Update.

.classpath

@@ -4,5 +4,6 @@
 	<classpathentry kind="src" output="test-classes" path="test"/>
 	<classpathentry kind="con" path="com.google.gwt.eclipse.core.GWT_CONTAINER"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
 	<classpathentry kind="output" path="war/WEB-INF/classes"/>
 </classpath>

.settings/com.google.gwt.eclipse.core.prefs

@@ -1,3 +1,3 @@
 eclipse.preferences.version=1
 filesCopiedToWebInfLib=gwt-servlet.jar
-gwtCompileSettings=PGd3dC1jb21waWxlLXNldHRpbmdzPjxsb2ctbGV2ZWw+VFJBQ0U8L2xvZy1sZXZlbD48b3V0cHV0LXN0eWxlPk9CRlVTQ0FURUQ8L291dHB1dC1zdHlsZT48ZXh0cmEtYXJncz48IVtDREFUQVtdXT48L2V4dHJhLWFyZ3M+PHZtLWFyZ3M+PCFbQ0RBVEFbLVhteDUxMm1dXT48L3ZtLWFyZ3M+PGVudHJ5LXBvaW50LW1vZHVsZT5zdGFyLmdlbmV0aWNzLlN0YXJnZW5ldGljc19nd3RfamF2YTwvZW50cnktcG9pbnQtbW9kdWxlPjwvZ3d0LWNvbXBpbGUtc2V0dGluZ3M+
+gwtCompileSettings=PGd3dC1jb21waWxlLXNldHRpbmdzPjxsb2ctbGV2ZWw+REVCVUc8L2xvZy1sZXZlbD48b3V0cHV0LXN0eWxlPk9CRlVTQ0FURUQ8L291dHB1dC1zdHlsZT48ZXh0cmEtYXJncz48IVtDREFUQVtdXT48L2V4dHJhLWFyZ3M+PHZtLWFyZ3M+PCFbQ0RBVEFbLVhteDUxMm1dXT48L3ZtLWFyZ3M+PGVudHJ5LXBvaW50LW1vZHVsZT5zdGFyLmdlbmV0aWNzLlN0YXJnZW5ldGljc19nd3RfamF2YTwvZW50cnktcG9pbnQtbW9kdWxlPjwvZ3d0LWNvbXBpbGUtc2V0dGluZ3M+

src/star/genetics/Stargenetics_gwt_java.gwt.xml

@@ -7,18 +7,18 @@
   "http://google-web-toolkit.googlecode.com/svn/tags/2.5.1/distro-source/core/src/gwt-module.dtd">
 <module rename-to='stargenetics_gwt_java'>
   <!-- Inherit the core Web Toolkit stuff.                        -->
-  <inherits name='com.google.gwt.user.User'/>
+     <inherits name='com.google.gwt.user.User'/> 
+     <!--   <inherits name="com.google.gwt.core.Core"/> -->
+  <inherits name="com.google.gwt.json.JSON" /> 
 
   <!-- Inherit the default GWT style sheet.  You can change       -->
   <!-- the theme of your GWT application by uncommenting          -->
   <!-- any one of the following lines.                            -->
-  <inherits name='com.google.gwt.user.theme.clean.Clean'/>
+  <!--   --><inherits name='com.google.gwt.user.theme.clean.Clean'/> -->
   <!-- <inherits name='com.google.gwt.user.theme.standard.Standard'/> -->
   <!-- <inherits name='com.google.gwt.user.theme.chrome.Chrome'/> -->
   <!-- <inherits name='com.google.gwt.user.theme.dark.Dark'/>     -->
 
-  <!-- Other module inherits                                      -->
-<inherits name="java.beans.JavaBeans"/>
   <!-- Specify the app entry point class.                         -->
   <entry-point class='star.genetics.client.Stargenetics_gwt_java'/>
 
@@ -29,5 +29,7 @@
   <source path='utils'/>
   <source path='visualizers'/>
   <source path='xls'/>
-
+  <source path='beans'/>
+  <source path='tests'/>
+  <source path='parser'/>
 </module>

src/java/beans/JavaBeans.gwt.xml → src/star/genetics/beans/JavaBeans.gwt.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE module PUBLIC "-//Google Inc.//DTD Google Web Toolkit 2.5.1//EN" "http://google-web-toolkit.googlecode.com/svn/tags/2.5.1/distro-source/core/src/gwt-module.dtd">
 <module>
-	<inherits name="com.google.gwt.user.User" />
+	<!--   <inherits name="com.google.gwt.user.User" /> -->
 	<source path=""/>
 </module>

src/java/beans/PropertyChangeEvent.java → src/star/genetics/beans/PropertyChangeEvent.java

@@ -1,4 +1,4 @@
-package java.beans;
+package star.genetics.beans;
 
 public class PropertyChangeEvent
 {

src/java/beans/PropertyChangeListener.java → src/star/genetics/beans/PropertyChangeListener.java

@@ -1,7 +1,6 @@
-package java.beans;
+package star.genetics.beans;
 
 public interface PropertyChangeListener
 {
     public void propertyChange(PropertyChangeEvent e);
-
 }

src/java/beans/PropertyChangeSupport.java → src/star/genetics/beans/PropertyChangeSupport.java

@@ -1,4 +1,4 @@
-package java.beans;
+package star.genetics.beans;
 
 import java.util.ArrayList;
 
@@ -22,7 +22,7 @@ public void firePropertyChange(PropertyChangeEvent propertyChangeEvent)
 
     }
 
-	public void addPropertyChangeListener(PropertyChangeListener listener)
+	public void addPropertyChangeListener(star.genetics.beans.PropertyChangeListener listener)
     {
 		listeners.add(listener);
     }

src/java/beans/StringTokenizer.java → src/star/genetics/beans/StringTokenizer.java

@@ -1,4 +1,4 @@
-package java.beans;
+package star.genetics.beans;
 
 public class StringTokenizer
 {

src/star/genetics/client/Stargenetics_gwt_java.java

@@ -10,20 +10,6 @@
 import star.genetics.shared.FieldVerifier;
 
 import com.google.gwt.core.client.EntryPoint;
-import com.google.gwt.core.client.GWT;
-import com.google.gwt.event.dom.client.ClickEvent;
-import com.google.gwt.event.dom.client.ClickHandler;
-import com.google.gwt.event.dom.client.KeyCodes;
-import com.google.gwt.event.dom.client.KeyUpEvent;
-import com.google.gwt.event.dom.client.KeyUpHandler;
-import com.google.gwt.user.client.rpc.AsyncCallback;
-import com.google.gwt.user.client.ui.Button;
-import com.google.gwt.user.client.ui.DialogBox;
-import com.google.gwt.user.client.ui.HTML;
-import com.google.gwt.user.client.ui.Label;
-import com.google.gwt.user.client.ui.RootPanel;
-import com.google.gwt.user.client.ui.TextBox;
-import com.google.gwt.user.client.ui.VerticalPanel;
 
 /**
  * Entry point classes define <code>onModuleLoad()</code>.
@@ -44,16 +30,17 @@ public void test2()
 		test(self, me);
 	}
 
-	public static int add(int a,int b)
+	public static String add(int a,int b)
 	{
-		return a+b;
+		return "" + a+b;
 	}
 
 	public native void test(Object self, MatingEngine me)
 	/*-{
 		$wnd.__sg_entry_point = self;
 		$wnd.__sg_me = me;
 		$wnd.__sg_add = $entry(@star.genetics.client.Stargenetics_gwt_java::add(II));
+		console.info( "Done!" );
 		return "Not A Number";
 	}-*/;
 
@@ -62,108 +49,14 @@ public native void test(Object self, MatingEngine me)
 	 */
 	public void onModuleLoad()
 	{
-		final Button sendButton = new Button("Send");
-		final TextBox nameField = new TextBox();
-		nameField.setText("GWT User");
-		final Label errorLabel = new Label();
-
-		// We can add style names to widgets
-		sendButton.addStyleName("sendButton");
-
-		// Add the nameField and sendButton to the RootPanel
-		// Use RootPanel.get() to get the entire body element
-		RootPanel.get("nameFieldContainer").add(nameField);
-		RootPanel.get("sendButtonContainer").add(sendButton);
-		RootPanel.get("errorLabelContainer").add(errorLabel);
-
-		// Focus the cursor on the name field when the app loads
-		nameField.setFocus(true);
-		nameField.selectAll();
-
-		// Create the popup dialog box
-		final DialogBox dialogBox = new DialogBox();
-		dialogBox.setText("Remote Procedure Call");
-		dialogBox.setAnimationEnabled(true);
-		final Button closeButton = new Button("Close");
-		// We can set the id of a widget by accessing its Element
-		closeButton.getElement().setId("closeButton");
-		final Label textToServerLabel = new Label();
-		final HTML serverResponseLabel = new HTML();
-		VerticalPanel dialogVPanel = new VerticalPanel();
-		dialogVPanel.addStyleName("dialogVPanel");
-		dialogVPanel.add(new HTML("<b>Sending name to the server:</b>"));
-		dialogVPanel.add(textToServerLabel);
-		dialogVPanel.add(new HTML("<br><b>Server replies:</b>"));
-		dialogVPanel.add(serverResponseLabel);
-		dialogVPanel.setHorizontalAlignment(VerticalPanel.ALIGN_RIGHT);
-		dialogVPanel.add(closeButton);
-		dialogBox.setWidget(dialogVPanel);
-		test2();
-		// Add a handler to close the DialogBox
-		closeButton.addClickHandler(new ClickHandler()
-		{
-			public void onClick(ClickEvent event)
-			{
-				dialogBox.hide();
-				sendButton.setEnabled(true);
-				sendButton.setFocus(true);
-
-			}
-		});
-
-		// Create a handler for the sendButton and nameField
-		class MyHandler implements ClickHandler, KeyUpHandler
-		{
-			/**
-			 * Fired when the user clicks on the sendButton.
-			 */
-			public void onClick(ClickEvent event)
-			{
-				sendNameToServer();
-				MatingEngineImpl_XY xy = new MatingEngineImpl_XY();
-				ModelImpl impl = new ModelImpl();
-				GenomeImpl genome = new GenomeImpl();
-				ChromosomeImpl c = new ChromosomeImpl("name", genome);
-				GeneImpl g = new GeneImpl("test", 2, c);
-				impl.setGenome(genome);
-				System.out.println(impl);
-			}
-
-			/**
-			 * Fired when the user types in the nameField.
-			 */
-			public void onKeyUp(KeyUpEvent event)
-			{
-				if (event.getNativeKeyCode() == KeyCodes.KEY_ENTER)
-				{
-					sendNameToServer();
-				}
-			}
-
-			/**
-			 * Send the name from the nameField to the server and wait for a response.
-			 */
-			private void sendNameToServer()
-			{
-				// First, we validate the input.
-				errorLabel.setText("");
-				String textToServer = nameField.getText();
-				if (!FieldVerifier.isValidName(textToServer))
-				{
-					errorLabel.setText("Please enter at least four characters");
-					return;
-				}
-
-				// Then, we send the input to the server.
-				sendButton.setEnabled(false);
-				textToServerLabel.setText(textToServer);
-				serverResponseLabel.setText("");
-			}
-		}
-
-		// Add a handler to send the name to the server
-		MyHandler handler = new MyHandler();
-		sendButton.addClickHandler(handler);
-		nameField.addKeyUpHandler(handler);
+		MatingEngineImpl_XY xy = new MatingEngineImpl_XY();
+		ModelImpl impl = new ModelImpl();
+		GenomeImpl genome = new GenomeImpl();
+		ChromosomeImpl c = new ChromosomeImpl("name", genome);
+		GeneImpl g = new GeneImpl("test", 2, c);
+		impl.setGenome(genome);
+		impl.setMater(xy);
+		System.out.println(impl);
+		test(this,xy);
 	}
 }

src/star/genetics/genetic/impl/CreatureSetImpl.java

@@ -1,12 +1,12 @@
 package star.genetics.genetic.impl;
 
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-import java.beans.PropertyChangeSupport;
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.Iterator;
 
+import star.genetics.beans.PropertyChangeEvent;
+import star.genetics.beans.PropertyChangeListener;
+import star.genetics.beans.PropertyChangeSupport;
 import star.genetics.genetic.model.Creature;
 
 public class CreatureSetImpl implements star.genetics.genetic.model.CreatureSet, Serializable

src/star/genetics/genetic/impl/RuleImpl.java

@@ -3,8 +3,8 @@
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.HashMap;
-import java.beans.StringTokenizer;
 
+import star.genetics.beans.StringTokenizer;
 import star.genetics.client.Messages;
 import star.genetics.genetic.model.Allele;
 import star.genetics.genetic.model.Chromosome;

src/star/genetics/parser/EngineParser.java

@@ -0,0 +1,46 @@
+package star.genetics.parser;
+
+import com.google.gwt.json.client.JSONNumber;
+import com.google.gwt.json.client.JSONObject;
+
+import star.genetics.genetic.impl.MatingEngineImpl_XY;
+import star.genetics.genetic.impl.ModelImpl;
+
+public class EngineParser
+{
+	public static void parse(ModelImpl model, JSONObject engine)
+	{
+		String sex_type = engine.get("sex_type").isString().toString();
+		if ("xy".equalsIgnoreCase(sex_type))
+		{
+			parse_XY(model, engine);
+		}
+	}
+
+	private static float get(JSONObject obj, String key, float default_value)
+	{
+		float ret = default_value;
+		if (obj.containsKey(key))
+		{
+			JSONNumber n = obj.get(key).isNumber();
+			if (n != null)
+			{
+				ret = (float) n.doubleValue();
+			}
+		}
+		return ret;
+	}
+
+	private static void parse_XY(ModelImpl model, JSONObject engine)
+	{
+		float maleRecombinationRate = get(engine, "male_recombination_rate", 1.0f);
+		float femaleRecombinationRate = get(engine, "female_recombination_rate", 1.0f);
+		float femaleSexRatio = get(engine, "female_sex_ratio", 1.0f);
+		int progeniesCount = Math.round(get(engine, "avg_offspring_count", 50.0f));
+		float twinningFrequency = get(engine, "twinning", 0.0f);
+		float identicalTwinsFrequency = get(engine, "identical_twins_frequency", 0.0f);
+
+		MatingEngineImpl_XY xy = new MatingEngineImpl_XY(maleRecombinationRate, femaleRecombinationRate, femaleSexRatio, progeniesCount, twinningFrequency, identicalTwinsFrequency);
+		model.setMater(xy);
+	}
+}

src/star/genetics/parser/GenomeParser.java

@@ -0,0 +1,75 @@
+package star.genetics.parser;
+
+import star.genetics.genetic.impl.AlleleImpl;
+import star.genetics.genetic.impl.ChromosomeImpl;
+import star.genetics.genetic.impl.GeneImpl;
+import star.genetics.genetic.impl.GenomeImpl;
+import star.genetics.genetic.impl.ModelImpl;
+
+import com.google.gwt.json.client.JSONArray;
+import com.google.gwt.json.client.JSONObject;
+
+public class GenomeParser
+{
+
+	public static void parse(ModelImpl model, JSONObject genome)
+    {
+		GenomeImpl ret = new GenomeImpl();
+		parseChromosomes( ret , genome.get("chromosomes").isObject());
+		model.setGenome(ret);
+    }
+
+
+	private static void parseChromosomes(GenomeImpl genome, JSONObject chromosomes)
+    {
+	    for( String chromosome_id : chromosomes.keySet() ) {
+	    	ChromosomeImpl c = new ChromosomeImpl(chromosome_id, genome);
+	    	parseChromosome( c, chromosomes.get(chromosome_id).isObject() );
+	    }
+    }
+
+
+	private static void parseChromosome(ChromosomeImpl c, JSONObject chromosome)
+    {
+		String name = chromosome.get("name").isString().toString();
+		parseGenes( c , chromosome.get("genes").isArray());
+    }
+
+
+	private static void parseGenes(ChromosomeImpl c, JSONArray genes)
+    {
+		for( int i = 0 ; i < genes.size() ; i++)
+		{
+			JSONObject gene = genes.get(i).isObject();
+			parseGene( c , gene );
+		}
+
+    }
+
+
+	private static void parseGene(ChromosomeImpl c, JSONObject gene)
+    {
+		String name = gene.get("name").isString().toString();
+		float position = (float)gene.get("position").isNumber().doubleValue();
+		GeneImpl g = new GeneImpl(name, position, c);
+		parseAlleles( g , gene.get("alleles").isArray());
+    }
+
+
+	private static void parseAlleles(GeneImpl gene, JSONArray alleles)
+    {
+		for( int i = 0 ; i < alleles.size() ; i++ )
+		{
+			parseAllele( gene , alleles.get(i).isObject());
+		}
+    }
+
+
+	private static void parseAllele(GeneImpl gene, JSONObject allele)
+    {
+		String name = allele.get("name").isString().toString();
+		AlleleImpl a = new AlleleImpl(name, gene);
+    }
+
+
+}