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
{\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
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
*/\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
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
\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