X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdatamodel%2Falphafold%2FPAEContactMatrix.java;h=41e677a6322897fe4b8032f0da665b191f2ac7dd;hb=115a611d005faab33f978a469578bcacbcecc112;hp=3ce1c83598e93da18dc5292b6d02e555b5f22c96;hpb=f83b6877ab7ff3fc5db5c946e16c74e016437311;p=jalview.git

diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
index 3ce1c83..41e677a 100644
--- a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
+++ b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
@@ -1,7 +1,9 @@
 package jalview.ws.datamodel.alphafold;
 
+import java.awt.Color;
 import java.util.ArrayList;
 import java.util.BitSet;
+import java.util.HashMap;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
@@ -262,10 +264,16 @@ public class PAEContactMatrix implements ContactMatrixI
     return groups!=null;
   }
   String newick=null;
-  public String getNewickString()
+  @Override
+  public String getNewick()
   {
     return newick;
   }
+  @Override
+  public boolean hasTree()
+  {
+    return newick!=null && newick.length()>0;
+  }
   boolean abs;
   double thresh;
   String treeType=null;
@@ -303,7 +311,14 @@ public class PAEContactMatrix implements ContactMatrixI
       groups.add(gpset);
     }
   }
-  
+  @Override
+  public void updateGroups(List<BitSet> colGroups)
+  {
+    if (colGroups!=null)
+    {
+      groups=colGroups;
+    }    
+  }
   @Override
   public BitSet getGroupsFor(int column)
   {
@@ -316,6 +331,25 @@ public class PAEContactMatrix implements ContactMatrixI
     return ContactMatrixI.super.getGroupsFor(column);
   }
 
+  HashMap<BitSet,Color> colorMap = new HashMap<>();
+  @Override 
+  public Color getColourForGroup(BitSet bs)
+  {
+    if (bs==null) {
+      return Color.white;
+    }
+    Color groupCol=colorMap.get(bs);
+    if (groupCol==null)
+    {
+      return Color.white;
+    }
+    return groupCol;
+  }
+  @Override 
+  public void setColorForGroup(BitSet bs,Color color)
+  {
+    colorMap.put(bs,color);
+  }
   public void restoreGroups(List<BitSet> newgroups, String treeMethod,
           String tree, double thresh2)
   {