+ void drawMarker(int i, int starty, int yoffset)\r
+ {\r
+\r
+ SequenceI[] hseqs = av.alignment.getHiddenSequences().hiddenSequences;\r
+ //Use this method here instead of calling hiddenSeq adjust\r
+ //3 times.\r
+ int hSize = hseqs.length;\r
+\r
+ int hiddenIndex = i;\r
+ int lastIndex = i - 1;\r
+ int nextIndex = i + 1;\r
+\r
+ for (int j = 0; j < hSize; j++)\r
+ {\r
+ if (hseqs[j] != null)\r
+ {\r
+ if (j - 1 < hiddenIndex)\r
+ {\r
+ hiddenIndex++;\r
+ }\r
+ if (j - 1 < lastIndex)\r
+ {\r
+ lastIndex++;\r
+ }\r
+ if (j - 1 < nextIndex)\r
+ {\r
+ nextIndex++;\r
+ }\r
+ }\r
+ }\r
+\r
+ boolean below = (hiddenIndex > lastIndex + 1);\r
+ boolean above = (nextIndex > hiddenIndex + 1);\r
+\r
+ gg.setColor(Color.blue);\r
+ if (below)\r
+ {\r
+ gg.fillPolygon(new int[]\r
+ {getWidth() - av.charHeight,\r
+ getWidth() - av.charHeight,\r
+ getWidth()},\r
+ new int[]\r
+ {\r
+ (i - starty) * av.charHeight + yoffset,\r
+ (i - starty) * av.charHeight + yoffset + av.charHeight / 4,\r
+ (i - starty) * av.charHeight + yoffset\r
+ }, 3);\r
+ }\r
+ if (above)\r
+ {\r
+ gg.fillPolygon(new int[]\r
+ {getWidth() - av.charHeight,\r
+ getWidth() - av.charHeight,\r
+ getWidth()},\r
+ new int[]\r
+ {\r
+ (i - starty + 1) * av.charHeight + yoffset,\r
+ (i - starty + 1) * av.charHeight + yoffset -\r
+ av.charHeight / 4,\r
+ (i - starty + 1) * av.charHeight + yoffset\r
+ }, 3);\r
+\r
+ }\r
+ }\r
+\r
+ void setHiddenFont(SequenceI seq)\r
+ {\r
+ Font bold = new Font(av.getFont().getName(), Font.BOLD,\r
+ av.getFont().getSize());\r
+\r
+ if (av.hiddenRepSequences != null &&\r
+ av.hiddenRepSequences.containsKey(seq))\r
+ {\r
+ gg.setFont(bold);\r
+ }\r
+ else\r
+ {\r
+ gg.setFont(idfont);\r
+ }\r