X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=ec52ee35c56572ccadff42af340733d18765fec3;hb=3e3378e2ccfea39a2b161600c5a2029716acd1b7;hp=016151766c1efed41c745622b5415ba2d6938d3b;hpb=8b7b2e3d4893991f29ab603c20ae826f7e3c8ffb;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 0161517..ec52ee3 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -112,6 +112,13 @@ public class AlignViewport
     Stack historyList = new Stack();
     Stack redoList = new Stack();
 
+    Hashtable sequenceColours;
+
+    int thresholdTextColour = 0;
+    Color textColour = Color.black;
+    Color textColour2 = Color.white;
+
+
     /**
      * Creates a new AlignViewport object.
      *
@@ -1536,6 +1543,22 @@ public class AlignViewport
           updateConservation(ap);
         }
 
+        //Reset endRes of groups if beyond alignment width
+        int alWidth = alignment.getWidth();
+        Vector groups = alignment.getGroups();
+        if(groups!=null)
+        {
+          for(int i=0; i<groups.size(); i++)
+          {
+            SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
+            if(sg.getEndRes()>alWidth)
+              sg.setEndRes(alWidth-1);
+          }
+        }
+
+        if(selectionGroup!=null && selectionGroup.getEndRes()>alWidth)
+          selectionGroup.setEndRes(alWidth-1);
+
         resetAllColourSchemes();
 
         alignment.adjustSequenceAnnotations();
@@ -1583,5 +1606,24 @@ public class AlignViewport
     }
 
 
+    public Color getSequenceColour(SequenceI seq)
+    {
+      if(sequenceColours==null || !sequenceColours.containsKey(seq))
+        return Color.white;
+      else
+        return (Color)sequenceColours.get(seq);
+    }
+
+    public void setSequenceColour(SequenceI seq, Color col)
+    {
+      if(sequenceColours==null)
+        sequenceColours = new Hashtable();
+
+      if(col == null)
+        sequenceColours.remove(seq);
+      else
+        sequenceColours.put(seq, col);
+    }
+
 
 }