X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=7145f7b2682c332c342d8e165f0dad88a3f938d5;hb=10ff37d2cb03f342ddbed679951d3e2fef0a404b;hp=1b42faf037a32f8ec693723f9c2d4c12a74abbd6;hpb=a300ed430003b3c0af3f1badee464c0f40de63a0;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 1b42faf..7145f7b 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -37,6 +37,7 @@ import jalview.schemes.Blosum62ColourScheme;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.PIDColourScheme;
 import jalview.schemes.ResidueProperties;
+import jalview.util.MappingUtils;
 import jalview.workers.AlignCalcManager;
 import jalview.workers.ConsensusThread;
 import jalview.workers.StrucConsensusThread;
@@ -44,6 +45,7 @@ import jalview.workers.StrucConsensusThread;
 import java.awt.Color;
 import java.util.ArrayList;
 import java.util.BitSet;
+import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
@@ -58,6 +60,12 @@ import java.util.Vector;
  */
 public abstract class AlignmentViewport implements AlignViewportI
 {
+  /*
+   * A viewport that hosts the cDna view of this (protein), or vice versa (if
+   * set).
+   */
+  AlignViewportI codingComplement = null;
+
   /**
    * alignment displayed in the viewport. Please use get/setter
    */
@@ -803,7 +811,7 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   protected boolean showConsensus = true;
 
-  Hashtable sequenceColours;
+  private Map<SequenceI, Color> sequenceColours = new HashMap<SequenceI, Color>();
 
   /**
    * Property change listener for changes in alignment
@@ -957,6 +965,17 @@ public abstract class AlignmentViewport implements AlignViewportI
 
     hideSequence(seqs);
 
+    AlignViewportI peer = getCodingComplement();
+    if (peer != null)
+    {
+      SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(
+              selectionGroup, this, peer);
+      ((AlignmentViewport) peer).hideSequence(mappedGroup
+              .getSequencesInOrder(peer.getAlignment()));
+      peer.setSelectionGroup(null);
+
+    }
+
     setSelectionGroup(null);
   }
 
@@ -1605,26 +1624,13 @@ public abstract class AlignmentViewport implements AlignViewportI
   @Override
   public Color getSequenceColour(SequenceI seq)
   {
-    Color sqc = Color.white;
-    if (sequenceColours != null)
-    {
-      sqc = (Color) sequenceColours.get(seq);
-      if (sqc == null)
-      {
-        sqc = Color.white;
-      }
-    }
-    return sqc;
+    Color sqc = sequenceColours.get(seq);
+    return (sqc == null ? Color.white : sqc);
   }
 
   @Override
   public void setSequenceColour(SequenceI seq, Color col)
   {
-    if (sequenceColours == null)
-    {
-      sequenceColours = new Hashtable();
-    }
-
     if (col == null)
     {
       sequenceColours.remove(seq);
@@ -1638,10 +1644,6 @@ public abstract class AlignmentViewport implements AlignViewportI
   @Override
   public void updateSequenceIdColours()
   {
-    if (sequenceColours == null)
-    {
-      sequenceColours = new Hashtable();
-    }
     for (SequenceGroup sg : alignment.getGroups())
     {
       if (sg.idColour != null)
@@ -1657,6 +1659,40 @@ public abstract class AlignmentViewport implements AlignViewportI
   @Override
   public void clearSequenceColours()
   {
-    sequenceColours = null;
+    sequenceColours.clear();
   };
+
+  @Override
+  public AlignViewportI getCodingComplement()
+  {
+    return this.codingComplement;
+  }
+
+  /**
+   * Set this as the (cDna/protein) complement of the given viewport. Also
+   * ensures the reverse relationship is set on the given viewport.
+   */
+  @Override
+  public void setCodingComplement(AlignViewportI av)
+  {
+    if (this == av)
+    {
+      System.err.println("Ignoring recursive setCodingComplement request");
+    }
+    else
+    {
+      this.codingComplement = av;
+      // avoid infinite recursion!
+      if (av.getCodingComplement() != this)
+      {
+        av.setCodingComplement(this);
+      }
+    }
+  }
+
+  @Override
+  public boolean isNucleotide()
+  {
+    return getAlignment() == null ? false : getAlignment().isNucleotide();
+  }
 }