+ /**\r
+ * If sequence ends in gaps, the end residue can\r
+ * be correctly calculated here\r
+ * @param seq SequenceI\r
+ * @return int\r
+ */\r
+ public int findEndRes(SequenceI seq)\r
+ {\r
+ int eres = 0;\r
+ char ch;\r
+\r
+ for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)\r
+ {\r
+ ch = seq.getCharAt(j);\r
+ if (!jalview.util.Comparison.isGap( (ch)))\r
+ {\r
+ eres++;\r
+ }\r
+ }\r
+\r
+ if (eres > 0)\r
+ {\r
+ eres += seq.getStart() - 1;\r
+ }\r
+\r
+ return eres;\r
+ }\r
+\r