[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/gui/detailviewers/blixem BlixemRunner.java,1.12,1.13

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

Update of /cvsroot/gmod/apollo/src/java/apollo/gui/detailviewers/blixem
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv3507/src/java/apollo/gui/detailviewers/blixem

Modified Files:
	BlixemRunner.java 
Log Message:
so peptide ids(accs) & names(formerly displayId) were being
erroneoulsly lumped on name changes. now settting of transcript name
ONLY changes the peptide name, peptide acc/id is left untouched. split
out a new PEPTIDE_ID subpart. next i need to add changing peptide id
on id changes. 

renamed SequenceI. displayId to name - if this is contentious its
trivial to switch it back - but i found displayId confusing - its
really a name i think (and once peptides become features thats what it
will be). 



Index: BlixemRunner.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/gui/detailviewers/blixem/BlixemRunner.java,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** BlixemRunner.java	2 Apr 2004 19:50:40 -0000	1.12
--- BlixemRunner.java	28 Apr 2005 18:43:47 -0000	1.13
***************
*** 211,216 ****
              System.out.println("Hitref " + hit.getRefSequence());
              if (hit.getRefSequence() != null) {
! 	    hitSeq = curationSet.getSequence(hit.getRefSequence().getDisplayId());
! 	    	    System.out.println("\nFor feature " + fp + ", hitSeq = null--trying to get sequence for " + hit.getRefSequence().getDisplayId()); // DEL
              }
  	    if (hitSeq != null) {
--- 211,216 ----
              System.out.println("Hitref " + hit.getRefSequence());
              if (hit.getRefSequence() != null) {
! 	    hitSeq = curationSet.getSequence(hit.getRefSequence().getName());
! 	    	    System.out.println("\nFor feature " + fp + ", hitSeq = null--trying to get sequence for " + hit.getRefSequence().getName()); // DEL
              }
  	    if (hitSeq != null) {