[Gmod-apollo-cmts] CVS: apollo/src/java/jalview/gui AlignFrame.java,1.11,1.12

[Mark G. <mg...@us...>]

Update of /cvsroot/gmod/apollo/src/java/jalview/gui
In directory sc8-pr-cvs1:/tmp/cvs-serv26114/src/java/jalview/gui

Modified Files:
	AlignFrame.java 
Log Message:
In game sometimes both the alignment sequence and hit sequence are
present. What you want in jalview preferably is the alignment sequence
as it will show alignment gaps. So I changed CondensedAlignment to
call FeaturePair.getAlignmentSequence() instead of
getHitSequence(). getAlignmentSequence returns the alignment sequence
if its non null. If its null it returns the hit sequence. I dont think
this will affect ensembl as I dont think ensembl stores alignment
sequence. This fixes game bug where some jalview alignments were
coming up without the dashes making the alignments all off.



Index: AlignFrame.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/jalview/gui/AlignFrame.java,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** AlignFrame.java	22 Apr 2003 00:00:22 -0000	1.11
--- AlignFrame.java	22 Apr 2003 20:36:01 -0000	1.12
***************
*** 134,180 ****
    }
  
!   /** Just copied this over from TierPopupMenu - replace with micheles blocking stuff...
!       Make DrawableSequence from SeqFeatureI feat */
!   private DrawableSequence makeDrawableSequence(SeqFeatureI feat) {
!     // feat.hasAlignmentSequence(), 
!     if (feat.isaFeaturePair()) {
!       FeaturePairI featPair = feat.getAsFeaturePair();
!       //SeqFeatureI hit = featPair.getHitFeature();
!       //seq = hit.getRefSequence().getResidues(hit.getLow(),hit.getHigh());
!       //String seq = hit.getProperty("subject_alignment");
!       // put in feat.getAlignmentSequence().getResidues()?
!       String seq =  featPair.getHitSequence().getResidues();
!       int resStart = feat.getStart();
!       int resEnd = feat.getEnd();
!       return new DrawableSequence(feat.getName(),seq,resStart,resEnd);
!     }
!     // FeatureSet of FeaturePairI's - make into one DrawbaleSeq with dots for 
!     // the introns
!     else if (feat.hasChildren()) {
!       String seq = "";
!       int endOfSeq = 0;
!       Vector kids = feat.getChildren();
!       for (int i=0; i<kids.size(); i++) {
! 	SeqFeatureI kid = (SeqFeatureI)kids.elementAt(i);
! 	if (kid.isaFeaturePair()) {
! 	  FeaturePairI fp = kid.getAsFeaturePair();
! 	  //DrawableSequence ds = featurePairToDrawableSequence(fp);
! 	  String s = fp.getHitSequence().getResidues();
! 	  if (endOfSeq > 0) {
! 	    for (int j=endOfSeq+1; j<fp.getStart(); j++) 
! 	      seq += ".";
! 	  } 
! 	  endOfSeq = fp.getEnd();
! 	  seq += s;
! 	}
!       }
!       return new DrawableSequence(feat.getName(),seq,feat.getStart(),feat.getEnd());
!     }
!     // non-FeaturePair leaf - eg Exon
!     else {
!       String seq = feat.getFeatureSequence().getResidues();
!       return new DrawableSequence(feat.getName(),seq,feat.getStart(),feat.getEnd());
!     }
!   }
  
    public void init() {
--- 134,180 ----
    }
  
! //   /** Just copied this over from TierPopupMenu - replace with micheles blocking stuff...
! //       Make DrawableSequence from SeqFeatureI feat */
! //   private DrawableSequence makeDrawableSequence(SeqFeatureI feat) {
! //     // feat.hasAlignmentSequence(), 
! //     if (feat.isaFeaturePair()) {
! //       FeaturePairI featPair = feat.getAsFeaturePair();
! //       //SeqFeatureI hit = featPair.getHitFeature();
! //       //seq = hit.getRefSequence().getResidues(hit.getLow(),hit.getHigh());
! //       //String seq = hit.getProperty("subject_alignment");
! //       // put in feat.getAlignmentSequence().getResidues()?
! //       String seq =  featPair.getHitSequence().getResidues();
! //       int resStart = feat.getStart();
! //       int resEnd = feat.getEnd();
! //       return new DrawableSequence(feat.getName(),seq,resStart,resEnd);
! //     }
! //     // FeatureSet of FeaturePairI's - make into one DrawbaleSeq with dots for 
! //     // the introns
! //     else if (feat.hasChildren()) {
! //       String seq = "";
! //       int endOfSeq = 0;
! //       Vector kids = feat.getChildren();
! //       for (int i=0; i<kids.size(); i++) {
! // 	SeqFeatureI kid = (SeqFeatureI)kids.elementAt(i);
! // 	if (kid.isaFeaturePair()) {
! // 	  FeaturePairI fp = kid.getAsFeaturePair();
! // 	  //DrawableSequence ds = featurePairToDrawableSequence(fp);
! // 	  String s = fp.getHitSequence().getResidues();
! // 	  if (endOfSeq > 0) {
! // 	    for (int j=endOfSeq+1; j<fp.getStart(); j++) 
! // 	      seq += ".";
! // 	  } 
! // 	  endOfSeq = fp.getEnd();
! // 	  seq += s;
! // 	}
! //       }
! //       return new DrawableSequence(feat.getName(),seq,feat.getStart(),feat.getEnd());
! //     }
! //     // non-FeaturePair leaf - eg Exon
! //     else {
! //       String seq = feat.getFeatureSequence().getResidues();
! //       return new DrawableSequence(feat.getName(),seq,feat.getStart(),feat.getEnd());
! //     }
! //   }
  
    public void init() {