[Gmod-apollo-cmts] CVS: apollo/doc todo,1.565,1.566 fixed-bugs,1.331,1.332

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

Update of /cvsroot/gmod/apollo/doc
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv31489

Modified Files:
	todo fixed-bugs 
Log Message:



Index: todo
===================================================================
RCS file: /cvsroot/gmod/apollo/doc/todo,v
retrieving revision 1.565
retrieving revision 1.566
diff -C2 -d -r1.565 -r1.566
*** todo	26 Feb 2004 18:16:44 -0000	1.565
--- todo	26 Feb 2004 23:48:57 -0000	1.566
***************
*** 976,994 ****
  org.bdgp.swing.widget.DataAdapterChooser, so not so simple to modify]
  
- Splice sites:
- Lynn Crosby suggests the following (instead of the more general splice
- site addition described after this):
- Apollo should have a visual flag for splices for which the cDNA alignment
- cannot be matched PRECISELY to a GT/AG.  In some cases, it may be close
- and sim4 may have fudged the alignment by a few bases; in other cases the
- alignment is so far from at GT/AG that it is shown as an atypical splice.
- In either case, we would like to see a flag.  Perhaps an edge mark of a
- different color?
- Latest suggestion: inward-pointing arrowhead:  ___
-                                                  /
-                                                  \
-                                                ---
- [Suzi said she can mark these non-matching alignments in BOP.]
- 
  Need way to annotate "this gene has unusual splice sites" (canned comment?)
  Tell user when they try to save, "You have a weird splice site that
--- 976,979 ----
***************
*** 1161,1168 ****
  Enable (what does that mean?) Sequence Ontology terms
  
! Intron editor: Suzi
  
! GenBank adapter: read data from GenBank, show or superimpose
! - Could we borrow code from Artemis to parse GenBank format?
  
  --------
--- 1146,1157 ----
  Enable (what does that mean?) Sequence Ontology terms
  
! - Way to view collapsed exons (no introns)
! - Intron editor?
  
! Need new adapters:
! - GenBank adapter: read data from GenBank, show or superimpose
!   (Could we borrow code from Artemis to parse GenBank format?)
! - GFF3 adapters
! - Chado adapter (JDBC)
  
  --------

Index: fixed-bugs
===================================================================
RCS file: /cvsroot/gmod/apollo/doc/fixed-bugs,v
retrieving revision 1.331
retrieving revision 1.332
diff -C2 -d -r1.331 -r1.332
*** fixed-bugs	25 Feb 2004 00:40:16 -0000	1.331
--- fixed-bugs	26 Feb 2004 23:48:58 -0000	1.332
***************
*** 4973,4974 ****
--- 4973,4990 ----
  Bev would like to start with smaller evidence panel.  Make this
  a configurable option.
+ 
+ Splice sites:
+ Lynn Crosby suggests the following (instead of the more general splice
+ site addition described after this):
+ Apollo should have a visual flag for splices for which the cDNA alignment
+ cannot be matched PRECISELY to a GT/AG.  In some cases, it may be close
+ and sim4 may have fudged the alignment by a few bases; in other cases the
+ alignment is so far from at GT/AG that it is shown as an atypical splice.
+ In either case, we would like to see a flag.  Perhaps an edge mark of a
+ different color?
+ Latest suggestion: inward-pointing arrowhead:  ___
+                                                  /
+                                                  \
+                                                ---
+ [Suzi said she can mark these non-matching alignments in BOP.]
+