[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/dataadapter/ensj EnsJAdapter.java, 1.114, 1.115

[Steve S. <se...@us...>]

Update of /cvsroot/gmod/apollo/src/java/apollo/dataadapter/ensj
In directory sc8-pr-cvs2.sourceforge.net:/tmp/cvs-serv7413

Modified Files:
	EnsJAdapter.java 
Log Message:
When fetching by stable id, the location generated was strand specific so
no genes on the other strand within the range of the wanted gene were 
retrieved. Now de-strand the location before fetching.


Index: EnsJAdapter.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/ensj/EnsJAdapter.java,v
retrieving revision 1.114
retrieving revision 1.115
diff -C2 -d -r1.114 -r1.115
*** EnsJAdapter.java	13 Sep 2007 04:32:29 -0000	1.114
--- EnsJAdapter.java	12 Oct 2007 13:25:00 -0000	1.115
***************
*** 360,364 ****
  
        if(gene != null){
!         return gene.getLocation();
        }
  
--- 360,364 ----
  
        if(gene != null){
!         return deStrandLocation(gene.getLocation());
        }
  
***************
*** 366,370 ****
  
        if(transcript != null){
!         return transcript.getLocation();
        }
  
--- 366,370 ----
  
        if(transcript != null){
!         return deStrandLocation(transcript.getLocation());
        }
  
***************
*** 372,376 ****
  
        if(translation != null){
!         return translation.getTranscript().getLocation();
        }
  
--- 372,376 ----
  
        if(translation != null){
!         return deStrandLocation(translation.getTranscript().getLocation());
        }
  
***************
*** 378,382 ****
  
        if(exon != null){
!         return exon.getLocation();
        }
      }catch(AdaptorException exception){
--- 378,382 ----
  
        if(exon != null){
!         return deStrandLocation(exon.getLocation());
        }
      }catch(AdaptorException exception){
***************
*** 390,393 ****
--- 390,399 ----
      throw new ApolloAdapterException("Cannot find a gene, transcript, translation or exon with input stableID: "+stableID);
    }
+ 
+   private Location deStrandLocation(Location strandedLoc) {
+     Location unstrandedLoc = strandedLoc.copy();
+     unstrandedLoc.setStrand(0);
+     return unstrandedLoc;
+   }
    
    // SMJS Temporary hack