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created converter, reader, and modelupgrader done creating conversion…
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| package org.sbml.layoutconverter; | ||
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| import java.io.File; | ||
| import java.io.IOException; | ||
| import java.util.Map; | ||
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| import javax.xml.stream.XMLStreamException; | ||
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| import org.sbml.jsbml.SBMLDocument; | ||
| import org.sbml.jsbml.SBMLReader; | ||
| import org.sbml.jsbml.ext.groups.GroupsConstants; | ||
| import org.sbml.jsbml.ext.layout.LayoutConstants; | ||
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| /** | ||
| * @author Kaito Ii | ||
| * | ||
| * Date Created: May 28, 2016 | ||
| */ | ||
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| public class ConverterSBMLReader { | ||
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| final static String cellDesignerNS = "http://www.sbml.org/2001/ns/celldesigner"; | ||
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| public static SBMLDocument read(File file) throws XMLStreamException, IOException{ | ||
| SBMLDocument document = SBMLReader.read(file); | ||
| int level = document.getLevel(); | ||
| int version = document.getVersion(); | ||
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| if(document.getLevel() < 3) | ||
| document = ModelUpgrader.upgrade(document); | ||
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| document.enablePackage(LayoutConstants.getNamespaceURI(level, version), true); | ||
| // document.enablePackage(GroupsConstants.getNamespaceURI(level, version), true); | ||
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| return document; | ||
| } | ||
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| public static boolean isSetCellDesignerNameSpace(SBMLDocument document){ | ||
| Map<String, String> nsMap = document.getDeclaredNamespaces(); | ||
| return nsMap.containsValue(cellDesignerNS); | ||
| } | ||
| } |
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| package org.sbml.layoutconverter; | ||
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| import java.io.File; | ||
| import java.io.IOException; | ||
| import java.util.List; | ||
| import java.util.Map; | ||
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| import javax.xml.bind.JAXBException; | ||
| import javax.xml.stream.XMLStreamException; | ||
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| import org.sbml._2001.ns.celldesigner.BaseProduct; | ||
| import org.sbml._2001.ns.celldesigner.BaseReactant; | ||
| import org.sbml._2001.ns.celldesigner.Bounds; | ||
| import org.sbml._2001.ns.celldesigner.BriefView; | ||
| import org.sbml._2001.ns.celldesigner.CompartmentAlias; | ||
| import org.sbml._2001.ns.celldesigner.ConnectScheme; | ||
| import org.sbml._2001.ns.celldesigner.Info; | ||
| import org.sbml._2001.ns.celldesigner.LineDirection; | ||
| import org.sbml._2001.ns.celldesigner.LinkAnchor; | ||
| import org.sbml._2001.ns.celldesigner.Modification; | ||
| import org.sbml._2001.ns.celldesigner.UsualView; | ||
| import org.sbml.jsbml.Model; | ||
| import org.sbml.jsbml.SBMLDocument; | ||
| import org.sbml.jsbml.SBMLException; | ||
| import org.sbml.jsbml.SBMLReader; | ||
| import org.sbml.jsbml.SBMLWriter; | ||
| import org.sbml.jsbml.ext.SBasePlugin; | ||
| import org.sbml.jsbml.ext.layout.BoundingBox; | ||
| import org.sbml.jsbml.ext.layout.CompartmentGlyph; | ||
| import org.sbml.jsbml.ext.layout.Dimensions; | ||
| import org.sbml.jsbml.ext.layout.Layout; | ||
| import org.sbml.jsbml.ext.layout.LayoutConstants; | ||
| import org.sbml.jsbml.ext.layout.LayoutModelPlugin; | ||
| import org.sbml.jsbml.ext.layout.Point; | ||
| import org.sbml.jsbml.ext.layout.TextGlyph; | ||
| import org.sbml.wrapper.CompartmentWrapper; | ||
| import org.sbml.wrapper.ModelWrapper; | ||
| import org.sbml.wrapper.ObjectFactory; | ||
| import org.sbml.wrapper.ReactionWrapper; | ||
| import org.sbml.wrapper.SpeciesAliasWrapper; | ||
| import org.sbml.wrapper.SpeciesWrapper; | ||
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| /** | ||
| * @author Kaito Ii | ||
| * | ||
| * Date Created: May 26, 2016 | ||
| */ | ||
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| public class LayoutConverter { | ||
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| ModelWrapper mWrapper; | ||
| List<ReactionWrapper> rwList; | ||
| List<SpeciesWrapper> swList; | ||
| List<CompartmentWrapper> cwList; | ||
| List<SpeciesAliasWrapper> sawList; | ||
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| SBMLDocument document; | ||
| Model model; | ||
| Layout layout; | ||
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| public LayoutConverter(File file) throws JAXBException, XMLStreamException, IOException{ | ||
| mWrapper = ObjectFactory.unmarshalSBML(file); | ||
| document = ConverterSBMLReader.read(file); | ||
| model = document.getModel(); | ||
| LayoutModelPlugin mplugin = (LayoutModelPlugin)(model.getPlugin("layout")); | ||
| layout = mplugin.createLayout(); | ||
| } | ||
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| public void print(){ | ||
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| // System.out.println(mWrapper.getId()); | ||
| // rwList = mWrapper.getListOfReactionWrapper(); | ||
| // swList = mWrapper.getListOfSpeciesWrapper(); | ||
| // cwList = mWrapper.getListOfCompartmentWrapper(); | ||
| // sawList = mWrapper.getListOfSpeciesAliasWrapper(); | ||
| // | ||
| // for(ReactionWrapper rw : rwList){ | ||
| // System.out.println(rw.getId()); | ||
| // System.out.println("reaction : " + rw.getReaction()); | ||
| // System.out.println("name " + rw.getName()); | ||
| // List<BaseReactant> rl = rw.getBaseReactants(); | ||
| // for(BaseReactant br : rl){ | ||
| // System.out.println("species : " + br.getSpecies()); | ||
| // System.out.println("alias : " + br.getAlias()); | ||
| // System.out.println("link anchor position : " + br.getLinkAnchor().getPosition()); | ||
| // } | ||
| // | ||
| // List<BaseProduct> pl = rw.getBaseProducts(); | ||
| // for(BaseProduct pr : pl){ | ||
| // System.out.println("species : " + pr.getSpecies()); | ||
| // System.out.println("alias : " + pr.getAlias()); | ||
| // System.out.println("link anchor position : " + pr.getLinkAnchor().getPosition()); | ||
| // } | ||
| // | ||
| // ConnectScheme cs = rw.getConnectScheme(); | ||
| // System.out.println("connect policy : " + cs.getConnectPolicy()); | ||
| // System.out.println("rectangle index : " + cs.getRectangleIndex()); | ||
| // | ||
| // List<LineDirection> ld = cs.getListOfLineDirection().getLineDirection(); | ||
| // for(LineDirection l : ld){ | ||
| // System.out.println("value : " + l.getValue()); | ||
| // System.out.println("index : " + l.getIndex()); | ||
| // System.out.println("arm : " + l.getArm()); | ||
| // } | ||
| // | ||
| // System.out.println("line color : " + rw.getLine().getColor()); | ||
| // System.out.println("width : " + rw.getLine().getWidth()); | ||
| // | ||
| // } | ||
| // | ||
| // for(SpeciesWrapper sw : swList){ | ||
| // System.out.println(sw.getId()); | ||
| // System.out.println("position to compartment : " + sw.getPositionToCompartment()); | ||
| // System.out.println("species identity : " + sw.getSpeciesIdentity().getClazz()); | ||
| // System.out.println("protein reference : " + sw.getSpeciesIdentity().getProteinReference()); | ||
| // System.out.println("antisenseRNA reference : " + sw.getSpeciesIdentity().getAntisensernaReference()); | ||
| // System.out.println("gene reference : " + sw.getSpeciesIdentity().getGeneReference()); | ||
| // System.out.println("rna reference : " + sw.getSpeciesIdentity().getRnaReference()); | ||
| // System.out.println("state : " + sw.getSpeciesIdentity().getState()); | ||
| // } | ||
| // | ||
| // for(CompartmentWrapper cw : cwList){ | ||
| // System.out.println(cw.getId()); | ||
| // if(cw.isSetName()) | ||
| // System.out.println("Name : " + cw.getName()); | ||
| // } | ||
| // | ||
| // for(SpeciesAliasWrapper saw : sawList){ | ||
| // System.out.println(saw.getId()); | ||
| // System.out.println("activity : " + saw.getActivity()); | ||
| // System.out.println("Bounds : " + " x = " + saw.getBounds().getX() + " y = " + saw.getBounds().getY() + " w = " + saw.getBounds().getW() + " h = " + saw.getBounds().getH()); | ||
| // System.out.println("view : " + saw.getView().getState()); | ||
| // | ||
| // UsualView uv = saw.getUsualView(); | ||
| // System.out.println("usual view"); | ||
| // System.out.println("inner position : " + uv.getInnerPosition().getX() + ", " + uv.getInnerPosition().getY()); | ||
| // System.out.println("single line : " + uv.getSingleLine().getWidth()); | ||
| // System.out.println("paint : " + "color " + uv.getPaint().getColor() + " scheme " + uv.getPaint().getScheme()); | ||
| // | ||
| // BriefView bv = saw.getBriefView(); | ||
| // System.out.println("usual view"); | ||
| // System.out.println("inner position : " + bv.getInnerPosition().getX() + ", " + bv.getInnerPosition().getY()); | ||
| // System.out.println("single line : " + bv.getSingleLine().getWidth()); | ||
| // System.out.println("paint : " + "color " + bv.getPaint().getColor() + " scheme " + uv.getPaint().getScheme()); | ||
| // | ||
| // Info info = saw.getInfo(); | ||
| // System.out.println("label : " + info.getLabel()); | ||
| // System.out.println("prefix : " + info.getPrefix()); | ||
| // System.out.println("state : " + info.getState()); | ||
| // System.out.println("angle : " + info.getAngle()); | ||
| // } | ||
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| try { | ||
| SBMLWriter.write(document, System.out, ' ', (short) 2); | ||
| } catch (SBMLException e) { | ||
| // TODO Auto-generated catch block | ||
| e.printStackTrace(); | ||
| } catch (XMLStreamException e) { | ||
| // TODO Auto-generated catch block | ||
| e.printStackTrace(); | ||
| } | ||
| } | ||
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| public void convert(){ | ||
| convertModel(); | ||
| convertCompartments(mWrapper.getListOfCompartmentAliases()); | ||
| } | ||
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| public void convertCompartments(List<CompartmentAlias> caList){ | ||
| for(CompartmentAlias ca : caList){ | ||
| CompartmentGlyph cg = layout.createCompartmentGlyph("CompartmentGlyph_" + ca.getId()); | ||
| ca.setCompartment(ca.getCompartment()); | ||
| Bounds bound = ca.getBounds(); | ||
| BoundingBox bb = cg.createBoundingBox(); | ||
| Dimensions dimension = bb.createDimensions(); | ||
| dimension.setWidth(bound.getW().doubleValue()); | ||
| dimension.setHeight(bound.getW().doubleValue()); | ||
| dimension.setDepth(1d); | ||
| bb.setDimensions(dimension); | ||
| Point point = bb.createPosition(); | ||
| point.setX(bound.getX().doubleValue()); | ||
| point.setY(bound.getY().doubleValue()); | ||
| point.setZ(0d); | ||
| bb.setPosition(point); | ||
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| TextGlyph tg = layout.createTextGlyph("TextGlyph_" + ca.getId()); | ||
| tg.setOriginOfText(ca.getId()); | ||
| tg.setGraphicalObject(cg); | ||
| BoundingBox bb2 = tg.createBoundingBox();; | ||
| Dimensions dimension2 = bb2.createDimensions(); | ||
| dimension2.setWidth(ca.getId().length() * 3); | ||
| dimension2.setHeight(10); | ||
| dimension.setDepth(1d); | ||
| Point point2 = bb.createPosition(); | ||
| point2.setX(ca.getNamePoint().getX().doubleValue()); | ||
| point2.setY(ca.getNamePoint().getX().doubleValue()); | ||
| point2.setZ(0d); | ||
| } | ||
| } | ||
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| public void convertModel(){ | ||
| layout.setId("Layout_" + model.getId()); | ||
| layout.createDimensions(mWrapper.getSizeX(), mWrapper.getSizeX(), 0); | ||
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| } | ||
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| public void convertReactions(){ | ||
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| } | ||
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| public void convertSpecies(){ | ||
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| } | ||
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| public static void main(String[] args){ | ||
| LayoutConverter converter; | ||
| try { | ||
| converter = new LayoutConverter(new File("sample/ex3.xml")); | ||
| } catch (JAXBException e) { | ||
| System.err.println("Error unmarshaling XML"); | ||
| e.printStackTrace(); | ||
| return; | ||
| } catch (XMLStreamException | IOException e) { | ||
| System.err.println("Error reading SBML model"); | ||
| e.printStackTrace(); | ||
| return; | ||
| } | ||
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| converter.convert(); | ||
| converter.print(); | ||
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| } | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,22 @@ | ||
| package org.sbml.layoutconverter; | ||
|
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| import org.sbml.jsbml.SBMLDocument; | ||
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| /** | ||
| * @author Kaito Ii | ||
| * | ||
| * Date Created: May 26, 2016 | ||
| */ | ||
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| public class ModelUpgrader { | ||
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| public static SBMLDocument upgrade(SBMLDocument document){ | ||
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| return document; | ||
| } | ||
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| public static void main(String[] args){ | ||
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| } | ||
| } |