+\r
+ public Color findFeatureColour(Color initialCol, SequenceI seq, int i)\r
+ {\r
+ if(!av.showSequenceFeatures)\r
+ return initialCol;\r
+\r
+ lastSequence = seq;\r
+ sequenceFeatures = lastSequence.getSequenceFeatures();\r
+ if(sequenceFeatures==null)\r
+ return initialCol;\r
+\r
+ sfSize = sequenceFeatures.length;\r
+\r
+ if(jalview.util.Comparison.isGap(lastSequence.getCharAt(i)))\r
+ return Color.white;\r
+\r
+ currentColour = null;\r
+\r
+ drawSequence(null, lastSequence, lastSequence.findPosition(i), -1,-1, -1, -1);\r
+\r
+ if(currentColour==null)\r
+ return initialCol;\r
+\r
+ return new Color( ((Integer)currentColour).intValue() );\r
+ }\r
+ /**\r
+ * This is used by the Molecule Viewer to get the accurate colour\r
+ * of the rendered sequence\r
+ */\r
+\r
+ boolean overview = false;\r
+\r
+ int white = Color.white.getRGB();\r
+ public int findFeatureColour(int initialCol, int seqIndex, int column)\r
+ {\r
+ if(!av.showSequenceFeatures)\r
+ return initialCol;\r
+\r
+ if(seqIndex!=lastSequenceIndex)\r
+ {\r
+ lastSequence = av.alignment.getSequenceAt(seqIndex);\r
+ lastSequenceIndex = seqIndex;\r
+ sequenceFeatures = lastSequence.getSequenceFeatures();\r
+ if(sequenceFeatures==null)\r
+ return initialCol;\r
+\r
+ sfSize = sequenceFeatures.length;\r
+ }\r
+\r
+\r
+ if(jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))\r
+ return Color.white.getRGB();\r
+\r
+ currentColour = null;\r
+\r
+ drawSequence(null, lastSequence, lastSequence.findPosition(column), -1,-1, -1, -1);\r
+\r
+ if(currentColour==null)\r
+ return initialCol;\r
+\r
+ return ((Integer)currentColour).intValue();\r
+ }\r
+\r
+\r