And more work!

starteam · Jan 17, 2014 · a5c3223 · a5c3223
1 parent 4d12c1a
commit a5c3223
Show file tree

Hide file tree

Showing 48 changed files with 13,134 additions and 6,368 deletions.
diff --git a/src/star/genetics/client/Helper.java b/src/star/genetics/client/Helper.java
@@ -8,7 +8,6 @@
 import star.genetics.genetic.model.Creature;
 import star.genetics.visualizers.Visualizer;
 
-import com.google.gwt.json.client.JSONNull;
 import com.google.gwt.json.client.JSONNumber;
 import com.google.gwt.json.client.JSONString;
 import com.google.gwt.json.client.JSONValue;
@@ -80,11 +79,15 @@ public static final JSONValue wrapString(String value)
 		{
 			return new JSONString(value);
 		}
-		return JSONNull.getInstance();
+		return new JSONString("");
 	}
 
 	public static final String unwrapString(JSONValue value)
 	{
+		if (value == null)
+		{
+			return null;
+		}
 		JSONString s = value.isString();
 		return s != null ? s.stringValue() : null;
 	}

diff --git a/src/star/genetics/client/JSONable.java b/src/star/genetics/client/JSONable.java
@@ -1,5 +1,7 @@
 package star.genetics.client;
 
+import star.genetics.genetic.model.Model;
+
 import com.google.gwt.json.client.JSONObject;
 
 public interface JSONable
@@ -48,4 +50,5 @@ public interface JSONable
 	static final String KIND = "kind";
 
 	JSONObject getJSON();
+	Model getModel();
 }
diff --git a/src/star/genetics/client/JSONableList.java b/src/star/genetics/client/JSONableList.java
@@ -19,8 +19,15 @@ public JSONableList(JSONArray array)
 
 	public void add(T element)
 	{
+		if( element instanceof String)
+		{
+			data.set(data.size(), Helper.wrapString((String)element));
+		}
+		else
+		{
 		JSONable e = (JSONable) element;
 		data.set(data.size(), e.getJSON());
+		}
 	}
 
 	public int size()
@@ -51,6 +58,10 @@ public T next()
 			{
 				JSONValue element = data.get(index);
 				index++;
+				if( element.isString() != null)
+				{
+					return (T)Helper.unwrapString(element);
+				}
 				return create(element.isObject());
 			}
 

diff --git a/src/star/genetics/client/StarGenetics.java b/src/star/genetics/client/StarGenetics.java
@@ -42,11 +42,12 @@ public void execute(Exec exec)
 	{
 		try
 		{
-			logger.log(Level.FINE, "in Execute.");
+			logger.log(Level.INFO, "in Execute.");
 			String command = exec.getCommand();
-			System.out.println("command " + command);
+			logger.log(Level.INFO, "in Command:" + command);
 			if (Commands.Open.is(command))
 			{
+				logger.log(Level.INFO, "in Command: OPEN -- " + command);
 				open(exec);
 			}
 			else if (Commands.ListStrains.is(command))
@@ -81,8 +82,11 @@ private void save(Exec exec)
 
 	private void open(Exec exec)
 	{
+		logger.log(Level.INFO, "in Command: QQ Open");
 		Open cmd = exec.cast();
+		logger.log(Level.INFO, "in Command: AA Open");
 		cmd.execute(this);
+		logger.log(Level.INFO, "in Command: WW Open");
 	}
 
 	private void listStrains(Exec exec)
@@ -101,9 +105,8 @@ private void updateExperiment(Exec exec)
 
 	private static native void log(String str)
 	/*-{
-		if( typeof(console) == 'object' && console && console.info )
-		{
-			console.info( str ) ;
+		if (typeof (console) == 'object' && console && console.info) {
+			console.info(str);
 		}
 	}-*/;
 

diff --git a/src/star/genetics/client/Stargenetics_gwt_java.java b/src/star/genetics/client/Stargenetics_gwt_java.java
@@ -49,12 +49,15 @@ public static void execute(Exec obj)
 				{
 					logger.log(Level.INFO, "New StarGenetics backend for token " + token);
 					map.put(token, new StarGenetics());
+
 				}
 				else
 				{
 					logger.log(Level.INFO, "Loading existing StarGenetics backend for token " + token);
 				}
+				logger.log(Level.INFO, "New StarGenetics backend for token " + token + " pre exec.");
 				map.get(token).execute(obj);
+				logger.log(Level.INFO, "New StarGenetics backend for token " + token + " post exec.");
 			}
 			else
 			{

diff --git a/src/star/genetics/client/messages/Open.java b/src/star/genetics/client/messages/Open.java
@@ -1,5 +1,8 @@
 package star.genetics.client.messages;
 
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
 import star.genetics.client.StarGenetics;
 import star.genetics.genetic.model.Model;
 import star.genetics.parser.ModelParser;
@@ -10,7 +13,6 @@
 
 public class Open extends Exec
 {
-
 	protected Open()
 	{
 	}
@@ -23,21 +25,29 @@ protected Open()
 
 	public final Model execute(StarGenetics starGenetics)
 	{
+		Logger logger = Logger.getLogger("Open");
 		final String VERSION_1 = "Version_1";
 		Model model = null;
+		logger.log(Level.INFO, "Open 1");
 		if (VERSION_1.equalsIgnoreCase(getProtocol()))
 		{
-			model = (ModelParser.parse(getJSONModel()));
+			logger.log(Level.INFO, "Open 2");
+			model = ModelParser.parse(getJSONModel());
+			logger.log(Level.INFO, "Open 3");
 			JSONObject ret = new JSONObject();
+			logger.log(Level.INFO, "Open 4");
 			starGenetics.setModel(model);
+			logger.log(Level.INFO,"Open 5");
 			onSuccess(ret.getJavaScriptObject());
+			logger.log(Level.INFO, "Open 6");
 		}
 		else
 		{
 			JSONObject ret = new JSONObject();
 			ret.put("error", new JSONString("Unrecognized protocol."));
 			onError(ret.getJavaScriptObject());
 		}
+		logger.log(Level.INFO, "Open 7");
 		return model;
 	}
 }
diff --git a/src/star/genetics/client/messages/Save.java b/src/star/genetics/client/messages/Save.java
@@ -6,9 +6,6 @@
 
 import com.google.gwt.json.client.JSONObject;
 import com.google.gwt.json.client.JSONString;
-import com.google.web.bindery.autobean.shared.AutoBean;
-import com.google.web.bindery.autobean.shared.AutoBeanCodex;
-import com.google.web.bindery.autobean.shared.AutoBeanUtils;
 
 public class Save extends Exec
 {
@@ -19,11 +16,9 @@ protected Save()
 
 	public final native String getProtocol() /*-{ return this.data.protocol; }-*/;
 
-	public final String serialize(ModelWriter model)
+	public final JSONObject serialize(ModelWriter model)
 	{
-
-		AutoBean<Model> m = AutoBeanUtils.getAutoBean(model);
-		return AutoBeanCodex.encode(m).getPayload();
+		return model.getJSON();
 	}
 
 	public final void execute(StarGenetics starGenetics, Model model)
@@ -32,7 +27,7 @@ public final void execute(StarGenetics starGenetics, Model model)
 		if (VERSION_1.equalsIgnoreCase(getProtocol()))
 		{
 			JSONObject ret = new JSONObject();
-			ret.put("model", new JSONString(serialize((ModelWriter) model)));
+			ret.put("model", serialize((ModelWriter) model));
 			ret.put("model2", new JSONString("test"));
 			starGenetics.setModel(model);
 			onSuccess(ret.getJavaScriptObject());

diff --git a/src/star/genetics/client/messages_en.properties b/src/star/genetics/client/messages_en.properties
@@ -1,5 +1,5 @@
 #en
-#Tue Jan 14 15:53:22 EST 2014
+#Thu Jan 16 19:56:22 EST 2014
 GroupBy.4={0} ({1}%)
 GroupBy.3=<html><b>Male</b></html>
 Cow.0=m\: 

diff --git a/src/star/genetics/genetic/impl/AlleleImpl.java b/src/star/genetics/genetic/impl/AlleleImpl.java
@@ -3,7 +3,10 @@
 import java.io.Serializable;
 
 import star.genetics.client.Helper;
+import star.genetics.genetic.model.Chromosome;
 import star.genetics.genetic.model.Gene;
+import star.genetics.genetic.model.Genome;
+import star.genetics.genetic.model.Model;
 
 import com.google.gwt.json.client.JSONObject;
 
@@ -12,16 +15,27 @@ public class AlleleImpl implements star.genetics.genetic.model.Allele, Serializa
 	private static final long serialVersionUID = 1L;
 	JSONObject data = new JSONObject();
 
-	public AlleleImpl(JSONObject data)
+	Model model;
+
+	@Override
+	public Model getModel()
+	{
+		return model;
+	}
+
+	public AlleleImpl(JSONObject data, Model model)
 	{
 		this.data = data;
+		this.model = model;
 	}
 
-	public AlleleImpl(String name, Gene gene)
+	public AlleleImpl(String name, Gene gene, Model model)
 	{
 		data.put(NAME, Helper.wrapString(name));
-		data.put(GENE, gene.getJSON());
+		data.put(CHROMOSOME, Helper.wrapString(gene.getChromosome().getName()));
+		data.put(GENE, Helper.wrapString(gene.getName()));
 		gene.getGeneTypes().add(this);
+		this.model = model;
 	}
 
 	public String getName()
@@ -31,7 +45,10 @@ public String getName()
 
 	public Gene getGene()
 	{
-		return new GeneImpl(data.get(GENE).isObject());
+		Genome g = getModel().getGenome();
+		Chromosome c= g.getChromosomeByName(Helper.unwrapString(data.get(CHROMOSOME)));
+		Gene gene = c.getGeneByName(Helper.unwrapString(data.get(GENE)));
+		return gene;
 	}
 
 	@Override

diff --git a/src/star/genetics/genetic/impl/ChromosomeImpl.java b/src/star/genetics/genetic/impl/ChromosomeImpl.java
@@ -7,6 +7,7 @@
 import star.genetics.genetic.model.Allele;
 import star.genetics.genetic.model.Gene;
 import star.genetics.genetic.model.Genome;
+import star.genetics.genetic.model.Model;
 
 import com.google.gwt.json.client.JSONArray;
 import com.google.gwt.json.client.JSONObject;
@@ -15,17 +16,25 @@ public class ChromosomeImpl implements star.genetics.genetic.model.Chromosome, S
 {
 	private static final long serialVersionUID = 1L;
 	private JSONObject data;
-
-	public ChromosomeImpl(JSONObject data)
+	private Model model ;
+	public Model getModel()
+    {
+	    return model;
+    }
+
+	public ChromosomeImpl(JSONObject data, Model model)
 	{
 		this.data = data;
+		this.model = model;
 	}
 
-	public ChromosomeImpl(String name, Genome genome)
+	public ChromosomeImpl(String name, Genome genome, Model model )
 	{
+		data = new JSONObject();
 		data.put(NAME, Helper.wrapString(name));
 		data.put(GENES, new JSONArray());
 		genome.addChromosome(this);
+		this.model = model;
 	}
 
 	public String getName()
@@ -39,7 +48,7 @@ public JSONableList<Gene> getGenes()
 		{
 			public Gene create(JSONObject d)
 			{
-				return new GeneImpl(d);
+				return new GeneImpl(d, getModel());
 			}
 		};
 	}