[Gmod-apollo-cmts] CVS: apollo/src/java/jalview/datamodel CondensedAlignment.java,1.4,1.5

[Michele C. <mc...@us...>]

Update of /cvsroot/gmod/apollo/src/java/jalview/datamodel
In directory sc8-pr-cvs1:/tmp/cvs-serv1789/jalview/datamodel

Modified Files:
	CondensedAlignment.java 
Log Message:
Ok - genomic is in and looks fine for ensembl
Game looks mostly fine but there are problems with odd
off by ones which I'll sort out tomorrow.

Reverse strand display is not reversed fully - i.e. it is
displayed as it is in the main panel.  This is presumably
what we want to see i.e. if the main panel is revcomped 
we want to see revcomp.



Index: CondensedAlignment.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/jalview/datamodel/CondensedAlignment.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** CondensedAlignment.java	19 Apr 2003 15:03:30 -0000	1.4
--- CondensedAlignment.java	19 Apr 2003 15:53:34 -0000	1.5
***************
*** 11,14 ****
--- 11,16 ----
  import jalview.gui.DrawableSequence;
  
+ import org.bdgp.util.DNAUtils;
+ 
  public class CondensedAlignment {
  
***************
*** 235,238 ****
--- 237,241 ----
  
      apollo.datamodel.SequenceI genseq = null;
+     int strand = 1;
  
      while (en.hasMoreElements()) {
***************
*** 264,271 ****
  	  apollo.datamodel.FeaturePair fp = (apollo.datamodel.FeaturePair)arr.get(i);
  
! 	  if (genseq != null) {
  
  	    genseq = fp.getRefSequence();
  
  	    System.out.println("Sequence " + genseq.getLength());
  	  }
--- 267,277 ----
  	  apollo.datamodel.FeaturePair fp = (apollo.datamodel.FeaturePair)arr.get(i);
  
! 	  if (genseq == null) {
  
  	    genseq = fp.getRefSequence();
  
+ 	    if (fp.getStrand() == -1) {
+ 	      strand = -1;
+ 	    }
  	    System.out.println("Sequence " + genseq.getLength());
  	  }
***************
*** 334,339 ****
  		}
  		    
- 
- 		    
  		StringBuffer  tmpstring = new StringBuffer();
  
--- 340,343 ----
***************
*** 436,443 ****
      }
  
-     jalview.datamodel.Sequence[] seqarr = new jalview.datamodel.Sequence[seqs.size()];
  
!     for (int i = 0; i < seqs.size(); i++) {
!       seqarr[i] = (jalview.datamodel.Sequence)seqs.get(i);
        
      }
--- 440,479 ----
      }
  
  
!     // Now generate the genomic sequence
! 
!     
!     StringBuffer genstr = new StringBuffer();
! 
!     for (int j = 0; j < blocks.size(); j++) {
! 
!       int blockstart = ((Integer)starts.get(j)).intValue();
!       int blockend   = ((Integer)ends.get(j)).intValue();
!       
!       // blockstart -= pad;
!       //blockend   += pad;
! 
!       if (blockstart < 1) { blockstart = 1;}
!  
!       System.out.println("Blockstart/end" + blockstart + " " + blockend);
!       String tmp = genseq.getResidues(blockstart,blockend-1);
!       if (strand == -1) {
! 	tmp = DNAUtils.complement(tmp);
!       }
!       genstr.append(tmp);
! 
!       
!       for (int k = 0; k < intron; k++) {
! 	genstr.append("-");
!       }
! 
!     }
!      
!     jalview.datamodel.Sequence[] seqarr = new jalview.datamodel.Sequence[seqs.size()+1];
! 
!     seqarr[0] = new jalview.datamodel.Sequence("GENOMIC",genstr.toString(),1,genstr.toString().length());
! 
!     for (int i = 1; i <= seqs.size(); i++) {
!       seqarr[i] = (jalview.datamodel.Sequence)seqs.get(i-1);
        
      }