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