[Gmod-apollo-cmts] CVS: apollo/doc/chado transaction-todo,1.20,1.21

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

Update of /cvsroot/gmod/apollo/doc/chado
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv4876/doc/chado

Modified Files:
	transaction-todo 
Log Message:
got feature loc updates to transcripts working more or less. this was
tricky as the datamodel would propigate range changes up from exons to
transcripts and genes. and the datamodel cant be firing annot change
events and it was way too much to rip out of there. i contemplated
doing something with all the annotation editor methods that effect
range - but i went with actually cloning the ranges set selection time
and then comparing them after all the ops are done (this also cuts
down on a bunch of spurious range changes). this worked out pretty
well. need to do the same for genes and translation start and stop
(protein) - shouldnt be too bad. i didnt notice theres times when it
fires and it shouldnt - looking into that. so annotation change
coalescer (which should perhaps be renamed as it isnt really
coalescing much) is where the post analysis happens and it adds in the
range changes before it fires off all the events.



Index: transaction-todo
===================================================================
RCS file: /cvsroot/gmod/apollo/doc/chado/transaction-todo,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** transaction-todo	10 Nov 2004 22:27:21 -0000	1.20
--- transaction-todo	12 Nov 2004 23:16:39 -0000	1.21
***************
*** 3,12 ****
  ------------------------
  1)Limits need to be propigated from exon to trans and gene
  2)syn,dbxref,comments on trans & gene merges - is this happening on
! gene merge? (consolidateGenes())
! 3) name propigation on merges to exons (trans deleted)
  4) split gene - name propigation, limits, copy stuff(2)
  5) need to fire events when translation stop and/or start changes
  
  AE.splitGene!
  AE.genesMerged
--- 3,23 ----
  ------------------------
  1)Limits need to be propigated from exon to trans and gene
+ - bug - splitting exon in ede causing transcript limits event
  2)syn,dbxref,comments on trans & gene merges - is this happening on
! gene merge? (consolidateGenes(),copyTranscriptData())
! 3) name propigation on gene/trans merges to exons (trans deleted)
  4) split gene - name propigation, limits, copy stuff(2)
  5) need to fire events when translation stop and/or start changes
  
+ start stop of translation (protein start stop) - often effected by
+ other changes - do this as post processing step like feat locs?
+ should event be translation range rather than separate start and stop??
+ - frameShift effects stop (fired as single change)
+ - getLongestOrf fires start event but not stop event
+ 
+ 
+ moveExonsToTranscript geneMerge case needs examining - is this now
+ covered somewhere else?
+ 
  AE.splitGene!
  AE.genesMerged
***************
*** 16,19 ****
--- 27,32 ----
  transcript name or is it implicit?
  
+ check if old objects need cloning
+ 
  on transcript merge trans stop not being calculated
  
***************
*** 46,49 ****
--- 59,65 ----
  comments - undo
  
+ comment internal state has to be preserved - forget how - i think it
+ might have to appended to comment string itself??
+ 
  commit and cancel for comments?
  
***************
*** 99,102 ****
--- 115,127 ----
  ----------------------
  
+ addSearchHits in jdbc reader has to be parameterized so it can handle
+ both hits with feat locs(rice) and not(fly) - tigr?
+ 
+ jdbc read to game save loses search hits - i wonder if this is because
+ the data structure/heiracrchy is not the same or something like that
+ 
+ addSearchHits should do != with rank instead of srcfeat != as that
+ will filter out self hits
+ 
  redo?
  
***************
*** 118,121 ****
--- 143,152 ----
  5) trans -> chado xml -> xort to chado -> jdbc read -> check values
  from trans
+ 6) jdbc read -> game save -> game read (jdbc and game jibing)
+ 
+ test that gene and trans feat locs get updated properly on exon
+ changes
+ 
+ test that exons have names corresponding to new gene after merges
  
  if i add an exon to a trans that overlaps with another gene - but the