fixed pom and output document handling

README.md

@@ -97,7 +97,7 @@ Interconvertable Layout Software for CellDesigner provides the way to convert fr
 
 
 ## How to convert file
-    java -jar layoutconverter-1.0.0-with-dependencies.jar /path/to/input.xml /path/to/output.xml
+    java -jar layoutconverter-1.0.0-jar-with-dependencies.jar /path/to/input.xml /path/to/output.xml
 ### Command Line Options
 **-h, --help**
 

pom.xml

@@ -1,10 +1,11 @@
 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
   <modelVersion>4.0.0</modelVersion>
-  <groupId>layoutconverter</groupId>
-  <artifactId>layoutconverter</artifactId>
+  <groupId>celldesigner-parser</groupId>
+  <artifactId>celldesigner-parser</artifactId>
   <version>1.0.0</version>
   <build>
     <sourceDirectory>src</sourceDirectory>
+    <finalName>layoutconverter-${version}</finalName>
     <plugins>
       <plugin>
         <artifactId>maven-compiler-plugin</artifactId>
@@ -25,9 +26,6 @@
           <descriptorRefs>
             <descriptorRef>jar-with-dependencies</descriptorRef>
           </descriptorRefs>
-          <descriptors>
-            <descriptor>descriptor.xml</descriptor>
-          </descriptors>
         </configuration>
         <executions>
           <execution>

src/org/sbml/layoutconverter/BaseLayoutConverter.java

@@ -27,6 +27,7 @@
 import org.sbml.jsbml.SBMLErrorLog;
 import org.sbml.jsbml.SBMLException;
 import org.sbml.jsbml.SBMLReader;
+import org.sbml.jsbml.SBMLWriter;
 import org.sbml.jsbml.TidySBMLWriter;
 import org.sbml.jsbml.ext.layout.Layout;
 import org.sbml.wrapper.ModelWrapper;
@@ -185,7 +186,13 @@ public void setModel(Model model) {
 	/**
 	 * Save.
 	 */
-	public abstract void save();
+	public void save(){
+		try {
+			SBMLWriter.write(document, new File(outputFileName), ' ', (short) 2);
+		} catch (SBMLException | XMLStreamException | IOException e) {
+			e.printStackTrace();
+		}
+	}
 
 	/**
 	 * Validate.

src/org/sbml/layoutconverter/CD2LayoutConverter.java

@@ -711,19 +711,4 @@ public void convertComplexAliasToLayout(
 		}
 	}
 
-	/**
-	 * Save.
-	 */
-	/* (non-Javadoc)
-	 * @see org.sbml.layoutconverter.abstractLayoutConverter#save()
-	 */
-	@Override
-	public void save() {
-		try {
-			SBMLWriter.write(document, new File(outputFileName), ' ', (short) 2);
-		} catch (SBMLException | XMLStreamException | IOException e) {
-			e.printStackTrace();
-		}
-	}
-
 }

src/org/sbml/layoutconverter/Layout2CDConverter.java

@@ -174,6 +174,16 @@ public void convert() {
 		convertSpeciesToCD(layout.getListOfSpeciesGlyphs());
 		convertReactionsToCD(layout.getListOfReactionGlyphs());
 		convertTextToCD(layout.getListOfTextGlyphs());
+
+		try {
+			String s = ObjectFactory.generateXMLString(mWrapper);
+			document = SBMLReader.read(s);
+			document = SBMLUtil.setMaths(document, downgrade_document);
+		} catch (JAXBException e) {		
+			e.printStackTrace();
+		} catch (XMLStreamException e) {
+			e.printStackTrace();
+		}
 	}
 
 	/**
@@ -641,22 +651,5 @@ public void convertTextToCD(List<TextGlyph> tgList){
 			}
 		}
 	}
-
-	/* (non-Javadoc)
-	 * @see org.sbml.layoutconverter.abstractLayoutConverter#save()
-	 */
-	@Override
-	public void save() {
-		try {
-			File file = ObjectFactory.saveModel(mWrapper, outputFileName);
-			document = SBMLUtil.setMaths(SBMLReader.read(file), downgrade_document);
-		} catch (JAXBException e) {
-			e.printStackTrace();
-		} catch (XMLStreamException e) {
-			e.printStackTrace();
-		} catch (IOException e) {
-			e.printStackTrace();
-		}
-	}
 
 }

src/org/sbml/wrapper/ModelWrapper.java

@@ -55,6 +55,7 @@
 import org.sbml.sbml.level2.version4.Compartment;
 import org.sbml.sbml.level2.version4.Model;
 import org.sbml.sbml.level2.version4.Reaction;
+import org.sbml.sbml.level2.version4.Sbml;
 import org.sbml.sbml.level2.version4.Species;
 
 // TODO: Auto-generated Javadoc
@@ -68,6 +69,9 @@
 
 public class ModelWrapper extends Model {
 
+	/** The sbml. */
+	private Sbml sbml;
+
   /** The model. */
   private Model model;
 
@@ -138,8 +142,10 @@ public class ModelWrapper extends Model {
 	 * Instantiates a new model wrapper.
 	 *
 	 * @param model the model
+	 * @param sbml the sbml
 	 */
-	public ModelWrapper(Model model){
+	public ModelWrapper(Model model, Sbml sbml){
+		this.sbml = sbml;
 		this.model = model;
 		this.id = model.getId();
 		this.name = model.getName();
@@ -272,25 +278,15 @@ void initAnnotations(){
 		model.setListOfRules(null);		// add later
 
 	}
-
-//
-//	/**
-//	 * @param species
-//	 * @return
-//	 * List<Species>
-//	 * TODO
-//	 */
-//	private List<Species> createIncludedSpeciesList(List<org.sbml._2001.ns.celldesigner.Species> speciesList) {
-//		List<Species> includedSpeciesList = new ArrayList<Species>(speciesList.size());
-//
-//		for(org.sbml._2001.ns.celldesigner.Species s : speciesList){
-//			Species species = new Species();
-//
-//			//includedSpeciesList
-//		}
-//
-//		return includedSpeciesList;
-//	}
+
+	/**
+	 * Gets the sbml.
+	 *
+	 * @return the sbml
+	 */
+	public Sbml getSbml() {
+		return sbml;
+	}
 
 	/**
 	 * Gets the w.

src/org/sbml/wrapper/ModifierSpeciesReferenceWrapper.java

@@ -248,7 +248,6 @@ public List<Point2D.Double> getEditPoints(){
 	 */
 	public void setEditPointList(List<String> editPointList) {
 		modification.getEditPoints().addAll(editPointList);
-		System.out.println(modification.getEditPoints());
 	}
 
 	/**

src/org/sbml/wrapper/ObjectFactory.java

@@ -20,6 +20,7 @@
 
 import java.io.File;
 import java.io.StringReader;
+import java.io.StringWriter;
 
 import javax.xml.bind.JAXBContext;
 import javax.xml.bind.JAXBException;
@@ -75,7 +76,7 @@ public static ModelWrapper unmarshalSBML(File file) throws JAXBException{
 		sbml = getSbml(file);
 
 		model = sbml.getModel();
-		modelWrapper = createModelWrapper(model);
+		modelWrapper = createModelWrapper(model, sbml);
 
 		return modelWrapper;
 	}
@@ -91,7 +92,7 @@ public static ModelWrapper unmarshalSBMLFromString(String xml) throws JAXBExcept
 		sbml = getSbml(xml);
 
 		model = sbml.getModel();
-		modelWrapper = createModelWrapper(model);
+		modelWrapper = createModelWrapper(model, sbml);
 
 		return modelWrapper;
 	}
@@ -133,10 +134,11 @@ public static Sbml getSbml(String xml) throws JAXBException{
 	 * Creates a new Object object.
 	 *
 	 * @param model the model
+	 * @param sbml the sbml
 	 * @return the model wrapper
 	 */
-	public static ModelWrapper createModelWrapper(Model model){
-		return new ModelWrapper(model);	
+	public static ModelWrapper createModelWrapper(Model model, Sbml sbml){
+		return new ModelWrapper(model, sbml);	
 	}
 
 	/**
@@ -147,13 +149,7 @@ public static ModelWrapper createModelWrapper(Model model){
 	 * @throws JAXBException the JAXB exception
 	 */
 	public static File saveModel(ModelWrapper modelWrapper) throws JAXBException{
-		File file = new File(modelWrapper.getId() + ".xml");
-		Marshaller marshaller = context.createMarshaller();
-		marshaller.setProperty(Marshaller.JAXB_ENCODING, "UTF-8");
-		marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
-		marshaller.marshal(sbml, file);
-
-		return file;
+		return saveModel(modelWrapper, modelWrapper.getId() + ".xml");
 	}
 
 	/**
@@ -169,8 +165,24 @@ public static File saveModel(ModelWrapper modelWrapper, String fileName) throws
 		Marshaller marshaller = context.createMarshaller();
 		marshaller.setProperty(Marshaller.JAXB_ENCODING, "UTF-8");
 		marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
-		marshaller.marshal(sbml, file);
+		marshaller.marshal(modelWrapper.getSbml(), file);
 
 		return file;
 	}
+
+	/**
+	 * Generate XML string.
+	 *
+	 * @param modelWrapper the model wrapper
+	 * @return the string
+	 * @throws JAXBException the JAXB exception
+	 */
+	public static String generateXMLString(ModelWrapper modelWrapper) throws JAXBException{
+		StringWriter sw = new StringWriter();
+		context = JAXBContext.newInstance(Sbml.class);
+		Marshaller marshaller = context.createMarshaller();
+		marshaller.marshal(modelWrapper.getSbml(), sw);
+
+		return sw.toString();
+	}
 }

src/org/sbml/wrapper/SpeciesAliasWrapper.java

@@ -401,7 +401,6 @@ public boolean isComplexSpecies(){
      * TODO
      */
     public boolean isSetComplexSpeciesAlias(){
-    	System.out.println(complexSpeciesAlias);
     	if(complexSpeciesAlias == null)
     		return false;
     	else