[Gmod-apollo-cmts] CVS: apollo/doc todo,1.464,1.465 fixed-bugs,1.269,1.270 synteny-todo,1.29,1.30

[Nomi H. <no...@us...>]

Update of /cvsroot/gmod/apollo/doc
In directory sc8-pr-cvs1:/tmp/cvs-serv26230

Modified Files:
	todo fixed-bugs synteny-todo 
Log Message:



Index: todo
===================================================================
RCS file: /cvsroot/gmod/apollo/doc/todo,v
retrieving revision 1.464
retrieving revision 1.465
diff -C2 -d -r1.464 -r1.465
*** todo	29 Oct 2003 00:33:37 -0000	1.464
--- todo	31 Oct 2003 00:16:59 -0000	1.465
***************
*** 24,27 ****
--- 24,31 ----
  may also need "generic.validation".
  
+ Rubberband:  only select sequence if no other features have been selected
+ (it's annoying to rubberband a bunch of annotations a bit sloppily and
+ end up with the sequence popping up when it's not wanted).
+ 
  -------
  Jalview
***************
*** 898,904 ****
  -------------------------------------------------------------------
  
! Record new genes, merges, and splits in XML.
! Also be sure to carry through any gene transaction records that were in
! the XML (they should persist across Apollo sessions).
  
  Synteny view (see synteny-todo)
--- 902,906 ----
  -------------------------------------------------------------------
  
! When running mac-set-jvm, also let Mac user choose Aqua or Metal look & feel
  
  Synteny view (see synteny-todo)

Index: fixed-bugs
===================================================================
RCS file: /cvsroot/gmod/apollo/doc/fixed-bugs,v
retrieving revision 1.269
retrieving revision 1.270
diff -C2 -d -r1.269 -r1.270
*** fixed-bugs	29 Oct 2003 00:33:37 -0000	1.269
--- fixed-bugs	31 Oct 2003 00:17:00 -0000	1.270
***************
*** 4156,4161 ****
  mac-set-jvm: more different status codes on exit; handle these with more
  informative reports from Apollo.
! Can we make Apollo capture and pass on the error messages printed by
! mac-set-jvm?
  
  When you save GAME from Apollo, it now doesn't save empty analyses, but
--- 4156,4160 ----
  mac-set-jvm: more different status codes on exit; handle these with more
  informative reports from Apollo.
! Make Apollo capture and pass on the error messages printed by mac-set-jvm
  
  When you save GAME from Apollo, it now doesn't save empty analyses, but
***************
*** 4166,4168 ****
--- 4165,4171 ----
  [Now have Chado differ from Harvard:  converts "before" and "after" GAME
  XML to chado, and diffs the two]
+ 
+ Record new genes, merges, and splits in XML.
+ Also be sure to carry through any gene transaction records that were in
+ the XML (they should persist across Apollo sessions).
  

Index: synteny-todo
===================================================================
RCS file: /cvsroot/gmod/apollo/doc/synteny-todo,v
retrieving revision 1.29
retrieving revision 1.30
diff -C2 -d -r1.29 -r1.30
*** synteny-todo	27 Oct 2003 22:56:24 -0000	1.29
--- synteny-todo	31 Oct 2003 00:17:00 -0000	1.30
***************
*** 1,2 ****
--- 1,10 ----
+ Top synteny bugs (10/30/2003):
+ 
+ 1. Correct endpoints of bottom edge of trapezoid 
+ 2. Enable start/stop view to be turned off from View menu [this would
+ also be useful for normal view, not just for synteny]
+ 
+ ---------------------------------------
+ 
  > home in/zoom to link:
  zoom both species