Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629

[jalview.git] / src / jalview / datamodel / ContactMatrix.java

diff --git a/src/jalview/datamodel/ContactMatrix.java b/src/jalview/datamodel/ContactMatrix.java
index 25aefd3..8434b4a 100644 (file)
--- a/src/jalview/datamodel/ContactMatrix.java
+++ b/src/jalview/datamodel/ContactMatrix.java
@@ -1,6 +1,9 @@
 package jalview.datamodel;
 
+import java.awt.Color;
 import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.HashMap;
 import java.util.List;
 import java.util.StringTokenizer;
 
@@ -170,6 +173,63 @@ public abstract class ContactMatrix implements ContactMatrixI
     return "Contact Matrix";
   }
 
+  List<BitSet> groups = null;
+
+  @Override
+  public void updateGroups(List<BitSet> colGroups)
+  {
+    groups = colGroups;
+    colorMap = new HashMap<>();
+  }
+
+  @Override
+  public boolean hasGroups()
+  {
+    return groups != null && groups.size() > 0;
+  }
+
+  @Override
+  public List<BitSet> getGroups()
+  {
+    return groups;
+  }
+
+  @Override
+  public BitSet getGroupsFor(int column)
+  {
+    for (BitSet gp : groups)
+    {
+      if (gp.get(column))
+      {
+        return gp;
+      }
+    }
+    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 static String contactToFloatString(ContactMatrixI cm)
   {
     StringBuilder sb = new StringBuilder();