+ resBoxColour = Color.white;\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
+ public void drawSequence(SequenceI seq, SequenceGroup[] sg,\r
+ int start, int end, int y1)\r
+ {\r
+ allGroups = sg;\r
+\r
+ drawBoxes(seq, start, end, y1);\r
+\r
+ if (av.validCharWidth)\r
+ {\r
+ drawText(seq, start, end, y1);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param seq 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
+ public synchronized void drawBoxes(SequenceI seq, int start, int end, int y1)\r
+ {\r
+ int i = start;\r
+ int length = seq.getLength();\r
+\r
+ int curStart = -1;\r
+ int curWidth = av.charWidth;\r
+\r
+ Color tempColour = null;\r
+\r
+ while (i <= end)\r
+ {\r
+ resBoxColour = Color.white;\r
+\r
+ if (i < length)\r
+ {\r
+ if (inCurrentSequenceGroup(i))\r