X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FContactMatrixI.java;h=925025fc3c70ba4ee4babe2bb1a2d9b2c1f54111;hb=1624d4fc89f17c4a6cdb80b7d4cc37a095b6fe67;hp=1d7391b617a009807695ac995693130c1c20e6dd;hpb=fdde9a078d7bdb46ed9fb7fe115ea83c84a19c81;p=jalview.git

diff --git a/src/jalview/datamodel/ContactMatrixI.java b/src/jalview/datamodel/ContactMatrixI.java
index 1d7391b..925025f 100644
--- a/src/jalview/datamodel/ContactMatrixI.java
+++ b/src/jalview/datamodel/ContactMatrixI.java
@@ -5,6 +5,9 @@ import java.util.Arrays;
 import java.util.BitSet;
 import java.util.List;
 
+import jalview.util.ColorUtils;
+import jalview.ws.datamodel.MappableContactMatrixI;
+
 public interface ContactMatrixI
 {
 
@@ -14,10 +17,6 @@ public interface ContactMatrixI
 
   float getMax();
 
-  boolean hasReferenceSeq();
-
-  SequenceI getReferenceSeq();
-
   String getAnnotDescr();
 
   String getAnnotLabel();
@@ -31,29 +30,45 @@ public interface ContactMatrixI
   String getType();
 
   int getWidth();
-
   int getHeight();
+  public GroupSetI getGroupSet();
+
+  /// proxy methods to simplify use of the interface
+  /// Mappable contact matrices can override these to perform mapping
+
+  default public boolean hasGroupSet()
+  {
+    return getGroupSet() != null;
+  }
 
   default boolean hasGroups()
   {
-    return false;
+    return hasGroupSet() && getGroupSet().hasGroups();
   }
 
   default BitSet getGroupsFor(int column)
   {
-    BitSet colbitset = new BitSet();
-    colbitset.set(column);
-    return colbitset;
+    if (!hasGroupSet())
+    {
+      BitSet colbitset = new BitSet();
+      colbitset.set(column);
+      return colbitset;
+    }
+    return getGroupSet().getGroupsFor(column);
   }
 
   default List<BitSet> getGroups()
   {
-    return Arrays.asList();
+    if (!hasGroupSet())
+    {
+      return Arrays.asList();
+    }
+    return getGroupSet().getGroups();
   }
 
   default boolean hasTree()
   {
-    return false;
+    return hasGroupSet() ? getGroupSet().hasTree() : false;
   }
 
   /**
@@ -63,30 +78,126 @@ public interface ContactMatrixI
    */
   default String getNewick()
   {
-    return null;
+    return hasGroupSet() ? getGroupSet().getNewick() : null;
   }
 
   default String getTreeMethod()
   {
-    return null;
+    return hasGroupSet() ? getGroupSet().getTreeMethod() : null;
   }
 
   default boolean hasCutHeight()
   {
-    return false;
+    return hasGroupSet() ? getGroupSet().hasCutHeight() : false;
   }
 
   default double getCutHeight()
   {
-    return 0;
+    return hasGroupSet() ? getGroupSet().getCutHeight() : 0;
   }
 
-  void updateGroups(List<BitSet> colGroups);
+  default void updateGroups(List<BitSet> colGroups)
+  {
+    if (hasGroupSet())
+    {
+      getGroupSet().updateGroups(colGroups);
+    }
+  }
 
-  void setColorForGroup(BitSet bs, Color color);
+  default void setColorForGroup(BitSet bs, Color color)
+  {
+    if (hasGroupSet())
+    {
+      getGroupSet().setColorForGroup(bs, color);
+    }
+  }
 
   default Color getColourForGroup(BitSet bs)
   {
+    if (hasGroupSet())
+    {
+      return getGroupSet().getColourForGroup(bs);
+    }
+    else
+    {
+      return Color.white;
+    }
+  }
+
+  void setGroupSet(GroupSet makeGroups);
+
+  default void randomlyReColourGroups() {
+    if (hasGroupSet())
+    {
+      GroupSetI groups = getGroupSet();
+      for (BitSet group:groups.getGroups())
+      {
+        groups.setColorForGroup(group, ColorUtils.getARandomColor());
+      }
+    }
+  }
+
+  default void transferGroupColorsTo(AlignmentAnnotation aa)
+  {
+    if (hasGroupSet())
+    {
+      GroupSetI groups = getGroupSet();
+      // stash colors in linked annotation row.
+      // doesn't work yet. TESTS!
+      int sstart = aa.sequenceRef != null ? aa.sequenceRef.getStart() - 1
+              : 0;
+      Annotation ae;
+      Color gpcol = null;
+      int[] seqpos = null;
+      for (BitSet gp : groups.getGroups())
+      {
+        gpcol = groups.getColourForGroup(gp);
+        for (int p = gp.nextSetBit(0); p >= 0
+                && p < Integer.MAX_VALUE; p = gp.nextSetBit(p + 1))
+        {
+          if (this instanceof MappableContactMatrixI)
+          {
+            MappableContactMatrixI mcm = (MappableContactMatrixI) this;
+            seqpos = mcm.getMappedPositionsFor(aa.sequenceRef, p);
+            if (seqpos == null)
+            {
+              // no mapping for this column.
+              continue;
+            }
+            // TODO: handle ranges...
+            ae = aa.getAnnotationForPosition(seqpos[0]);
+          }
+          else
+          {
+            ae = aa.getAnnotationForPosition(p + sstart);
+          }
+          if (ae != null)
+          {
+            ae.colour = gpcol.brighter().darker();
+          }
+        }
+      }
+    }
+  }
+  
+  /**
+   * look up the colour for a column in the associated contact matrix 
+   * @return Color.white or assigned colour
+   */
+  default Color getGroupColorForPosition(int column)
+  {
+    if (hasGroupSet())
+    {
+      GroupSetI groups = getGroupSet();
+      for (BitSet gp:groups.getGroups())
+      {
+        if (gp.get(column))
+        {
+          return groups.getColourForGroup(gp);
+        }
+      }
+    }
     return Color.white;
-  };
+  }
+  
 }