@link ListOfCatalyzedReactions } - * + * Create an instance of {@link ListOfCatalyzedReactions }. + * + * @return the list of catalyzed reactions */ public ListOfCatalyzedReactions createListOfCatalyzedReactions() { return new ListOfCatalyzedReactions(); } /** - * Create an instance of {@link Catalyzed } - * + * Create an instance of {@link Catalyzed }. + * + * @return the catalyzed */ public Catalyzed createCatalyzed() { return new Catalyzed(); } /** - * Create an instance of {@link Layer } - * + * Create an instance of {@link Layer }. + * + * @return the layer */ public Layer createLayer() { return new Layer(); } /** - * Create an instance of {@link ListOfSpeciesAliases } - * + * Create an instance of {@link ListOfSpeciesAliases }. + * + * @return the list of species aliases */ public ListOfSpeciesAliases createListOfSpeciesAliases() { return new ListOfSpeciesAliases(); } /** - * Create an instance of {@link SpeciesTag } - * + * Create an instance of {@link SpeciesTag }. + * + * @return the species tag */ public SpeciesTag createSpeciesTag() { return new SpeciesTag(); } /** - * Create an instance of {@link ListOfStructuralStates } - * + * Create an instance of {@link ListOfStructuralStates }. + * + * @return the list of structural states */ public ListOfStructuralStates createListOfStructuralStates() { return new ListOfStructuralStates(); } /** - * Create an instance of {@link SpeciesIdentity } - * + * Create an instance of {@link SpeciesIdentity }. + * + * @return the species identity */ public SpeciesIdentity createSpeciesIdentity() { return new SpeciesIdentity(); } /** - * Create an instance of {@link BaseProduct } - * + * Create an instance of {@link BaseProduct }. + * + * @return the base product */ public BaseProduct createBaseProduct() { return new BaseProduct(); } /** - * Create an instance of {@link ListOfExternalNamesForResidue } - * + * Create an instance of {@link ListOfExternalNamesForResidue }. + * + * @return the list of external names for residue */ public ListOfExternalNamesForResidue createListOfExternalNamesForResidue() { return new ListOfExternalNamesForResidue(); } /** - * Create an instance of {@link ModificationResidue } - * + * Create an instance of {@link ModificationResidue }. + * + * @return the modification residue */ public ModificationResidue createModificationResidue() { return new ModificationResidue(); } /** - * Create an instance of {@link EffectSiteInBlockDiagram } - * + * Create an instance of {@link EffectSiteInBlockDiagram }. + * + * @return the effect site in block diagram */ public EffectSiteInBlockDiagram createEffectSiteInBlockDiagram() { return new EffectSiteInBlockDiagram(); } /** - * Create an instance of {@link ListOfInternalLinksInBlockDiagram } - * + * Create an instance of {@link ListOfInternalLinksInBlockDiagram }. + * + * @return the list of internal links in block diagram */ public ListOfInternalLinksInBlockDiagram createListOfInternalLinksInBlockDiagram() { return new ListOfInternalLinksInBlockDiagram(); } /** - * Create an instance of {@link AntisenseRNA } - * + * Create an instance of {@link AntisenseRNA }. + * + * @return the antisense RNA */ public AntisenseRNA createAntisenseRNA() { return new AntisenseRNA(); } /** - * Create an instance of {@link ExternalConnectionInBlockDiagram } - * + * Create an instance of {@link ExternalConnectionInBlockDiagram }. + * + * @return the external connection in block diagram */ public ExternalConnectionInBlockDiagram createExternalConnectionInBlockDiagram() { return new ExternalConnectionInBlockDiagram(); } /** - * Create an instance of {@link ListOfGenes } - * + * Create an instance of {@link ListOfGenes }. + * + * @return the list of genes */ public ListOfGenes createListOfGenes() { return new ListOfGenes(); } /** - * Create an instance of {@link LinkAnchor } - * + * Create an instance of {@link LinkAnchor }. + * + * @return the link anchor */ public LinkAnchor createLinkAnchor() { return new LinkAnchor(); } /** - * Create an instance of {@link UsualView } - * + * Create an instance of {@link UsualView }. + * + * @return the usual view */ public UsualView createUsualView() { return new UsualView(); } /** - * Create an instance of {@link ListOfLayers } - * + * Create an instance of {@link ListOfLayers }. + * + * @return the list of layers */ public ListOfLayers createListOfLayers() { return new ListOfLayers(); } /** - * Create an instance of {@link Notes } - * + * Create an instance of {@link Notes }. + * + * @return the notes */ public Notes createNotes() { return new Notes(); } /** - * Create an instance of {@link RNA } - * + * Create an instance of {@link RNA }. + * + * @return the rna */ public RNA createRNA() { return new RNA(); } /** - * Create an instance of {@link DegradedInBlockDiagram } - * + * Create an instance of {@link DegradedInBlockDiagram }. + * + * @return the degraded in block diagram */ public DegradedInBlockDiagram createDegradedInBlockDiagram() { return new DegradedInBlockDiagram(); } /** - * Create an instance of {@link ExternalNameForResidue } - * + * Create an instance of {@link ExternalNameForResidue }. + * + * @return the external name for residue */ public ExternalNameForResidue createExternalNameForResidue() { return new ExternalNameForResidue(); } /** - * Create an instance of {@link View } - * + * Create an instance of {@link View }. + * + * @return the view */ public View createView() { return new View(); } /** - * Create an instance of {@link ListOfLineDirection } - * + * Create an instance of {@link ListOfLineDirection }. + * + * @return the list of line direction */ public ListOfLineDirection createListOfLineDirection() { return new ListOfLineDirection(); } /** - * Create an instance of {@link TagBounds } - * + * Create an instance of {@link TagBounds }. + * + * @return the tag bounds */ public TagBounds createTagBounds() { return new TagBounds(); } /** - * Create an instance of {@link TagEdgeLine } - * + * Create an instance of {@link TagEdgeLine }. + * + * @return the tag edge line */ public TagEdgeLine createTagEdgeLine() { return new TagEdgeLine(); } /** - * Create an instance of {@link ListOfBindingSitesInBlockDiagram } - * + * Create an instance of {@link ListOfBindingSitesInBlockDiagram }. + * + * @return the list of binding sites in block diagram */ public ListOfBindingSitesInBlockDiagram createListOfBindingSitesInBlockDiagram() { return new ListOfBindingSitesInBlockDiagram(); } /** - * Create an instance of {@link ProductLink } - * + * Create an instance of {@link ProductLink }. + * + * @return the product link */ public ProductLink createProductLink() { return new ProductLink(); } /** - * Create an instance of {@link ListOfTexts } - * + * Create an instance of {@link ListOfTexts }. + * + * @return the list of texts */ public ListOfTexts createListOfTexts() { return new ListOfTexts(); } /** - * Create an instance of {@link InternalLinkInBlockDiagram } - * + * Create an instance of {@link InternalLinkInBlockDiagram }. + * + * @return the internal link in block diagram */ public InternalLinkInBlockDiagram createInternalLinkInBlockDiagram() { return new InternalLinkInBlockDiagram(); } /** - * Create an instance of {@link ListOfModification } - * + * Create an instance of {@link ListOfModification }. + * + * @return the list of modification */ public ListOfModification createListOfModification() { return new ListOfModification(); } /** - * Create an instance of {@link Group } - * + * Create an instance of {@link Group }. + * + * @return the group */ public Group createGroup() { return new Group(); } /** - * Create an instance of {@link LineDirection } - * + * Create an instance of {@link LineDirection }. + * + * @return the line direction */ public LineDirection createLineDirection() { return new LineDirection(); } /** - * Create an instance of {@link ListOfReactantLinks } - * + * Create an instance of {@link ListOfReactantLinks }. + * + * @return the list of reactant links */ public ListOfReactantLinks createListOfReactantLinks() { return new ListOfReactantLinks(); } /** - * Create an instance of {@link Info } - * + * Create an instance of {@link Info }. + * + * @return the info */ public Info createInfo() { return new Info(); } /** - * Create an instance of {@link Offset } - * + * Create an instance of {@link Offset }. + * + * @return the offset */ public Offset createOffset() { return new Offset(); } /** - * Create an instance of {@link InnerPosition } - * + * Create an instance of {@link InnerPosition }. + * + * @return the inner position */ public InnerPosition createInnerPosition() { return new InnerPosition(); @@ -738,39 +866,44 @@ public InnerPosition createInnerPosition() { /** * Create an instance of {@link org.sbml._2001.ns.celldesigner.Modification } - * + * + * @return the modification */ public org.sbml._2001.ns.celldesigner.Modification createModification() { return new org.sbml._2001.ns.celldesigner.Modification(); } /** - * Create an instance of {@link ListOfEffectSitesInBlockDiagram } - * + * Create an instance of {@link ListOfEffectSitesInBlockDiagram }. + * + * @return the list of effect sites in block diagram */ public ListOfEffectSitesInBlockDiagram createListOfEffectSitesInBlockDiagram() { return new ListOfEffectSitesInBlockDiagram(); } /** - * Create an instance of {@link LayerFreeLine } - * + * Create an instance of {@link LayerFreeLine }. + * + * @return the layer free line */ public LayerFreeLine createLayerFreeLine() { return new LayerFreeLine(); } /** - * Create an instance of {@link ListOfSpeciesTag } - * + * Create an instance of {@link ListOfSpeciesTag }. + * + * @return the list of species tag */ public ListOfSpeciesTag createListOfSpeciesTag() { return new ListOfSpeciesTag(); } /** - * Create an instance of {@link EditPoints } - * + * Create an instance of {@link EditPoints }. + * + * @return the edits the points */ public EditPoints createEditPoints() { return new EditPoints(); @@ -778,151 +911,170 @@ public EditPoints createEditPoints() { /** * Create an instance of {@link org.sbml._2001.ns.celldesigner.Region } - * + * + * @return the region */ public org.sbml._2001.ns.celldesigner.Region createRegion() { return new org.sbml._2001.ns.celldesigner.Region(); } /** - * Create an instance of {@link ListOfProductLinks } - * + * Create an instance of {@link ListOfProductLinks }. + * + * @return the list of product links */ public ListOfProductLinks createListOfProductLinks() { return new ListOfProductLinks(); } /** - * Create an instance of {@link ResidueInBlockDiagram } - * + * Create an instance of {@link ResidueInBlockDiagram }. + * + * @return the residue in block diagram */ public ResidueInBlockDiagram createResidueInBlockDiagram() { return new ResidueInBlockDiagram(); } /** - * Create an instance of {@link BindingRegion } - * + * Create an instance of {@link BindingRegion }. + * + * @return the binding region */ public BindingRegion createBindingRegion() { return new BindingRegion(); } /** - * Create an instance of {@link Line } - * + * Create an instance of {@link Line }. + * + * @return the line */ public Line createLine() { return new Line(); } /** - * Create an instance of {@link ListOfCompartmentAliases } - * + * Create an instance of {@link ListOfCompartmentAliases }. + * + * @return the list of compartment aliases */ public ListOfCompartmentAliases createListOfCompartmentAliases() { return new ListOfCompartmentAliases(); } /** - * Create an instance of {@link LinkTarget } - * + * Create an instance of {@link LinkTarget }. + * + * @return the link target */ public LinkTarget createLinkTarget() { return new LinkTarget(); } /** - * Create an instance of {@link Point } - * + * Create an instance of {@link Point }. + * + * @return the point */ public Point createPoint() { return new Point(); } /** - * Create an instance of {@link ListOfGroups } - * + * Create an instance of {@link ListOfGroups }. + * + * @return the list of groups */ public ListOfGroups createListOfGroups() { return new ListOfGroups(); } /** - * Create an instance of {@link ListOfResiduesInBlockDiagram } - * + * Create an instance of {@link ListOfResiduesInBlockDiagram }. + * + * @return the list of residues in block diagram */ public ListOfResiduesInBlockDiagram createListOfResiduesInBlockDiagram() { return new ListOfResiduesInBlockDiagram(); } /** - * Create an instance of {@link BindingSiteInBlockDiagram } - * + * Create an instance of {@link BindingSiteInBlockDiagram }. + * + * @return the binding site in block diagram */ public BindingSiteInBlockDiagram createBindingSiteInBlockDiagram() { return new BindingSiteInBlockDiagram(); } /** - * Create an instance of {@link ListOfBindingRegions } - * + * Create an instance of {@link ListOfBindingRegions }. + * + * @return the list of binding regions */ public ListOfBindingRegions createListOfBindingRegions() { return new ListOfBindingRegions(); } /** - * Create an instance of {@link ListOfModificationResidues } - * + * Create an instance of {@link ListOfModificationResidues }. + * + * @return the list of modification residues */ public ListOfModificationResidues createListOfModificationResidues() { return new ListOfModificationResidues(); } /** - * Create an instance of {@link EffectInBlockDiagram } - * + * Create an instance of {@link EffectInBlockDiagram }. + * + * @return the effect in block diagram */ public EffectInBlockDiagram createEffectInBlockDiagram() { return new EffectInBlockDiagram(); } /** - * Create an instance of {@link SpeciesAlias } - * + * Create an instance of {@link SpeciesAlias }. + * + * @return the species alias */ public SpeciesAlias createSpeciesAlias() { return new SpeciesAlias(); } /** - * Create an instance of {@link StartingPointInBlockDiagram } - * + * Create an instance of {@link StartingPointInBlockDiagram }. + * + * @return the starting point in block diagram */ public StartingPointInBlockDiagram createStartingPointInBlockDiagram() { return new StartingPointInBlockDiagram(); } /** - * Create an instance of {@link BaseProducts } - * + * Create an instance of {@link BaseProducts }. + * + * @return the base products */ public BaseProducts createBaseProducts() { return new BaseProducts(); } /** - * Create an instance of {@link ListOfExternalConnectionsInBlockDiagram } - * + * Create an instance of {@link ListOfExternalConnectionsInBlockDiagram }. + * + * @return the list of external connections in block diagram */ public ListOfExternalConnectionsInBlockDiagram createListOfExternalConnectionsInBlockDiagram() { return new ListOfExternalConnectionsInBlockDiagram(); } /** - * Create an instance of {@link LineType2 } - * + * Create an instance of {@link LineType2 }. + * + * @return the line type 2 */ public LineType2 createLineType2() { return new LineType2(); @@ -930,7 +1082,8 @@ public LineType2 createLineType2() { /** * Create an instance of {@link ListOfRegions.Region } - * + * + * @return the region */ public ListOfRegions.Region createListOfRegionsRegion() { return new ListOfRegions.Region(); @@ -938,7 +1091,8 @@ public ListOfRegions.Region createListOfRegionsRegion() { /** * Create an instance of {@link LayerSpeciesAlias.Font } - * + * + * @return the font */ public LayerSpeciesAlias.Font createLayerSpeciesAliasFont() { return new LayerSpeciesAlias.Font(); @@ -946,7 +1100,8 @@ public LayerSpeciesAlias.Font createLayerSpeciesAliasFont() { /** * Create an instance of {@link ListOfModifications.Modification } - * + * + * @return the modification */ public ListOfModifications.Modification createListOfModificationsModification() { return new ListOfModifications.Modification(); @@ -954,7 +1109,8 @@ public ListOfModifications.Modification createListOfModificationsModification() /** * Create an instance of {@link Species.Annotation } - * + * + * @return the annotation */ public Species.Annotation createSpeciesAnnotation() { return new Species.Annotation(); @@ -962,7 +1118,8 @@ public Species.Annotation createSpeciesAnnotation() { /** * Create an instance of {@link ListOfComplexSpeciesAliases.ComplexSpeciesAlias } - * + * + * @return the complex species alias */ public ListOfComplexSpeciesAliases.ComplexSpeciesAlias createListOfComplexSpeciesAliasesComplexSpeciesAlias() { return new ListOfComplexSpeciesAliases.ComplexSpeciesAlias(); @@ -970,7 +1127,8 @@ public ListOfComplexSpeciesAliases.ComplexSpeciesAlias createListOfComplexSpecie /** * Create an instance of {@link org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias.BackupSize } - * + * + * @return the backup size */ public org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias.BackupSize createComplexSpeciesAliasBackupSize() { return new org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias.BackupSize(); @@ -978,7 +1136,8 @@ public org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias.BackupSize createCompl /** * Create an instance of {@link ReactionAnnotationType.Extension } - * + * + * @return the extension */ public ReactionAnnotationType.Extension createReactionAnnotationTypeExtension() { return new ReactionAnnotationType.Extension(); @@ -986,7 +1145,8 @@ public ReactionAnnotationType.Extension createReactionAnnotationTypeExtension() /** * Create an instance of {@link ModelAnnotationType.Extension } - * + * + * @return the extension */ public ModelAnnotationType.Extension createModelAnnotationTypeExtension() { return new ModelAnnotationType.Extension(); @@ -994,7 +1154,8 @@ public ModelAnnotationType.Extension createModelAnnotationTypeExtension() { /** * Create an instance of {@link SpeciesAnnotationType.Extension } - * + * + * @return the extension */ public SpeciesAnnotationType.Extension createSpeciesAnnotationTypeExtension() { return new SpeciesAnnotationType.Extension(); @@ -1002,7 +1163,8 @@ public SpeciesAnnotationType.Extension createSpeciesAnnotationTypeExtension() { /** * Create an instance of {@link CompartmentAnnotationType.Extension } - * + * + * @return the extension */ public CompartmentAnnotationType.Extension createCompartmentAnnotationTypeExtension() { return new CompartmentAnnotationType.Extension(); @@ -1010,15 +1172,18 @@ public CompartmentAnnotationType.Extension createCompartmentAnnotationTypeExtens /** * Create an instance of {@link SpeciesReferenceAnnotationType.Extension } - * + * + * @return the extension */ public SpeciesReferenceAnnotationType.Extension createSpeciesReferenceAnnotationTypeExtension() { return new SpeciesReferenceAnnotationType.Extension(); } /** - * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}}. + * + * @param value the value + * @return the JAXB element< string> */ @XmlElementDecl(namespace = "http://www.sbml.org/2001/ns/celldesigner", name = "reactionType") public JAXBElement createReactionType(String value) { @@ -1026,8 +1191,10 @@ public JAXBElement createReactionType(String value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link Boolean }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link Boolean }{@code >}}. + * + * @param value the value + * @return the JAXB element< boolean> */ @XmlElementDecl(namespace = "http://www.sbml.org/2001/ns/celldesigner", name = "hypothetical") public JAXBElement createHypothetical(Boolean value) { @@ -1035,8 +1202,10 @@ public JAXBElement createHypothetical(Boolean value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}}. + * + * @param value the value + * @return the JAXB element< string> */ @XmlElementDecl(namespace = "http://www.sbml.org/2001/ns/celldesigner", name = "antisensernaReference") public JAXBElement createAntisensernaReference(String value) { @@ -1044,8 +1213,10 @@ public JAXBElement createAntisensernaReference(String value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}}. + * + * @param value the value + * @return the JAXB element< string> */ @XmlElementDecl(namespace = "http://www.sbml.org/2001/ns/celldesigner", name = "complexSpecies") public JAXBElement createComplexSpecies(String value) { @@ -1053,8 +1224,10 @@ public JAXBElement createComplexSpecies(String value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}}. + * + * @param value the value + * @return the JAXB element< string> */ @XmlElementDecl(namespace = "http://www.sbml.org/2001/ns/celldesigner", name = "class") public JAXBElement createClass(String value) { @@ -1062,8 +1235,10 @@ public JAXBElement createClass(String value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link BigInteger }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link BigInteger }{@code >}}. + * + * @param value the value + * @return the JAXB element< big integer> */ @XmlElementDecl(namespace = "http://www.sbml.org/2001/ns/celldesigner", name = "homodimer") public JAXBElement createHomodimer(BigInteger value) { @@ -1071,8 +1246,10 @@ public JAXBElement createHomodimer(BigInteger value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}}. + * + * @param value the value + * @return the JAXB element< string> */ @XmlElementDecl(namespace = "http://www.sbml.org/2001/ns/celldesigner", name = "name") public JAXBElement createName(String value) { @@ -1080,8 +1257,10 @@ public JAXBElement createName(String value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}}. + * + * @param value the value + * @return the JAXB element< string> */ @XmlElementDecl(namespace = "http://www.sbml.org/2001/ns/celldesigner", name = "alias") public JAXBElement createAlias(String value) { @@ -1089,8 +1268,10 @@ public JAXBElement createAlias(String value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}}. + * + * @param value the value + * @return the JAXB element< string> */ @XmlElementDecl(namespace = "http://www.sbml.org/2001/ns/celldesigner", name = "activity") public JAXBElement createActivity(String value) { @@ -1098,8 +1279,10 @@ public JAXBElement createActivity(String value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link BigDecimal }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link BigDecimal }{@code >}}. + * + * @param value the value + * @return the JAXB element< big decimal> */ @XmlElementDecl(namespace = "http://www.sbml.org/2001/ns/celldesigner", name = "modelVersion") public JAXBElement createModelVersion(BigDecimal value) { @@ -1107,8 +1290,10 @@ public JAXBElement createModelVersion(BigDecimal value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}}. + * + * @param value the value + * @return the JAXB element< string> */ @XmlElementDecl(namespace = "http://www.sbml.org/2001/ns/celldesigner", name = "proteinReference") public JAXBElement createProteinReference(String value) { @@ -1116,8 +1301,10 @@ public JAXBElement createProteinReference(String value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}}. + * + * @param value the value + * @return the JAXB element< string> */ @XmlElementDecl(namespace = "http://www.sbml.org/2001/ns/celldesigner", name = "rnaReference") public JAXBElement createRnaReference(String value) { @@ -1125,8 +1312,10 @@ public JAXBElement createRnaReference(String value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}}. + * + * @param value the value + * @return the JAXB element< string> */ @XmlElementDecl(namespace = "http://www.sbml.org/2001/ns/celldesigner", name = "positionToCompartment") public JAXBElement createPositionToCompartment(String value) { @@ -1134,8 +1323,10 @@ public JAXBElement createPositionToCompartment(String value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}}. + * + * @param value the value + * @return the JAXB element< string> */ @XmlElementDecl(namespace = "http://www.sbml.org/2001/ns/celldesigner", name = "geneReference") public JAXBElement createGeneReference(String value) { diff --git a/src/org/sbml/_2001/ns/celldesigner/Offset.java b/src/org/sbml/_2001/ns/celldesigner/Offset.java index 359a291..bb6cc72 100644 --- a/src/org/sbml/_2001/ns/celldesigner/Offset.java +++ b/src/org/sbml/_2001/ns/celldesigner/Offset.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Offset of a link from default position(center to center). * @@ -50,8 +66,11 @@ @XmlType(name = "offset") public class Offset { + /** The x. */ @XmlAttribute(name = "x", required = true) protected BigDecimal x; + + /** The y. */ @XmlAttribute(name = "y", required = true) protected BigDecimal y; diff --git a/src/org/sbml/_2001/ns/celldesigner/Paint.java b/src/org/sbml/_2001/ns/celldesigner/Paint.java index fbc0053..9299624 100644 --- a/src/org/sbml/_2001/ns/celldesigner/Paint.java +++ b/src/org/sbml/_2001/ns/celldesigner/Paint.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Paint scheme to paint object. * @@ -51,8 +67,11 @@ @XmlType(name = "paint") public class Paint { + /** The color. */ @XmlAttribute(name = "color", required = true) protected String color; + + /** The scheme. */ @XmlAttribute(name = "scheme") protected String scheme; diff --git a/src/org/sbml/_2001/ns/celldesigner/Point.java b/src/org/sbml/_2001/ns/celldesigner/Point.java index 5550ef7..8e32499 100644 --- a/src/org/sbml/_2001/ns/celldesigner/Point.java +++ b/src/org/sbml/_2001/ns/celldesigner/Point.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Point of an object on canvas. * @@ -50,8 +66,11 @@ @XmlType(name = "point") public class Point { + /** The x. */ @XmlAttribute(name = "x", required = true) protected BigDecimal x; + + /** The y. */ @XmlAttribute(name = "y", required = true) protected BigDecimal y; diff --git a/src/org/sbml/_2001/ns/celldesigner/ProductLink.java b/src/org/sbml/_2001/ns/celldesigner/ProductLink.java index 94d1f00..6fef572 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ProductLink.java +++ b/src/org/sbml/_2001/ns/celldesigner/ProductLink.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -15,6 +30,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Product link type. * @@ -58,13 +74,22 @@ }) public class ProductLink { + /** The link anchor. */ protected LinkAnchor linkAnchor; + + /** The line. */ @XmlElement(required = true) protected LineType2 line; + + /** The alias. */ @XmlAttribute(name = "alias", required = true) protected String alias; + + /** The product. */ @XmlAttribute(name = "product", required = true) protected String product; + + /** The target line index. */ @XmlAttribute(name = "targetLineIndex", required = true) protected String targetLineIndex; diff --git a/src/org/sbml/_2001/ns/celldesigner/Protein.java b/src/org/sbml/_2001/ns/celldesigner/Protein.java index 4d5ccac..4db82df 100644 --- a/src/org/sbml/_2001/ns/celldesigner/Protein.java +++ b/src/org/sbml/_2001/ns/celldesigner/Protein.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * For protein. * @@ -69,14 +85,27 @@ }) public class Protein { + /** The notes. */ protected Notes notes; + + /** The list of binding regions. */ protected ListOfBindingRegions listOfBindingRegions; + + /** The list of modification residues. */ protected ListOfModificationResidues listOfModificationResidues; + + /** The list of structural states. */ protected ListOfStructuralStates listOfStructuralStates; + + /** The id. */ @XmlAttribute(name = "id", required = true) protected String id; + + /** The name. */ @XmlAttribute(name = "name", required = true) protected String name; + + /** The type. */ @XmlAttribute(name = "type", required = true) protected String type; diff --git a/src/org/sbml/_2001/ns/celldesigner/RNA.java b/src/org/sbml/_2001/ns/celldesigner/RNA.java index 4c25e96..92e8b9b 100644 --- a/src/org/sbml/_2001/ns/celldesigner/RNA.java +++ b/src/org/sbml/_2001/ns/celldesigner/RNA.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * For RNA. * @@ -62,12 +78,21 @@ }) public class RNA { + /** The notes. */ protected Notes notes; + + /** The list of regions. */ protected ListOfRegions listOfRegions; + + /** The id. */ @XmlAttribute(name = "id", required = true) protected String id; + + /** The name. */ @XmlAttribute(name = "name", required = true) protected String name; + + /** The type. */ @XmlAttribute(name = "type", required = true) protected String type; diff --git a/src/org/sbml/_2001/ns/celldesigner/ReactantLink.java b/src/org/sbml/_2001/ns/celldesigner/ReactantLink.java index 85ddbba..57480ec 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ReactantLink.java +++ b/src/org/sbml/_2001/ns/celldesigner/ReactantLink.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -15,6 +30,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Reactant link type. * @@ -58,13 +74,22 @@ }) public class ReactantLink { + /** The link anchor. */ protected LinkAnchor linkAnchor; + + /** The line. */ @XmlElement(required = true) protected LineType2 line; + + /** The alias. */ @XmlAttribute(name = "alias", required = true) protected String alias; + + /** The reactant. */ @XmlAttribute(name = "reactant", required = true) protected String reactant; + + /** The target line index. */ @XmlAttribute(name = "targetLineIndex", required = true) protected String targetLineIndex; diff --git a/src/org/sbml/_2001/ns/celldesigner/ReactionAnnotationType.java b/src/org/sbml/_2001/ns/celldesigner/ReactionAnnotationType.java index 283acd2..7dfd4b1 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ReactionAnnotationType.java +++ b/src/org/sbml/_2001/ns/celldesigner/ReactionAnnotationType.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Annotation for reaction. * @@ -61,6 +77,7 @@ }) public class ReactionAnnotationType { + /** The extension. */ @XmlElement(required = true) protected ReactionAnnotationType.Extension extension; @@ -134,21 +151,42 @@ public void setExtension(ReactionAnnotationType.Extension value) { }) public static class Extension { + /** The name. */ protected String name; + + /** The reaction type. */ @XmlElement(required = true) protected String reactionType; + + /** The base reactants. */ @XmlElement(required = true) protected BaseReactants baseReactants; + + /** The base products. */ @XmlElement(required = true) protected BaseProducts baseProducts; + + /** The list of reactant links. */ protected ListOfReactantLinks listOfReactantLinks; + + /** The list of product links. */ protected ListOfProductLinks listOfProductLinks; + + /** The connect scheme. */ @XmlElement(required = true) protected ConnectScheme connectScheme; + + /** The offset. */ protected Offset offset; + + /** The edit points. */ protected EditPoints editPoints; + + /** The line. */ @XmlElement(required = true) protected Line line; + + /** The list of modification. */ protected ListOfModification listOfModification; /** diff --git a/src/org/sbml/_2001/ns/celldesigner/Region.java b/src/org/sbml/_2001/ns/celldesigner/Region.java index 15de203..d8d27b2 100644 --- a/src/org/sbml/_2001/ns/celldesigner/Region.java +++ b/src/org/sbml/_2001/ns/celldesigner/Region.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Specific region on nucleotide. * @@ -84,16 +100,27 @@ }) public class Region { + /** The id. */ @XmlAttribute(name = "id", required = true) protected String id; + + /** The size. */ @XmlAttribute(name = "size", required = true) protected BigDecimal size; + + /** The pos. */ @XmlAttribute(name = "pos") protected BigDecimal pos; + + /** The type. */ @XmlAttribute(name = "type") protected String type; + + /** The name. */ @XmlAttribute(name = "name") protected String name; + + /** The active. */ @XmlAttribute(name = "active") protected Boolean active; diff --git a/src/org/sbml/_2001/ns/celldesigner/ResidueInBlockDiagram.java b/src/org/sbml/_2001/ns/celldesigner/ResidueInBlockDiagram.java index ce9b7bb..794e905 100644 --- a/src/org/sbml/_2001/ns/celldesigner/ResidueInBlockDiagram.java +++ b/src/org/sbml/_2001/ns/celldesigner/ResidueInBlockDiagram.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Residue on the upper side of a block(protein). * @@ -100,18 +116,31 @@ @XmlType(name = "residueInBlockDiagram") public class ResidueInBlockDiagram { + /** The residue. */ @XmlAttribute(name = "residue") protected String residue; + + /** The type. */ @XmlAttribute(name = "type", required = true) protected String type; + + /** The id. */ @XmlAttribute(name = "id", required = true) protected short id; + + /** The offset X. */ @XmlAttribute(name = "offsetX", required = true) protected BigDecimal offsetX; + + /** The name. */ @XmlAttribute(name = "name") protected String name; + + /** The name offset X. */ @XmlAttribute(name = "nameOffsetX") protected BigDecimal nameOffsetX; + + /** The name offset Y. */ @XmlAttribute(name = "nameOffsetY") protected BigDecimal nameOffsetY; @@ -165,7 +194,8 @@ public void setType(String value) { /** * Gets the value of the id property. - * + * + * @return the id */ public short getId() { return id; @@ -173,7 +203,8 @@ public short getId() { /** * Sets the value of the id property. - * + * + * @param value the new id */ public void setId(short value) { this.id = value; diff --git a/src/org/sbml/_2001/ns/celldesigner/SingleLine.java b/src/org/sbml/_2001/ns/celldesigner/SingleLine.java index d846a63..4042fb9 100644 --- a/src/org/sbml/_2001/ns/celldesigner/SingleLine.java +++ b/src/org/sbml/_2001/ns/celldesigner/SingleLine.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Single line type to draw object. * @@ -45,6 +61,7 @@ @XmlType(name = "singleLine") public class SingleLine { + /** The width. */ @XmlAttribute(name = "width", required = true) protected BigDecimal width; diff --git a/src/org/sbml/_2001/ns/celldesigner/Species.java b/src/org/sbml/_2001/ns/celldesigner/Species.java index 0302488..a551f80 100644 --- a/src/org/sbml/_2001/ns/celldesigner/Species.java +++ b/src/org/sbml/_2001/ns/celldesigner/Species.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Species inside complexes. * @@ -72,29 +88,54 @@ }) public class Species { + /** The notes. */ protected Notes notes; + + /** The annotation. */ @XmlElement(required = true) protected Species.Annotation annotation; + + /** The id. */ @XmlAttribute(name = "id", required = true) protected String id; + + /** The name. */ @XmlAttribute(name = "name") protected String name; + + /** The compartment. */ @XmlAttribute(name = "compartment") protected String compartment; + + /** The initial amount. */ @XmlAttribute(name = "initialAmount") protected Double initialAmount; + + /** The initial concentration. */ @XmlAttribute(name = "initialConcentration") protected Double initialConcentration; + + /** The substance units. */ @XmlAttribute(name = "substanceUnits") protected String substanceUnits; + + /** The spatial size units. */ @XmlAttribute(name = "spatialSizeUnits") protected String spatialSizeUnits; + + /** The has only substance units. */ @XmlAttribute(name = "hasOnlySubstanceUnits") protected Boolean hasOnlySubstanceUnits; + + /** The boundary condition. */ @XmlAttribute(name = "boundaryCondition") protected Boolean boundaryCondition; + + /** The charge. */ @XmlAttribute(name = "charge") protected BigInteger charge; + + /** The constant. */ @XmlAttribute(name = "constant") protected Boolean constant; @@ -456,10 +497,17 @@ public void setConstant(Boolean value) { }) public static class Annotation { + /** The position to compartment. */ protected String positionToCompartment; + + /** The complex species. */ protected String complexSpecies; + + /** The species identity. */ @XmlElement(required = true) protected SpeciesIdentity speciesIdentity; + + /** The list of catalyzed reactions. */ protected ListOfCatalyzedReactions listOfCatalyzedReactions; /** diff --git a/src/org/sbml/_2001/ns/celldesigner/SpeciesAlias.java b/src/org/sbml/_2001/ns/celldesigner/SpeciesAlias.java index 83a9b7e..ec6ba52 100644 --- a/src/org/sbml/_2001/ns/celldesigner/SpeciesAlias.java +++ b/src/org/sbml/_2001/ns/celldesigner/SpeciesAlias.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -15,6 +30,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * For species aliases not forming complexes. * @@ -75,26 +91,49 @@ }) public class SpeciesAlias { + /** The activity. */ @XmlElement(required = true) protected String activity; + + /** The bounds. */ @XmlElement(required = true) protected Bounds bounds; + + /** The view. */ @XmlElement(required = true) protected View view; + + /** The structural state. */ protected StructuralStateAngle structuralState; + + /** The usual view. */ @XmlElement(required = true) protected UsualView usualView; + + /** The brief view. */ @XmlElement(required = true) protected BriefView briefView; + + /** The list of species tag. */ protected ListOfSpeciesTag listOfSpeciesTag; + + /** The info. */ @XmlElement(required = true) protected Info info; + + /** The id. */ @XmlAttribute(name = "id", required = true) protected String id; + + /** The species. */ @XmlAttribute(name = "species", required = true) protected String species; + + /** The compartment alias. */ @XmlAttribute(name = "compartmentAlias") protected String compartmentAlias; + + /** The complex species alias. */ @XmlAttribute(name = "complexSpeciesAlias") protected String complexSpeciesAlias; diff --git a/src/org/sbml/_2001/ns/celldesigner/SpeciesAnnotationType.java b/src/org/sbml/_2001/ns/celldesigner/SpeciesAnnotationType.java index 7fab5a2..d44a1f5 100644 --- a/src/org/sbml/_2001/ns/celldesigner/SpeciesAnnotationType.java +++ b/src/org/sbml/_2001/ns/celldesigner/SpeciesAnnotationType.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Annotation for species. * @@ -56,6 +72,7 @@ }) public class SpeciesAnnotationType { + /** The extension. */ @XmlElement(required = true) protected SpeciesAnnotationType.Extension extension; @@ -117,10 +134,17 @@ public void setExtension(SpeciesAnnotationType.Extension value) { }) public static class Extension { + /** The position to compartment. */ protected String positionToCompartment; + + /** The complex species. */ protected String complexSpecies; + + /** The species identity. */ @XmlElement(required = true) protected SpeciesIdentity speciesIdentity; + + /** The list of catalyzed reactions. */ protected ListOfCatalyzedReactions listOfCatalyzedReactions; /** diff --git a/src/org/sbml/_2001/ns/celldesigner/SpeciesIdentity.java b/src/org/sbml/_2001/ns/celldesigner/SpeciesIdentity.java index aeb0da5..c63f3f3 100644 --- a/src/org/sbml/_2001/ns/celldesigner/SpeciesIdentity.java +++ b/src/org/sbml/_2001/ns/celldesigner/SpeciesIdentity.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Identity to distinguish chemical species of CellDesigner's model. * @@ -57,14 +73,29 @@ }) public class SpeciesIdentity { + /** The clazz. */ @XmlElement(name = "class", required = true) protected String clazz; + + /** The hypothetical. */ protected Boolean hypothetical; + + /** The name. */ protected String name; + + /** The protein reference. */ protected String proteinReference; + + /** The rna reference. */ protected String rnaReference; + + /** The gene reference. */ protected String geneReference; + + /** The antisenserna reference. */ protected String antisensernaReference; + + /** The state. */ protected State state; /** diff --git a/src/org/sbml/_2001/ns/celldesigner/SpeciesReferenceAnnotationType.java b/src/org/sbml/_2001/ns/celldesigner/SpeciesReferenceAnnotationType.java index 7a88f50..6e44038 100644 --- a/src/org/sbml/_2001/ns/celldesigner/SpeciesReferenceAnnotationType.java +++ b/src/org/sbml/_2001/ns/celldesigner/SpeciesReferenceAnnotationType.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Annotation for (modifier)speciesReference. * @@ -51,6 +67,7 @@ }) public class SpeciesReferenceAnnotationType { + /** The extension. */ @XmlElement(required = true) protected SpeciesReferenceAnnotationType.Extension extension; @@ -104,6 +121,7 @@ public void setExtension(SpeciesReferenceAnnotationType.Extension value) { }) public static class Extension { + /** The alias. */ @XmlElement(required = true) protected String alias; diff --git a/src/org/sbml/_2001/ns/celldesigner/SpeciesTag.java b/src/org/sbml/_2001/ns/celldesigner/SpeciesTag.java index 0390772..bcf9127 100644 --- a/src/org/sbml/_2001/ns/celldesigner/SpeciesTag.java +++ b/src/org/sbml/_2001/ns/celldesigner/SpeciesTag.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for SpeciesTag complex type. * @@ -45,12 +61,19 @@ }) public class SpeciesTag { + /** The key info. */ @XmlElement(name = "KeyInfo", required = true) protected KeyInfo keyInfo; + + /** The tag bounds. */ @XmlElement(name = "TagBounds", required = true) protected TagBounds tagBounds; + + /** The tag edge line. */ @XmlElement(name = "TagEdgeLine", required = true) protected TagEdgeLine tagEdgeLine; + + /** The tag frame paint. */ @XmlElement(name = "TagFramePaint", required = true) protected Paint tagFramePaint; diff --git a/src/org/sbml/_2001/ns/celldesigner/StartingPointInBlockDiagram.java b/src/org/sbml/_2001/ns/celldesigner/StartingPointInBlockDiagram.java index d57d04c..e1e6d0a 100644 --- a/src/org/sbml/_2001/ns/celldesigner/StartingPointInBlockDiagram.java +++ b/src/org/sbml/_2001/ns/celldesigner/StartingPointInBlockDiagram.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Starting point (residue, binding site, operator) of the link. * @@ -71,14 +87,23 @@ @XmlType(name = "startingPointInBlockDiagram") public class StartingPointInBlockDiagram { + /** The offset X. */ @XmlAttribute(name = "offsetX", required = true) protected BigDecimal offsetX; + + /** The offset Y. */ @XmlAttribute(name = "offsetY", required = true) protected BigDecimal offsetY; + + /** The residue. */ @XmlAttribute(name = "residue") protected Short residue; + + /** The binding site. */ @XmlAttribute(name = "bindingSite") protected Short bindingSite; + + /** The operator. */ @XmlAttribute(name = "operator") protected Short operator; diff --git a/src/org/sbml/_2001/ns/celldesigner/State.java b/src/org/sbml/_2001/ns/celldesigner/State.java index 7a337fc..a6c7b8a 100644 --- a/src/org/sbml/_2001/ns/celldesigner/State.java +++ b/src/org/sbml/_2001/ns/celldesigner/State.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -15,6 +30,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Chemical "state" to distinguish chemical species derived from a root chemical. * @@ -46,8 +62,13 @@ }) public class State { + /** The homodimer. */ protected BigInteger homodimer; + + /** The list of modifications. */ protected ListOfModifications listOfModifications; + + /** The list of structural states. */ protected ListOfStructuralStates listOfStructuralStates; /** diff --git a/src/org/sbml/_2001/ns/celldesigner/StructuralStateAngle.java b/src/org/sbml/_2001/ns/celldesigner/StructuralStateAngle.java index e70f753..9dd326b 100644 --- a/src/org/sbml/_2001/ns/celldesigner/StructuralStateAngle.java +++ b/src/org/sbml/_2001/ns/celldesigner/StructuralStateAngle.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for structuralStateAngle complex type. * @@ -35,6 +51,7 @@ @XmlType(name = "structuralStateAngle") public class StructuralStateAngle { + /** The angle. */ @XmlAttribute(name = "angle") protected Double angle; diff --git a/src/org/sbml/_2001/ns/celldesigner/StructuralStates.java b/src/org/sbml/_2001/ns/celldesigner/StructuralStates.java index 92de8a8..69a53d1 100644 --- a/src/org/sbml/_2001/ns/celldesigner/StructuralStates.java +++ b/src/org/sbml/_2001/ns/celldesigner/StructuralStates.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for StructuralStates complex type. * @@ -35,6 +51,7 @@ @XmlType(name = "StructuralStates") public class StructuralStates { + /** The structural state. */ @XmlAttribute(name = "structuralState") protected String structuralState; diff --git a/src/org/sbml/_2001/ns/celldesigner/TagBounds.java b/src/org/sbml/_2001/ns/celldesigner/TagBounds.java index 9a397d2..068ba0e 100644 --- a/src/org/sbml/_2001/ns/celldesigner/TagBounds.java +++ b/src/org/sbml/_2001/ns/celldesigner/TagBounds.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for TagBounds complex type. * @@ -38,12 +54,19 @@ @XmlType(name = "TagBounds") public class TagBounds { + /** The x. */ @XmlAttribute(name = "x") protected Double x; + + /** The y. */ @XmlAttribute(name = "y") protected Double y; + + /** The w. */ @XmlAttribute(name = "w") protected Double w; + + /** The h. */ @XmlAttribute(name = "h") protected Double h; diff --git a/src/org/sbml/_2001/ns/celldesigner/TagEdgeLine.java b/src/org/sbml/_2001/ns/celldesigner/TagEdgeLine.java index bc03e08..8c21dda 100644 --- a/src/org/sbml/_2001/ns/celldesigner/TagEdgeLine.java +++ b/src/org/sbml/_2001/ns/celldesigner/TagEdgeLine.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for TagEdgeLine complex type. * @@ -35,6 +51,7 @@ @XmlType(name = "TagEdgeLine") public class TagEdgeLine { + /** The width. */ @XmlAttribute(name = "width") protected Double width; diff --git a/src/org/sbml/_2001/ns/celldesigner/UsualView.java b/src/org/sbml/_2001/ns/celldesigner/UsualView.java index 7e26141..eba3d29 100644 --- a/src/org/sbml/_2001/ns/celldesigner/UsualView.java +++ b/src/org/sbml/_2001/ns/celldesigner/UsualView.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * Data for drawing object with usual view. * @@ -47,11 +63,18 @@ }) public class UsualView { + /** The inner position. */ protected InnerPosition innerPosition; + + /** The box size. */ @XmlElement(required = true) protected BoxSize boxSize; + + /** The single line. */ @XmlElement(required = true) protected SingleLine singleLine; + + /** The paint. */ @XmlElement(required = true) protected Paint paint; diff --git a/src/org/sbml/_2001/ns/celldesigner/View.java b/src/org/sbml/_2001/ns/celldesigner/View.java index d027786..f9636ca 100644 --- a/src/org/sbml/_2001/ns/celldesigner/View.java +++ b/src/org/sbml/_2001/ns/celldesigner/View.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** * View state. * @@ -47,6 +63,7 @@ @XmlType(name = "view") public class View { + /** The state. */ @XmlAttribute(name = "state", required = true) protected String state; diff --git a/src/org/sbml/_2001/ns/celldesigner/package-info.java b/src/org/sbml/_2001/ns/celldesigner/package-info.java index cad91db..28ca535 100644 --- a/src/org/sbml/_2001/ns/celldesigner/package-info.java +++ b/src/org/sbml/_2001/ns/celldesigner/package-info.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb diff --git a/src/org/sbml/layoutconverter/Application.java b/src/org/sbml/layoutconverter/Application.java index 5ebb44b..79cacbd 100644 --- a/src/org/sbml/layoutconverter/Application.java +++ b/src/org/sbml/layoutconverter/Application.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ package org.sbml.layoutconverter; import java.io.File; @@ -20,7 +35,8 @@ public class Application { - LayoutConverter converter; + /** The converter. */ + private LayoutConverter converter; /** * Instantiates a new application. diff --git a/src/org/sbml/layoutconverter/ApplicationOption.java b/src/org/sbml/layoutconverter/ApplicationOption.java index 93a291b..db7b91f 100644 --- a/src/org/sbml/layoutconverter/ApplicationOption.java +++ b/src/org/sbml/layoutconverter/ApplicationOption.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ package org.sbml.layoutconverter; import org.kohsuke.args4j.Argument; @@ -14,6 +29,7 @@ public class ApplicationOption { + /** The help. */ @Option(name = "-h", aliases= {"--help"}, required = false, usage = "help") private boolean help = false; @@ -38,6 +54,8 @@ public class ApplicationOption { private String output; /** + * Checks if is help. + * * @return the help */ public boolean isHelp() { diff --git a/src/org/sbml/layoutconverter/BaseLayoutConverter.java b/src/org/sbml/layoutconverter/BaseLayoutConverter.java index a6b7c74..eeacb33 100644 --- a/src/org/sbml/layoutconverter/BaseLayoutConverter.java +++ b/src/org/sbml/layoutconverter/BaseLayoutConverter.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ package org.sbml.layoutconverter; import java.io.File; @@ -46,13 +61,13 @@ public abstract class BaseLayoutConverter { protected boolean convertDefaultCompartment = false; /** The Constant DEFAULT_SPECIES_WIDTH. */ - static final double DEFAULT_SPECIES_WIDTH = 80.0; + protected static final double DEFAULT_SPECIES_WIDTH = 80.0; /** The Constant DEFAULT_SPECIES_HEIGHT. */ - static final double DEFAULT_SPECIES_HEIGHT = 40.0; + protected static final double DEFAULT_SPECIES_HEIGHT = 40.0; /** The Constant DEFAULT_SPECIES_DEPTH. */ - static final double DEFAULT_SPECIES_DEPTH = 1.0; + protected static final double DEFAULT_SPECIES_DEPTH = 1.0; /** * Instantiates a new base layout converter. diff --git a/src/org/sbml/layoutconverter/CD2LayoutConverter.java b/src/org/sbml/layoutconverter/CD2LayoutConverter.java index 6bf7381..7f31e5e 100644 --- a/src/org/sbml/layoutconverter/CD2LayoutConverter.java +++ b/src/org/sbml/layoutconverter/CD2LayoutConverter.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ package org.sbml.layoutconverter; import java.awt.geom.Point2D; @@ -271,7 +286,7 @@ public void convertReactionsToLayout(List rList) { BoundingBox reactionBB = rg.createBoundingBox(); double xmin = Integer.MAX_VALUE, xmax = Integer.MIN_VALUE, ymin = Integer.MAX_VALUE, ymax = Integer.MIN_VALUE; - // System.out.println(rw.getId()); + System.out.println(rw.getId() + srgList.size()); for(SpeciesReferenceGlyph srg : srgList){ Point position = srg.getBoundingBox().getPosition(); Dimensions dim = srg.getBoundingBox().getDimensions(); @@ -287,7 +302,7 @@ public void convertReactionsToLayout(List rList) { if(ymax < position.getY() + dim.getHeight()) ymax = position.getY() + dim.getHeight(); - // System.out.println(srg + srg.getSpeciesGlyph()); + System.out.println(srg + srg.getSpeciesGlyph()); } Dimensions dim = new Dimensions(SBMLUtil.DEFAULT_SBML_LEVEL, SBMLUtil.DEFAULT_SBML_VERSION); dim.setWidth(xmax - xmin); @@ -298,14 +313,14 @@ public void convertReactionsToLayout(List rList) { if (brsList.size() == 1 && prsList.size() == 1) { BaseReactant br = brsList.get(0); BaseProduct bp = prsList.get(0); -// System.out.println(br.getAlias() + " " + br.getSpecies()); -// System.out.println(bp.getAlias() + " " + bp.getSpecies()); + System.out.println(br.getAlias() + " " + br.getSpecies()); + System.out.println(bp.getAlias() + " " + bp.getSpecies()); SpeciesReferenceGlyph srg1 = srgList.get("srGlyphReactant_" + rg.getReaction() + "_" + br.getSpecies()); //SpeciesGlyph sg1 = srg1.getSpeciesGlyphInstance(); SpeciesReferenceGlyph srg2 = srgList.get("srGlyphProduct_" + rg.getReaction() + "_" + bp.getSpecies()); //SpeciesGlyph sg2 = srg2.getSpeciesGlyphInstance(); -// System.out.println("srg1 " + srg1); -// System.out.println("srg2 " + srg2); + System.out.println("srg1 " + srg1); + System.out.println("srg2 " + srg2); Point startPoint = LayoutUtil.createAdjustedPoint(srg1, br.getLinkAnchor().getPosition()); Point endPoint = LayoutUtil.createAdjustedPoint(srg2, bp.getLinkAnchor().getPosition()); Point reactantPoint = LayoutUtil.createCenterPoint(srg1); @@ -340,9 +355,9 @@ public void convertReactionsToLayout(List rList) { SpeciesReferenceGlyph srg3 = srgList.get("srGlyphProduct_" + rg.getReaction() + "_" + bp1.getSpecies()); SpeciesGlyph sg3 = srg3.getSpeciesGlyphInstance(); Point endPoint2 = LayoutUtil.createAdjustedPoint(sg3, bp1.getLinkAnchor().getPosition()); -// System.out.println("srg1 " + srg1); -// System.out.println("srg2 " + srg2); -// System.out.println("srg3 " + srg3); + System.out.println("srg1 " + srg1); + System.out.println("srg2 " + srg2); + System.out.println("srg3 " + srg3); Point reactantPoint1 = LayoutUtil.createCenterPoint(sg1); Point reactantPoint2 = LayoutUtil.createCenterPoint(sg2); @@ -383,12 +398,12 @@ public void convertReactionsToLayout(List rList) { SpeciesReferenceGlyph srg1 = srgList.get("srGlyphReactant_" + rg.getReaction() + "_" + br1.getSpecies()); //SpeciesGlyph sg1 = srg1.getSpeciesGlyphInstance(); Point startPoint = LayoutUtil.createAdjustedPoint(srg1, br1.getLinkAnchor().getPosition()); -// System.out.println(br1.getAlias() + " " + br1.getSpecies()); -// System.out.println( "srg1 " + srg1); + System.out.println(br1.getAlias() + " " + br1.getSpecies()); + System.out.println( "srg1 " + srg1); BaseProduct bp1 = prsList.get(0); SpeciesReferenceGlyph srg2 = srgList.get("srGlyphProduct_" + rg.getReaction() + "_" + bp1.getSpecies()); -// System.out.println(bp1.getAlias() + " " + bp1.getSpecies()); -// System.out.println( "srg2 " + srg2); + System.out.println(bp1.getAlias() + " " + bp1.getSpecies()); + System.out.println( "srg2 " + srg2); //SpeciesGlyph sg2 = srg2.getSpeciesGlyphInstance(); Point endPoint1 = LayoutUtil.createAdjustedPoint(srg2, bp1.getLinkAnchor().getPosition()); @@ -397,7 +412,7 @@ public void convertReactionsToLayout(List rList) { //SpeciesGlyph sg3 = layout.getSpeciesGlyph("SpeciesGlyph_" + bp2.getAlias()); Point endPoint2 = LayoutUtil.createAdjustedPoint(srg3, bp2.getLinkAnchor().getPosition()); -// System.out.println("srg3 " + srg3); + System.out.println("srg3 " + srg3); Point reactantPoint = LayoutUtil.createCenterPoint(srg1); Point productPoint1 = LayoutUtil.createCenterPoint(srg2); diff --git a/src/org/sbml/layoutconverter/FBCConverter.java b/src/org/sbml/layoutconverter/FBCConverter.java index cf0d599..274d94f 100644 --- a/src/org/sbml/layoutconverter/FBCConverter.java +++ b/src/org/sbml/layoutconverter/FBCConverter.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ package org.sbml.layoutconverter; import java.util.List; @@ -44,8 +59,6 @@ public class FBCConverter { public FBCConverter(Model model, ModelWrapper mWrapper) { this.model = model; this.mWrapper = mWrapper; - - model.getSBMLDocument().setPackageRequired("fbc", false); } /** diff --git a/src/org/sbml/layoutconverter/Layout2CDConverter.java b/src/org/sbml/layoutconverter/Layout2CDConverter.java index 3f0a023..442331b 100644 --- a/src/org/sbml/layoutconverter/Layout2CDConverter.java +++ b/src/org/sbml/layoutconverter/Layout2CDConverter.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ package org.sbml.layoutconverter; import java.awt.geom.Point2D; diff --git a/src/org/sbml/layoutconverter/LayoutConverter.java b/src/org/sbml/layoutconverter/LayoutConverter.java index 77b5880..f00f057 100644 --- a/src/org/sbml/layoutconverter/LayoutConverter.java +++ b/src/org/sbml/layoutconverter/LayoutConverter.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ /* * */ @@ -151,9 +166,9 @@ public void save() { public static void main(String[] args) { LayoutConverter converter; //String filepath = "EcoliCore.sbml.xml"; - String filepath = "1752-0509-7-97-S4.xml"; + String filepath = "h.xml"; String outputpath = ""; - Boolean isCD2Layout = true; + Boolean isCD2Layout = false; Boolean defaultCompartment = false; for(int i = 0 ; i < args.length; i++){ diff --git a/src/org/sbml/layoutconverter/LayoutUtil.java b/src/org/sbml/layoutconverter/LayoutUtil.java index f315fce..b150d6c 100644 --- a/src/org/sbml/layoutconverter/LayoutUtil.java +++ b/src/org/sbml/layoutconverter/LayoutUtil.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ /* * */ @@ -262,7 +277,7 @@ public static Point createAdjustedPoint(double x, double y, double width, double /** * Creates the adjusted point. * - * @param sg the sg + * @param go the go * @param direction the direction * @return Point * TODO @@ -728,30 +743,42 @@ public static String convertLineTypeToCDString(String type){ } } + /** + * Adjust overlapping end point. + * + * @param cs the cs + * @param go the go + * @return the point + */ public static Point adjustOverlappingEndPoint(CurveSegment cs, GraphicalObject go){ Line2D.Double reactionLine = new Line2D.Double(cs.getStart().getX(), cs.getStart().getY(), cs.getEnd().getX(), cs.getEnd().getY()); Rectangle2D.Double glyph = new Rectangle2D.Double(go.getBoundingBox().getPosition().getX(), go.getBoundingBox().getPosition().getY(), go.getBoundingBox().getDimensions().getWidth(), go.getBoundingBox().getDimensions().getWidth()); if(reactionLine.intersectsLine(glyph.getMinX(), glyph.getMinY(), glyph.getMaxX(), glyph.getMinY())){ //up - System.out.println("up"); return getIntersectingPoint(cs.getStart(), cs.getEnd(), new Point(glyph.getMinX(), glyph.getMinY()), new Point(glyph.getMaxX(), glyph.getMinY())); } else if(reactionLine.intersectsLine(glyph.getMaxX(), glyph.getMinY(), glyph.getMaxX(), glyph.getMaxY())){ //right - System.out.println("right"); return getIntersectingPoint(cs.getStart(), cs.getEnd(), new Point(glyph.getMaxX(), glyph.getMinY()), new Point( glyph.getMaxX(), glyph.getMaxY())); } else if(reactionLine.intersectsLine(glyph.getMinX(), glyph.getMaxY(), glyph.getMaxX(), glyph.getMaxY())){ //down - System.out.println("down"); return getIntersectingPoint(cs.getStart(), cs.getEnd(), new Point(glyph.getMinX(), glyph.getMaxY()), new Point(glyph.getMaxX(), glyph.getMaxY())); } else if(reactionLine.intersectsLine(glyph.getMinX(), glyph.getMinY(), glyph.getMinX(), glyph.getMaxY())){ //left - System.out.println("left"); return getIntersectingPoint(cs.getStart(), cs.getEnd(), new Point(glyph.getMinX(), glyph.getMinY()), new Point(glyph.getMinX(), glyph.getMaxY())); } return cs.getEnd(); } + /** + * Gets the intersecting point. + * + * @param p1Start the p 1 start + * @param p1End the p 1 end + * @param p2Start the p 2 start + * @param p2End the p 2 end + * @return the intersecting point + */ public static Point getIntersectingPoint(Point p1Start, Point p1End, Point p2Start, Point p2End){ Point point = new Point(SBMLUtil.DEFAULT_SBML_LEVEL, SBMLUtil.DEFAULT_SBML_VERSION); double area1 = crossProduct(p2Start, p2Start, p2End, p1Start) / 2; @@ -763,6 +790,15 @@ public static Point getIntersectingPoint(Point p1Start, Point p1End, Point p2Sta return point; } + /** + * Cross product. + * + * @param startPoint1 the start point 1 + * @param startPoint2 the start point 2 + * @param endPoint1 the end point 1 + * @param endPoint2 the end point 2 + * @return the double + */ public static double crossProduct(Point startPoint1, Point startPoint2, Point endPoint1, Point endPoint2){ return (endPoint1.getX() - startPoint1.getX())*(endPoint2.getY() - startPoint2.getY()) - (endPoint1.getY() - startPoint1.getY()) * (endPoint2.getX() - startPoint2.getX()); } diff --git a/src/org/sbml/layoutconverter/MultiConverter.java b/src/org/sbml/layoutconverter/MultiConverter.java index fb5280c..8e436fd 100644 --- a/src/org/sbml/layoutconverter/MultiConverter.java +++ b/src/org/sbml/layoutconverter/MultiConverter.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ package org.sbml.layoutconverter; import org.sbml.jsbml.Model; @@ -30,8 +45,6 @@ public class MultiConverter { public MultiConverter(Model model, ModelWrapper mWrapper){ this.model = model; this.mWrapper = mWrapper; - - model.getSBMLDocument().setPackageRequired(MultiConstants.shortLabel, false); } /** diff --git a/src/org/sbml/layoutconverter/SBMLLevelandVersionHandler.java b/src/org/sbml/layoutconverter/SBMLLevelandVersionHandler.java index 6a41b49..237930a 100644 --- a/src/org/sbml/layoutconverter/SBMLLevelandVersionHandler.java +++ b/src/org/sbml/layoutconverter/SBMLLevelandVersionHandler.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ /* * */ @@ -31,9 +46,6 @@ public static SBMLDocument upgrade(SBMLDocument document){ document.setLevelAndVersion(SBMLUtil.DEFAULT_SBML_LEVEL, SBMLUtil.DEFAULT_SBML_VERSION); System.out.println("SBML Model converted to Level " + SBMLUtil.DEFAULT_SBML_LEVEL + " Version " + SBMLUtil.DEFAULT_SBML_VERSION); } - - //if(!SBMLUtil.isSetSBOTerm(document)) - //System.err.println("Missing sboterms"); document = SBMLModelCompleter.autoCompleteRequiredAttributes(document); diff --git a/src/org/sbml/layoutconverter/SBMLModelCompleter.java b/src/org/sbml/layoutconverter/SBMLModelCompleter.java index bcf928b..b024c42 100644 --- a/src/org/sbml/layoutconverter/SBMLModelCompleter.java +++ b/src/org/sbml/layoutconverter/SBMLModelCompleter.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ /* * */ diff --git a/src/org/sbml/layoutconverter/SBMLUtil.java b/src/org/sbml/layoutconverter/SBMLUtil.java index 5e023f8..30e0abb 100644 --- a/src/org/sbml/layoutconverter/SBMLUtil.java +++ b/src/org/sbml/layoutconverter/SBMLUtil.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ package org.sbml.layoutconverter; import java.io.File; @@ -31,6 +46,7 @@ import org.sbml.jsbml.SpeciesReference; import org.sbml.jsbml.StoichiometryMath; import org.sbml.jsbml.Trigger; +import org.sbml.jsbml.ext.fbc.FBCConstants; import org.sbml.jsbml.ext.layout.LayoutConstants; // TODO: Auto-generated Javadoc @@ -42,6 +58,7 @@ * Date Created: Jun 24, 2016 */ +@SuppressWarnings("deprecation") public class SBMLUtil { /** The defaultsbmllevel. */ @@ -293,6 +310,29 @@ public static SBMLDocument addExtensionPackageLayout(SBMLDocument document){ return document; } + + /** + * Adds the extension package fbc. + * + * @param document the document + * @return the SBML document + */ + public static SBMLDocument addExtensionPackageFBC(SBMLDocument document){ + document.enablePackage(FBCConstants.getNamespaceURI(SBMLUtil.DEFAULT_SBML_LEVEL, SBMLUtil.DEFAULT_SBML_VERSION), true); + document.setPackageRequired(FBCConstants.getNamespaceURI(SBMLUtil.DEFAULT_SBML_LEVEL, SBMLUtil.DEFAULT_SBML_VERSION), false); + + return document; + } + + /** + * Adds the extension package fbc. + * + * @param model the model + * @return the SBML document + */ + public static Model addExtensionPackageFBC(Model model){ + return addExtensionPackageFBC(model.getSBMLDocument()).getModel(); + } /** * Checks if is level and version match with CD. @@ -316,40 +356,6 @@ public static boolean isLevelAndVersionMatchWithCD(SBMLDocument document){ return (document.getLevel() == DEFAULT_CELLDESIGNER_SBML_LEVEL) && (document.getVersion() == DEFAULT_CELLDESIGNER_SBML_VERSION); } - /** - * The main method. - * - * @param args the arguments - */ - public static void main(String[] args){ - try { - SBMLDocument d = SBMLReader.read(new File("sample/layout_example1_L3.xml")); - Map nsMap = d.getDeclaredNamespaces(); - for(java.util.Map.Entry e: nsMap.entrySet()) - System.out.println(e.toString()); - System.out.println(LayoutConstants.namespaceURI_L3V1V1); - } catch (XMLStreamException | IOException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } - } - - /** - * Checks if is set SBO term. - * - * @param node the node - */ - public static void isSetSBOTerm(TreeNode node){ - for(int i = 0; i < node.getChildCount(); i++){ - TreeNode n = node.getChildAt(i); - if(n instanceof SBase && !((SBase)n ).isSetSBOTerm()){ - System.out.println(n.getClass()); - SBMLLevelandVersionHandler.isSetSBOTerm = false; - } - isSetSBOTerm(n); - } - } - /** * Checks if is sets the SBO term. * @@ -671,7 +677,6 @@ public static void setMaths(SBMLDocument d1, TreeNode node2){ * @param d the d * @param math the math */ - @SuppressWarnings("deprecation") public static void setMathObject(SBMLDocument d, AbstractMathContainer math){ if(math instanceof FunctionDefinition){ diff --git a/src/org/sbml/layoutconverter/package-info.java b/src/org/sbml/layoutconverter/package-info.java index a56af5b..02a832a 100644 --- a/src/org/sbml/layoutconverter/package-info.java +++ b/src/org/sbml/layoutconverter/package-info.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ /** * @author Kaito Ii * diff --git a/src/org/sbml/sbml/level2/version4/AlgebraicRule.java b/src/org/sbml/sbml/level2/version4/AlgebraicRule.java index 31dc9c1..1adab1e 100644 --- a/src/org/sbml/sbml/level2/version4/AlgebraicRule.java +++ b/src/org/sbml/sbml/level2/version4/AlgebraicRule.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb diff --git a/src/org/sbml/sbml/level2/version4/AssignmentRule.java b/src/org/sbml/sbml/level2/version4/AssignmentRule.java index 2f119e7..7d977f3 100644 --- a/src/org/sbml/sbml/level2/version4/AssignmentRule.java +++ b/src/org/sbml/sbml/level2/version4/AssignmentRule.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for AssignmentRule complex type. * @@ -37,6 +53,7 @@ public class AssignmentRule extends Rule { + /** The variable. */ @XmlAttribute(name = "variable", required = true) protected String variable; diff --git a/src/org/sbml/sbml/level2/version4/Compartment.java b/src/org/sbml/sbml/level2/version4/Compartment.java index 4884dd1..7151d61 100644 --- a/src/org/sbml/sbml/level2/version4/Compartment.java +++ b/src/org/sbml/sbml/level2/version4/Compartment.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -15,6 +30,7 @@ import org.sbml._2001.ns.celldesigner.CompartmentAnnotationType; +// TODO: Auto-generated Javadoc /** * Redefined compartment. * @@ -66,6 +82,7 @@ public class Compartment extends OriginalCompartment { + /** The annotation. */ protected CompartmentAnnotationType annotation; /** diff --git a/src/org/sbml/sbml/level2/version4/Event.java b/src/org/sbml/sbml/level2/version4/Event.java index 1fd965e..cc28bbb 100644 --- a/src/org/sbml/sbml/level2/version4/Event.java +++ b/src/org/sbml/sbml/level2/version4/Event.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -15,6 +30,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for Event complex type. * @@ -49,15 +65,26 @@ public class Event extends SBase { + /** The trigger. */ @XmlElement(required = true) protected MathField trigger; + + /** The delay. */ protected MathField delay; + + /** The list of event assignments. */ @XmlElement(required = true) protected ListOfEventAssignments listOfEventAssignments; + + /** The id. */ @XmlAttribute(name = "id") protected String id; + + /** The name. */ @XmlAttribute(name = "name") protected String name; + + /** The time units. */ @XmlAttribute(name = "timeUnits") protected String timeUnits; diff --git a/src/org/sbml/sbml/level2/version4/EventAssignment.java b/src/org/sbml/sbml/level2/version4/EventAssignment.java index 2e3068a..93106c6 100644 --- a/src/org/sbml/sbml/level2/version4/EventAssignment.java +++ b/src/org/sbml/sbml/level2/version4/EventAssignment.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import org.w3._1998.math.mathml.Math; +// TODO: Auto-generated Javadoc /** *

Java class for EventAssignment complex type. * @@ -45,8 +61,11 @@ public class EventAssignment extends SBase { + /** The math. */ @XmlElement(namespace = "http://www.w3.org/1998/Math/MathML", required = true) protected Math math; + + /** The variable. */ @XmlAttribute(name = "variable", required = true) protected String variable; diff --git a/src/org/sbml/sbml/level2/version4/FunctionDefinition.java b/src/org/sbml/sbml/level2/version4/FunctionDefinition.java index 651e8b7..4ba3f3a 100644 --- a/src/org/sbml/sbml/level2/version4/FunctionDefinition.java +++ b/src/org/sbml/sbml/level2/version4/FunctionDefinition.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import org.w3._1998.math.mathml.Math; +// TODO: Auto-generated Javadoc /** *

Java class for FunctionDefinition complex type. * @@ -46,10 +62,15 @@ public class FunctionDefinition extends SBase { + /** The math. */ @XmlElement(namespace = "http://www.w3.org/1998/Math/MathML", required = true) protected Math math; + + /** The id. */ @XmlAttribute(name = "id", required = true) protected String id; + + /** The name. */ @XmlAttribute(name = "name") protected String name; diff --git a/src/org/sbml/sbml/level2/version4/KineticLaw.java b/src/org/sbml/sbml/level2/version4/KineticLaw.java index 5611b8e..8e2b5d0 100644 --- a/src/org/sbml/sbml/level2/version4/KineticLaw.java +++ b/src/org/sbml/sbml/level2/version4/KineticLaw.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import org.w3._1998.math.mathml.Math; +// TODO: Auto-generated Javadoc /** *

Java class for KineticLaw complex type. * @@ -48,11 +64,18 @@ public class KineticLaw extends SBase { + /** The math. */ @XmlElement(namespace = "http://www.w3.org/1998/Math/MathML", required = true) protected Math math; + + /** The list of parameters. */ protected ListOfParameters listOfParameters; + + /** The time units. */ @XmlAttribute(name = "timeUnits") protected String timeUnits; + + /** The substance units. */ @XmlAttribute(name = "substanceUnits") protected String substanceUnits; diff --git a/src/org/sbml/sbml/level2/version4/ListOfEventAssignments.java b/src/org/sbml/sbml/level2/version4/ListOfEventAssignments.java index 0447f0e..737a870 100644 --- a/src/org/sbml/sbml/level2/version4/ListOfEventAssignments.java +++ b/src/org/sbml/sbml/level2/version4/ListOfEventAssignments.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for ListOfEventAssignments complex type. * @@ -44,6 +60,7 @@ public class ListOfEventAssignments extends SBase { + /** The event assignment. */ @XmlElement(required = true) protected List eventAssignment; @@ -66,8 +83,8 @@ public class ListOfEventAssignments *

* Objects of the following type(s) are allowed in the list * {@link EventAssignment } - * - * + * + * @return the event assignment */ public List getEventAssignment() { if (eventAssignment == null) { diff --git a/src/org/sbml/sbml/level2/version4/ListOfModifierSpeciesReferences.java b/src/org/sbml/sbml/level2/version4/ListOfModifierSpeciesReferences.java index 0e7a96a..66aba99 100644 --- a/src/org/sbml/sbml/level2/version4/ListOfModifierSpeciesReferences.java +++ b/src/org/sbml/sbml/level2/version4/ListOfModifierSpeciesReferences.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for ListOfModifierSpeciesReferences complex type. * @@ -44,6 +60,7 @@ public class ListOfModifierSpeciesReferences extends SBase { + /** The modifier species reference. */ @XmlElement(required = true) protected List modifierSpeciesReference; @@ -66,8 +83,8 @@ public class ListOfModifierSpeciesReferences *

* Objects of the following type(s) are allowed in the list * {@link ModifierSpeciesReference } - * - * + * + * @return the modifier species reference */ public List getModifierSpeciesReference() { if (modifierSpeciesReference == null) { diff --git a/src/org/sbml/sbml/level2/version4/ListOfParameters.java b/src/org/sbml/sbml/level2/version4/ListOfParameters.java index c8e4435..f9c54b2 100644 --- a/src/org/sbml/sbml/level2/version4/ListOfParameters.java +++ b/src/org/sbml/sbml/level2/version4/ListOfParameters.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for ListOfParameters complex type. * @@ -44,6 +60,7 @@ public class ListOfParameters extends SBase { + /** The parameter. */ @XmlElement(required = true) protected List parameter; @@ -66,8 +83,8 @@ public class ListOfParameters *

* Objects of the following type(s) are allowed in the list * {@link Parameter } - * - * + * + * @return the parameter */ public List getParameter() { if (parameter == null) { diff --git a/src/org/sbml/sbml/level2/version4/ListOfSpeciesReferences.java b/src/org/sbml/sbml/level2/version4/ListOfSpeciesReferences.java index 198e502..81bee62 100644 --- a/src/org/sbml/sbml/level2/version4/ListOfSpeciesReferences.java +++ b/src/org/sbml/sbml/level2/version4/ListOfSpeciesReferences.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for ListOfSpeciesReferences complex type. * @@ -44,6 +60,7 @@ public class ListOfSpeciesReferences extends SBase { + /** The species reference. */ @XmlElement(required = true) protected List speciesReference; @@ -66,8 +83,8 @@ public class ListOfSpeciesReferences *

* Objects of the following type(s) are allowed in the list * {@link SpeciesReference } - * - * + * + * @return the species reference */ public List getSpeciesReference() { if (speciesReference == null) { diff --git a/src/org/sbml/sbml/level2/version4/ListOfUnits.java b/src/org/sbml/sbml/level2/version4/ListOfUnits.java index 1b51966..007c259 100644 --- a/src/org/sbml/sbml/level2/version4/ListOfUnits.java +++ b/src/org/sbml/sbml/level2/version4/ListOfUnits.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for ListOfUnits complex type. * @@ -44,6 +60,7 @@ public class ListOfUnits extends SBase { + /** The unit. */ @XmlElement(required = true) protected List unit; @@ -66,8 +83,8 @@ public class ListOfUnits *

* Objects of the following type(s) are allowed in the list * {@link Unit } - * - * + * + * @return the unit */ public List getUnit() { if (unit == null) { diff --git a/src/org/sbml/sbml/level2/version4/MathField.java b/src/org/sbml/sbml/level2/version4/MathField.java index f39c8bc..c6964a1 100644 --- a/src/org/sbml/sbml/level2/version4/MathField.java +++ b/src/org/sbml/sbml/level2/version4/MathField.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import org.w3._1998.math.mathml.Math; +// TODO: Auto-generated Javadoc /** *

Java class for MathField complex type. * @@ -43,6 +59,7 @@ public class MathField extends SBase { + /** The math. */ @XmlElement(namespace = "http://www.w3.org/1998/Math/MathML", required = true) protected Math math; diff --git a/src/org/sbml/sbml/level2/version4/Model.java b/src/org/sbml/sbml/level2/version4/Model.java index 609f51d..e3e30f8 100644 --- a/src/org/sbml/sbml/level2/version4/Model.java +++ b/src/org/sbml/sbml/level2/version4/Model.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -15,6 +30,7 @@ import org.sbml._2001.ns.celldesigner.ModelAnnotationType; +// TODO: Auto-generated Javadoc /** * Redefined model. * @@ -146,6 +162,7 @@ public class Model extends OriginalModel { + /** The annotation. */ protected ModelAnnotationType annotation; /** diff --git a/src/org/sbml/sbml/level2/version4/ModifierSpeciesReference.java b/src/org/sbml/sbml/level2/version4/ModifierSpeciesReference.java index 3b6f851..9c4d227 100644 --- a/src/org/sbml/sbml/level2/version4/ModifierSpeciesReference.java +++ b/src/org/sbml/sbml/level2/version4/ModifierSpeciesReference.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -15,6 +30,7 @@ import org.sbml._2001.ns.celldesigner.SpeciesReferenceAnnotationType; +// TODO: Auto-generated Javadoc /** * Redefined modifierSpeciesReference. * @@ -52,6 +68,7 @@ public class ModifierSpeciesReference extends OriginalModifierSpeciesReference { + /** The annotation. */ protected SpeciesReferenceAnnotationType annotation; /** diff --git a/src/org/sbml/sbml/level2/version4/ObjectFactory.java b/src/org/sbml/sbml/level2/version4/ObjectFactory.java index ffbef1b..ddbced1 100644 --- a/src/org/sbml/sbml/level2/version4/ObjectFactory.java +++ b/src/org/sbml/sbml/level2/version4/ObjectFactory.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.namespace.QName; +// TODO: Auto-generated Javadoc /** * This object contains factory methods for each * Java content interface and Java element interface @@ -31,6 +47,7 @@ @XmlRegistry public class ObjectFactory { + /** The Constant _Sbml_QNAME. */ private final static QName _Sbml_QNAME = new QName("http://www.sbml.org/sbml/level2/version4", "sbml"); /** @@ -41,72 +58,81 @@ public ObjectFactory() { } /** - * Create an instance of {@link OriginalModel } - * + * Create an instance of {@link OriginalModel }. + * + * @return the original model */ public OriginalModel createOriginalModel() { return new OriginalModel(); } /** - * Create an instance of {@link Sbml } - * + * Create an instance of {@link Sbml }. + * + * @return the sbml */ public Sbml createSbml() { return new Sbml(); } /** - * Create an instance of {@link StoichiometryMath } - * + * Create an instance of {@link StoichiometryMath }. + * + * @return the stoichiometry math */ public StoichiometryMath createStoichiometryMath() { return new StoichiometryMath(); } /** - * Create an instance of {@link Compartment } - * + * Create an instance of {@link Compartment }. + * + * @return the compartment */ public Compartment createCompartment() { return new Compartment(); } /** - * Create an instance of {@link Unit } - * + * Create an instance of {@link Unit }. + * + * @return the unit */ public Unit createUnit() { return new Unit(); } /** - * Create an instance of {@link MathField } - * + * Create an instance of {@link MathField }. + * + * @return the math field */ public MathField createMathField() { return new MathField(); } /** - * Create an instance of {@link AlgebraicRule } - * + * Create an instance of {@link AlgebraicRule }. + * + * @return the algebraic rule */ public AlgebraicRule createAlgebraicRule() { return new AlgebraicRule(); } /** - * Create an instance of {@link ListOfSpeciesReferences } - * + * Create an instance of {@link ListOfSpeciesReferences }. + * + * @return the list of species references */ public ListOfSpeciesReferences createListOfSpeciesReferences() { return new ListOfSpeciesReferences(); } /** - * Create an instance of {@link SpeciesReference } - * + * Create an instance of {@link SpeciesReference }. + * + * @return the species reference */ public SpeciesReference createSpeciesReference() { return new SpeciesReference(); @@ -114,127 +140,143 @@ public SpeciesReference createSpeciesReference() { /** * Create an instance of {@link org.sbml.sbml.level2.version4.ListOfParameters } - * + * + * @return the list of parameters */ public org.sbml.sbml.level2.version4.ListOfParameters createListOfParameters() { return new org.sbml.sbml.level2.version4.ListOfParameters(); } /** - * Create an instance of {@link ListOfEventAssignments } - * + * Create an instance of {@link ListOfEventAssignments }. + * + * @return the list of event assignments */ public ListOfEventAssignments createListOfEventAssignments() { return new ListOfEventAssignments(); } /** - * Create an instance of {@link RateRule } - * + * Create an instance of {@link RateRule }. + * + * @return the rate rule */ public RateRule createRateRule() { return new RateRule(); } /** - * Create an instance of {@link FunctionDefinition } - * + * Create an instance of {@link FunctionDefinition }. + * + * @return the function definition */ public FunctionDefinition createFunctionDefinition() { return new FunctionDefinition(); } /** - * Create an instance of {@link Species } - * + * Create an instance of {@link Species }. + * + * @return the species */ public Species createSpecies() { return new Species(); } /** - * Create an instance of {@link ModifierSpeciesReference } - * + * Create an instance of {@link ModifierSpeciesReference }. + * + * @return the modifier species reference */ public ModifierSpeciesReference createModifierSpeciesReference() { return new ModifierSpeciesReference(); } /** - * Create an instance of {@link UnitDefinition } - * + * Create an instance of {@link UnitDefinition }. + * + * @return the unit definition */ public UnitDefinition createUnitDefinition() { return new UnitDefinition(); } /** - * Create an instance of {@link ListOfModifierSpeciesReferences } - * + * Create an instance of {@link ListOfModifierSpeciesReferences }. + * + * @return the list of modifier species references */ public ListOfModifierSpeciesReferences createListOfModifierSpeciesReferences() { return new ListOfModifierSpeciesReferences(); } /** - * Create an instance of {@link EventAssignment } - * + * Create an instance of {@link EventAssignment }. + * + * @return the event assignment */ public EventAssignment createEventAssignment() { return new EventAssignment(); } /** - * Create an instance of {@link AssignmentRule } - * + * Create an instance of {@link AssignmentRule }. + * + * @return the assignment rule */ public AssignmentRule createAssignmentRule() { return new AssignmentRule(); } /** - * Create an instance of {@link Reaction } - * + * Create an instance of {@link Reaction }. + * + * @return the reaction */ public Reaction createReaction() { return new Reaction(); } /** - * Create an instance of {@link Model } - * + * Create an instance of {@link Model }. + * + * @return the model */ public Model createModel() { return new Model(); } /** - * Create an instance of {@link Parameter } - * + * Create an instance of {@link Parameter }. + * + * @return the parameter */ public Parameter createParameter() { return new Parameter(); } /** - * Create an instance of {@link Event } - * + * Create an instance of {@link Event }. + * + * @return the event */ public Event createEvent() { return new Event(); } /** - * Create an instance of {@link ListOfUnits } - * + * Create an instance of {@link ListOfUnits }. + * + * @return the list of units */ public ListOfUnits createListOfUnits() { return new ListOfUnits(); } /** - * Create an instance of {@link KineticLaw } - * + * Create an instance of {@link KineticLaw }. + * + * @return the kinetic law */ public KineticLaw createKineticLaw() { return new KineticLaw(); @@ -242,7 +284,8 @@ public KineticLaw createKineticLaw() { /** * Create an instance of {@link org.sbml.sbml.level2.version4.SBase.Notes } - * + * + * @return the notes */ public org.sbml.sbml.level2.version4.SBase.Notes createSBaseNotes() { return new org.sbml.sbml.level2.version4.SBase.Notes(); @@ -250,7 +293,8 @@ public org.sbml.sbml.level2.version4.SBase.Notes createSBaseNotes() { /** * Create an instance of {@link OriginalModel.ListOfFunctionDefinitions } - * + * + * @return the list of function definitions */ public OriginalModel.ListOfFunctionDefinitions createOriginalModelListOfFunctionDefinitions() { return new OriginalModel.ListOfFunctionDefinitions(); @@ -258,7 +302,8 @@ public OriginalModel.ListOfFunctionDefinitions createOriginalModelListOfFunction /** * Create an instance of {@link OriginalModel.ListOfUnitDefinitions } - * + * + * @return the list of unit definitions */ public OriginalModel.ListOfUnitDefinitions createOriginalModelListOfUnitDefinitions() { return new OriginalModel.ListOfUnitDefinitions(); @@ -266,7 +311,8 @@ public OriginalModel.ListOfUnitDefinitions createOriginalModelListOfUnitDefiniti /** * Create an instance of {@link OriginalModel.ListOfCompartments } - * + * + * @return the list of compartments */ public OriginalModel.ListOfCompartments createOriginalModelListOfCompartments() { return new OriginalModel.ListOfCompartments(); @@ -274,7 +320,8 @@ public OriginalModel.ListOfCompartments createOriginalModelListOfCompartments() /** * Create an instance of {@link OriginalModel.ListOfSpecies } - * + * + * @return the list of species */ public OriginalModel.ListOfSpecies createOriginalModelListOfSpecies() { return new OriginalModel.ListOfSpecies(); @@ -282,7 +329,8 @@ public OriginalModel.ListOfSpecies createOriginalModelListOfSpecies() { /** * Create an instance of {@link OriginalModel.ListOfParameters } - * + * + * @return the list of parameters */ public OriginalModel.ListOfParameters createOriginalModelListOfParameters() { return new OriginalModel.ListOfParameters(); @@ -290,7 +338,8 @@ public OriginalModel.ListOfParameters createOriginalModelListOfParameters() { /** * Create an instance of {@link OriginalModel.ListOfRules } - * + * + * @return the list of rules */ public OriginalModel.ListOfRules createOriginalModelListOfRules() { return new OriginalModel.ListOfRules(); @@ -298,7 +347,8 @@ public OriginalModel.ListOfRules createOriginalModelListOfRules() { /** * Create an instance of {@link OriginalModel.ListOfReactions } - * + * + * @return the list of reactions */ public OriginalModel.ListOfReactions createOriginalModelListOfReactions() { return new OriginalModel.ListOfReactions(); @@ -306,55 +356,63 @@ public OriginalModel.ListOfReactions createOriginalModelListOfReactions() { /** * Create an instance of {@link OriginalModel.ListOfEvents } - * + * + * @return the list of events */ public OriginalModel.ListOfEvents createOriginalModelListOfEvents() { return new OriginalModel.ListOfEvents(); } /** - * Create an instance of {@link OriginalReaction } - * + * Create an instance of {@link OriginalReaction }. + * + * @return the original reaction */ public OriginalReaction createOriginalReaction() { return new OriginalReaction(); } /** - * Create an instance of {@link OriginalModifierSpeciesReference } - * + * Create an instance of {@link OriginalModifierSpeciesReference }. + * + * @return the original modifier species reference */ public OriginalModifierSpeciesReference createOriginalModifierSpeciesReference() { return new OriginalModifierSpeciesReference(); } /** - * Create an instance of {@link OriginalSpecies } - * + * Create an instance of {@link OriginalSpecies }. + * + * @return the original species */ public OriginalSpecies createOriginalSpecies() { return new OriginalSpecies(); } /** - * Create an instance of {@link OriginalSpeciesReference } - * + * Create an instance of {@link OriginalSpeciesReference }. + * + * @return the original species reference */ public OriginalSpeciesReference createOriginalSpeciesReference() { return new OriginalSpeciesReference(); } /** - * Create an instance of {@link OriginalCompartment } - * + * Create an instance of {@link OriginalCompartment }. + * + * @return the original compartment */ public OriginalCompartment createOriginalCompartment() { return new OriginalCompartment(); } /** - * Create an instance of {@link JAXBElement }{@code <}{@link Sbml }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link Sbml }{@code >}}. + * + * @param value the value + * @return the JAXB element< sbml> */ @XmlElementDecl(namespace = "http://www.sbml.org/sbml/level2/version4", name = "sbml") public JAXBElement createSbml(Sbml value) { diff --git a/src/org/sbml/sbml/level2/version4/OriginalCompartment.java b/src/org/sbml/sbml/level2/version4/OriginalCompartment.java index aa74024..360cad4 100644 --- a/src/org/sbml/sbml/level2/version4/OriginalCompartment.java +++ b/src/org/sbml/sbml/level2/version4/OriginalCompartment.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -15,6 +30,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for Compartment complex type. * @@ -54,18 +70,31 @@ public class OriginalCompartment extends SBase { + /** The id. */ @XmlAttribute(name = "id", required = true) protected String id; + + /** The name. */ @XmlAttribute(name = "name") protected String name; + + /** The size. */ @XmlAttribute(name = "size") protected Double size; + + /** The spatial dimensions. */ @XmlAttribute(name = "spatialDimensions") protected Integer spatialDimensions; + + /** The units. */ @XmlAttribute(name = "units") protected String units; + + /** The outside. */ @XmlAttribute(name = "outside") protected String outside; + + /** The constant. */ @XmlAttribute(name = "constant") protected Boolean constant; diff --git a/src/org/sbml/sbml/level2/version4/OriginalModel.java b/src/org/sbml/sbml/level2/version4/OriginalModel.java index 3d3d53c..ff8029a 100644 --- a/src/org/sbml/sbml/level2/version4/OriginalModel.java +++ b/src/org/sbml/sbml/level2/version4/OriginalModel.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -20,6 +35,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for Model complex type. * @@ -148,16 +164,35 @@ public class OriginalModel extends SBase { + /** The list of function definitions. */ protected OriginalModel.ListOfFunctionDefinitions listOfFunctionDefinitions; + + /** The list of unit definitions. */ protected OriginalModel.ListOfUnitDefinitions listOfUnitDefinitions; + + /** The list of compartments. */ protected OriginalModel.ListOfCompartments listOfCompartments; + + /** The list of species. */ protected OriginalModel.ListOfSpecies listOfSpecies; + + /** The list of parameters. */ protected OriginalModel.ListOfParameters listOfParameters; + + /** The list of rules. */ protected OriginalModel.ListOfRules listOfRules; + + /** The list of reactions. */ protected OriginalModel.ListOfReactions listOfReactions; + + /** The list of events. */ protected OriginalModel.ListOfEvents listOfEvents; + + /** The id. */ @XmlAttribute(name = "id") protected String id; + + /** The name. */ @XmlAttribute(name = "name") protected String name; @@ -429,6 +464,7 @@ public static class ListOfCompartments extends SBase { + /** The compartment. */ @XmlElement(required = true) protected List compartment; @@ -451,8 +487,8 @@ public static class ListOfCompartments *

* Objects of the following type(s) are allowed in the list * {@link Compartment } - * - * + * + * @return the compartment */ public List getCompartment() { if (compartment == null) { @@ -491,6 +527,7 @@ public static class ListOfEvents extends SBase { + /** The event. */ @XmlElement(required = true) protected List event; @@ -513,8 +550,8 @@ public static class ListOfEvents *

* Objects of the following type(s) are allowed in the list * {@link Event } - * - * + * + * @return the event */ public List getEvent() { if (event == null) { @@ -553,6 +590,7 @@ public static class ListOfFunctionDefinitions extends SBase { + /** The function definition. */ @XmlElement(required = true) protected List functionDefinition; @@ -575,8 +613,8 @@ public static class ListOfFunctionDefinitions *

* Objects of the following type(s) are allowed in the list * {@link FunctionDefinition } - * - * + * + * @return the function definition */ public List getFunctionDefinition() { if (functionDefinition == null) { @@ -615,6 +653,7 @@ public static class ListOfParameters extends SBase { + /** The parameter. */ @XmlElement(required = true) protected List parameter; @@ -637,8 +676,8 @@ public static class ListOfParameters *

* Objects of the following type(s) are allowed in the list * {@link Parameter } - * - * + * + * @return the parameter */ public List getParameter() { if (parameter == null) { @@ -677,6 +716,7 @@ public static class ListOfReactions extends SBase { + /** The reaction. */ @XmlElement(required = true) protected List reaction; @@ -699,8 +739,8 @@ public static class ListOfReactions *

* Objects of the following type(s) are allowed in the list * {@link Reaction } - * - * + * + * @return the reaction */ public List getReaction() { if (reaction == null) { @@ -741,6 +781,7 @@ public static class ListOfRules extends SBase { + /** The algebraic rule or assignment rule or rate rule. */ @XmlElements({ @XmlElement(name = "algebraicRule", type = AlgebraicRule.class), @XmlElement(name = "assignmentRule", type = AssignmentRule.class), @@ -769,8 +810,8 @@ public static class ListOfRules * {@link AlgebraicRule } * {@link AssignmentRule } * {@link RateRule } - * - * + * + * @return the algebraic rule or assignment rule or rate rule */ public List getAlgebraicRuleOrAssignmentRuleOrRateRule() { if (algebraicRuleOrAssignmentRuleOrRateRule == null) { @@ -809,6 +850,7 @@ public static class ListOfSpecies extends SBase { + /** The species. */ @XmlElement(required = true) protected List species; @@ -831,8 +873,8 @@ public static class ListOfSpecies *

* Objects of the following type(s) are allowed in the list * {@link Species } - * - * + * + * @return the species */ public List getSpecies() { if (species == null) { @@ -871,6 +913,7 @@ public static class ListOfUnitDefinitions extends SBase { + /** The unit definition. */ @XmlElement(required = true) protected List unitDefinition; @@ -893,8 +936,8 @@ public static class ListOfUnitDefinitions *

* Objects of the following type(s) are allowed in the list * {@link UnitDefinition } - * - * + * + * @return the unit definition */ public List getUnitDefinition() { if (unitDefinition == null) { diff --git a/src/org/sbml/sbml/level2/version4/OriginalModifierSpeciesReference.java b/src/org/sbml/sbml/level2/version4/OriginalModifierSpeciesReference.java index 7655129..b7646f8 100644 --- a/src/org/sbml/sbml/level2/version4/OriginalModifierSpeciesReference.java +++ b/src/org/sbml/sbml/level2/version4/OriginalModifierSpeciesReference.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb diff --git a/src/org/sbml/sbml/level2/version4/OriginalReaction.java b/src/org/sbml/sbml/level2/version4/OriginalReaction.java index 1fd4e14..9131c67 100644 --- a/src/org/sbml/sbml/level2/version4/OriginalReaction.java +++ b/src/org/sbml/sbml/level2/version4/OriginalReaction.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -15,6 +30,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for Reaction complex type. * @@ -55,16 +71,31 @@ public class OriginalReaction extends SBase { + /** The list of reactants. */ protected ListOfSpeciesReferences listOfReactants; + + /** The list of products. */ protected ListOfSpeciesReferences listOfProducts; + + /** The list of modifiers. */ protected ListOfModifierSpeciesReferences listOfModifiers; + + /** The kinetic law. */ protected KineticLaw kineticLaw; + + /** The id. */ @XmlAttribute(name = "id", required = true) protected String id; + + /** The name. */ @XmlAttribute(name = "name") protected String name; + + /** The reversible. */ @XmlAttribute(name = "reversible") protected Boolean reversible; + + /** The fast. */ @XmlAttribute(name = "fast") protected Boolean fast; diff --git a/src/org/sbml/sbml/level2/version4/OriginalSpecies.java b/src/org/sbml/sbml/level2/version4/OriginalSpecies.java index 68c642d..1e4f53e 100644 --- a/src/org/sbml/sbml/level2/version4/OriginalSpecies.java +++ b/src/org/sbml/sbml/level2/version4/OriginalSpecies.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for Species complex type. * @@ -53,26 +69,47 @@ public class OriginalSpecies extends SBase { + /** The id. */ @XmlAttribute(name = "id", required = true) protected String id; + + /** The name. */ @XmlAttribute(name = "name") protected String name; + + /** The compartment. */ @XmlAttribute(name = "compartment") protected String compartment; + + /** The initial amount. */ @XmlAttribute(name = "initialAmount") protected Double initialAmount; + + /** The initial concentration. */ @XmlAttribute(name = "initialConcentration") protected Double initialConcentration; + + /** The substance units. */ @XmlAttribute(name = "substanceUnits") protected String substanceUnits; + + /** The spatial size units. */ @XmlAttribute(name = "spatialSizeUnits") protected String spatialSizeUnits; + + /** The has only substance units. */ @XmlAttribute(name = "hasOnlySubstanceUnits") protected Boolean hasOnlySubstanceUnits; + + /** The boundary condition. */ @XmlAttribute(name = "boundaryCondition") protected Boolean boundaryCondition; + + /** The charge. */ @XmlAttribute(name = "charge") protected BigInteger charge; + + /** The constant. */ @XmlAttribute(name = "constant") protected Boolean constant; diff --git a/src/org/sbml/sbml/level2/version4/OriginalSpeciesReference.java b/src/org/sbml/sbml/level2/version4/OriginalSpeciesReference.java index 4c98274..39609fb 100644 --- a/src/org/sbml/sbml/level2/version4/OriginalSpeciesReference.java +++ b/src/org/sbml/sbml/level2/version4/OriginalSpeciesReference.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -15,6 +30,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for SpeciesReference complex type. * @@ -46,7 +62,10 @@ public class OriginalSpeciesReference extends SimpleSpeciesReference { + /** The stoichiometry math. */ protected StoichiometryMath stoichiometryMath; + + /** The stoichiometry. */ @XmlAttribute(name = "stoichiometry") protected Double stoichiometry; diff --git a/src/org/sbml/sbml/level2/version4/Parameter.java b/src/org/sbml/sbml/level2/version4/Parameter.java index 10dcad4..89e2873 100644 --- a/src/org/sbml/sbml/level2/version4/Parameter.java +++ b/src/org/sbml/sbml/level2/version4/Parameter.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for Parameter complex type. * @@ -41,14 +57,23 @@ public class Parameter extends SBase { + /** The id. */ @XmlAttribute(name = "id", required = true) protected String id; + + /** The name. */ @XmlAttribute(name = "name") protected String name; + + /** The value. */ @XmlAttribute(name = "value") protected Double value; + + /** The units. */ @XmlAttribute(name = "units") protected String units; + + /** The constant. */ @XmlAttribute(name = "constant") protected Boolean constant; diff --git a/src/org/sbml/sbml/level2/version4/RateRule.java b/src/org/sbml/sbml/level2/version4/RateRule.java index 3601a90..647d935 100644 --- a/src/org/sbml/sbml/level2/version4/RateRule.java +++ b/src/org/sbml/sbml/level2/version4/RateRule.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for RateRule complex type. * @@ -37,6 +53,7 @@ public class RateRule extends Rule { + /** The variable. */ @XmlAttribute(name = "variable", required = true) protected String variable; diff --git a/src/org/sbml/sbml/level2/version4/Reaction.java b/src/org/sbml/sbml/level2/version4/Reaction.java index de9c08d..1f34496 100644 --- a/src/org/sbml/sbml/level2/version4/Reaction.java +++ b/src/org/sbml/sbml/level2/version4/Reaction.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -15,6 +30,7 @@ import org.sbml._2001.ns.celldesigner.ReactionAnnotationType; +// TODO: Auto-generated Javadoc /** * Redefined reaction. * @@ -62,6 +78,7 @@ public class Reaction extends OriginalReaction { + /** The annotation. */ protected ReactionAnnotationType annotation; /** diff --git a/src/org/sbml/sbml/level2/version4/Rule.java b/src/org/sbml/sbml/level2/version4/Rule.java index fac87c8..e493827 100644 --- a/src/org/sbml/sbml/level2/version4/Rule.java +++ b/src/org/sbml/sbml/level2/version4/Rule.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import org.w3._1998.math.mathml.Math; +// TODO: Auto-generated Javadoc /** *

Java class for Rule complex type. * @@ -49,6 +65,7 @@ public abstract class Rule extends SBase { + /** The math. */ @XmlElement(namespace = "http://www.w3.org/1998/Math/MathML", required = true) protected Math math; diff --git a/src/org/sbml/sbml/level2/version4/SBase.java b/src/org/sbml/sbml/level2/version4/SBase.java index 8b28203..1c787b0 100644 --- a/src/org/sbml/sbml/level2/version4/SBase.java +++ b/src/org/sbml/sbml/level2/version4/SBase.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -25,6 +40,7 @@ import org.w3c.dom.Element; +// TODO: Auto-generated Javadoc /** * The SBase type is the base type of all main components in SBML. It supports attaching metadata, notes and annotations to components. * @@ -94,7 +110,10 @@ }) public abstract class SBase { + /** The notes. */ protected SBase.Notes notes; + + /** The metaid. */ @XmlAttribute(name = "metaid") @XmlJavaTypeAdapter(CollapsedStringAdapter.class) @XmlID @@ -175,6 +194,7 @@ public void setMetaid(String value) { }) public static class Notes { + /** The any. */ @XmlAnyElement protected List any; @@ -197,8 +217,8 @@ public static class Notes { *

* Objects of the following type(s) are allowed in the list * {@link Element } - * - * + * + * @return the any */ public List getAny() { if (any == null) { diff --git a/src/org/sbml/sbml/level2/version4/Sbml.java b/src/org/sbml/sbml/level2/version4/Sbml.java index a8ffeac..050bb23 100644 --- a/src/org/sbml/sbml/level2/version4/Sbml.java +++ b/src/org/sbml/sbml/level2/version4/Sbml.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -19,6 +34,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for Sbml complex type. * @@ -49,11 +65,16 @@ public class Sbml extends SBase { + /** The model. */ @XmlElement(required = true) protected Model model; + + /** The level. */ @XmlAttribute(name = "level", required = true) @XmlSchemaType(name = "positiveInteger") protected BigInteger level; + + /** The version. */ @XmlAttribute(name = "version", required = true) @XmlSchemaType(name = "positiveInteger") protected BigInteger version; diff --git a/src/org/sbml/sbml/level2/version4/SimpleSpeciesReference.java b/src/org/sbml/sbml/level2/version4/SimpleSpeciesReference.java index 251a335..c0fa9da 100644 --- a/src/org/sbml/sbml/level2/version4/SimpleSpeciesReference.java +++ b/src/org/sbml/sbml/level2/version4/SimpleSpeciesReference.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -15,6 +30,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for SimpleSpeciesReference complex type. * @@ -42,6 +58,7 @@ public abstract class SimpleSpeciesReference extends SBase { + /** The species. */ @XmlAttribute(name = "species", required = true) protected String species; diff --git a/src/org/sbml/sbml/level2/version4/Species.java b/src/org/sbml/sbml/level2/version4/Species.java index cfe186a..a7fd854 100644 --- a/src/org/sbml/sbml/level2/version4/Species.java +++ b/src/org/sbml/sbml/level2/version4/Species.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -15,6 +30,7 @@ import org.sbml._2001.ns.celldesigner.SpeciesAnnotationType; +// TODO: Auto-generated Javadoc /** * Redefined species. * @@ -63,6 +79,7 @@ public class Species extends OriginalSpecies { + /** The annotation. */ protected SpeciesAnnotationType annotation; /** diff --git a/src/org/sbml/sbml/level2/version4/SpeciesReference.java b/src/org/sbml/sbml/level2/version4/SpeciesReference.java index dd336a1..736ac6f 100644 --- a/src/org/sbml/sbml/level2/version4/SpeciesReference.java +++ b/src/org/sbml/sbml/level2/version4/SpeciesReference.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -15,6 +30,7 @@ import org.sbml._2001.ns.celldesigner.SpeciesReferenceAnnotationType; +// TODO: Auto-generated Javadoc /** * Redefined speciesReference. * @@ -56,6 +72,7 @@ public class SpeciesReference extends OriginalSpeciesReference { + /** The annotation. */ protected SpeciesReferenceAnnotationType annotation; /** diff --git a/src/org/sbml/sbml/level2/version4/StoichiometryMath.java b/src/org/sbml/sbml/level2/version4/StoichiometryMath.java index 628f952..4e1ee64 100644 --- a/src/org/sbml/sbml/level2/version4/StoichiometryMath.java +++ b/src/org/sbml/sbml/level2/version4/StoichiometryMath.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import org.w3._1998.math.mathml.Math; +// TODO: Auto-generated Javadoc /** *

Java class for StoichiometryMath complex type. * @@ -43,6 +59,7 @@ public class StoichiometryMath extends SBase { + /** The math. */ @XmlElement(namespace = "http://www.w3.org/1998/Math/MathML", required = true) protected Math math; diff --git a/src/org/sbml/sbml/level2/version4/Unit.java b/src/org/sbml/sbml/level2/version4/Unit.java index 5ee03e9..a801eb3 100644 --- a/src/org/sbml/sbml/level2/version4/Unit.java +++ b/src/org/sbml/sbml/level2/version4/Unit.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for Unit complex type. * @@ -43,14 +59,23 @@ public class Unit extends SBase { + /** The kind. */ @XmlAttribute(name = "kind", required = true) protected UnitKind kind; + + /** The exponent. */ @XmlAttribute(name = "exponent") protected BigInteger exponent; + + /** The scale. */ @XmlAttribute(name = "scale") protected BigInteger scale; + + /** The multiplier. */ @XmlAttribute(name = "multiplier") protected Double multiplier; + + /** The offset. */ @XmlAttribute(name = "offset") protected Double offset; diff --git a/src/org/sbml/sbml/level2/version4/UnitDefinition.java b/src/org/sbml/sbml/level2/version4/UnitDefinition.java index ead2b0f..c23066a 100644 --- a/src/org/sbml/sbml/level2/version4/UnitDefinition.java +++ b/src/org/sbml/sbml/level2/version4/UnitDefinition.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -15,6 +30,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for UnitDefinition complex type. * @@ -44,10 +60,15 @@ public class UnitDefinition extends SBase { + /** The list of units. */ @XmlElement(required = true) protected ListOfUnits listOfUnits; + + /** The id. */ @XmlAttribute(name = "id", required = true) protected String id; + + /** The name. */ @XmlAttribute(name = "name") protected String name; diff --git a/src/org/sbml/sbml/level2/version4/UnitKind.java b/src/org/sbml/sbml/level2/version4/UnitKind.java index 149b46b..7c5fb30 100644 --- a/src/org/sbml/sbml/level2/version4/UnitKind.java +++ b/src/org/sbml/sbml/level2/version4/UnitKind.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -13,6 +28,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for UnitKind. * @@ -63,82 +79,165 @@ @XmlEnum public enum UnitKind { + /** The ampere. */ @XmlEnumValue("ampere") AMPERE("ampere"), + + /** The becquerel. */ @XmlEnumValue("becquerel") BECQUEREL("becquerel"), + + /** The candela. */ @XmlEnumValue("candela") CANDELA("candela"), + + /** The celsius. */ @XmlEnumValue("Celsius") CELSIUS("Celsius"), + + /** The coulomb. */ @XmlEnumValue("coulomb") COULOMB("coulomb"), + + /** The dimensionless. */ @XmlEnumValue("dimensionless") DIMENSIONLESS("dimensionless"), + + /** The farad. */ @XmlEnumValue("farad") FARAD("farad"), + + /** The gram. */ @XmlEnumValue("gram") GRAM("gram"), + + /** The gray. */ @XmlEnumValue("gray") GRAY("gray"), + + /** The henry. */ @XmlEnumValue("henry") HENRY("henry"), + + /** The hertz. */ @XmlEnumValue("hertz") HERTZ("hertz"), + + /** The item. */ @XmlEnumValue("item") ITEM("item"), + + /** The joule. */ @XmlEnumValue("joule") JOULE("joule"), + + /** The katal. */ @XmlEnumValue("katal") KATAL("katal"), + + /** The kelvin. */ @XmlEnumValue("kelvin") KELVIN("kelvin"), + + /** The kilogram. */ @XmlEnumValue("kilogram") KILOGRAM("kilogram"), + + /** The litre. */ @XmlEnumValue("litre") LITRE("litre"), + + /** The lumen. */ @XmlEnumValue("lumen") LUMEN("lumen"), + + /** The lux. */ @XmlEnumValue("lux") LUX("lux"), + + /** The metre. */ @XmlEnumValue("metre") METRE("metre"), + + /** The mole. */ @XmlEnumValue("mole") MOLE("mole"), + + /** The newton. */ @XmlEnumValue("newton") NEWTON("newton"), + + /** The ohm. */ @XmlEnumValue("ohm") OHM("ohm"), + + /** The pascal. */ @XmlEnumValue("pascal") PASCAL("pascal"), + + /** The radian. */ @XmlEnumValue("radian") RADIAN("radian"), + + /** The second. */ @XmlEnumValue("second") SECOND("second"), + + /** The siemens. */ @XmlEnumValue("siemens") SIEMENS("siemens"), + + /** The sievert. */ @XmlEnumValue("sievert") SIEVERT("sievert"), + + /** The steradian. */ @XmlEnumValue("steradian") STERADIAN("steradian"), + + /** The tesla. */ @XmlEnumValue("tesla") TESLA("tesla"), + + /** The volt. */ @XmlEnumValue("volt") VOLT("volt"), + + /** The watt. */ @XmlEnumValue("watt") WATT("watt"), + + /** The weber. */ @XmlEnumValue("weber") WEBER("weber"); + + /** The value. */ private final String value; + /** + * Instantiates a new unit kind. + * + * @param v the v + */ UnitKind(String v) { value = v; } + /** + * Value. + * + * @return the string + */ public String value() { return value; } + /** + * From value. + * + * @param v the v + * @return the unit kind + */ public static UnitKind fromValue(String v) { for (UnitKind c: UnitKind.values()) { if (c.value.equals(v)) { diff --git a/src/org/sbml/sbml/level2/version4/package-info.java b/src/org/sbml/sbml/level2/version4/package-info.java index f8446a7..08ecd76 100644 --- a/src/org/sbml/sbml/level2/version4/package-info.java +++ b/src/org/sbml/sbml/level2/version4/package-info.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb diff --git a/src/org/sbml/wrapper/CompartmentAliasWrapper.java b/src/org/sbml/wrapper/CompartmentAliasWrapper.java index 4c6f502..9cdd202 100644 --- a/src/org/sbml/wrapper/CompartmentAliasWrapper.java +++ b/src/org/sbml/wrapper/CompartmentAliasWrapper.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ /* * */ diff --git a/src/org/sbml/wrapper/CompartmentWrapper.java b/src/org/sbml/wrapper/CompartmentWrapper.java index 1d3132b..5fde06d 100644 --- a/src/org/sbml/wrapper/CompartmentWrapper.java +++ b/src/org/sbml/wrapper/CompartmentWrapper.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ /* * */ diff --git a/src/org/sbml/wrapper/ComplexSpeciesAliasWrapper.java b/src/org/sbml/wrapper/ComplexSpeciesAliasWrapper.java index a60ef09..a3e8016 100644 --- a/src/org/sbml/wrapper/ComplexSpeciesAliasWrapper.java +++ b/src/org/sbml/wrapper/ComplexSpeciesAliasWrapper.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ /* * */ diff --git a/src/org/sbml/wrapper/ModelWrapper.java b/src/org/sbml/wrapper/ModelWrapper.java index 1b15719..8762fae 100644 --- a/src/org/sbml/wrapper/ModelWrapper.java +++ b/src/org/sbml/wrapper/ModelWrapper.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ /* * */ diff --git a/src/org/sbml/wrapper/ModifierSpeciesReferenceWrapper.java b/src/org/sbml/wrapper/ModifierSpeciesReferenceWrapper.java index 99602b1..7ef03da 100644 --- a/src/org/sbml/wrapper/ModifierSpeciesReferenceWrapper.java +++ b/src/org/sbml/wrapper/ModifierSpeciesReferenceWrapper.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ /* * */ @@ -227,9 +242,9 @@ public List getEditPoints(){ } /** - * @param editPointListToStringList - * void - * TODO + * Sets the edits the point list. + * + * @param editPointList the new edits the point list */ public void setEditPointList(List editPointList) { modification.getEditPoints().addAll(editPointList); diff --git a/src/org/sbml/wrapper/ObjectFactory.java b/src/org/sbml/wrapper/ObjectFactory.java index 993f05b..ac004fd 100644 --- a/src/org/sbml/wrapper/ObjectFactory.java +++ b/src/org/sbml/wrapper/ObjectFactory.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ /* * */ @@ -27,16 +42,16 @@ public class ObjectFactory { /** The model. */ - static Model model; + private static Model model; /** The model wrapper. */ - static ModelWrapper modelWrapper; + private static ModelWrapper modelWrapper; /** The context. */ - static JAXBContext context; + private static JAXBContext context; /** The sbml. */ - static Sbml sbml; + private static Sbml sbml; /** * Unmarshal SBML. diff --git a/src/org/sbml/wrapper/ReactionWrapper.java b/src/org/sbml/wrapper/ReactionWrapper.java index bea5dfb..50f2714 100644 --- a/src/org/sbml/wrapper/ReactionWrapper.java +++ b/src/org/sbml/wrapper/ReactionWrapper.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ /* * */ diff --git a/src/org/sbml/wrapper/SpeciesAliasWrapper.java b/src/org/sbml/wrapper/SpeciesAliasWrapper.java index cc4386d..10f9a5a 100644 --- a/src/org/sbml/wrapper/SpeciesAliasWrapper.java +++ b/src/org/sbml/wrapper/SpeciesAliasWrapper.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ /* * */ @@ -370,6 +385,11 @@ public void setComplexSpeciesAliased(ComplexSpeciesAlias value) { setComplexSpeciesAlias(value.getId()); } + /** + * Checks if is complex species. + * + * @return true, if is complex species + */ public boolean isComplexSpecies(){ return isSetComplexSpeciesAlias(); } diff --git a/src/org/sbml/wrapper/SpeciesReferenceWrapper.java b/src/org/sbml/wrapper/SpeciesReferenceWrapper.java index 5a6531f..f8ebf00 100644 --- a/src/org/sbml/wrapper/SpeciesReferenceWrapper.java +++ b/src/org/sbml/wrapper/SpeciesReferenceWrapper.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ /* * */ diff --git a/src/org/sbml/wrapper/SpeciesWrapper.java b/src/org/sbml/wrapper/SpeciesWrapper.java index bf81bc3..155d920 100644 --- a/src/org/sbml/wrapper/SpeciesWrapper.java +++ b/src/org/sbml/wrapper/SpeciesWrapper.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ /* * */ diff --git a/src/org/sbml/wrapper/package-info.java b/src/org/sbml/wrapper/package-info.java index 6c5c743..122209c 100644 --- a/src/org/sbml/wrapper/package-info.java +++ b/src/org/sbml/wrapper/package-info.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ /** * @author Kaito Ii * diff --git a/src/org/w3/_1998/math/mathml/Annotation.java b/src/org/w3/_1998/math/mathml/Annotation.java index 668a476..f660e2d 100644 --- a/src/org/w3/_1998/math/mathml/Annotation.java +++ b/src/org/w3/_1998/math/mathml/Annotation.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -22,6 +37,7 @@ import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter; +// TODO: Auto-generated Javadoc /** *

Java class for Annotation complex type. * @@ -45,15 +61,24 @@ }) public class Annotation { + /** The value. */ @XmlValue protected String value; + + /** The encoding. */ @XmlAttribute(name = "encoding", required = true) protected String encoding; + + /** The clazz. */ @XmlAttribute(name = "class") @XmlSchemaType(name = "NMTOKENS") protected List clazz; + + /** The style. */ @XmlAttribute(name = "style") protected String style; + + /** The id. */ @XmlAttribute(name = "id") @XmlJavaTypeAdapter(CollapsedStringAdapter.class) @XmlID @@ -127,8 +152,8 @@ public void setEncoding(String value) { *

* Objects of the following type(s) are allowed in the list * {@link String } - * - * + * + * @return the clazz */ public List getClazz() { if (clazz == null) { diff --git a/src/org/w3/_1998/math/mathml/AnnotationXml.java b/src/org/w3/_1998/math/mathml/AnnotationXml.java index e0d03e5..fe30ae5 100644 --- a/src/org/w3/_1998/math/mathml/AnnotationXml.java +++ b/src/org/w3/_1998/math/mathml/AnnotationXml.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -24,6 +39,7 @@ import org.w3c.dom.Element; +// TODO: Auto-generated Javadoc /** *

Java class for Annotation-xml complex type. * @@ -50,15 +66,24 @@ }) public class AnnotationXml { + /** The any. */ @XmlAnyElement protected List any; + + /** The encoding. */ @XmlAttribute(name = "encoding", required = true) protected String encoding; + + /** The clazz. */ @XmlAttribute(name = "class") @XmlSchemaType(name = "NMTOKENS") protected List clazz; + + /** The style. */ @XmlAttribute(name = "style") protected String style; + + /** The id. */ @XmlAttribute(name = "id") @XmlJavaTypeAdapter(CollapsedStringAdapter.class) @XmlID @@ -84,8 +109,8 @@ public class AnnotationXml { *

* Objects of the following type(s) are allowed in the list * {@link Element } - * - * + * + * @return the any */ public List getAny() { if (any == null) { @@ -137,8 +162,8 @@ public void setEncoding(String value) { *

* Objects of the following type(s) are allowed in the list * {@link String } - * - * + * + * @return the clazz */ public List getClazz() { if (clazz == null) { diff --git a/src/org/w3/_1998/math/mathml/Apply.java b/src/org/w3/_1998/math/mathml/Apply.java index 8f0b6ce..7972fa4 100644 --- a/src/org/w3/_1998/math/mathml/Apply.java +++ b/src/org/w3/_1998/math/mathml/Apply.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -19,6 +34,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for Apply complex type. * @@ -154,57 +170,160 @@ public class Apply extends MathBase { + /** The ci. */ protected Ci ci; + + /** The csymbol. */ protected Csymbol csymbol; + + /** The eq. */ protected MathBase eq; + + /** The neq. */ protected MathBase neq; + + /** The gt. */ protected MathBase gt; + + /** The lt. */ protected MathBase lt; + + /** The geq. */ protected MathBase geq; + + /** The leq. */ protected MathBase leq; + + /** The plus. */ protected MathBase plus; + + /** The minus. */ protected MathBase minus; + + /** The times. */ protected MathBase times; + + /** The divide. */ protected MathBase divide; + + /** The power. */ protected MathBase power; + + /** The root. */ protected MathBase root; + + /** The degree. */ protected NodeContainer degree; + + /** The abs. */ protected MathBase abs; + + /** The exp. */ protected MathBase exp; + + /** The ln. */ protected MathBase ln; + + /** The log. */ protected MathBase log; + + /** The logbase. */ protected NodeContainer logbase; + + /** The floor. */ protected MathBase floor; + + /** The ceiling. */ protected MathBase ceiling; + + /** The factorial. */ protected MathBase factorial; + + /** The and. */ protected MathBase and; + + /** The or. */ protected MathBase or; + + /** The xor. */ protected MathBase xor; + + /** The not. */ protected MathBase not; + + /** The sin. */ protected MathBase sin; + + /** The cos. */ protected MathBase cos; + + /** The tan. */ protected MathBase tan; + + /** The sec. */ protected MathBase sec; + + /** The csc. */ protected MathBase csc; + + /** The cot. */ protected MathBase cot; + + /** The sinh. */ protected MathBase sinh; + + /** The cosh. */ protected MathBase cosh; + + /** The tanh. */ protected MathBase tanh; + + /** The sech. */ protected MathBase sech; + + /** The csch. */ protected MathBase csch; + + /** The coth. */ protected MathBase coth; + + /** The arcsin. */ protected MathBase arcsin; + + /** The arccos. */ protected MathBase arccos; + + /** The arctan. */ protected MathBase arctan; + + /** The arcsec. */ protected MathBase arcsec; + + /** The arccsc. */ protected MathBase arccsc; + + /** The arccot. */ protected MathBase arccot; + + /** The arcsinh. */ protected MathBase arcsinh; + + /** The arccosh. */ protected MathBase arccosh; + + /** The arctanh. */ protected MathBase arctanh; + + /** The arcsech. */ protected MathBase arcsech; + + /** The arccsch. */ protected MathBase arccsch; + + /** The arccoth. */ protected MathBase arccoth; + + /** The node. */ @XmlElementRefs({ @XmlElementRef(name = "infinity", namespace = "http://www.w3.org/1998/Math/MathML", type = JAXBElement.class, required = false), @XmlElementRef(name = "notanumber", namespace = "http://www.w3.org/1998/Math/MathML", type = JAXBElement.class, required = false), @@ -1475,8 +1594,8 @@ public void setArccoth(MathBase value) { * {@link JAXBElement }{@code <}{@link Piecewise }{@code >} * {@link JAXBElement }{@code <}{@link Ci }{@code >} * {@link JAXBElement }{@code <}{@link MathBase }{@code >} - * - * + * + * @return the node */ public List> getNode() { if (node == null) { diff --git a/src/org/w3/_1998/math/mathml/Bvar.java b/src/org/w3/_1998/math/mathml/Bvar.java index 10ffd3a..d17af93 100644 --- a/src/org/w3/_1998/math/mathml/Bvar.java +++ b/src/org/w3/_1998/math/mathml/Bvar.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for Bvar complex type. * @@ -41,6 +57,7 @@ public class Bvar extends MathBase { + /** The ci. */ @XmlElement(required = true) protected Ci ci; diff --git a/src/org/w3/_1998/math/mathml/Ci.java b/src/org/w3/_1998/math/mathml/Ci.java index 7cbac86..7fde3d4 100644 --- a/src/org/w3/_1998/math/mathml/Ci.java +++ b/src/org/w3/_1998/math/mathml/Ci.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -22,6 +37,7 @@ import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter; +// TODO: Auto-generated Javadoc /** *

Java class for Ci complex type. * @@ -46,15 +62,24 @@ }) public class Ci { + /** The value. */ @XmlValue protected String value; + + /** The definition URL. */ @XmlAttribute(name = "definitionURL") protected String definitionURL; + + /** The clazz. */ @XmlAttribute(name = "class") @XmlSchemaType(name = "NMTOKENS") protected List clazz; + + /** The style. */ @XmlAttribute(name = "style") protected String style; + + /** The id. */ @XmlAttribute(name = "id") @XmlJavaTypeAdapter(CollapsedStringAdapter.class) @XmlID @@ -128,8 +153,8 @@ public void setDefinitionURL(String value) { *

* Objects of the following type(s) are allowed in the list * {@link String } - * - * + * + * @return the clazz */ public List getClazz() { if (clazz == null) { diff --git a/src/org/w3/_1998/math/mathml/Cn.java b/src/org/w3/_1998/math/mathml/Cn.java index 176050c..aeba9ee 100644 --- a/src/org/w3/_1998/math/mathml/Cn.java +++ b/src/org/w3/_1998/math/mathml/Cn.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -25,6 +40,7 @@ import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter; +// TODO: Auto-generated Javadoc /** *

Java class for Cn complex type. * @@ -51,17 +67,26 @@ }) public class Cn { + /** The content. */ @XmlElementRef(name = "sep", namespace = "http://www.w3.org/1998/Math/MathML", type = JAXBElement.class, required = false) @XmlMixed protected List content; + + /** The type. */ @XmlAttribute(name = "type") @XmlJavaTypeAdapter(CollapsedStringAdapter.class) protected String type; + + /** The clazz. */ @XmlAttribute(name = "class") @XmlSchemaType(name = "NMTOKENS") protected List clazz; + + /** The style. */ @XmlAttribute(name = "style") protected String style; + + /** The id. */ @XmlAttribute(name = "id") @XmlJavaTypeAdapter(CollapsedStringAdapter.class) @XmlID @@ -88,8 +113,8 @@ public class Cn { * Objects of the following type(s) are allowed in the list * {@link JAXBElement }{@code <}{@link SepType }{@code >} * {@link String } - * - * + * + * @return the content */ public List getContent() { if (content == null) { @@ -141,8 +166,8 @@ public void setType(String value) { *

* Objects of the following type(s) are allowed in the list * {@link String } - * - * + * + * @return the clazz */ public List getClazz() { if (clazz == null) { diff --git a/src/org/w3/_1998/math/mathml/Csymbol.java b/src/org/w3/_1998/math/mathml/Csymbol.java index 1742f0a..58e32ac 100644 --- a/src/org/w3/_1998/math/mathml/Csymbol.java +++ b/src/org/w3/_1998/math/mathml/Csymbol.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -22,6 +37,7 @@ import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter; +// TODO: Auto-generated Javadoc /** *

Java class for Csymbol complex type. * @@ -47,18 +63,29 @@ }) public class Csymbol { + /** The value. */ @XmlValue protected String value; + + /** The encoding. */ @XmlAttribute(name = "encoding", required = true) @XmlSchemaType(name = "anySimpleType") protected String encoding; + + /** The definition URL. */ @XmlAttribute(name = "definitionURL", required = true) protected CsymbolURI definitionURL; + + /** The clazz. */ @XmlAttribute(name = "class") @XmlSchemaType(name = "NMTOKENS") protected List clazz; + + /** The style. */ @XmlAttribute(name = "style") protected String style; + + /** The id. */ @XmlAttribute(name = "id") @XmlJavaTypeAdapter(CollapsedStringAdapter.class) @XmlID @@ -160,8 +187,8 @@ public void setDefinitionURL(CsymbolURI value) { *

* Objects of the following type(s) are allowed in the list * {@link String } - * - * + * + * @return the clazz */ public List getClazz() { if (clazz == null) { diff --git a/src/org/w3/_1998/math/mathml/CsymbolURI.java b/src/org/w3/_1998/math/mathml/CsymbolURI.java index e8f82a5..0d9e601 100644 --- a/src/org/w3/_1998/math/mathml/CsymbolURI.java +++ b/src/org/w3/_1998/math/mathml/CsymbolURI.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -13,6 +28,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for CsymbolURI. * @@ -32,20 +48,41 @@ @XmlEnum public enum CsymbolURI { + /** The http www sbml org sbml symbols time. */ @XmlEnumValue("http://www.sbml.org/sbml/symbols/time") HTTP_WWW_SBML_ORG_SBML_SYMBOLS_TIME("http://www.sbml.org/sbml/symbols/time"), + + /** The http www sbml org sbml symbols delay. */ @XmlEnumValue("http://www.sbml.org/sbml/symbols/delay") HTTP_WWW_SBML_ORG_SBML_SYMBOLS_DELAY("http://www.sbml.org/sbml/symbols/delay"); + + /** The value. */ private final String value; + /** + * Instantiates a new csymbol URI. + * + * @param v the v + */ CsymbolURI(String v) { value = v; } + /** + * Value. + * + * @return the string + */ public String value() { return value; } + /** + * From value. + * + * @param v the v + * @return the csymbol URI + */ public static CsymbolURI fromValue(String v) { for (CsymbolURI c: CsymbolURI.values()) { if (c.value.equals(v)) { diff --git a/src/org/w3/_1998/math/mathml/Lambda.java b/src/org/w3/_1998/math/mathml/Lambda.java index 88f289f..e9307dd 100644 --- a/src/org/w3/_1998/math/mathml/Lambda.java +++ b/src/org/w3/_1998/math/mathml/Lambda.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -17,6 +32,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for Lambda complex type. * @@ -57,20 +73,45 @@ public class Lambda extends MathBase { + /** The bvar. */ protected List bvar; + + /** The apply. */ protected Apply apply; + + /** The cn. */ protected Cn cn; + + /** The ci. */ protected Ci ci; + + /** The csymbol. */ protected Csymbol csymbol; + + /** The true. */ @XmlElement(name = "true") protected MathBase _true; + + /** The false. */ @XmlElement(name = "false") protected MathBase _false; + + /** The notanumber. */ protected MathBase notanumber; + + /** The pi. */ protected MathBase pi; + + /** The infinity. */ protected MathBase infinity; + + /** The exponentiale. */ protected MathBase exponentiale; + + /** The semantics. */ protected Semantics semantics; + + /** The piecewise. */ protected Piecewise piecewise; /** @@ -92,8 +133,8 @@ public class Lambda *

* Objects of the following type(s) are allowed in the list * {@link Bvar } - * - * + * + * @return the bvar */ public List getBvar() { if (bvar == null) { diff --git a/src/org/w3/_1998/math/mathml/Math.java b/src/org/w3/_1998/math/mathml/Math.java index db4b64f..cc4102b 100644 --- a/src/org/w3/_1998/math/mathml/Math.java +++ b/src/org/w3/_1998/math/mathml/Math.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for Math complex type. * @@ -54,20 +70,45 @@ public class Math extends MathBase { + /** The apply. */ protected Apply apply; + + /** The cn. */ protected Cn cn; + + /** The ci. */ protected Ci ci; + + /** The csymbol. */ protected Csymbol csymbol; + + /** The true. */ @XmlElement(name = "true") protected MathBase _true; + + /** The false. */ @XmlElement(name = "false") protected MathBase _false; + + /** The notanumber. */ protected MathBase notanumber; + + /** The pi. */ protected MathBase pi; + + /** The infinity. */ protected MathBase infinity; + + /** The exponentiale. */ protected MathBase exponentiale; + + /** The semantics. */ protected Semantics semantics; + + /** The piecewise. */ protected Piecewise piecewise; + + /** The lambda. */ protected Lambda lambda; /** diff --git a/src/org/w3/_1998/math/mathml/MathBase.java b/src/org/w3/_1998/math/mathml/MathBase.java index 163a80c..2477685 100644 --- a/src/org/w3/_1998/math/mathml/MathBase.java +++ b/src/org/w3/_1998/math/mathml/MathBase.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -22,6 +37,7 @@ import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter; +// TODO: Auto-generated Javadoc /** *

Java class for MathBase complex type. * @@ -54,11 +70,16 @@ }) public class MathBase { + /** The clazz. */ @XmlAttribute(name = "class") @XmlSchemaType(name = "NMTOKENS") protected List clazz; + + /** The style. */ @XmlAttribute(name = "style") protected String style; + + /** The id. */ @XmlAttribute(name = "id") @XmlJavaTypeAdapter(CollapsedStringAdapter.class) @XmlID @@ -84,8 +105,8 @@ public class MathBase { *

* Objects of the following type(s) are allowed in the list * {@link String } - * - * + * + * @return the clazz */ public List getClazz() { if (clazz == null) { diff --git a/src/org/w3/_1998/math/mathml/NodeContainer.java b/src/org/w3/_1998/math/mathml/NodeContainer.java index 10e3660..dbd11f7 100644 --- a/src/org/w3/_1998/math/mathml/NodeContainer.java +++ b/src/org/w3/_1998/math/mathml/NodeContainer.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for NodeContainer complex type. * @@ -50,19 +66,42 @@ public class NodeContainer extends MathBase { + /** The apply. */ protected Apply apply; + + /** The cn. */ protected Cn cn; + + /** The ci. */ protected Ci ci; + + /** The csymbol. */ protected Csymbol csymbol; + + /** The true. */ @XmlElement(name = "true") protected MathBase _true; + + /** The false. */ @XmlElement(name = "false") protected MathBase _false; + + /** The notanumber. */ protected MathBase notanumber; + + /** The pi. */ protected MathBase pi; + + /** The infinity. */ protected MathBase infinity; + + /** The exponentiale. */ protected MathBase exponentiale; + + /** The semantics. */ protected Semantics semantics; + + /** The piecewise. */ protected Piecewise piecewise; /** diff --git a/src/org/w3/_1998/math/mathml/ObjectFactory.java b/src/org/w3/_1998/math/mathml/ObjectFactory.java index 927b2ae..b63245f 100644 --- a/src/org/w3/_1998/math/mathml/ObjectFactory.java +++ b/src/org/w3/_1998/math/mathml/ObjectFactory.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.namespace.QName; +// TODO: Auto-generated Javadoc /** * This object contains factory methods for each * Java content interface and Java element interface @@ -31,19 +47,46 @@ @XmlRegistry public class ObjectFactory { + /** The Constant _Math_QNAME. */ private final static QName _Math_QNAME = new QName("http://www.w3.org/1998/Math/MathML", "math"); + + /** The Constant _ApplyCsymbol_QNAME. */ private final static QName _ApplyCsymbol_QNAME = new QName("http://www.w3.org/1998/Math/MathML", "csymbol"); + + /** The Constant _ApplyPi_QNAME. */ private final static QName _ApplyPi_QNAME = new QName("http://www.w3.org/1998/Math/MathML", "pi"); + + /** The Constant _ApplyTrue_QNAME. */ private final static QName _ApplyTrue_QNAME = new QName("http://www.w3.org/1998/Math/MathML", "true"); + + /** The Constant _ApplyFalse_QNAME. */ private final static QName _ApplyFalse_QNAME = new QName("http://www.w3.org/1998/Math/MathML", "false"); + + /** The Constant _ApplyCn_QNAME. */ private final static QName _ApplyCn_QNAME = new QName("http://www.w3.org/1998/Math/MathML", "cn"); + + /** The Constant _ApplySemantics_QNAME. */ private final static QName _ApplySemantics_QNAME = new QName("http://www.w3.org/1998/Math/MathML", "semantics"); + + /** The Constant _ApplyInfinity_QNAME. */ private final static QName _ApplyInfinity_QNAME = new QName("http://www.w3.org/1998/Math/MathML", "infinity"); + + /** The Constant _ApplyPiecewise_QNAME. */ private final static QName _ApplyPiecewise_QNAME = new QName("http://www.w3.org/1998/Math/MathML", "piecewise"); + + /** The Constant _ApplyNotanumber_QNAME. */ private final static QName _ApplyNotanumber_QNAME = new QName("http://www.w3.org/1998/Math/MathML", "notanumber"); + + /** The Constant _ApplyApply_QNAME. */ private final static QName _ApplyApply_QNAME = new QName("http://www.w3.org/1998/Math/MathML", "apply"); + + /** The Constant _ApplyExponentiale_QNAME. */ private final static QName _ApplyExponentiale_QNAME = new QName("http://www.w3.org/1998/Math/MathML", "exponentiale"); + + /** The Constant _ApplyCi_QNAME. */ private final static QName _ApplyCi_QNAME = new QName("http://www.w3.org/1998/Math/MathML", "ci"); + + /** The Constant _CnSep_QNAME. */ private final static QName _CnSep_QNAME = new QName("http://www.w3.org/1998/Math/MathML", "sep"); /** @@ -54,136 +97,154 @@ public ObjectFactory() { } /** - * Create an instance of {@link Math } - * + * Create an instance of {@link Math }. + * + * @return the math */ public Math createMath() { return new Math(); } /** - * Create an instance of {@link Csymbol } - * + * Create an instance of {@link Csymbol }. + * + * @return the csymbol */ public Csymbol createCsymbol() { return new Csymbol(); } /** - * Create an instance of {@link Ci } - * + * Create an instance of {@link Ci }. + * + * @return the ci */ public Ci createCi() { return new Ci(); } /** - * Create an instance of {@link Apply } - * + * Create an instance of {@link Apply }. + * + * @return the apply */ public Apply createApply() { return new Apply(); } /** - * Create an instance of {@link SepType } - * + * Create an instance of {@link SepType }. + * + * @return the sep type */ public SepType createSepType() { return new SepType(); } /** - * Create an instance of {@link NodeContainer } - * + * Create an instance of {@link NodeContainer }. + * + * @return the node container */ public NodeContainer createNodeContainer() { return new NodeContainer(); } /** - * Create an instance of {@link Cn } - * + * Create an instance of {@link Cn }. + * + * @return the cn */ public Cn createCn() { return new Cn(); } /** - * Create an instance of {@link AnnotationXml } - * + * Create an instance of {@link AnnotationXml }. + * + * @return the annotation xml */ public AnnotationXml createAnnotationXml() { return new AnnotationXml(); } /** - * Create an instance of {@link Annotation } - * + * Create an instance of {@link Annotation }. + * + * @return the annotation */ public Annotation createAnnotation() { return new Annotation(); } /** - * Create an instance of {@link Otherwise } - * + * Create an instance of {@link Otherwise }. + * + * @return the otherwise */ public Otherwise createOtherwise() { return new Otherwise(); } /** - * Create an instance of {@link Semantics } - * + * Create an instance of {@link Semantics }. + * + * @return the semantics */ public Semantics createSemantics() { return new Semantics(); } /** - * Create an instance of {@link Piece } - * + * Create an instance of {@link Piece }. + * + * @return the piece */ public Piece createPiece() { return new Piece(); } /** - * Create an instance of {@link Piecewise } - * + * Create an instance of {@link Piecewise }. + * + * @return the piecewise */ public Piecewise createPiecewise() { return new Piecewise(); } /** - * Create an instance of {@link Bvar } - * + * Create an instance of {@link Bvar }. + * + * @return the bvar */ public Bvar createBvar() { return new Bvar(); } /** - * Create an instance of {@link MathBase } - * + * Create an instance of {@link MathBase }. + * + * @return the math base */ public MathBase createMathBase() { return new MathBase(); } /** - * Create an instance of {@link Lambda } - * + * Create an instance of {@link Lambda }. + * + * @return the lambda */ public Lambda createLambda() { return new Lambda(); } /** - * Create an instance of {@link JAXBElement }{@code <}{@link Math }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link Math }{@code >}}. + * + * @param value the value + * @return the JAXB element< math> */ @XmlElementDecl(namespace = "http://www.w3.org/1998/Math/MathML", name = "math") public JAXBElement createMath(Math value) { @@ -191,8 +252,10 @@ public JAXBElement createMath(Math value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link Csymbol }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link Csymbol }{@code >}}. + * + * @param value the value + * @return the JAXB element< csymbol> */ @XmlElementDecl(namespace = "http://www.w3.org/1998/Math/MathML", name = "csymbol", scope = Apply.class) public JAXBElement createApplyCsymbol(Csymbol value) { @@ -200,8 +263,10 @@ public JAXBElement createApplyCsymbol(Csymbol value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link MathBase }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link MathBase }{@code >}}. + * + * @param value the value + * @return the JAXB element< math base> */ @XmlElementDecl(namespace = "http://www.w3.org/1998/Math/MathML", name = "pi", scope = Apply.class) public JAXBElement createApplyPi(MathBase value) { @@ -209,8 +274,10 @@ public JAXBElement createApplyPi(MathBase value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link MathBase }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link MathBase }{@code >}}. + * + * @param value the value + * @return the JAXB element< math base> */ @XmlElementDecl(namespace = "http://www.w3.org/1998/Math/MathML", name = "true", scope = Apply.class) public JAXBElement createApplyTrue(MathBase value) { @@ -218,8 +285,10 @@ public JAXBElement createApplyTrue(MathBase value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link MathBase }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link MathBase }{@code >}}. + * + * @param value the value + * @return the JAXB element< math base> */ @XmlElementDecl(namespace = "http://www.w3.org/1998/Math/MathML", name = "false", scope = Apply.class) public JAXBElement createApplyFalse(MathBase value) { @@ -227,8 +296,10 @@ public JAXBElement createApplyFalse(MathBase value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link Cn }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link Cn }{@code >}}. + * + * @param value the value + * @return the JAXB element< cn> */ @XmlElementDecl(namespace = "http://www.w3.org/1998/Math/MathML", name = "cn", scope = Apply.class) public JAXBElement createApplyCn(Cn value) { @@ -236,8 +307,10 @@ public JAXBElement createApplyCn(Cn value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link Semantics }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link Semantics }{@code >}}. + * + * @param value the value + * @return the JAXB element< semantics> */ @XmlElementDecl(namespace = "http://www.w3.org/1998/Math/MathML", name = "semantics", scope = Apply.class) public JAXBElement createApplySemantics(Semantics value) { @@ -245,8 +318,10 @@ public JAXBElement createApplySemantics(Semantics value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link MathBase }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link MathBase }{@code >}}. + * + * @param value the value + * @return the JAXB element< math base> */ @XmlElementDecl(namespace = "http://www.w3.org/1998/Math/MathML", name = "infinity", scope = Apply.class) public JAXBElement createApplyInfinity(MathBase value) { @@ -254,8 +329,10 @@ public JAXBElement createApplyInfinity(MathBase value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link Piecewise }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link Piecewise }{@code >}}. + * + * @param value the value + * @return the JAXB element< piecewise> */ @XmlElementDecl(namespace = "http://www.w3.org/1998/Math/MathML", name = "piecewise", scope = Apply.class) public JAXBElement createApplyPiecewise(Piecewise value) { @@ -263,8 +340,10 @@ public JAXBElement createApplyPiecewise(Piecewise value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link MathBase }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link MathBase }{@code >}}. + * + * @param value the value + * @return the JAXB element< math base> */ @XmlElementDecl(namespace = "http://www.w3.org/1998/Math/MathML", name = "notanumber", scope = Apply.class) public JAXBElement createApplyNotanumber(MathBase value) { @@ -272,8 +351,10 @@ public JAXBElement createApplyNotanumber(MathBase value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link Apply }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link Apply }{@code >}}. + * + * @param value the value + * @return the JAXB element< apply> */ @XmlElementDecl(namespace = "http://www.w3.org/1998/Math/MathML", name = "apply", scope = Apply.class) public JAXBElement createApplyApply(Apply value) { @@ -281,8 +362,10 @@ public JAXBElement createApplyApply(Apply value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link MathBase }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link MathBase }{@code >}}. + * + * @param value the value + * @return the JAXB element< math base> */ @XmlElementDecl(namespace = "http://www.w3.org/1998/Math/MathML", name = "exponentiale", scope = Apply.class) public JAXBElement createApplyExponentiale(MathBase value) { @@ -290,8 +373,10 @@ public JAXBElement createApplyExponentiale(MathBase value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link Ci }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link Ci }{@code >}}. + * + * @param value the value + * @return the JAXB element< ci> */ @XmlElementDecl(namespace = "http://www.w3.org/1998/Math/MathML", name = "ci", scope = Apply.class) public JAXBElement createApplyCi(Ci value) { @@ -299,8 +384,10 @@ public JAXBElement createApplyCi(Ci value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link SepType }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link SepType }{@code >}}. + * + * @param value the value + * @return the JAXB element< sep type> */ @XmlElementDecl(namespace = "http://www.w3.org/1998/Math/MathML", name = "sep", scope = Cn.class) public JAXBElement createCnSep(SepType value) { @@ -308,8 +395,10 @@ public JAXBElement createCnSep(SepType value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link Csymbol }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link Csymbol }{@code >}}. + * + * @param value the value + * @return the JAXB element< csymbol> */ @XmlElementDecl(namespace = "http://www.w3.org/1998/Math/MathML", name = "csymbol", scope = Piece.class) public JAXBElement createPieceCsymbol(Csymbol value) { @@ -317,8 +406,10 @@ public JAXBElement createPieceCsymbol(Csymbol value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link MathBase }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link MathBase }{@code >}}. + * + * @param value the value + * @return the JAXB element< math base> */ @XmlElementDecl(namespace = "http://www.w3.org/1998/Math/MathML", name = "pi", scope = Piece.class) public JAXBElement createPiecePi(MathBase value) { @@ -326,8 +417,10 @@ public JAXBElement createPiecePi(MathBase value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link MathBase }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link MathBase }{@code >}}. + * + * @param value the value + * @return the JAXB element< math base> */ @XmlElementDecl(namespace = "http://www.w3.org/1998/Math/MathML", name = "true", scope = Piece.class) public JAXBElement createPieceTrue(MathBase value) { @@ -335,8 +428,10 @@ public JAXBElement createPieceTrue(MathBase value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link MathBase }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link MathBase }{@code >}}. + * + * @param value the value + * @return the JAXB element< math base> */ @XmlElementDecl(namespace = "http://www.w3.org/1998/Math/MathML", name = "false", scope = Piece.class) public JAXBElement createPieceFalse(MathBase value) { @@ -344,8 +439,10 @@ public JAXBElement createPieceFalse(MathBase value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link Cn }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link Cn }{@code >}}. + * + * @param value the value + * @return the JAXB element< cn> */ @XmlElementDecl(namespace = "http://www.w3.org/1998/Math/MathML", name = "cn", scope = Piece.class) public JAXBElement createPieceCn(Cn value) { @@ -353,8 +450,10 @@ public JAXBElement createPieceCn(Cn value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link Semantics }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link Semantics }{@code >}}. + * + * @param value the value + * @return the JAXB element< semantics> */ @XmlElementDecl(namespace = "http://www.w3.org/1998/Math/MathML", name = "semantics", scope = Piece.class) public JAXBElement createPieceSemantics(Semantics value) { @@ -362,8 +461,10 @@ public JAXBElement createPieceSemantics(Semantics value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link MathBase }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link MathBase }{@code >}}. + * + * @param value the value + * @return the JAXB element< math base> */ @XmlElementDecl(namespace = "http://www.w3.org/1998/Math/MathML", name = "infinity", scope = Piece.class) public JAXBElement createPieceInfinity(MathBase value) { @@ -371,8 +472,10 @@ public JAXBElement createPieceInfinity(MathBase value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link Piecewise }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link Piecewise }{@code >}}. + * + * @param value the value + * @return the JAXB element< piecewise> */ @XmlElementDecl(namespace = "http://www.w3.org/1998/Math/MathML", name = "piecewise", scope = Piece.class) public JAXBElement createPiecePiecewise(Piecewise value) { @@ -380,8 +483,10 @@ public JAXBElement createPiecePiecewise(Piecewise value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link MathBase }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link MathBase }{@code >}}. + * + * @param value the value + * @return the JAXB element< math base> */ @XmlElementDecl(namespace = "http://www.w3.org/1998/Math/MathML", name = "notanumber", scope = Piece.class) public JAXBElement createPieceNotanumber(MathBase value) { @@ -389,8 +494,10 @@ public JAXBElement createPieceNotanumber(MathBase value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link Apply }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link Apply }{@code >}}. + * + * @param value the value + * @return the JAXB element< apply> */ @XmlElementDecl(namespace = "http://www.w3.org/1998/Math/MathML", name = "apply", scope = Piece.class) public JAXBElement createPieceApply(Apply value) { @@ -398,8 +505,10 @@ public JAXBElement createPieceApply(Apply value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link MathBase }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link MathBase }{@code >}}. + * + * @param value the value + * @return the JAXB element< math base> */ @XmlElementDecl(namespace = "http://www.w3.org/1998/Math/MathML", name = "exponentiale", scope = Piece.class) public JAXBElement createPieceExponentiale(MathBase value) { @@ -407,8 +516,10 @@ public JAXBElement createPieceExponentiale(MathBase value) { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link Ci }{@code >}} - * + * Create an instance of {@link JAXBElement }{@code <}{@link Ci }{@code >}}. + * + * @param value the value + * @return the JAXB element< ci> */ @XmlElementDecl(namespace = "http://www.w3.org/1998/Math/MathML", name = "ci", scope = Piece.class) public JAXBElement createPieceCi(Ci value) { diff --git a/src/org/w3/_1998/math/mathml/Otherwise.java b/src/org/w3/_1998/math/mathml/Otherwise.java index 91ab63d..81caf94 100644 --- a/src/org/w3/_1998/math/mathml/Otherwise.java +++ b/src/org/w3/_1998/math/mathml/Otherwise.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -14,6 +29,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for Otherwise complex type. * @@ -50,19 +66,42 @@ public class Otherwise extends MathBase { + /** The apply. */ protected Apply apply; + + /** The cn. */ protected Cn cn; + + /** The ci. */ protected Ci ci; + + /** The csymbol. */ protected Csymbol csymbol; + + /** The true. */ @XmlElement(name = "true") protected MathBase _true; + + /** The false. */ @XmlElement(name = "false") protected MathBase _false; + + /** The notanumber. */ protected MathBase notanumber; + + /** The pi. */ protected MathBase pi; + + /** The infinity. */ protected MathBase infinity; + + /** The exponentiale. */ protected MathBase exponentiale; + + /** The semantics. */ protected Semantics semantics; + + /** The piecewise. */ protected Piecewise piecewise; /** diff --git a/src/org/w3/_1998/math/mathml/Piece.java b/src/org/w3/_1998/math/mathml/Piece.java index a8cffee..8ad517a 100644 --- a/src/org/w3/_1998/math/mathml/Piece.java +++ b/src/org/w3/_1998/math/mathml/Piece.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -19,6 +34,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for Piece complex type. * @@ -44,6 +60,7 @@ public class Piece extends MathBase { + /** The node. */ @XmlElementRefs({ @XmlElementRef(name = "true", namespace = "http://www.w3.org/1998/Math/MathML", type = JAXBElement.class, required = false), @XmlElementRef(name = "apply", namespace = "http://www.w3.org/1998/Math/MathML", type = JAXBElement.class, required = false), @@ -90,8 +107,8 @@ public class Piece * {@link JAXBElement }{@code <}{@link Csymbol }{@code >} * {@link JAXBElement }{@code <}{@link MathBase }{@code >} * {@link JAXBElement }{@code <}{@link MathBase }{@code >} - * - * + * + * @return the node */ public List> getNode() { if (node == null) { diff --git a/src/org/w3/_1998/math/mathml/Piecewise.java b/src/org/w3/_1998/math/mathml/Piecewise.java index 77c8e76..a691446 100644 --- a/src/org/w3/_1998/math/mathml/Piecewise.java +++ b/src/org/w3/_1998/math/mathml/Piecewise.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -16,6 +31,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for Piecewise complex type. * @@ -45,7 +61,10 @@ public class Piecewise extends MathBase { + /** The piece. */ protected List piece; + + /** The otherwise. */ protected Otherwise otherwise; /** @@ -67,8 +86,8 @@ public class Piecewise *

* Objects of the following type(s) are allowed in the list * {@link Piece } - * - * + * + * @return the piece */ public List getPiece() { if (piece == null) { diff --git a/src/org/w3/_1998/math/mathml/Semantics.java b/src/org/w3/_1998/math/mathml/Semantics.java index 69390df..a1fff61 100644 --- a/src/org/w3/_1998/math/mathml/Semantics.java +++ b/src/org/w3/_1998/math/mathml/Semantics.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb @@ -20,6 +35,7 @@ import javax.xml.bind.annotation.XmlType; +// TODO: Auto-generated Javadoc /** *

Java class for Semantics complex type. * @@ -70,26 +86,55 @@ public class Semantics extends MathBase { + /** The apply. */ protected Apply apply; + + /** The cn. */ protected Cn cn; + + /** The ci. */ protected Ci ci; + + /** The csymbol. */ protected Csymbol csymbol; + + /** The true. */ @XmlElement(name = "true") protected MathBase _true; + + /** The false. */ @XmlElement(name = "false") protected MathBase _false; + + /** The notanumber. */ protected MathBase notanumber; + + /** The pi. */ protected MathBase pi; + + /** The infinity. */ protected MathBase infinity; + + /** The exponentiale. */ protected MathBase exponentiale; + + /** The semantics. */ protected Semantics semantics; + + /** The piecewise. */ protected Piecewise piecewise; + + /** The lambda. */ protected Lambda lambda; + + /** The annotation or annotation xml. */ @XmlElements({ @XmlElement(name = "annotation", type = Annotation.class), @XmlElement(name = "annotation-xml", type = AnnotationXml.class) }) protected List annotationOrAnnotationXml; + + /** The definition URL. */ @XmlAttribute(name = "definitionURL") @XmlSchemaType(name = "anyURI") protected String definitionURL; @@ -426,8 +471,8 @@ public void setLambda(Lambda value) { * Objects of the following type(s) are allowed in the list * {@link Annotation } * {@link AnnotationXml } - * - * + * + * @return the annotation or annotation xml */ public List getAnnotationOrAnnotationXml() { if (annotationOrAnnotationXml == null) { diff --git a/src/org/w3/_1998/math/mathml/SepType.java b/src/org/w3/_1998/math/mathml/SepType.java index 54ff51c..6e5bb72 100644 --- a/src/org/w3/_1998/math/mathml/SepType.java +++ b/src/org/w3/_1998/math/mathml/SepType.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb diff --git a/src/org/w3/_1998/math/mathml/package-info.java b/src/org/w3/_1998/math/mathml/package-info.java index 292f0fe..66a8834 100644 --- a/src/org/w3/_1998/math/mathml/package-info.java +++ b/src/org/w3/_1998/math/mathml/package-info.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ // // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb diff --git a/src/sample/APITest.java b/src/sample/APITest.java index e7c8fc9..042958f 100644 --- a/src/sample/APITest.java +++ b/src/sample/APITest.java @@ -1,3 +1,18 @@ +/******************************************************************************* + * Copyright 2016 Kaito Ii + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + *******************************************************************************/ package sample; import java.util.List;