/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
\r
String [] renderOrder;\r
\r
- boolean newFeatureAdded = false;\r
-\r
-\r
/**\r
* Creates a new FeatureRenderer object.\r
*\r
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
|| seq.getDatasetSequence().getSequenceFeatures().length==0)\r
return;\r
\r
-\r
if(g!=null)\r
fm = g.getFontMetrics();\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
}\r
}\r
\r
- int count = 0;\r
- synchronized public void featuresAdded()\r
+\r
+ boolean newFeatureAdded = false;\r
+\r
+ public void featuresAdded()\r
{\r
- newFeatureAdded = true;\r
findAllFeatures();\r
- newFeatureAdded = false;\r
}\r
\r
+ boolean findingFeatures = false;\r
synchronized void findAllFeatures()\r
{\r
+ newFeatureAdded = false;\r
+\r
+ if(findingFeatures)\r
+ {\r
+ newFeatureAdded = true;\r
+ return;\r
+ }\r
+\r
+ findingFeatures = true;\r
jalview.schemes.UserColourScheme ucs = new\r
jalview.schemes.UserColourScheme();\r
\r
renderOrder[i] = en.nextElement().toString();\r
i--;\r
}\r
+\r
+ findingFeatures = false;\r
}\r
\r
public Color getColour(String featureType)\r