From 5b10b4b6ed0c979c114d2511925a6a7570cc3bc8 Mon Sep 17 00:00:00 2001
From: Marcel Kronfeld <makron@gmx.net>
Date: Tue, 1 Feb 2011 12:43:04 +0000
Subject: [PATCH] Minor addition to GI individual

---
 .../individuals/GIIndividualIntegerData.java  | 17 +++++++--
 .../distancemetric/GenotypeMetricBitSet.java  |  4 +++
 .../server/go/populations/Population.java     | 35 ++++++++++++-------
 3 files changed, 41 insertions(+), 15 deletions(-)

diff --git a/src/eva2/server/go/individuals/GIIndividualIntegerData.java b/src/eva2/server/go/individuals/GIIndividualIntegerData.java
index 7662f6f7..6f58a6f6 100644
--- a/src/eva2/server/go/individuals/GIIndividualIntegerData.java
+++ b/src/eva2/server/go/individuals/GIIndividualIntegerData.java
@@ -21,7 +21,7 @@ public class GIIndividualIntegerData extends AbstractEAIndividual implements Int
     protected int[]                     m_Genotype;
 
     public GIIndividualIntegerData() {
-        this.m_MutationProbability  = 0.1;
+        this.m_MutationProbability  = 0.2;
         this.m_MutationOperator     = new MutateDefault();
         this.m_CrossoverProbability = 0.7;
         this.m_CrossoverOperator    = new CrossoverGIDefault();
@@ -276,7 +276,20 @@ public class GIIndividualIntegerData extends AbstractEAIndividual implements Int
 
     public void defaultInit(InterfaceOptimizationProblem prob) {
     	int[][] range = m_Range;
-        if ((prob != null) && (prob instanceof InterfaceHasInitRange) && (((InterfaceHasInitRange)prob).getInitRange()!=null)) range = (int[][])((InterfaceHasInitRange)prob).getInitRange();
+        if ((prob != null) && (prob instanceof InterfaceHasInitRange) && (((InterfaceHasInitRange)prob).getInitRange()!=null)) {
+        	Object rng = ((InterfaceHasInitRange)prob).getInitRange();
+        	if (rng instanceof double[][]) {
+        		double[][] dblRng = (double[][])rng;
+        		range = new int[dblRng.length][dblRng[0].length];
+        		for (int i=0; i<range.length; i++) {
+        			for (int j=0; j<range[0].length ; j++) {
+        				range[i][j]=(int)dblRng[i][j];
+        			}
+        		}
+        	} else if (rng instanceof int[][]){
+        		range = (int[][])rng;
+        	} else System.err.println("Error, invalid initial range provided by " + prob + ", expecting int[][] or double[][], disregarding initialization range");
+        }
     	
         for (int i = 0; i < this.m_Genotype.length; i++) {
             this.m_Genotype[i] = RNG.randomInt(range[i][0], range[i][1]);
diff --git a/src/eva2/server/go/operators/distancemetric/GenotypeMetricBitSet.java b/src/eva2/server/go/operators/distancemetric/GenotypeMetricBitSet.java
index 6a5d2b93..5eeadc55 100644
--- a/src/eva2/server/go/operators/distancemetric/GenotypeMetricBitSet.java
+++ b/src/eva2/server/go/operators/distancemetric/GenotypeMetricBitSet.java
@@ -34,6 +34,10 @@ public class GenotypeMetricBitSet implements InterfaceDistanceMetric, java.io.Se
      * @return double
      */
     public double distance(AbstractEAIndividual indy1, AbstractEAIndividual indy2) {
+    	return GenotypeMetricBitSet.dist(indy1, indy2);
+    }
+    
+    public static double dist(AbstractEAIndividual indy1, AbstractEAIndividual indy2) {
         BitSet      dIndy1, dIndy2;
         double      result = 0;
         int         length = 0;
diff --git a/src/eva2/server/go/populations/Population.java b/src/eva2/server/go/populations/Population.java
index 5d19ac0d..bc59c698 100644
--- a/src/eva2/server/go/populations/Population.java
+++ b/src/eva2/server/go/populations/Population.java
@@ -17,6 +17,7 @@ import eva2.server.go.PopulationInterface;
 import eva2.server.go.individuals.AbstractEAIndividual;
 import eva2.server.go.individuals.AbstractEAIndividualComparator;
 import eva2.server.go.individuals.InterfaceDataTypeDouble;
+import eva2.server.go.individuals.InterfaceESIndividual;
 import eva2.server.go.individuals.InterfaceGAIndividual;
 import eva2.server.go.operators.distancemetric.EuclideanMetric;
 import eva2.server.go.operators.distancemetric.InterfaceDistanceMetric;
@@ -1788,19 +1789,27 @@ public class Population extends ArrayList implements PopulationInterface, Clonea
     	double maxDist = Double.MIN_VALUE;
     	double minDist = Double.MAX_VALUE;
     	
-        for (int i = 0; i < pop.size(); i++) {
-        	for (int j = i+1; j < pop.size(); j++) {
-        		try {
-        			if (metric == null) d = EuclideanMetric.euclideanDistance(AbstractEAIndividual.getDoublePositionShallow(pop.get(i)), 
-        					AbstractEAIndividual.getDoublePositionShallow(pop.get(j)));
-        			else d = metric.distance((AbstractEAIndividual)pop.get(i), (AbstractEAIndividual)pop.get(j));
-        		} catch (Exception e) {
-        			EVAERROR.errorMsgOnce("Exception when calculating population measures ... possibly no double position available?");
-        			d = 0;
-        		}
-        		distSum += d;
-                if (d < minDist) minDist = d;
-                if (d > maxDist) maxDist = d;
+    	for (int i = 0; i < pop.size(); i++) {
+    		for (int j = i+1; j < pop.size(); j++) {
+    			try {
+    				if (metric == null) {
+    					if (pop.get(i) instanceof InterfaceESIndividual) { 
+    						// short cut if the distance may directly work on the genotype 
+    						d = EuclideanMetric.euclideanDistance(AbstractEAIndividual.getDoublePositionShallow(pop.get(i)), 
+    	    						AbstractEAIndividual.getDoublePositionShallow(pop.get(j)));
+    					} else {
+    						d = PhenotypeMetric.dist(pop.get(i), pop.get(j));
+    					}
+    				} else {
+    					d = metric.distance((AbstractEAIndividual)pop.get(i), (AbstractEAIndividual)pop.get(j));
+    				}
+    			} catch (Exception e) {
+    				EVAERROR.errorMsgOnce("Exception when calculating population measures ... possibly no double position available?");
+    				d = 0;
+    			}
+    			distSum += d;
+    			if (d < minDist) minDist = d;
+    			if (d > maxDist) maxDist = d;
             }
         }
         res[1] = minDist;