Updates

diff.sh

@@ -0,0 +1,4 @@
+echo "========= DIFF ==========="
+echo $1
+
+diff ../stargenetics_java/$1 $1

i18n.sh

@@ -0,0 +1,7 @@
+#!/bin/bash
+
+java -cp ../star_xls2i18_java/bin/:../star_xls2i18_java/lib/poi-3.2-FINAL-20081019.jar xls.MessagesBuilder ../stargenetics_java/src/StarGenetics_Properties_en.xls src/star/genetics/client/messages.properties
+mkdir -p war/stargenetics_gwt_java/messages
+cp src/star/genetics/client/messages*.json war/stargenetics_gwt_java/messages
+
+

ignore/.classpath

@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" path="src"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="lib" path="/Applications/eclipse-4.3/plugins/com.google.gwt.eclipse.sdkbundle_2.5.1/gwt-2.5.1/gwt-user.jar">
+		<attributes>
+			<attribute name="javadoc_location" value="file:/Applications/eclipse-4.3/plugins/com.google.gwt.eclipse.sdkbundle_2.5.1/gwt-2.5.1/doc/javadoc/"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="lib" path="/Applications/eclipse-4.3/plugins/com.google.gwt.eclipse.sdkbundle_2.5.1/gwt-2.5.1/gwt-dev.jar">
+		<attributes>
+			<attribute name="javadoc_location" value="file:/Applications/eclipse-4.3/plugins/com.google.gwt.eclipse.sdkbundle_2.5.1/gwt-2.5.1/doc/javadoc/"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="lib" path="/Applications/eclipse-4.3/plugins/com.google.gwt.eclipse.sdkbundle_2.5.1/gwt-2.5.1/validation-api-1.0.0.GA-sources.jar"/>
+	<classpathentry kind="lib" path="/Applications/eclipse-4.3/plugins/com.google.gwt.eclipse.sdkbundle_2.5.1/gwt-2.5.1/validation-api-1.0.0.GA.jar" sourcepath="/Applications/eclipse-4.3/plugins/com.google.gwt.eclipse.sdkbundle_2.5.1/gwt-2.5.1/validation-api-1.0.0.GA-sources.jar"/>
+	<classpathentry kind="output" path="war/WEB-INF/classes"/>
+</classpath>

src/star/genetics/client/messages/UpdateExperimentImpl.java

@@ -1,5 +1,8 @@
 package star.genetics.client.messages;
 
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
 import star.genetics.client.StrainHelper;
 import star.genetics.genetic.impl.MatingException;
 import star.genetics.genetic.model.CrateModel;
@@ -16,50 +19,55 @@
 public class UpdateExperimentImpl
 {
 	private UpdateExperiment exp;
-
+
+	private static Logger logger = Logger.getLogger("UpdateExperiment");
+
 	public UpdateExperimentImpl(UpdateExperiment e)
 	{
-		this.exp = e ;
+		this.exp = e;
 	}
-	
+
 	public final void execute(Model model)
-	{		
+	{
 		Experiment experiment = exp.getExperiment();
 		String id = experiment.getId();
 		if (id == null)
 		{
 			CrateModel cratemodel = model.getCrateSet().newCrateModel();
 			if ("mate".equalsIgnoreCase(exp.getExperimentCommand()))
 			{
-				cratemodel.setName(experiment.getName());
+				if( experiment.getName() != null )
+				{
+					cratemodel.setName(experiment.getName());
+				}
 				for (JavaScriptObject so : experiment.getParents())
 				{
 					Strain s = so.cast();
-					System.out.println( new JSONObject(s));
+					System.out.println(new JSONObject(s));
 					Creature c = getCreature(s, model);
-					System.out.println( c );
+					System.out.println(c);
 					cratemodel.getParents().add(c);
 				}
 				try
-                {
-	                CreatureSet children = model.getMatingEngine().getProgenies(cratemodel.getName(), cratemodel.getParents(), cratemodel.getProgenies().size()+1, 1, model.getRules());
-	                for( Creature c : children )
-	                {
-	                	cratemodel.getProgenies().add(c);
-	                }
-                }
-                catch (MatingException e)
-                {
-                	JSONObject err = new JSONObject();
-    				err.put("error", new JSONString("Mating exception." + e.getMessage() ));
-    				exp.onError(err.getJavaScriptObject());
-	                e.printStackTrace();
-                }
+				{
+					CreatureSet children = model.getMatingEngine().getProgenies(cratemodel.getName(), cratemodel.getParents(), cratemodel.getProgenies().size() + 1, 1, model.getRules());
+					for (Creature c : children)
+					{
+						cratemodel.getProgenies().add(c);
+					}
+				}
+				catch (MatingException e)
+				{
+					JSONObject err = new JSONObject();
+					err.put("error", new JSONString("Mating exception." + e.getMessage()));
+					exp.onError(err.getJavaScriptObject());
+					e.printStackTrace();
+				}
 				JSONObject ret = new JSONObject();
-				ret.put("name", new JSONString(cratemodel.getName()));
+				ret.put("name", new JSONString(cratemodel.getName() != null ? cratemodel.getName() : "-- No Name --"));
 				ret.put("id", new JSONString(cratemodel.getUUID()));
-				ret.put("parents", getCrateSetToJSON(cratemodel.getParents(),model));
-				ret.put("children", getCrateSetToJSON(cratemodel.getProgenies(),model));			
+				ret.put("parents", getCrateSetToJSON(cratemodel.getParents(), model));
+				ret.put("children", getCrateSetToJSON(cratemodel.getProgenies(), model));
 				exp.onSuccess(ret.getJavaScriptObject());
 			}
 			else if ("metadata".equalsIgnoreCase(exp.getExperimentCommand()))
@@ -100,17 +108,21 @@ else if ("metadata".equalsIgnoreCase(exp.getExperimentCommand()))
 		}
 	}
 
-
-
 	private final JSONValue getCrateSetToJSON(CreatureSet creatures, Model model)
-    {
+	{
+		logger.log(Level.INFO, " getCrateSetToJSON " + creatures + " " + model);
 		JSONArray ret = new JSONArray();
-		for( Creature c : creatures )
+		logger.log(Level.INFO, " getCrateSetToJSON 2");
+		for (Creature c : creatures)
 		{
-			ret.set(ret.size(),StrainHelper.getLong(c, model.getRules()));
+			logger.log(Level.INFO, " getCrateSetToJSON 3 ");
+			logger.log(Level.INFO, " getCrateSetToJSON 3 " + c);
+			logger.log(Level.INFO, " getCrateSetToJSON 3 " + model.getRules());
+			ret.set(ret.size(), StrainHelper.getLong(c, model.getRules()));
 		}
-	    return ret;
-    }
+		logger.log(Level.INFO, " getCrateSetToJSON 4");
+		return ret;
+	}
 
 	private final Creature getCreature(Strain s, Model model)
 	{

src/star/genetics/client/messages_en.properties

@@ -1,5 +1,5 @@
 #en
-#Thu Aug 22 15:14:45 EDT 2013
+#Wed Dec 11 17:50:40 EST 2013
 GroupBy.4={0} ({1}%)
 GroupBy.3=<html><b>Male</b></html>
 Cow.0=m\: 
@@ -412,7 +412,7 @@ ChooseExperiment.0=Choose experimental setup
 CrateModelImpl.0=Exp. {0}
 Sex.10=Unknown sex type
 Fly.wingsize=Wing size
-MatingEngineImpl_Common.4=Parents can not mate\\\!
+MatingEngineImpl_Common.4=These parents cannot perform any more matings.
 MatingEngineImpl_Common.3=All progenies are dead\\\!
 Fly.sex=Sex
 MainPanel.9=Unsupported visualizer class, supported classes\: {0}

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

@@ -65,8 +65,9 @@ public Iterator<CrateModel> iterator()
 	public CrateModel newCrateModel()
 	{
 		clearInvisibleCrates();
-		add(new CrateModelImpl(id++));
-		return current();
+		CrateModel ret = new CrateModelImpl(id++);
+		add(ret);
+		return ret;
 	}
 
 	private void clearInvisibleCrates()

war/Stargenetics_gwt_java.css

@@ -32,3 +32,4 @@ h1 {
 #closeButton {
   margin: 15px 6px 6px;
 }
+

war/Stargenetics_gwt_java.html

@@ -60,3 +60,4 @@ <h1>Web Application Starter Project</h1>
     </table>
   </body>
 </html>
+

war/WEB-INF/web.xml

@@ -11,3 +11,4 @@
   </welcome-file-list>
 
 </web-app>
+