[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/analysis AnalysisGUI.java, 1.2, 1.3

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

Update of /cvsroot/gmod/apollo/src/java/apollo/analysis
In directory ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv4931

Modified Files:
	AnalysisGUI.java 
Log Message:
+ Due to issues with different Sequence.getSubsequence() implementations,
ended up writing outside one to behave the same regardless of Sequence



Index: AnalysisGUI.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/analysis/AnalysisGUI.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** AnalysisGUI.java	27 Feb 2009 17:03:09 -0000	1.2
--- AnalysisGUI.java	17 Jul 2009 18:28:46 -0000	1.3
***************
*** 32,35 ****
--- 32,37 ----
  import apollo.config.TierProperty;
  import apollo.datamodel.CurationSet;
+ import apollo.datamodel.Sequence;
+ import apollo.datamodel.SequenceI;
  import apollo.gui.genomemap.StrandedZoomableApolloPanel;
  import apollo.gui.synteny.CurationManager;
***************
*** 598,602 ****
            getOptions());
        CurationSet cs = CurationManager.getActiveCurationState().getCurationSet();
!       String type = blast.runAnalysis(cs, cs.getRefSequence().getSubSequence(start, end), strand, start - 1);
        AnalysisFilter filter = new AnalysisFilter();
        AnalysisInput ai = new AnalysisInput();
--- 600,617 ----
            getOptions());
        CurationSet cs = CurationManager.getActiveCurationState().getCurationSet();
!       // too much weirdness going on with the different implementation of Sequence objects, just create our own subsequence here
!       int seqStart;
!       int seqEnd;
!       if (strand == 1) {
!         seqStart = start - cs.getLow();
!         seqEnd = end - cs.getLow() + 1;
!       }
!       else {
!         seqStart = start - cs.getLow() - 1;
!         seqEnd = end - cs.getLow();
!       }
!       SequenceI region = new Sequence(cs.getRefSequence().getName(), cs.getRefSequence().getResidues().substring(seqStart, seqEnd));
!       //String type = blast.runAnalysis(cs, cs.getRefSequence().getSubSequence(start, end), strand, start - 1);      
!       String type = blast.runAnalysis(cs, region, strand, start - 1);
        AnalysisFilter filter = new AnalysisFilter();
        AnalysisInput ai = new AnalysisInput();