Corrected hidden row feature render bug

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

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 714eec6..2933841 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -281,11 +281,9 @@ public class OverviewPanel extends JPanel implements Runnable
             seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);\r
             if (seq == null)\r
             {\r
-\r
               int index =\r
                  av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(lastrow);\r
 \r
-\r
              seq = av.alignment.getSequenceAt(index);\r
             }\r
             else\r
@@ -319,7 +317,7 @@ public class OverviewPanel extends JPanel implements Runnable
                   seq, lastcol).getRGB();\r
 \r
               if (av.showSequenceFeatures)\r
-                color = fr.findFeatureColour(color, lastrow, lastcol);\r
+                color = fr.findFeatureColour(color, seq, lastcol);\r
             }\r
             else\r
             {\r