From 87a6f444f7e215abd2a0d5081eb646d7da88e4ec Mon Sep 17 00:00:00 2001
From: Marcel Kronfeld <makron@gmx.net>
Date: Fri, 29 Apr 2011 16:23:23 +0000
Subject: [PATCH] New interfaces for density based clustering

---
 .../cluster/ClusteringDensityBased.java       | 32 ++++++++++---------
 .../InterfaceClusteringDistanceParam.java     | 12 +++++++
 .../InterfaceClusteringMetricBased.java       | 14 ++++++++
 3 files changed, 43 insertions(+), 15 deletions(-)
 create mode 100644 src/eva2/server/go/operators/cluster/InterfaceClusteringDistanceParam.java
 create mode 100644 src/eva2/server/go/operators/cluster/InterfaceClusteringMetricBased.java

diff --git a/src/eva2/server/go/operators/cluster/ClusteringDensityBased.java b/src/eva2/server/go/operators/cluster/ClusteringDensityBased.java
index f95a2bb9..1ccfb061 100644
--- a/src/eva2/server/go/operators/cluster/ClusteringDensityBased.java
+++ b/src/eva2/server/go/operators/cluster/ClusteringDensityBased.java
@@ -17,7 +17,7 @@ import eva2.tools.Pair;
  * Time: 15:17:53
  * To change this template use Options | File Templates.
  */
-public class ClusteringDensityBased implements InterfaceClustering, java.io.Serializable {
+public class ClusteringDensityBased implements InterfaceClusteringDistanceParam, InterfaceClusteringMetricBased, java.io.Serializable {
 
     private InterfaceDistanceMetric     m_Metric            = new PhenotypeMetric();
     private double                      m_ClusterDistance   = 0.1;
@@ -105,7 +105,10 @@ public class ClusteringDensityBased implements InterfaceClustering, java.io.Seri
             ConnectionMatrix[i][i] = true;
             for (int j = i+1; j < pop.size(); j++) {
                 tmpIndy2 = (AbstractEAIndividual)pop.get(j);
-                if (this.m_Metric.distance(tmpIndy1, tmpIndy2) < this.m_ClusterDistance) {
+                if (tmpIndy1==null || (tmpIndy2==null)) {
+                	System.err.println("Warning: Individual should not be null (ClusteringDensityBased)!");
+                }
+                if ((tmpIndy1!=null) && (tmpIndy2!=null) && (this.m_Metric.distance(tmpIndy1, tmpIndy2) < this.m_ClusterDistance)) {
                     ConnectionMatrix[i][j] = true;
                     ConnectionMatrix[j][i] = true;
                 } else {
@@ -241,19 +244,7 @@ public class ClusteringDensityBased implements InterfaceClustering, java.io.Seri
     public String metricTipText() {
         return "Choose the distance metric to use.";
     }
-    /** This method allows you to set/get the distance threshhold of the DBSCAN method.
-     * @return The currently used distance threshhold.
-     */
-    public double getClusterDistance() {
-        return this.m_ClusterDistance;
-    }
-    public void setClusterDistance(double m){
-        if (m < 0) m = 0;
-        this.m_ClusterDistance = m;
-    }
-    public String clusterDistanceTipText() {
-        return "Set the distance threshhold for the DBSCAN method.";
-    }
+
     /** This method allows you to set/get the minimal group size of the DBSCAN method.
      * @return The currently used minimal group size.
      */
@@ -272,6 +263,17 @@ public class ClusteringDensityBased implements InterfaceClustering, java.io.Seri
 		return null;
 	}
 
+	public double getClustDistParam() {
+		return this.m_ClusterDistance;
+	}
+	public void setClustDistParam(double m) {
+        if (m < 0) m = 0;
+        this.m_ClusterDistance = m;
+	}
+    public String clustDistTipText() {
+        return "Set the distance threshhold for the DBSCAN method.";
+    }
+
 
 //    /** For debuggy only
 //     * @param plot TopoPlot
diff --git a/src/eva2/server/go/operators/cluster/InterfaceClusteringDistanceParam.java b/src/eva2/server/go/operators/cluster/InterfaceClusteringDistanceParam.java
new file mode 100644
index 00000000..596a1d45
--- /dev/null
+++ b/src/eva2/server/go/operators/cluster/InterfaceClusteringDistanceParam.java
@@ -0,0 +1,12 @@
+package eva2.server.go.operators.cluster;
+
+/**
+ * A clustering method which has a cluster parameter - the niche radius for example.
+ * 
+ * @author mkron
+ *
+ */
+public interface InterfaceClusteringDistanceParam extends InterfaceClustering {
+	public double getClustDistParam();
+	public void setClustDistParam(double param);
+}
diff --git a/src/eva2/server/go/operators/cluster/InterfaceClusteringMetricBased.java b/src/eva2/server/go/operators/cluster/InterfaceClusteringMetricBased.java
new file mode 100644
index 00000000..921c7010
--- /dev/null
+++ b/src/eva2/server/go/operators/cluster/InterfaceClusteringMetricBased.java
@@ -0,0 +1,14 @@
+package eva2.server.go.operators.cluster;
+
+import eva2.server.go.operators.distancemetric.InterfaceDistanceMetric;
+
+/**
+ * A clustering method which is associated with a metric.
+ * 
+ * @author mkron
+ *
+ */
+public interface InterfaceClusteringMetricBased {
+    public InterfaceDistanceMetric getMetric();
+    public void setMetric(InterfaceDistanceMetric m);
+}