JAL-1385 JAL-535 refactor sequence colour settings to abstract alignment view model

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

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index dc352f4..cceff86 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -40,6 +40,7 @@ import jalview.workers.AlignCalcManager;
 import jalview.workers.ConsensusThread;
 import jalview.workers.StrucConsensusThread;
 
+import java.awt.Color;
 import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
@@ -783,6 +784,8 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   protected boolean showConsensus = true;
 
+  Hashtable sequenceColours;
+
   /**
    * Property change listener for changes in alignment
    * 
@@ -1542,4 +1545,60 @@ public abstract class AlignmentViewport implements AlignViewportI
     oldrfs.clear();
   }
 
+  @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;
+  }
+
+  @Override
+  public void setSequenceColour(SequenceI seq, Color col)
+  {
+    if (sequenceColours == null)
+    {
+      sequenceColours = new Hashtable();
+    }
+
+    if (col == null)
+    {
+      sequenceColours.remove(seq);
+    }
+    else
+    {
+      sequenceColours.put(seq, col);
+    }
+  }
+
+  @Override
+  public void updateSequenceIdColours()
+  {
+    if (sequenceColours == null)
+    {
+      sequenceColours = new Hashtable();
+    }
+    for (SequenceGroup sg : alignment.getGroups())
+    {
+      if (sg.idColour != null)
+      {
+        for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
+        {
+          sequenceColours.put(s, sg.idColour);
+        }
+      }
+    }
+  }
+
+  @Override
+  public void clearSequenceColours()
+  {
+    sequenceColours = null;
+  };
 }