[Gmod-apollo-cmts] CVS: apollo/doc/html dataadapter_cookbook.html,1.34,1.35

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

Update of /cvsroot/gmod/apollo/doc/html
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv20072/doc/html

Modified Files:
	dataadapter_cookbook.html 
Log Message:
updated dataadapter cookbook about ref seqs. added ref seq to sample
adapter - also took out annoying windows "^M". comment in feat set.



Index: dataadapter_cookbook.html
===================================================================
RCS file: /cvsroot/gmod/apollo/doc/html/dataadapter_cookbook.html,v
retrieving revision 1.34
retrieving revision 1.35
diff -C2 -d -r1.34 -r1.35
*** dataadapter_cookbook.html	29 Nov 2004 23:09:58 -0000	1.34
--- dataadapter_cookbook.html	30 Nov 2004 16:15:01 -0000	1.35
***************
*** 542,547 ****
  no boolean has an implicit false for this param.
  <p>
! Automatic figuring of start and stop will only happen if the curation
! sets ref sequence is set (see Sequence below)
  <br>
  <h3>Sequence</h3>
--- 542,559 ----
  no boolean has an implicit false for this param.
  <p>
! You have to set the transcripts reference sequence for translation
! stops and starts to work properly (especially the automatic
! setting). This is done with: 
! <p>
! transcript.setRefSequence(SequenceI mainGenomicSequence)
! <p>
! The sequence is usually (always?) the main genomic sequence. See
! "Sequence" below. 
! <p>
! I noticed the GAME adapter sets its exons ref sequence as well. Its
! unclear if this is necasary but it doesnt hurt. It seems the GAME
! adapter sets ref sequences for most or all of its features. (check out
! source src/java/apollo/dataadapter/gamexml/GAMEAdapter setRange method).
! 
  <br>
  <h3>Sequence</h3>