[Gmod-apollo-cmts] CVS: apollo/doc fixed-bugs,1.236,1.237 todo,1.401,1.402

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

Update of /cvsroot/gmod/apollo/doc
In directory sc8-pr-cvs1:/tmp/cvs-serv11226/doc

Modified Files:
	fixed-bugs todo 
Log Message:
Fixed jalview bug:
JV83) Genomic sequence slippping into the ends of some sequences
example: align 2nd feat of Q9V4UO with 2nd feat of P07190 (seems ok now)
example2: Q9GZT9 3rd exon on a multi align with its neighbors (in example.xml)

extendAlignment() was padding seq with consensus genomic instead of dots - not sure why


Index: fixed-bugs
===================================================================
RCS file: /cvsroot/gmod/apollo/doc/fixed-bugs,v
retrieving revision 1.236
retrieving revision 1.237
diff -C2 -d -r1.236 -r1.237
*** fixed-bugs	24 Jul 2003 00:39:17 -0000	1.236
--- fixed-bugs	24 Jul 2003 01:56:29 -0000	1.237
***************
*** 3892,3894 ****
  BE015368 in ~suzi/raw_data/temp.xml shows dna seq in feat and pep in alignment.
  
! 
--- 3892,3896 ----
  BE015368 in ~suzi/raw_data/temp.xml shows dna seq in feat and pep in alignment.
  
! JV83) Genomic sequence slippping into the ends of some sequences
! example: align 2nd feat of Q9V4UO with 2nd feat of P07190 (seems ok now)
! example2: Q9GZT9 3rd exon on a multi align with its neighbors (in example.xml)

Index: todo
===================================================================
RCS file: /cvsroot/gmod/apollo/doc/todo,v
retrieving revision 1.401
retrieving revision 1.402
diff -C2 -d -r1.401 -r1.402
*** todo	24 Jul 2003 00:39:17 -0000	1.401
--- todo	24 Jul 2003 01:56:31 -0000	1.402
***************
*** 84,90 ****
  believe is the way we want it which is to give the coordinates of the
  actual features
- JV83) Genomic sequence slippping into the ends of some sequences
- example: align 2nd feat of Q9V4UO with 2nd feat of P07190 (seems ok now)
- example2: Q9GZT9 on a multi align with its neighbors (in example.xml)
  JV87) Merging of blocks not working right. This can most easily seen
  by creating 2 exons that are 5 bp apart - they get put into 2
--- 84,87 ----