[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/analysis AnalysisGUI.java, 1.3, 1.4 BlastXMLParser.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-serv28330

Modified Files:
	AnalysisGUI.java BlastXMLParser.java 
Log Message:
+ Fixed some offset issues when dealing with analysis on minus strand



Index: AnalysisGUI.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/analysis/AnalysisGUI.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** AnalysisGUI.java	17 Jul 2009 18:28:46 -0000	1.3
--- AnalysisGUI.java	24 Jul 2009 19:56:48 -0000	1.4
***************
*** 603,614 ****
        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);      
--- 603,608 ----
        int seqStart;
        int seqEnd;
!       seqStart = start - cs.getLow();
!       seqEnd = end - cs.getLow() + 1;
        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);      

Index: BlastXMLParser.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/analysis/BlastXMLParser.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** BlastXMLParser.java	27 Feb 2009 17:03:09 -0000	1.2
--- BlastXMLParser.java	24 Jul 2009 19:56:48 -0000	1.3
***************
*** 150,155 ****
      }
      else {
!       queryBegin = offset + genomicLength - Integer.parseInt(getTextContent(elt.getElementsByTagName("Hsp_query-to").item(0)));
!       queryEnd = offset + genomicLength - Integer.parseInt(getTextContent(elt.getElementsByTagName("Hsp_query-from").item(0)));
        queryStrand *= -1;
      }
--- 150,155 ----
      }
      else {
!       queryBegin = offset + genomicLength - Integer.parseInt(getTextContent(elt.getElementsByTagName("Hsp_query-to").item(0))) + 1;
!       queryEnd = offset + genomicLength - Integer.parseInt(getTextContent(elt.getElementsByTagName("Hsp_query-from").item(0))) + 1;
        queryStrand *= -1;
      }