Updating SG to output phenotypes

starteam · Sep 16, 2013 · b31b8e5 · b31b8e5
1 parent ff45882
commit b31b8e5
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Showing 8 changed files with 71 additions and 18 deletions.
diff --git a/src/star/genetics/beans/StringTokenizer.java b/src/star/genetics/beans/StringTokenizer.java
@@ -6,24 +6,35 @@ public class StringTokenizer
 	private String str;
 	private String split;
 	private int index;
+	private boolean hasMoreTokens = true;
 
 	public StringTokenizer(String str, String split)
     {
 		this.str = str;
 		this.split = split;
 		this.index = 0;
+
     }
 
 	public boolean hasMoreTokens()
     {
-	    return str.indexOf(split,index) > 0; 
+	    return hasMoreTokens; 
     }
 
 	public String nextToken()
-    {
+    {		
 		int next_index = str.indexOf(split,index);
-		String ret = str.substring(index, next_index);
-		index = next_index;
+		String ret;
+		if( next_index == -1 )
+		{
+			hasMoreTokens = false;
+			ret = str.substring(index);
+		}
+		else
+		{
+			ret = str.substring(index, next_index );					
+			index = next_index + split.length();
+		}
 		return ret;
     }
 

diff --git a/src/star/genetics/client/StarGenetics.java b/src/star/genetics/client/StarGenetics.java
@@ -90,7 +90,8 @@ private void listStrains(Exec exec)
 		CreatureSet strains = model.getCreatures();
 		for (int i = 0; i < strains.size(); i++)
 		{
-			retset.set(i, StrainHelper.getShort(strains.get(i)));
+//			retset.set(i, StrainHelper.getShort(strains.get(i)));
+			retset.set(i, StrainHelper.getLong(strains.get(i),model.getRules()));
 		}
 		exec.onSuccess(ret.getJavaScriptObject());
 	}

diff --git a/src/star/genetics/client/Stargenetics_gwt_java.java b/src/star/genetics/client/Stargenetics_gwt_java.java
@@ -25,24 +25,27 @@ public class Stargenetics_gwt_java implements EntryPoint
 	private static Logger logger = Logger.getLogger("StarGenetics");
 	private static HashMap<String, StarGenetics> map = new HashMap<String, StarGenetics>();
 
+
+
 	public void onModuleLoad()
 	{
 		setupInterface();
 	}
-
-	static {
-		setupInterface();
-	}
 
 	private static native void setupInterface()
 	/*-{
 		$wnd.__sg_bg_exec = $entry(@star.genetics.client.Stargenetics_gwt_java::execute(*));
-		console.info( "setup interface" ) ;
+		if( typeof(console) == 'object' && console && console.info ) {
+			console.info( "setup interface" ) ;
+		}
 	}-*/;
 
 	private static native void log( String str )
 	/*-{
-		console.info( str ) ;
+		if( typeof(console) == 'object' && console && console.info )
+		{
+			console.info( str ) ;
+		}
 	}-*/;
 	public static void execute(Exec obj)
 	{	

diff --git a/src/star/genetics/client/StrainHelper.java b/src/star/genetics/client/StrainHelper.java
@@ -1,9 +1,14 @@
 package star.genetics.client;
 
+import java.util.Map;
+import java.util.Map.Entry;
+
 import com.google.gwt.json.client.JSONObject;
 import com.google.gwt.json.client.JSONString;
 
 import star.genetics.genetic.model.Creature;
+import star.genetics.genetic.model.Rule;
+import star.genetics.genetic.model.RuleSet;
 
 public class StrainHelper
 {
@@ -12,6 +17,23 @@ public static JSONObject getShort(Creature creature)
 		JSONObject ret = new JSONObject();
 		ret.put( "name", new JSONString(creature.getName()));
 		ret.put( "id" , new JSONString(creature.getUUID()));
+		ret.put( "export_type" , new JSONString("short"));
 		return ret;
     }
+
+	public static JSONObject getLong(Creature creature, RuleSet rules)
+	{
+		JSONObject ret = new JSONObject();
+		Map<String,String> properties = rules.getProperties(creature.getMakeup(), creature.getSex());
+		for( Entry<String,String> e : properties.entrySet() )
+		{
+			ret.put(e.getKey(), new JSONString(e.getValue()));
+		}
+		ret.put( "name", new JSONString(creature.getName()));
+		ret.put( "id" , new JSONString(creature.getUUID()));
+		ret.put( "export_type" , new JSONString("long"));
+
+		return ret;
+
+	}
 }
diff --git a/src/star/genetics/genetic/impl/RuleImpl.java b/src/star/genetics/genetic/impl/RuleImpl.java
@@ -26,7 +26,10 @@ public RuleImpl(String rule, HashMap<String, String> properties, Genome g)
 	{
 		this.rule = rule;
 		this.properties = properties;
-		parseRules(rule, g);
+		if(!isDefault())
+		{
+			parseRules(rule, g);
+		}
 	}
 
 	private void parseRules(String rule, Genome g)
@@ -139,6 +142,7 @@ private void parseOneRule(String oneRule, Genome g)
 				{
 					chromosome = gene.getChromosome();
 					chromosomeName = chromosome.getName();
+					break;
 				}
 			}
 		}
@@ -191,7 +195,7 @@ private ChromosomeRuleImpl makeChromosomeRule(String alleles, Chromosome chromos
 
 	public boolean isDefault()
 	{
-		return DEFAULT.equalsIgnoreCase(rule);
+		return DEFAULT.equalsIgnoreCase(rule) || "*".equalsIgnoreCase(rule);
 	}
 
 	public boolean isMatching(GeneticMakeup makeup, Creature.Sex sex)

diff --git a/test-classes/star/genetics/tests/setupmodel.json b/test-classes/star/genetics/tests/setupmodel.json
@@ -45,14 +45,14 @@
             },
             {
                 "name": "white eyes",
-                "matches": "aa",
+                "matches": "a,a",
                 "phenotype": {
                     "eyes": "white"
                 }
             },
             {
                 "name": "wingless",
-                "matches": "bb",
+                "matches": "b,b",
                 "phenotype": {
                     "wings": 0
                 }

diff --git a/test/star/genetics/tests/JSONModel.java b/test/star/genetics/tests/JSONModel.java
@@ -1,5 +1,6 @@
 package star.genetics.tests;
 
+import star.genetics.beans.StringTokenizer;
 import star.genetics.client.Exec;
 import star.genetics.client.Stargenetics_gwt_java;
 
@@ -38,9 +39,20 @@ private final native String toJSON(JavaScriptObject that) /*-{
 	String getJson()
 	{
 		// getJSON("setupmodel.json");
-		return "{\"genetics\":{\"visualizer\":{\"name\":\"fly\"},\"model_metadata\":{},\"experiments\":{},\"engine\":{\"sex_type\":\"XY\",\"male_recombination_rate\":1,\"female_sex_ratio\":0.51,\"avg_offspring_count\":50,\"female_recombination_rate\":1,\"twinning\":0,\"identical_twins_frequency\":0},\"strains\":{\"initial\":{\"name\":\"Initial Strains\",\"list\":[{\"sex\":\"M\",\"alleles\":[\"A,A\",\"B,B\"],\"name\":\"Wildtype M\"},{\"sex\":\"F\",\"alleles\":[\"A,A\",\"B,B\"],\"name\":\"Wildtype F\"},{\"sex\":\"M\",\"alleles\":[\"a,a\",\"b,b\"],\"name\":\"Double Mutant M\"},{\"sex\":\"F\",\"alleles\":[\"a,a\",\"b,b\"],\"name\":\"Double Mutant F\"}]}},\"gel_rules\":{},\"phenotype_rules\":[{\"matches\":\"*\",\"name\":\"default\",\"phenotype\":{\"wings\":1,\"eyes\":\"red\"}},{\"matches\":\"aa\",\"name\":\"white eyes\",\"phenotype\":{\"eyes\":\"white\"}},{\"matches\":\"bb\",\"name\":\"wingless\",\"phenotype\":{\"wings\":0}}],\"genome\":{\"chromosomes\":{\"C_1\":{\"genes\":[{\"position\":25,\"alleles\":[{\"name\":\"A\"},{\"name\":\"a\"}],\"name\":\"red_eyes\"},{\"position\":40,\"alleles\":[{\"name\":\"B\"},{\"name\":\"b\"}],\"name\":\"wingless\"}],\"name\":\"Chromosome 1\"}}}}}\n";
+		return "{\"genetics\":{\"visualizer\":{\"name\":\"fly\"},\"model_metadata\":{},\"experiments\":{},\"engine\":{\"sex_type\":\"XY\",\"male_recombination_rate\":1,\"female_sex_ratio\":0.51,\"avg_offspring_count\":50,\"female_recombination_rate\":1,\"twinning\":0,\"identical_twins_frequency\":0},\"strains\":{\"initial\":{\"name\":\"Initial Strains\",\"list\":[{\"sex\":\"M\",\"alleles\":[\"A,A\",\"B,B\"],\"name\":\"Wildtype M\"},{\"sex\":\"F\",\"alleles\":[\"A,A\",\"B,B\"],\"name\":\"Wildtype F\"},{\"sex\":\"M\",\"alleles\":[\"a,a\",\"b,b\"],\"name\":\"Double Mutant M\"},{\"sex\":\"F\",\"alleles\":[\"a,a\",\"b,b\"],\"name\":\"Double Mutant F\"}]}},\"gel_rules\":{},\"phenotype_rules\":[{\"matches\":\"*\",\"name\":\"default\",\"phenotype\":{\"wings\":1,\"eyes\":\"red\"}},{\"matches\":\"a,a\",\"name\":\"white eyes\",\"phenotype\":{\"eyes\":\"white\"}},{\"matches\":\"b,b\",\"name\":\"wingless\",\"phenotype\":{\"wings\":0}}],\"genome\":{\"chromosomes\":{\"C_1\":{\"genes\":[{\"position\":25,\"alleles\":[{\"name\":\"A\"},{\"name\":\"a\"}],\"name\":\"red_eyes\"},{\"position\":40,\"alleles\":[{\"name\":\"B\"},{\"name\":\"b\"}],\"name\":\"wingless\"}],\"name\":\"Chromosome 1\"}}}}}\n";
 	}
 
+	public void st_test()
+	{
+		if( true )
+		{
+		StringTokenizer st = new StringTokenizer("a,b" , ",");
+		assertTrue(st.hasMoreTokens());
+		assertEquals("a", st.nextToken().trim());
+		assertTrue(st.hasMoreTokens());
+		assertEquals("b", st.nextToken().trim());
+		}
+	}
 	public void test()
 	{
 		open();

diff --git a/test/star/genetics/tests/setupmodel.json b/test/star/genetics/tests/setupmodel.json
@@ -45,14 +45,14 @@
             },
             {
                 "name": "white eyes",
-                "matches": "aa",
+                "matches": "a,a",
                 "phenotype": {
                     "eyes": "white"
                 }
             },
             {
                 "name": "wingless",
-                "matches": "bb",
+                "matches": "b,b",
                 "phenotype": {
                     "wings": 0
                 }