added util methods

src/org/sbml/wrapper/CompartmentWrapper.java

@@ -36,4 +36,11 @@ public String getName(){
 	public void setName(String value){
 		annotation.getExtension().setName(value);;
 	}
+
+	public boolean isSetName(){
+		if(annotation == null || annotation.getExtension().getName() == null)
+			return false;
+
+		return true;
+	}
 }

src/org/sbml/wrapper/ModelWrapper.java

@@ -94,14 +94,31 @@ public ModelWrapper(Model model){
 		this.setListOfRNAs(annotation.getExtension().getListOfRNAs());
 		this.setModelDisplay(annotation.getExtension().getModelDisplay());
 		this.setModelVersion(annotation.getExtension().getModelVersion());
-
 		this.cWrapperList = createCompartmentWrapperList(model.getListOfCompartments().getCompartment());
 		this.rWrapperList = createReactionWrapperList(model.getListOfReactions().getReaction());
 		this.sWrapperList = createSpeciesWrapperList(model.getListOfSpecies().getSpecies());
 		this.sAliasWrapperList = createSpeciesAliasWrapperList(annotation.getExtension().getListOfSpeciesAliases().getSpeciesAlias());
-
 	}
 
+	/**
+	 * 
+	 * @return
+	 * short
+	 * TODO
+	 */
+	public short getSizeX(){
+		return annotation.getExtension().getModelDisplay().getSizeX();
+	}
+
+	/**
+	 * 
+	 * @return
+	 * short
+	 * TODO
+	 */
+	public short getSizeY(){
+		return annotation.getExtension().getModelDisplay().getSizeY();
+	}
 
 	/**
 	 * 

src/org/sbml/wrapper/ReactionWrapper.java

@@ -1,8 +1,11 @@
 package org.sbml.wrapper;
 
+import java.util.ArrayList;
 import java.util.List;
 
+import org.sbml._2001.ns.celldesigner.BaseProduct;
 import org.sbml._2001.ns.celldesigner.BaseProducts;
+import org.sbml._2001.ns.celldesigner.BaseReactant;
 import org.sbml._2001.ns.celldesigner.BaseReactants;
 import org.sbml._2001.ns.celldesigner.ConnectScheme;
 import org.sbml._2001.ns.celldesigner.EditPoints;
@@ -14,7 +17,9 @@
 import org.sbml._2001.ns.celldesigner.Offset;
 import org.sbml._2001.ns.celldesigner.ProductLink;
 import org.sbml._2001.ns.celldesigner.ReactantLink;
+import org.sbml.sbml.level2.version4.ModifierSpeciesReference;
 import org.sbml.sbml.level2.version4.Reaction;
+import org.sbml.sbml.level2.version4.SpeciesReference;
 
 /**
  * @author Kaito Ii
@@ -29,21 +34,28 @@ public class ReactionWrapper extends Reaction{
 
 		Reaction reaction;
 		ModelWrapper modelWrapper;
-
+		List<SpeciesReferenceWrapper> reactantWrapperList;
+		List<SpeciesReferenceWrapper> productWrapperList;
+		List<ModifierSpeciesReferenceWrapper> modifierWrapperList;
+
 		public ReactionWrapper(Reaction reaction, ModelWrapper modelWrapper){
 			this.reaction = reaction;
 			this.modelWrapper = modelWrapper;
 			this.annotation = reaction.getAnnotation();
 			this.fast = reaction.isFast();
 			this.id = reaction.getId();
 			this.kineticLaw = reaction.getKineticLaw();
-//			this.listOfModifiers = reaction.getListOfModifiers();
-//			this.listOfProducts = reaction.getListOfProducts();
-//			this.listOfReactants = reaction.getListOfReactants();
+			this.listOfModifiers = reaction.getListOfModifiers();
+			this.listOfProducts = reaction.getListOfProducts();
+			this.listOfReactants = reaction.getListOfReactants();
 			this.metaid = reaction.getMetaid();
 			this.name = reaction.getName();
 			this.notes = reaction.getNotes();
 			this.reversible = reaction.isReversible();
+
+			reactantWrapperList = createReactantWrapperList(listOfReactants.getSpeciesReference());
+			productWrapperList = createProductWrapperList(listOfProducts.getSpeciesReference());
+			//modifierWrapperList = createModifierWrapperList(listOfModifiers.getModifierSpeciesReference());					
 		}
 
 	   public String getName() {
@@ -80,8 +92,8 @@ public void setReaction(String value) {
         * BaseReactants
         * TODO
         */
-       public BaseReactants getBaseReactants() {
-           return annotation.getExtension().getBaseReactants();
+       public List<BaseReactant> getBaseReactants() {
+           return annotation.getExtension().getBaseReactants().getBaseReactant();
        }
 
        /**
@@ -100,8 +112,8 @@ public void setBaseReactants(BaseReactants value) {
         * BaseProducts
         * TODO
         */
-       public BaseProducts getBaseProducts() {
-           return annotation.getExtension().getBaseProducts();
+       public List<BaseProduct> getBaseProducts() {
+           return annotation.getExtension().getBaseProducts().getBaseProduct();
        }
 
        /**
@@ -313,4 +325,28 @@ public void addModification(Modification modification){
        public void removeModification(Modification modification){
     	   annotation.getExtension().getListOfModification().getModification().remove(modification);
        }
+
+       public List<SpeciesReferenceWrapper> createReactantWrapperList(List<SpeciesReference> srList){
+    	   List<SpeciesReferenceWrapper> srwList = new ArrayList<SpeciesReferenceWrapper>(srList.size());
+    	   for(SpeciesReference sr : srList)
+    		   srwList.add(new SpeciesReferenceWrapper(sr, modelWrapper));
+
+    	   return srwList;
+       }
+
+       public List<SpeciesReferenceWrapper> createProductWrapperList(List<SpeciesReference> srList){
+    	   List<SpeciesReferenceWrapper> srwList = new ArrayList<SpeciesReferenceWrapper>(srList.size());
+    	   for(SpeciesReference sr : srList)
+    		   srwList.add(new SpeciesReferenceWrapper(sr, modelWrapper));
+
+    	   return srwList;
+       }
+
+       public List<ModifierSpeciesReferenceWrapper> createModifierWrapperList(List<ModifierSpeciesReference> msrList){
+    	   List<ModifierSpeciesReferenceWrapper> msrwList = new ArrayList<ModifierSpeciesReferenceWrapper>(msrList.size());
+    	   for(ModifierSpeciesReference msr : msrList)
+    		   msrwList.add(new ModifierSpeciesReferenceWrapper(msr, modelWrapper));
+
+    	   return msrwList;
+       }
 }

src/org/sbml/wrapper/SpeciesAliasWrapper.java

@@ -38,7 +38,7 @@ public SpeciesAliasWrapper(SpeciesAlias speciesAlias, ModelWrapper modelWrapper)
 		this.compartmentAlias = modelWrapper.getCompartmentAliasById(speciesAlias.getCompartmentAlias());
 		this.complexSpeciesAlias = modelWrapper.getComplexSpeciesAliasById(speciesAlias.getComplexSpeciesAlias());
 		this.speciesWrapper = modelWrapper.getSpeciesWrapperById(speciesAlias.getSpecies());
-
+		this.view = speciesAlias.getView();
 	}
 
 	/**

src/org/sbml/wrapper/SpeciesWrapper.java

@@ -5,7 +5,6 @@
 import org.sbml._2001.ns.celldesigner.Catalyzed;
 import org.sbml._2001.ns.celldesigner.ListOfCatalyzedReactions;
 import org.sbml._2001.ns.celldesigner.SpeciesIdentity;
-import org.sbml.sbml.level2.version4.Compartment;
 import org.sbml.sbml.level2.version4.Species;
 
 /**
@@ -18,15 +17,14 @@ public class SpeciesWrapper extends Species{
 
 	ModelWrapper modelWrapper;
 	Species species;
-	Compartment compartment;
+	CompartmentWrapper compartmentWrapper;
 
 	public SpeciesWrapper(Species species, ModelWrapper modelWrapper){
 		this.modelWrapper = modelWrapper;
 		this.species = species;
 		this.annotation = species.getAnnotation();
 		this.boundaryCondition = species.isBoundaryCondition();
 		this.charge = species.getCharge();
-		//this.compartment = species.getCompartment();
 		this.constant = species.isConstant();
 		this.hasOnlySubstanceUnits = species.isHasOnlySubstanceUnits();
 		this.id = species.getId();
@@ -37,6 +35,8 @@ public SpeciesWrapper(Species species, ModelWrapper modelWrapper){
 		this.notes = species.getNotes();
 		this.spatialSizeUnits = species.getSpatialSizeUnits();
 		this.substanceUnits = species.getSubstanceUnits();
+
+		this.compartmentWrapper = modelWrapper.getCompartmentWrapperById(species.getCompartment());
 	}
 
 	/**

src/sample/APITest.java

@@ -9,7 +9,9 @@
 import javax.xml.bind.JAXBIntrospector;
 import javax.xml.bind.Unmarshaller;
 
+import org.sbml._2001.ns.celldesigner.ConnectScheme;
 import org.sbml._2001.ns.celldesigner.SpeciesAlias;
+import org.sbml.sbml.level2.version4.Reaction;
 import org.sbml.sbml.level2.version4.Sbml;
 import org.sbml.sbml.level2.version4.Species;
 
@@ -53,7 +55,14 @@ public static void main(String[] args) {
       String str = s.getAnnotation().getExtension().getPositionToCompartment();
       System.out.println(s.getId() + ":" + str);
     }
-
+
+    List<Reaction> rList = sbml.getModel().getListOfReactions().getReaction();
+    for(Reaction r : rList){
+    	System.out.println(r.getId() + ":" + r.getAnnotation().getExtension().getReaction() + ", " + r.getAnnotation().getExtension().getName());
+    	ConnectScheme cs = r.getAnnotation().getExtension().getConnectScheme();
+    	System.out.println("connect policy " + cs.getConnectPolicy());
+    }
+
   }
 
 }