[Gmod-apollo-cmts] CVS: apollo/doc todo,1.658,1.659 fixed-bugs,1.388,1.389

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

Update of /cvsroot/gmod/apollo/doc
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv10381

Modified Files:
	todo fixed-bugs 
Log Message:


Index: todo
===================================================================
RCS file: /cvsroot/gmod/apollo/doc/todo,v
retrieving revision 1.658
retrieving revision 1.659
diff -C2 -d -r1.658 -r1.659
*** todo	17 Nov 2004 19:07:28 -0000	1.658
--- todo	18 Nov 2004 00:38:27 -0000	1.659
***************
*** 5,70 ****
  ----------------------------------------------------
  
! changing result tag to incomplete cds has a repaint issue
! 
! Add GAME version number in GAME output (but where to get version #?).
! 
! on changing the range of an exon in Hph (annot-types.xml) in the EDE
! it seemed to erroneously split the gene and get all wack - need to
! look into this more. - happens on making intron on highest exon (3'
! forward, 3' reverse)
! 
! sequencing error should cause a recalc of translation start - doesnt
! seem to - where translation stop does get recalculated.
! 
! Add ability to add publication to synonyms. need in gui and game.
! 
! When a comment is changed (via the comment editor), change the author and
! datestamp.
! 
! Release 1.4.5 doesn't make--it is missing src/java/apollo/dataadapter/ensj19
! (which I added) but it still is having trouble compiling
! src/java/apollo/dataadapter/ensj19/AnnotationEnsJAdapterGUI.java
! src/java/apollo/dataadapter/ensj19/AnnotationEnsJAdapter.java
! Make a new release 1.4.6 (might as well) tar for sourceforge.
  
! These are my thoughts on redoing the gui for comments (yes i know we did a
! which really helped but I think we need to go one step further)
! In main annot info window have comment list - of comment text not author/date
! or maybe both but minimally comment text (maybe just 1st 30 chars?) - anyways
! there would be an add,delete and edit buttons. Edit and delete buttons would be
! greyed out unless a comment was selected. If add comment was pressed the
! commentator box would come up (minus the comment list, add button, and delete
! buttons). The comment would then be constructed via the dropdown list and editing.
! and close would be hit - I suppose there could also be a cancel button to cancel
! the add. If a comment was selected in the comment list (in the main window NOT
! the commentator) edit and delete would be enabled (ungreyed). Delete would just
! delete it. Edit would popup the commentator as with add. With comments in this
! list in main window comments could be taken out of "comments" window. Comments
! window could turn into a "properties" window and show all the other properties
! as it does now.
  
! unless/until the annot info gui is changed have to make sure empty
! comments get wiped out on commentator window clsing - only get wiped
! on close button at the moment. - no biggie
!                                    
! minor bug: after changing type from gene to something non-coding like
! snoRNA the start and stop are still drawn in the main window.
  
! Don't let users create new transcript by dragging a collapsed tier.  This
! should be popping up a warning message, but Mark isn't getting one--why?
  
! serialized files seem to fail to read in and only get vague error
! popup message: "Exception from java.lang.NullPointerException". Bug
! should be fixed and error message should be made more informative
! (a stack trace would be good).
  
! get the installed version to tell you how much
! memory it's allocating (could grep from Apollo.lax)
  
! synonyms, dbxrefs, and comments are being copied on just moving one
! exon (not a transcript merge - and its going from target transcript to
! source transcript). On transcript merge the new transcript does not
! have the deleted transcripts stuff - i suspect that this is because
! the merged stuff went to the deleted and not vice versa.
  
  Cant delete synonyms in info editor. can only add. if you delete one
--- 5,42 ----
  ----------------------------------------------------
  
! New bugs introduced since r1.4.6:
! --------------------------------
! Load tiny.xml; try to save.
! Warning: couldn't find file conf/null anywhere
! GAMEAdapter.saveTransactions(): java.lang.IllegalStateException: ChadoTransactionXML.commitTransactions(): Cannot find xml template for chado transaction.
! java.lang.IllegalStateException: ChadoTransactionXML.commitTransactions(): Cannot find xml template for chado transaction.
! 	at apollo.dataadapter.chadoxml.ChadoTransactionXMLWriter.commitTransactions(ChadoTransactionXMLWriter.java:73)
! 	at apollo.dataadapter.TransactionOutputAdapter.commit(TransactionOutputAdapter.java:87)
! 	at apollo.dataadapter.gamexml.GAMEAdapter.saveTransactions(GAMEAdapter.java:334)
! 	at apollo.dataadapter.gamexml.GAMEAdapter.commitChanges(GAMEAdapter.java:298)
  
! Reading from backup file broken (null pointer--no informative message).
  
! If you load the example GFF file and then load a GAME file, none of the
! GAME results show up (only the annotations).  (If you load the GAME file
! first, or load it after first loading a GenBank file, it works fine--it
! only seems to be a problem after loading a GFF file.)
! Also, if you load a GAME file (e.g. annot-types.xml) and then load the
! sample GFF file, it comes up with all the results tiny and gray.  If you
! load the GFF file first, it's fine.
! In both cases, it seems that the tiers are coming up collapsed to the
! point of (near-)invisibility; if you say "Expand all tiers," they show up.
  
! Annot info editor:  Undo doesn't work for symbols, ID, synonyms, or
! changes to comments.  [Mark says these issues are already on his list
! (doc/chado/transaction-todo)]
  
! --------------------------------
! (End of new bugs introduced since r1.4.6)
  
! Add GAME version number in GAME output (but where to get version #?).
  
! Add ability to add publications (database literature IDs--e.g. FBrf or
! PubmedID) to synonyms. need in gui and game.
  
  Cant delete synonyms in info editor. can only add. if you delete one
***************
*** 72,75 ****
--- 44,50 ----
  changing selection.
  
+ get the installed version to tell you how much
+ memory it's allocating (could grep from Apollo.lax)
+ 
  <arm> tag is not always written out (it should be)--this is because
  Apollo expects the arm to have a name different from the seqid, and the
***************
*** 80,84 ****
  using the old method and is writing the seq.getDisplayId
  
! Can't click "select" boxes in restriction enzyme table.
  
  produces_seq field being lost from <feature_set> records after roundtrip
--- 55,61 ----
  using the old method and is writing the seq.getDisplayId
  
! Can't click "select" boxes in restriction enzyme table.  (Broke between
! r1.4.4 and r1.4.5.)
! http://cvs.sourceforge.net/viewcvs.py/gmod/apollo/src/java/apollo/gui/tweeker/RestrictionEnzymeSelector.java?r1=1.14&r2=1.15
  
  produces_seq field being lost from <feature_set> records after roundtrip
***************
*** 91,98 ****
  I have a feeling this was a problem that was fixed before that has now returned.
  
- Peptide spacing can be buggy (most of the time gets it right). 
- RE54776 DCG cdna dark green feature in AE003689 result seq has peptide
- spacing in its zoomed in main panel feat though it's nucleotide seq.
- 
  i just noticed a rather obscure and not-very-important bug that possibly
  hints at other as-yet-undiscovered issues.  i tried reading from
--- 68,71 ----
***************
*** 107,131 ****
  properly in the backup (although i didn't see any other bad symptoms).
  
! Sima reported problems editing gene symbols and IDs in annot info
! editor.  Can't replicate.  Sima wrote:
! I'm in internal mode, and looking at genes in the "gadflyst" database.
! For example, if I query for "gene" "HP1679" from gadflyst, and then select
! "ST:X:15590323:15589211:GENSCAN" and I open up the Annotation Info editor,
! and then I select some text at the end of the "Symbol", delete it, then go
! to the middle, and try to delete the X, the cursor goes the end of the
! string.  Then if I go the beginning of the string and try to type
! "CG:temp", the cursor goes to the end of the string after every 1 or 2
! strokes I type (e.g. if I type "te" really fast it lets me get those 2 in
! before the cursor ends up at the end of the string).
! [Sima sees this on Linux and on Mac.]
! 
! Inappropriately asking if you want to split genes you weren't working on
! (see Kathryn Campbell's message of Tue, 16 Mar 2004 18:20:27).
! to see this behavior, select gene CG12147 in the old (jan 30) example (i
! have it saved as ~nomi/apollo/data/example.old.xml), click somewhere in
! the middle of it, and say "split exon".  now select the first exon and
! say "delete selection".  you are asked, "Are you sure you want gene
! CG12163 to be split"?  CG12163 is clear on the other side of the rev
! strand.
  
  Show axis in view menu needs a repaint.
--- 80,85 ----
  properly in the backup (although i didn't see any other bad symptoms).
  
! Don't let users create new transcript by dragging a collapsed tier.  This
! should pop up a warning message (it seems to do so only sporadically).
  
  Show axis in view menu needs a repaint.
***************
*** 133,145 ****
  Annotation labels don't slide along as you scroll if you're revcomped.
  
- Put translational exceptions (selenocysteine for stop, +/-1 frameshift,
- one base pair genomic sequencing errors) into the transaction records.
- [They are already there, but just as FeatureChangeEvent.REPLACE or LIMIT
- events on TRANSLATION--is that not sufficient for now?]
- 
- After much fiddling with editing I managed to get in a state where
- sequencing errors i was doing in EDE were not coming up in annot
- info. Sporatic - dont have repeatable.
- 
  URLs for "Show gene report" need to be updated.
  internal: ProjectRefURL "http://www.fruitfly.org/cgi-bin/annot/mini-search.pl?query="
--- 87,90 ----
***************
*** 221,227 ****
  worse;  it clears the main window, leaving it blank!]
  
  Split up gui from non-gui config - so bop can run without apollo gui classes.
  
- Minor bug: 
  Cant move feature to other strand if there exists no feature of that
  type on other strand - will throw exception - no model being made for
--- 166,173 ----
  worse;  it clears the main window, leaving it blank!]
  
+ changing result tag to incomplete cds has a repaint issue
+ 
  Split up gui from non-gui config - so bop can run without apollo gui classes.
  
  Cant move feature to other strand if there exists no feature of that
  type on other strand - will throw exception - no model being made for
***************
*** 265,268 ****
--- 211,226 ----
  - If user changes annotation ID, make it show up in a different color in
  the annot info window.
+ - Sima reported problems editing gene symbols and IDs in annot info
+ editor.  Can't replicate.  Sima wrote:
+ I'm in internal mode, and looking at genes in the "gadflyst" database.
+ For example, if I query for "gene" "HP1679" from gadflyst, and then select
+ "ST:X:15590323:15589211:GENSCAN" and I open up the Annotation Info editor,
+ and then I select some text at the end of the "Symbol", delete it, then go
+ to the middle, and try to delete the X, the cursor goes the end of the
+ string.  Then if I go the beginning of the string and try to type
+ "CG:temp", the cursor goes to the end of the string after every 1 or 2
+ strokes I type (e.g. if I type "te" really fast it lets me get those 2 in
+ before the cursor ends up at the end of the string).
+ [Sima sees this on Linux and on Mac.]
  
  InstallAnywhere issues:
***************
*** 418,421 ****
--- 376,383 ----
  JV118) If just viewing protein alignments, genomic sequence gets
  protein seq - should be genomic.
+ JV119) If we have only cigars in the input, and not alignments, the
+ genomic sequence appears only as nucleotides, even when aligned with a
+ peptide--it should be using the cigar to fill in the genomic translation,
+ but apparently it's not.
  
  --------------
***************
*** 461,464 ****
--- 423,428 ----
  - When type changes, right detail panel doesn't change (though left
  one does!)
+ - After changing type from gene to something non-coding like
+ snoRNA the start and stop are still drawn in the main window.
  - What options should be turned off for non-gene annots--e.g. Exon Detail
  Editor, calculate longest ORF, ...?
***************
*** 733,736 ****
--- 697,716 ----
          at apollo.gui.AnnotationEditor.addGeneOrTranscript(AnnotationEditor.java:1701)
          at apollo.gui.AnnotationEditor.addGeneOrTranscript(AnnotationEditor.java:1687)
+ AE51) Inappropriately asking if you want to split genes you weren't working on
+ (see Kathryn Campbell's message of Tue, 16 Mar 2004 18:20:27).
+ to see this behavior, select gene CG12147 in the old (jan 30) example (i
+ have it saved as ~nomi/apollo/data/example.old.xml), click somewhere in
+ the middle of it, and say "split exon".  now select the first exon and
+ say "delete selection".  you are asked, "Are you sure you want gene
+ CG12163 to be split"?  CG12163 is clear on the other side of the rev
+ strand.
+ AE52) sequencing error should cause a recalc of translation start - doesnt
+ seem to - where translation stop does get recalculated.
+ AE53) synonyms, dbxrefs, and comments are being copied on just moving one
+ exon (not a transcript merge - and its going from target transcript to
+ source transcript). On transcript merge the new transcript does not
+ have the deleted transcripts stuff - i suspect that this is because
+ the merged stuff went to the deleted and not vice versa.
+ 
  
  ---------------------
***************
*** 750,757 ****
--- 730,761 ----
  annotation info window even appears?
  - Should add variable (GOURL?) to style instead of just hardcoding it in GeneEditPanel.
+ 
+ Annotation comments:
+ - When a comment is changed (via the comment editor), change the author and
+ datestamp.
+ - unless/until the annot info gui is changed have to make sure empty
+ comments get wiped out on commentator window clsing - only get wiped
+ on close button at the moment. - no biggie
  - It's weird to have the list of comments be by author name and date.
  Should have the comment text in that list.  Panel to right is really just
  a panel for adding/editing comments, which should be a popup that comes
  up when you want to add or edit rather than living there full-time.
+ - These are my [Mark's] thoughts on redoing the gui for comments (yes i
+ know we did a which really helped but I think we need to go one step
+ further) In main annot info window have comment list - of comment text
+ not author/date or maybe both but minimally comment text (maybe just 1st
+ 30 chars?) - anyways there would be an add,delete and edit buttons. Edit
+ and delete buttons would be greyed out unless a comment was selected. If
+ add comment was pressed the commentator box would come up (minus the
+ comment list, add button, and delete buttons). The comment would then be
+ constructed via the dropdown list and editing.  and close would be hit -
+ I suppose there could also be a cancel button to cancel the add. If a
+ comment was selected in the comment list (in the main window NOT the
+ commentator) edit and delete would be enabled (ungreyed). Delete would
+ just delete it. Edit would popup the commentator as with add. With
+ comments in this list in main window comments could be taken out of
+ "comments" window. Comments window could turn into a "properties" window
+ and show all the other properties as it does now.
+ 
  
  -----------------
***************
*** 786,789 ****
--- 790,796 ----
  like C's  Maybe choose a different font?  Or maybe we shouldn't show the
  bases until the user zooms in a teensy bit more?  (See ScaleView:drawSequence)
+ - Peptide spacing can be buggy (most of the time gets it right). 
+ RE54776 DCG cdna dark green feature in AE003689 result seq has peptide
+ spacing in its zoomed in main panel feat though it's nucleotide seq.
  
  Annotation creator colors and names:
***************
*** 862,865 ****
--- 869,876 ----
          at java.awt.EventDispatchThread.run(EventDispatchThread.java:80)
  
+ Right-menu option sometimes says "Set owner to FlyBase (taking from
+ FlyBase)".  It doesn't make sense to offer a set-owner change when the
+ new value is the same as the old.  (Very minor issue, though.)
+ 
  ----
  Exon Detail Editor (BOFE):
***************
*** 986,990 ****
  change, not for just any gene. But if I remove the deletion, I still can't
  see the black rectangle when I don't show introns for the sdk gene.
! EDE81) creating exons (in introns) seems to repeatably produce this
  message:
  DEBUG: Range.isContainedByRefSeq() feature has null reference seq Returning true even though we dont really know
--- 997,1001 ----
  change, not for just any gene. But if I remove the deletion, I still can't
  see the black rectangle when I don't show introns for the sdk gene.
! EDE82) creating exons (in introns) seems to repeatably produce this
  message:
  DEBUG: Range.isContainedByRefSeq() feature has null reference seq Returning true even though we dont really know
***************
*** 998,1001 ****
--- 1009,1024 ----
          at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1786)
          at javax.swing.AbstractButton$ForwardActionEvents.actionPerformed(AbstractButton.java:1
+ EDE83) on changing the range of an exon in Hph (annot-types.xml) in the EDE
+ it seemed to erroneously split the gene and get all wack - need to
+ look into this more. - happens on making intron on highest exon (3'
+ forward, 3' reverse)
+ EDE84) After much fiddling with editing I managed to get in a state where
+ sequencing errors i was doing in EDE were not coming up in annot
+ info. Sporatic - dont have repeatable.
+ EDE85) it seems like the "adjust for sequencing error" functionality in
+ the EDE does not work right.  (this is not a new problem--it seems to be
+ the same in r1.4.4.)  if i try to add an insertion, it asks me which base
+ i want to add, but then it frequently adds a different base--i asked for
+ an N and got a T; asked for a G and got an A.
  
  --------------------

Index: fixed-bugs
===================================================================
RCS file: /cvsroot/gmod/apollo/doc/fixed-bugs,v
retrieving revision 1.388
retrieving revision 1.389
diff -C2 -d -r1.388 -r1.389
*** fixed-bugs	11 Nov 2004 00:43:49 -0000	1.388
--- fixed-bugs	18 Nov 2004 00:38:27 -0000	1.389
***************
*** 5528,5531 ****
--- 5528,5532 ----
  being re-entity-ized when being written out.  Sequence names weren't; now
  they are, too.]
+ [Also fixed this in current version.]
  - Guanming's buffered save fix
  (These fixes were added on top of the June 2004 patches to v1.4.4.)
***************
*** 5536,5537 ****
--- 5537,5550 ----
  as db for prediction analysis and like, and xml has empty database
  element.  (See /users/sshu/tmp/CG1234_chado.game.xml)
+ 
+ serialized files seem to fail to read in and only get vague error
+ popup message: "Exception from java.lang.NullPointerException". Bug
+ should be fixed and error message should be made more informative
+ (a stack trace would be good).
+ 
+ Release 1.4.5 doesn't make--it is missing src/java/apollo/dataadapter/ensj19
+ (which I added) but it still is having trouble compiling
+ src/java/apollo/dataadapter/ensj19/AnnotationEnsJAdapterGUI.java
+ src/java/apollo/dataadapter/ensj19/AnnotationEnsJAdapter.java
+ Make a new release 1.4.6 (might as well) tar for sourceforge.
+