[Gmod-apollo-cmts] CVS: apollo/doc synteny-fixed,1.28,1.29 synteny-todo,1.79,1.80

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

Update of /cvsroot/gmod/apollo/doc
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv24214/doc

Modified Files:
	synteny-fixed synteny-todo 
Log Message:
game synteny was querying all transcripts with getPeptideSeq!=null -
on non-gene annots this was causing the messages to fly in FS.get_ORF
and getFeaturePos as they had a translation start of 0 - which is to
say no real trans start. Now queried with hasPeptideSequence which
checks if translation start == 0.



Index: synteny-fixed
===================================================================
RCS file: /cvsroot/gmod/apollo/doc/synteny-fixed,v
retrieving revision 1.28
retrieving revision 1.29
diff -C2 -d -r1.28 -r1.29
*** synteny-fixed	26 Mar 2004 19:58:26 -0000	1.28
--- synteny-fixed	26 Mar 2004 21:01:36 -0000	1.29
***************
*** 331,333 ****
--- 331,339 ----
  in vertical ev pan need to be able to make ev pan as big as ya want
  
+ Annoying error message:
+ tRNA:R:83AB-RA does not have translation start
+ featureSet.getFeaturePosition: tRNA:R:83AB-RA has no feature containing 0 (1213947-1214019)
+ snRNA:U4atac:83A-RA does not have translation start
+ featureSet.getFeaturePosition: snRNA:U4atac:83A-RA has no feature containing 0 (1216883-1217004)
+ HB{}1219-RA does not have translation start
  

Index: synteny-todo
===================================================================
RCS file: /cvsroot/gmod/apollo/doc/synteny-todo,v
retrieving revision 1.79
retrieving revision 1.80
diff -C2 -d -r1.79 -r1.80
*** synteny-todo	26 Mar 2004 19:58:26 -0000	1.79
--- synteny-todo	26 Mar 2004 21:01:36 -0000	1.80
***************
*** 16,25 ****
  Had to create sequence CG2669-PA
  Had to create sequence CG14667-PA
- Completed XML parse of Contig3681_Contig434:191972-243563
- tRNA:R:83AB-RA does not have translation start
- featureSet.getFeaturePosition: tRNA:R:83AB-RA has no feature containing 0 (1213947-1214019)
- snRNA:U4atac:83A-RA does not have translation start
- featureSet.getFeaturePosition: snRNA:U4atac:83A-RA has no feature containing 0 (1216883-1217004)
- HB{}1219-RA does not have translation start
  
  After loading synteny region, if you then load a regular game xml file,
--- 16,19 ----
***************
*** 84,89 ****
  Config evidence panel width(for vertical) and height(for horizontal)?
  or config percentage?
! evidence panel vertical should be default for synteny
! in vertical need to be able to make ev pan as big as ya want
  
  Going from 2 species to 1 (regular load) bottom species gets split out
--- 78,83 ----
  Config evidence panel width(for vertical) and height(for horizontal)?
  or config percentage?
! evidence panel vertical should be default for synteny - make this a
! style param?
  
  Going from 2 species to 1 (regular load) bottom species gets split out