+ 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
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ * @param seq DOCUMENT ME!\r
+ * @param sg DOCUMENT ME!\r
+ * @param start DOCUMENT ME!\r
+ * @param end DOCUMENT ME!\r
+ * @param x1 DOCUMENT ME!\r
+ * @param y1 DOCUMENT ME!\r
+ * @param width DOCUMENT ME!\r
+ * @param height DOCUMENT ME!\r
+ */\r
+ // String type;\r
+ // SequenceFeature sf;\r
+ int lastSequenceIndex=-1;\r
+ SequenceI lastSequence;\r
+ SequenceFeature [] sequenceFeatures;\r
+ int sfSize, sfindex, spos, epos;\r
+\r
+ public void drawSequence(Graphics g, SequenceI seq,\r
+ int start, int end, int y1, int width, int height)\r
+ {\r
+ if ( seq.getSequenceFeatures() == null\r
+ || seq.getSequenceFeatures().length==0)\r
+ return;\r
+\r
+ if(transparencySetter!=null && g!=null)\r
+ {\r
+ transparencySetter.setTransparency(g, transparency);\r
+ }\r
+\r
+ if (av.featuresDisplayed == null || renderOrder==null)\r
+ {\r
+ findAllFeatures();\r
+ if(av.featuresDisplayed.size()<1)\r
+ return;\r
+\r
+ sequenceFeatures = seq.getSequenceFeatures();\r
+ sfSize = sequenceFeatures.length;\r
+ }\r
+ if(lastSequence==null || seq!=lastSequence)\r
+ {\r
+ lastSequence = seq;\r
+ sequenceFeatures = seq.getSequenceFeatures();\r
+ sfSize = sequenceFeatures.length;\r
+ }\r
+ if(!overview)\r
+ {\r
+ spos = lastSequence.findPosition(start);\r
+ epos = lastSequence.findPosition(end);\r
+ if(g!=null)\r
+ fm = g.getFontMetrics();\r
+ }\r
+ String type;\r
+ for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)\r
+ {\r
+ type = renderOrder[renderIndex];\r
+ if(!av.featuresDisplayed.containsKey(type))\r
+ continue;\r
+\r
+ // loop through all features in sequence to find\r
+ // current feature to render\r
+ for (sfindex = 0; sfindex < sfSize; sfindex++)\r