updated license and readme, created util methods

LICENSE

@@ -186,7 +186,7 @@
       same "printed page" as the copyright notice for easier
       identification within third-party archives.
 
-   Copyright {2016} {hogehoge}
+   Copyright {2016} {Kaito Ii, Akira Funahashi}
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.

README.md

@@ -118,6 +118,7 @@ Convert SBML Layout package to CellDesigner Annotation
 ## So, what's next?
 - Alter schema to add editPoints into reactant links and product links
 - Convert complex species and included species to [SBML Multi package](http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/multi)
+- Convert Layers in CellDesigner Annotation
 
 ## License
 This content is licensed under the [Apache License](http://www.apache.org/licenses/LICENSE-2.0) .

src/org/sbml/wrapper/CompartmentAliasWrapper.java

@@ -303,4 +303,11 @@ public void setCompartmentAliased(Compartment compartment){
     public CompartmentWrapper getCompartmentWrapperAliased(){
     	return compartmentWrapper;
     }
+
+	/**
+	 * @return the modelWrapper
+	 */
+	public ModelWrapper getModelWrapper() {
+		return modelWrapper;
+	}
 }

src/org/sbml/wrapper/CompartmentWrapper.java

@@ -133,4 +133,11 @@ public CompartmentWrapper getOutsideInstance(){
 	public CompartmentAliasWrapper getAliasWrapper() {
 		return modelWrapper.getCompartmentAliasWrapperByCompartmentId(id);
 	}
+
+	/**
+	 * @return the modelWrapper
+	 */
+	public ModelWrapper getModelWrapper() {
+		return modelWrapper;
+	}
 }

src/org/sbml/wrapper/ComplexSpeciesAliasWrapper.java

@@ -225,5 +225,41 @@ public void setListOfSpeciesTags(ListOfSpeciesTag value) {
     public ComplexSpeciesAlias getComplexSpeciesAliased() {
         return complexSpeciesAlias;
     }
+
+	/**
+	 * @return the speciesWrapper
+	 */
+	public SpeciesWrapper getSpeciesWrapper() {
+		return speciesWrapper;
+	}
+
+	/**
+	 * @param speciesWrapper the speciesWrapper to set
+	 */
+	public void setSpeciesWrapper(SpeciesWrapper speciesWrapper) {
+		this.speciesWrapper = speciesWrapper;
+	}
+
+	/**
+	 * @return the compartmentAliasWrapper
+	 */
+	public CompartmentAliasWrapper getCompartmentAliasWrapper() {
+		return compartmentAliasWrapper;
+	}
+
+	/**
+	 * @param compartmentAliasWrapper the compartmentAliasWrapper to set
+	 */
+	public void setCompartmentAliasWrapper(
+			CompartmentAliasWrapper compartmentAliasWrapper) {
+		this.compartmentAliasWrapper = compartmentAliasWrapper;
+	}
+
+	/**
+	 * @return the modelWrapper
+	 */
+	public ModelWrapper getModelWrapper() {
+		return modelWrapper;
+	}
 
 }

src/org/sbml/wrapper/ModifierSpeciesReferenceWrapper.java

@@ -251,4 +251,11 @@ public void setEditPointList(List<String> editPointList) {
 		System.out.println(modification.getEditPoints());
 	}
 
+	/**
+	 * @return the modelWrapper
+	 */
+	public ModelWrapper getModelWrapper() {
+		return modelWrapper;
+	}
+
 }

src/org/sbml/wrapper/ReactionWrapper.java

@@ -934,4 +934,11 @@ public void createBaseProduct(SpeciesReferenceWrapper srw) {
 		baseProducts.add(bp);
 	}
 
+	/**
+	 * @return the modelWrapper
+	 */
+	public ModelWrapper getModelWrapper() {
+		return modelWrapper;
+	}
+
 }

src/org/sbml/wrapper/SpeciesReferenceWrapper.java

@@ -115,4 +115,11 @@ public SpeciesAliasWrapper getAliased(){
 		return modelWrapper.getSpeciesAliasWrapperById(getAlias());
 	}
 
+	/**
+	 * @return the modelWrapper
+	 */
+	public ModelWrapper getModelWrapper() {
+		return modelWrapper;
+	}
+
 }

src/org/sbml/wrapper/SpeciesWrapper.java

@@ -88,7 +88,6 @@ public SpeciesWrapper(Species species, ModelWrapper modelWrapper){
 			setAnnotations();
 		else
 			initAnnotations();
-
 	}
 
 	/**
@@ -318,4 +317,25 @@ public Catalyzed createCatalyzedReaction(String reaction){
 		return catalyzed;
 	}
 
+	/**
+	 * @return the modelWrapper
+	 */
+	public ModelWrapper getModelWrapper() {
+		return modelWrapper;
+	}
+
+	/**
+	 * @return the compartmentWrapper
+	 */
+	public CompartmentWrapper getCompartmentWrapper() {
+		return compartmentWrapper;
+	}
+
+	/**
+	 * @param compartmentWrapper the compartmentWrapper to set
+	 */
+	public void setCompartmentWrapper(CompartmentWrapper compartmentWrapper) {
+		this.compartmentWrapper = compartmentWrapper;
+	}
+
 }