X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=b6094170350b4e4dd2dc7333fd359dd5513bfd8e;hb=ddf3aca722d27da4bd2c58e9f0ab0909ba9639c0;hp=b275611b74cd426731f481678960d0655f120c4d;hpb=f5a39f4861d0f1ffdb3c5b542e00907b2cc18a73;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index b275611..b609417 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -112,6 +112,15 @@ public class AlignViewport
     Stack historyList = new Stack();
     Stack redoList = new Stack();
 
+    Hashtable sequenceColours;
+
+    int thresholdTextColour = 0;
+    Color textColour = Color.black;
+    Color textColour2 = Color.white;
+
+    boolean idsAlignRight = false;
+
+
     /**
      * Creates a new AlignViewport object.
      *
@@ -1599,5 +1608,24 @@ 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);
+    }
+
 
 }