[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/dataadapter/gff3 GFF3Adapter.java, 1.18, 1.19

[elee <gk...@us...>]

Update of /cvsroot/gmod/apollo/src/java/apollo/dataadapter/gff3
In directory ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv25339

Modified Files:
	GFF3Adapter.java 
Log Message:
+ Check to make sure a match has the hit sequence data in case of id collisions before comparison



Index: GFF3Adapter.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/gff3/GFF3Adapter.java,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** GFF3Adapter.java	15 Jul 2009 20:34:44 -0000	1.18
--- GFF3Adapter.java	10 Aug 2009 14:35:44 -0000	1.19
***************
*** 355,359 ****
          // collisions back - if there's a collision, append a counter to the sequence
          // identifier
!         if (seqs.containsKey(hitSeq.getName()) && !seqs.get(hitSeq.getName()).getResidues().equals(hitSeq.getResidues())) {
            String oldHitName = hitSeq.getName();
            seqIds.put(hitSeq.getName(), seqIds.get(hitSeq.getName()) + 1);
--- 355,360 ----
          // collisions back - if there's a collision, append a counter to the sequence
          // identifier
!         
!         if (seqs.containsKey(hitSeq.getName()) && hitSeq.getResidues() != null && !seqs.get(hitSeq.getName()).getResidues().equals(hitSeq.getResidues())) {
            String oldHitName = hitSeq.getName();
            seqIds.put(hitSeq.getName(), seqIds.get(hitSeq.getName()) + 1);