[Gmod-apollo-cmts] CVS: apollo/doc todo,1.264,1.265 fixed-bugs,1.163,1.164

SourceForge Headquarters 225 Broadway Suite 1600 San Diego, CA 92101 +1 (858) 454-5900

Update of /cvsroot/gmod/apollo/doc
In directory sc8-pr-cvs1:/tmp/cvs-serv18895

Modified Files:
	todo fixed-bugs 
Log Message:


Index: todo
===================================================================
RCS file: /cvsroot/gmod/apollo/doc/todo,v
retrieving revision 1.264
retrieving revision 1.265
diff -C2 -d -r1.264 -r1.265
*** todo	21 Apr 2003 19:04:56 -0000	1.264
--- todo	21 Apr 2003 19:08:00 -0000	1.265
***************
*** 42,45 ****
--- 42,47 ----
  xJV20) Null pointer in example.xml bringing up Fly ESTs (light green).
  JV21) genomic dna and translated have N's in introns. Change to '-'.
+ JV22) Can't view features from GFF or Ensembl data because it can't
+ pfetch the sequences.  Michele said she'll set something up to enable this.
  --------------
  end of jalview
***************
*** 259,268 ****
  java 1.3.1 popup mem leak. This is fixed in 1.4.1 so we'll just wait for the 
  migration. Old curation sets are not being held onto.
- - If I open the annot info window for any annotation that has INTERNAL
- comments, and I'm in public mode, then when I hit the x, it asks if I want
- to save changes (even though I didn't make any changes).
- (Example: Hph:CG31543)
- This is because the internal comments are not getting copied somewhere.
- Need to copy them into clones, but not show them.
  - Uncommited edits are lost if edits are done in the main window. 
  Annotation change events wipe out the edited uncommited clone. 
--- 261,264 ----
***************
*** 345,359 ****
  
  GenBank writer:
! - You're supposed to choose a directory, but it doesn't tell you that,
! and the browser will only let you choose a file.  If you select a file,
! you get:
! java.lang.NullPointerException
!         at apollo.dataadapter.genbank.GenbankAdapterGUI.doOperation(GenbankAdapterGUI.java:30)
!         at org.bdgp.swing.widget.DataAdapterChooser.doCommitWithExceptions(DataAdapterChooser.java:355)
!         at org.bdgp.swing.widget.DataAdapterChooser.doCommit(DataAdapterChooser.java:408)
!         at apollo.gui.menus.FileMenu$SaveAdapterChooser.doCommit(FileMenu.java:349)
!         at org.bdgp.swing.widget.DataAdapterChooser$CommitRunnable.run(DataAdapterChooser.java:132)
!         at java.lang.Thread.run(Thread.java:479)
! - But if you choose a directory, you're also hosed:
  caught exception writing AE003603.Sept.tbl
  null
--- 341,348 ----
  
  GenBank writer:
! - File browser won't let you choose a directory (even though that's what
! GenBank writer requires).  Can we make it let you choose a directory?  If
! not, can we accept a file and chop off the filename to get a directory?
! - Even if you choose a directory, you're hosed:
  caught exception writing AE003603.Sept.tbl
  null
***************
*** 639,649 ****
  Need to be more robust and informative when user makes bad GFF or Ensembl
  CGI requests:
- - If you ask for a gff file that's not found, you get a popup that just
- says Exception from apollo.dataadapter.DataAdapterException.  Message
- "Error: could not open file foo for reading." is just printed to
- terminal.
  - Ensembl CGI data adapter doesn't deal gracefully with bad ranges.  For example, if you
  ask for a range starting at 0, you get many exceptions.  It should pop up a box saying
  "The valid range for chromosome N is 1-3592309" or whatever.
  - If you put letters instead of numbers in the boxes, it appears to freeze up.
  - Ensj/Otter also behaves badly if you request nonexistent chromosomes or
--- 628,635 ----
  Need to be more robust and informative when user makes bad GFF or Ensembl
  CGI requests:
  - Ensembl CGI data adapter doesn't deal gracefully with bad ranges.  For example, if you
  ask for a range starting at 0, you get many exceptions.  It should pop up a box saying
  "The valid range for chromosome N is 1-3592309" or whatever.
+ [Now it seems ok with 0, but other bad ranges still make it throw an exception.]
  - If you put letters instead of numbers in the boxes, it appears to freeze up.
  - Ensj/Otter also behaves badly if you request nonexistent chromosomes or
***************
*** 653,664 ****
  you're zoomed in enough to see all the bases!  Also get message
  "Warning: No features to getEnd() for".
- 
- A lot of Ensembl results, when you click on them, show names like
- "sptrembl: no_name" in the righthand detail panel.  If second part of
- name is "no_name", don't show it.  But there are some results that seem
- like they should have real names.
- - Got rid of the no_name by changing SetDetailPanel:featureDisplayString,
- but line below colored line on right has nothing in it--should have
- something.
  
  GFF parsing problems:
--- 639,642 ----

Index: fixed-bugs
===================================================================
RCS file: /cvsroot/gmod/apollo/doc/fixed-bugs,v
retrieving revision 1.163
retrieving revision 1.164
diff -C2 -d -r1.163 -r1.164
*** fixed-bugs	18 Apr 2003 19:43:32 -0000	1.163
--- fixed-bugs	21 Apr 2003 19:08:01 -0000	1.164
***************
*** 3056,3057 ****
--- 3056,3090 ----
  StringIndexOutOfBoundsException with Sequence residueOffset adding one 
  and asking for more sequence than is there - why is it adding one anyways?
+ 
+ GenBank writer:
+ - You're supposed to choose a directory, but it doesn't tell you that,
+ and the browser will only let you choose a file.  If you select a file,
+ you get:
+ java.lang.NullPointerException
+         at apollo.dataadapter.genbank.GenbankAdapterGUI.doOperation(GenbankAdapterGUI.java:30)
+         at org.bdgp.swing.widget.DataAdapterChooser.doCommitWithExceptions(DataAdapterChooser.java:355)
+         at org.bdgp.swing.widget.DataAdapterChooser.doCommit(DataAdapterChooser.java:408)
+         at apollo.gui.menus.FileMenu$SaveAdapterChooser.doCommit(FileMenu.java:349)
+         at org.bdgp.swing.widget.DataAdapterChooser$CommitRunnable.run(DataAdapterChooser.java:132)
+         at java.lang.Thread.run(Thread.java:479)
+ 
+ A lot of Ensembl results, when you click on them, show names like
+ "sptrembl: no_name" in the righthand detail panel.  If second part of
+ name is "no_name", don't show it.  But there are some results that seem
+ like they should have real names.
+ - Got rid of the no_name by changing SetDetailPanel:featureDisplayString,
+ but line below colored line on right has nothing in it--should have
+ something. 
+ [Oh well, whatever.]
+ 
+ x If you ask for a gff file that's not found, you get a popup that just
+ says Exception from apollo.dataadapter.DataAdapterException.  Message
+ "Error: could not open file foo for reading." is just printed to
+ terminal.
+ 
+ x If I open the annot info window for any annotation that has INTERNAL
+ comments, and I'm in public mode, then when I hit the x, it asks if I want
+ to save changes (even though I didn't make any changes).
+ (Example: Hph:CG31543)
+ This is because the internal comments are not getting copied somewhere.
+ Need to copy them into clones, but not show them.