- SequenceI seq = av.alignment.getSequenceAt(results[0]);\r
- int start = seq.findIndex(results[1]) - 1;\r
- int end = seq.findIndex(results[2]) - 1;\r
- if (av.getStartRes() > start\r
- || av.getEndRes() < end\r
- || (av.getStartSeq() > results[0]\r
- || av.getEndSeq() < results[0]))\r
- {\r
- setScrollValues(start, results[0]);\r
- }\r
+ SequenceI seq = results.getResultSequence(0);\r
+ int seqIndex = av.alignment.findIndex(seq);\r
+ int start = seq.findIndex(results.getResultStart(0)) - 1;\r
+ int end = seq.findIndex(results.getResultEnd(0)) - 1;\r
+\r
+ if(!av.wrapAlignment)\r
+ {\r
+ if ( (av.getStartRes() > end) || (av.getEndRes() < start) ||\r
+ ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))\r
+ {\r
+ if (start > av.alignment.getWidth() - hextent)\r
+ {\r
+ start = av.alignment.getWidth() - hextent;\r
+ if (start < 0)\r
+ start = 0;\r
+ }\r
+ if (seqIndex > av.alignment.getHeight() - vextent)\r
+ {\r
+ seqIndex = av.alignment.getHeight() - vextent;\r
+ if (seqIndex < 0)\r
+ seqIndex = 0;\r
+ }\r
+ setScrollValues(start, seqIndex);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ scrollToWrappedVisible(start);\r
+ }\r