JAL-845 linked protein/dna 'slave' further PoC functionality

[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 1b42faf..ed63e0f 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -44,6 +44,7 @@ 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 +59,11 @@ import java.util.Vector;
  */
 public abstract class AlignmentViewport implements AlignViewportI
 {
+  /*
+   * A viewport that is a slave of (driven by) this one in some sense.
+   */
+  AlignViewportI slave = null;
+
   /**
    * alignment displayed in the viewport. Please use get/setter
    */
@@ -803,7 +809,7 @@ 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
@@ -1605,26 +1611,13 @@ 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 +1631,6 @@ 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 +1646,25 @@ public abstract class AlignmentViewport implements AlignViewportI
   @Override
   public void clearSequenceColours()
   {
-    sequenceColours = null;
+    sequenceColours.clear();
   };
+
+  @Override
+  public AlignViewportI getSlave()
+  {
+    return this.slave;
+  }
+
+  @Override
+  public void setSlave(AlignViewportI sl)
+  {
+    if (this == sl.getSlave())
+    {
+      System.err.println("Ignoring recursive setSlave request");
+    }
+    else
+    {
+      this.slave = sl;
+    }
+  }
 }