[Gmod-apollo-cmts] CVS: apollo/src/java/jalview/gui DrawableSequence.java,1.17,1.18

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

Update of /cvsroot/gmod/apollo/src/java/jalview/gui
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv29055/src/java/jalview/gui

Modified Files:
	DrawableSequence.java 
Log Message:
fixed alignement seq/jalview bug where "genomic" 
sequence for peptide alignments was
coming up with the unspaced peptide alignment - now its with the
spaced peptide alignment. the problem was
SeqFeature.alignmentIsPeptide was querying the feats sequence for its
residue type and if there was one, assumed that the type of the
alignment was the same and didnt go through the seq length hack. but
this is a wrong assumption. the feature sequence can be dna and the
alignment sequence can be aa, the alignment can use the translated
feat seq. the only assumption you can make is if the feats seq is aa
then the alignment seq must surely be aa as well (its not doing aa ->
dna). 

also put in a test in TestApollo for this.



Index: DrawableSequence.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/jalview/gui/DrawableSequence.java,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** DrawableSequence.java	28 Apr 2005 18:43:49 -0000	1.17
--- DrawableSequence.java	30 Jun 2005 13:47:02 -0000	1.18
***************
*** 511,514 ****
--- 511,516 ----
    }
  
+   public boolean isAA() { return sequence.isAA(); }
+ 
    public void setLength (int len) {
      sequence.setLength(len);