X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=7c6032716287cee54db9b9818b34690d2d0628c2;hb=f5f5806de6923a8a62906c5a62c6276ba56ae0da;hp=b06cace9cd24551ad5567c96480b89a7af39e8bc;hpb=d2f3c59deebfd9ea52b0021ab31467c18b9d2c14;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index b06cace..7c60327 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -79,33 +79,30 @@ public class FeatureRenderer
     boolean offscreenRender = false;
     public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
     {
-      int seqindex = av.alignment.findIndex(seq);
-
       return new Color( findFeatureColour (initialCol.getRGB(),
-                        seqindex, res ));
+                        seq, res ));
     }
 
     /**
-     * This is used by the Molecule Viewer to get the accurate colour
-     * of the rendered sequence
+     * This is used by the Molecule Viewer and Overview to
+     * get the accurate colourof the rendered sequence
      */
-    public int findFeatureColour(int initialCol, int seqIndex, int column)
+    public int findFeatureColour(int initialCol, SequenceI seq, int column)
     {
       if(!av.showSequenceFeatures)
         return initialCol;
 
-      if(seqIndex!=lastSequenceIndex)
+      if(seq!=lastSeq)
       {
-        lastSequence = av.alignment.getSequenceAt(seqIndex);
-        lastSequenceIndex = seqIndex;
-        sequenceFeatures = lastSequence.getDatasetSequence().getSequenceFeatures();
+        lastSeq = seq;
+        sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
         if(sequenceFeatures==null)
           return initialCol;
 
         sfSize = sequenceFeatures.length;
       }
 
-      if(jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))
+      if(jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))
         return Color.white.getRGB();
 
 
@@ -123,7 +120,7 @@ public class FeatureRenderer
       {
         offscreenImage.setRGB(0,0,initialCol);
         drawSequence(offscreenImage.getGraphics(),
-                     lastSequence,
+                     lastSeq,
                      column,column,0);
 
         return offscreenImage.getRGB(0,0);
@@ -131,8 +128,8 @@ public class FeatureRenderer
       else
       {
         drawSequence(null,
-                    lastSequence,
-                    lastSequence.findPosition(column),
+                    lastSeq,
+                    lastSeq.findPosition(column),
                     -1, -1);
 
         if (currentColour == null)
@@ -160,8 +157,7 @@ public class FeatureRenderer
      */
    // String type;
    // SequenceFeature sf;
-    int lastSequenceIndex=-1;
-    SequenceI lastSequence;
+    SequenceI lastSeq;
     SequenceFeature [] sequenceFeatures;
     int sfSize, sfindex, spos, epos;
 
@@ -189,9 +185,9 @@ public class FeatureRenderer
          sfSize = sequenceFeatures.length;
        }
 
-       if(lastSequence==null || seq!=lastSequence)
+       if(lastSeq==null || seq!=lastSeq)
       {
-        lastSequence = seq;
+        lastSeq = seq;
         sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
         sfSize = sequenceFeatures.length;
       }
@@ -207,8 +203,8 @@ public class FeatureRenderer
 
       if(!offscreenRender)
       {
-        spos = lastSequence.findPosition(start);
-        epos = lastSequence.findPosition(end);
+        spos = lastSeq.findPosition(start);
+        epos = lastSeq.findPosition(end);
       }