+ //Now draw the id strings\r
+ int tmp, hiddenIndex = starty;\r
+ boolean markHidden = false;\r
+ for (int i = starty; i < endy; i++)\r
+ {\r
+ if (av.hasHiddenRows)\r
+ {\r
+ tmp = av.adjustForHiddenSeqs(i);\r
+ if(hiddenIndex != tmp)\r
+ {\r
+ hiddenIndex = tmp;\r
+ markHidden = true;\r
+ }\r
+ else\r
+ markHidden = false;\r
+\r
+ hiddenIndex++;\r
+ }\r
+\r
+ if(av.hasHiddenRows && av.alignment.getSequenceAt(i).getHiddenSequences()!=null)\r
+ {\r
+ currentTextColor = Color.blue;\r
+ }\r
+ else\r
+ // Selected sequence colours\r
+ if ((searchResults != null) &&\r
+ searchResults.contains(av.alignment.getSequenceAt(i)))\r
+ {\r
+ currentColor = Color.black;\r
+ currentTextColor = Color.white;\r
+ }\r
+ else if ((av.getSelectionGroup() != null) &&\r
+ av.getSelectionGroup().sequences.contains(\r
+ av.alignment.getSequenceAt(i)))\r
+ {\r
+ currentColor = Color.lightGray;\r
+ currentTextColor = Color.black;\r
+ }\r
+ else\r
+ {\r
+ currentColor = av.alignment.getSequenceAt(i).getColor();\r
+ currentTextColor = Color.black;\r
+ }\r
+\r
+ gg.setColor(currentColor);\r
+\r
+ gg.fillRect(0, (i - starty) * av.charHeight, getWidth(),\r
+ av.charHeight);\r
+\r
+ if (markHidden)\r
+ {\r
+ gg.setColor(Color.blue);\r
+ // gg.drawLine(0, (i-starty)*av.charHeight, getWidth(),(i-starty)*av.charHeight);\r
+ gg.fillPolygon(new int[] { getWidth() - av.charHeight,\r
+ getWidth() - av.charHeight,\r
+ getWidth() },\r
+ new int[]\r
+ {\r
+ (i-starty)*av.charHeight -av.charHeight/4,\r
+ (i-starty)*av.charHeight +av.charHeight/4,\r
+ (i-starty)*av.charHeight\r
+ }, 3);\r
+\r
+ }\r
+\r
+ gg.setColor(currentTextColor);\r
+\r
+ String string = av.alignment.getSequenceAt(i).getDisplayId( av.getShowJVSuffix());\r
+\r
+ gg.drawString(string, 0,\r
+ (((i - starty) * av.charHeight) + av.charHeight) -\r
+ (av.charHeight / 5));\r
+ }\r
+\r
+ // add a border\r
+ // gg.setColor(Color.cyan);\r
+ // gg.fillRect(getWidth() - 4, 0, 4, getHeight());\r