catch (Exception ex)\r
{\r
refSeqIndex = 1;\r
+ refSeq=null;\r
}\r
\r
continue ;\r
if (refSeq != null)\r
{\r
annotation.createSequenceMapping(refSeq, refSeqIndex, false);\r
+ annotation.adjustForAlignment();\r
refSeq.addAlignmentAnnotation(annotation);\r
}\r
\r