[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/dataadapter/analysis BlatParser.java,1.1,1.2

Update of /cvsroot/gmod/apollo/src/java/apollo/dataadapter/analysis
In directory sc8-pr-cvs1:/tmp/cvs-serv7130/apollo/dataadapter/analysis

Modified Files:
	BlatParser.java 
Log Message:
Made changes for reverse strand coordinates on query


Index: BlatParser.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/analysis/BlatParser.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** BlatParser.java	3 Sep 2003 21:19:53 -0000	1.1
--- BlatParser.java	4 Sep 2003 21:26:15 -0000	1.2
***************
*** 70,73 ****
--- 70,74 ----
  		else
  		    reverse_analysis.addFeature (hit, true);
+ 
  		System.out.println ("Hit size is " + hit.size());
  		//parsedData.errorCheck();
***************
*** 83,86 ****
--- 84,88 ----
  	return (parsed ? getAnalysisType() : null);
      }
+     
      public FeatureSetI createFP () {
  	//generate exon pairs of query and target exons
***************
*** 99,145 ****
  	hit.setName(queryName);
  	for (int index = 0; index < blocks; index++) {
- 	    //	while (index < blocks) {
  	    //------------------------------------------------------------//
  	    //------------------Set query range---------------------------//
! 	    int qStart = Integer.parseInt(
! 					  (String)splitQueryStarts.elementAt(index)
! 					  );
! 	   
! 	    //find end point by adding blockSize to qStart 
! 	    int qEnd = qStart + Integer.parseInt(
! 						 (String)splitBlockSizes.elementAt(index)
! 						 );
! 
! 	    //add one to qStart to make this base rather than
  	    //interbase coordinates
! 	    qStart ++;
  	    
  	    //make seqFeature 
  	    SeqFeatureI query = new SeqFeature();
- 	    query.setLow(qStart);
- 	    System.out.print("STRAND" + strand + "  LOWER" + qStart +  "--");
- 	    query.setHigh(qEnd);
- 	    System.out.println("HIGHER" + qEnd);
- 	    query.setRefSequence(query_seq);
  	    query.setStrand(query_strand);
  	    query.setName(queryName);
  	    //------------------------------------------------------------//
  	    //------------------Set target range---------------------------//
! 	    int tStart = Integer.parseInt(
! 					  (String)splitTargetStarts.elementAt(index)
! 	    				  );
! 	    int tEnd = tStart + Integer.parseInt(
! 	    					 (String)splitBlockSizes.elementAt(index)
! 						 );
! 	    tStart ++;
  
  	    //make seqFeature 
  	    SeqFeatureI target = new SeqFeature();
- 	    target.setLow(tStart);
- 	    System.out.print("TARGET" + strand + "  LOWER" + tStart +  "--");
- 	    target.setHigh(tEnd);
- 	    System.out.println("HIGHER" + tEnd);
- 	    target.setRefSequence(target_seq);
  	    target.setStrand(1);
  
  	    //-------------------------------------------------------------
--- 101,172 ----
  	hit.setName(queryName);
  	for (int index = 0; index < blocks; index++) {
  	    //------------------------------------------------------------//
  	    //------------------Set query range---------------------------//
! 	    
! 	    int qLow, qHigh;
! 	    
! 	    //use strand information here
! 	    //because this is blat, the output is similar to the
! 	    //sim4 output.  
! 	    //when query is forward, everything is as expected.  
! 	    
! 	    if (query_strand == 1) {
! 		qLow = 
! 		    Integer.parseInt((String)splitQueryStarts.elementAt(index));
! 		//find end point by adding blockSize to qLow 
! 		qHigh = 
! 		    qLow  + Integer.parseInt((String)splitBlockSizes.elementAt(index));
! 	    }
! 	    //when query is reverse, you have to adjust the coordinates
! 	    //essentially, the minus strand blockSizes and qStarts are what
! 	    //you would get if you revcomped the query.  But, the qStart and
! 	    //qEnd are non-reveresed
! 	    else {
! 		qHigh = 
! 		    Integer.parseInt(querySize) -
! 		    Integer.parseInt((String)splitQueryStarts.elementAt(index));
! 		
! 		qLow  =  
! 		    Integer.parseInt(querySize) -
! 		    Integer.parseInt((String)splitQueryStarts.elementAt(index)) -
! 		    Integer.parseInt((String)splitBlockSizes.elementAt(index));
! 	    }
! 		    
! 	    //add one to qLow to make this base rather than
  	    //interbase coordinates
! 	    qLow ++;
  	    
  	    //make seqFeature 
  	    SeqFeatureI query = new SeqFeature();
  	    query.setStrand(query_strand);
+ 	    query.setLow(qLow);
+ 	    //query.setStart(qLow);
+ 	    query.setHigh(qHigh);
+ 	    //query.setEnd(qHigh);
+ 	    System.out.print("STRAND" + strand + "  LOWER" + qLow +  "--");
+ 	    System.out.println("HIGHER" + qHigh);
+ 	    System.out.println("SETTING Start as" + qLow + "  End" + qHigh +  "--");
+ 	    query.setRefSequence(query_seq);
  	    query.setName(queryName);
  	    //------------------------------------------------------------//
  	    //------------------Set target range---------------------------//
! 	    int tLow = 
! 		Integer.parseInt((String)splitTargetStarts.elementAt(index));
! 	    int tHigh = 
! 		tLow + Integer.parseInt((String)splitBlockSizes.elementAt(index));
! 	    tLow ++;
  
  	    //make seqFeature 
  	    SeqFeatureI target = new SeqFeature();
  	    target.setStrand(1);
+ 	    //target.setStart(tLow);
+ 	    target.setLow(tLow);
+ 	    //target.setEnd(tHigh);
+ 	    target.setHigh(tHigh);
+ 	    System.out.print("TARGET" + strand + "  LOWER" + tLow +  "--");
+ 	    System.out.println("HIGHER" + tHigh);
+ 	    System.out.println("SETTING Start as" + tLow + "  End" + tHigh +  "--");
+ 	    target.setRefSequence(target_seq);
+ 
  
  	    //-------------------------------------------------------------
***************
*** 150,154 ****
  	    System.out.println ("Added feature " + fp.getName());
   	    
! 	    System.out.println(tStart + "-" + tEnd + " (" +qStart + "-" + qEnd + ")");
  	    System.out.println("made seqfeature object for each pair");
  	}
--- 177,181 ----
  	    System.out.println ("Added feature " + fp.getName());
   	    
! 	    System.out.println(tLow + "-" + tHigh + " (" +qLow + "-" + qHigh + ")");
  	    System.out.println("made seqfeature object for each pair");
  	}