organized external packages and options

src/org/sbml/extconverter/EXTConverter.java

@@ -0,0 +1,53 @@
+/*******************************************************************************
+ * 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.extconverter;
+
+import org.sbml.jsbml.Model;
+import org.sbml.wrapper.ModelWrapper;
+
+// TODO: Auto-generated Javadoc
+/**
+ * The Class EXTConverter.
+ *
+ * @author Kaito Ii
+ * 
+ * Date Created: Aug 22, 2016
+ */
+
+public abstract class EXTConverter {
+
+	/** The model. */
+	protected Model model;
+
+	/** The m wrapper. */
+	protected ModelWrapper mWrapper;
+
+	/**
+	 * Instantiates a new EXT converter.
+	 *
+	 * @param model the model
+	 * @param mWrapper the m wrapper
+	 */
+	public EXTConverter(Model model, ModelWrapper mWrapper){
+		this.model = model;
+		this.mWrapper = mWrapper;
+	}
+
+	/**
+	 * Convert.
+	 */
+	public abstract void convert();
+}

src/org/sbml/layoutconverter/FBCConverter.java → src/org/sbml/extconverter/FBCConverter.java

@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  *******************************************************************************/
-package org.sbml.layoutconverter;
+package org.sbml.extconverter;
 
 import java.util.List;
 
@@ -44,13 +44,7 @@
  * Date Created: Aug 6, 2016
  */
 
-public class FBCConverter {
-
-	/** The model. */
-	private Model model;
-
-	/** The m wrapper. */
-	private ModelWrapper mWrapper;
+public class FBCConverter extends EXTConverter{
 
 	/** The fbc plugin. */
 	private FBCModelPlugin fbcPlugin;
@@ -62,8 +56,7 @@ public class FBCConverter {
 	 * @param mWrapper the m wrapper
 	 */
 	public FBCConverter(Model model, ModelWrapper mWrapper) {
-		this.model = model;
-		this.mWrapper = mWrapper;
+		super(model, mWrapper);
 	}
 
 	/**

src/org/sbml/layoutconverter/MultiConverter.java → src/org/sbml/extconverter/MultiConverter.java

@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  *******************************************************************************/
-package org.sbml.layoutconverter;
+package org.sbml.extconverter;
 
 import org.sbml.jsbml.Model;
 import org.sbml.wrapper.ModelWrapper;
@@ -27,13 +27,7 @@
  * Date Created: Aug 7, 2016
  */
 //TODO convert complex species and included species from CellDesigner Annootation to SBML Multi package
-public class MultiConverter {
-
-	/** The model. */
-	private Model model;
-
-	/** The m wrapper. */
-	private ModelWrapper mWrapper;
+public class MultiConverter extends EXTConverter{
 
 	/**
 	 * Instantiates a new multi converter.
@@ -42,8 +36,7 @@ public class MultiConverter {
 	 * @param mWrapper the m wrapper
 	 */
 	public MultiConverter(Model model, ModelWrapper mWrapper){
-		this.model = model;
-		this.mWrapper = mWrapper;
+		super(model, mWrapper);
 	}
 
 	/**

src/org/sbml/extconverter/package-info.java

@@ -0,0 +1,21 @@
+/*******************************************************************************
+ * 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
+ *
+ * Date Created: Aug 22, 2016
+ */
+package org.sbml.extconverter;

src/org/sbml/layoutconverter/ApplicationOption.java

@@ -44,6 +44,10 @@ public class ApplicationOption {
 	/** The default compartment. */
 	@Option(name = "-d", aliases= {"--defaultCompartment"}, required = false, usage = "convert default compartment")
 	private Boolean defaultCompartment;
+
+	/** The convert 2 FBC. */
+	@Option(name = "-f", aliases= {"--fbc"}, required = false, usage = "add FBC packages")
+	private boolean convert2FBC;
 
 	/** The input. */
 	@Argument(index = 0, metaVar = "input files", required = true, usage = "input file")
@@ -104,6 +108,31 @@ public boolean issetLayout2CD() {
 		return true;
 	}
 
+	/**
+	 * Checks if is sets the conversion direction.
+	 *
+	 * @return true, if is sets the conversion direction
+	 */
+	public boolean isSetConversionDirection(){
+		if(issetLayout2CD() || issetCD2Layout())
+			return false;
+
+		return true;
+	}
+
+	/**
+	 * Checks if is 2 CD 2 layout.
+	 *
+	 * @return true, if is 2 CD 2 layout
+	 */
+	public boolean is2CD2Layout(){
+		if(issetCD2Layout())
+			return CD2Layout;
+
+		else
+			return Layout2CD;
+	}
+
 	/**
 	 * Checks if is default compartment.
 	 *
@@ -125,6 +154,18 @@ public String getInput() {
 		return input;
 	}
 
+	/**
+	 * Checks if is sets the output.
+	 *
+	 * @return true, if is sets the output
+	 */
+	public boolean isSetOutput(){
+		if(output == null)
+			return false;
+
+		return true;
+	}
+
 	/**
 	 * Gets the output.
 	 *
@@ -137,4 +178,12 @@ public String getOutput() {
 		return output;
 	}
 
+	/**
+	 * Gets the convert 2 FBC.
+	 *
+	 * @return the convert 2 FBC
+	 */
+	public boolean isConvert2FBC() {
+		return convert2FBC;
+	}
 }

src/org/sbml/layoutconverter/BaseLayoutConverter.java

@@ -69,6 +69,12 @@ public abstract class BaseLayoutConverter {
 	/** The Constant DEFAULT_SPECIES_DEPTH. */
 	protected static final double DEFAULT_SPECIES_DEPTH = 1.0;
 
+	/** The convert 2 FBC. */
+	protected boolean convert2FBC = false;
+
+	/** The convert 2 multi. */
+	protected boolean convert2Multi = false;
+
 	/**
 	 * Instantiates a new base layout converter.
 	 *
@@ -121,6 +127,20 @@ public BaseLayoutConverter(File file, boolean defaultCompartment, String outputF
 		this.convertDefaultCompartment = defaultCompartment;
 	}
 
+	/**
+	 * Instantiates a new base layout converter.
+	 *
+	 * @param file the file
+	 * @param options the options
+	 * @throws XMLStreamException the XML stream exception
+	 * @throws IOException Signals that an I/O exception has occurred.
+	 */
+	public BaseLayoutConverter(File file, ApplicationOption options) throws XMLStreamException, IOException{
+		this(file);
+		this.outputFileName = options.isSetOutput() ? options.getOutput() : SBMLUtil.createOutputFileName(file);
+		this.convertDefaultCompartment = options.isDefaultCompartment();
+	}
+
 	/**
 	 * Gets the document.
 	 *
@@ -166,9 +186,9 @@ public void setModel(Model model) {
 	 * Save.
 	 */
 	public abstract void save();
-	
+
 	/**
-	 * void TODO.
+	 * Validate.
 	 */
 	public void validate() {
 		document.checkConsistency();
@@ -180,7 +200,7 @@ public void validate() {
 	}
 
 	/**
-	 * void TODO.
+	 * Print
 	 */
 	public void print() {
 		try {
@@ -192,5 +212,59 @@ public void print() {
 			e.printStackTrace();
 		}
 	}
+
+	/**
+	 * Checks if is convert default compartment.
+	 *
+	 * @return the convertDefaultCompartment
+	 */
+	public boolean isConvertDefaultCompartment() {
+		return convertDefaultCompartment;
+	}
+
+	/**
+	 * Sets the convert default compartment.
+	 *
+	 * @param convertDefaultCompartment the convertDefaultCompartment to set
+	 */
+	public void setConvertDefaultCompartment(boolean convertDefaultCompartment) {
+		this.convertDefaultCompartment = convertDefaultCompartment;
+	}
+
+	/**
+	 * Checks if is convert 2 FBC.
+	 *
+	 * @return the convert2FBC
+	 */
+	public boolean isConvert2FBC() {
+		return convert2FBC;
+	}
+
+	/**
+	 * Sets the convert 2 FBC.
+	 *
+	 * @param convert2fbc the convert2FBC to set
+	 */
+	public void setConvert2FBC(boolean convert2fbc) {
+		convert2FBC = convert2fbc;
+	}
+
+	/**
+	 * Checks if is convert 2 multi.
+	 *
+	 * @return the convert2Multi
+	 */
+	public boolean isConvert2Multi() {
+		return convert2Multi;
+	}
+
+	/**
+	 * Sets the convert 2 multi.
+	 *
+	 * @param convert2Multi the convert2Multi to set
+	 */
+	public void setConvert2Multi(boolean convert2Multi) {
+		this.convert2Multi = convert2Multi;
+	}
 
 }

src/org/sbml/layoutconverter/CD2LayoutConverter.java

@@ -30,6 +30,8 @@
 import org.sbml._2001.ns.celldesigner.Modification;
 import org.sbml._2001.ns.celldesigner.ProductLink;
 import org.sbml._2001.ns.celldesigner.ReactantLink;
+import org.sbml.extconverter.FBCConverter;
+import org.sbml.extconverter.MultiConverter;
 import org.sbml.jsbml.ListOf;
 import org.sbml.jsbml.Reaction;
 import org.sbml.jsbml.SBMLException;
@@ -67,12 +69,6 @@
 
 public class CD2LayoutConverter extends BaseLayoutConverter {
 
-	/** The convert 2 FBC. */
-	private boolean convert2FBC = true;
-
-	/** The convert 2 multi. */
-	private boolean convert2Multi = false;
-
 	/**
 	 * Instantiates a new CD 2 layout converter.
 	 *
@@ -130,6 +126,19 @@ public CD2LayoutConverter(File file, boolean defaultCompartment) throws XMLStrea
 		init(file);
 	}
 
+	/**
+	 * @param file
+	 * @param options
+	 * @throws IOException 
+	 * @throws XMLStreamException 
+	 * @throws JAXBException 
+	 */
+	public CD2LayoutConverter(File file, ApplicationOption options) throws XMLStreamException, IOException, JAXBException {
+		super(file, options);
+		convert2FBC = options.isConvert2FBC();
+		init(file);
+	}
+
 	/**
 	 * Inits the.
 	 *