Issue 3810: section 2.1.9 (p. 2-24) BioSequence                                                                                                                                                                     (biomolecular-ftf)
Source: SciTegic Inc. (Scott Markel, Ph.D., smarkel@scitegic.com smarkel@san.rr.com)
Nature: Uncategorized Issue
Severity: 
Summary: section 2.1.9 (p. 2-24) BioSequence
seq_intervals()'s lone exception IntervalOutOfBounds is insufficient to
handle cases where the Interval is actually a SeqRegion that has an
invalid StrandType or SeqRegionOperator.

I suggest adding SeqRegionInvalid to cover this case.  I don't think we
need to add SeqRegionOutOfBounds; IntervalOutOfBounds seems sufficient
for coordinate problems.

Resolution: accepted
Revised Text: Add SeqRegionInvalid to the IDL for seq_interval(). Add

Raise SeqRegionInvalid if interval is a SeqRegion and has an incorrect StrandType or SeqRegionOperator. to the exception row in
the description box. Change the IDL in C.1.
Actions taken:
September 7, 2000: received issue
May 24, 2001: closed issue
Discussion: 

End of Annotations:=====
Date: Wed, 06 Sep 2000 16:12:18 -0700
From: Scott Markel <smarkel@netgenics.com>
Organization: NetGenics, Inc.
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To: BSA FTF <biomolecular-ftf@omg.org>
Subject: BSA issues
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Here are a few more BSA issues.  Most are small changes to the text
and
involve no IDL changes.


section 2.1.9 (p. 2-24) BioSequence
seq_intervals()'s lone exception IntervalOutOfBounds is insufficient
to
handle cases where the Interval is actually a SeqRegion that has an
invalid StrandType or SeqRegionOperator.

I suggest adding SeqRegionInvalid to cover this case.  I don't think
we
need to add SeqRegionOutOfBounds; IntervalOutOfBounds seems sufficient
for coordinate problems.

Date: Tue, 19 Sep 2000 20:21:40 -0700
From: Scott Markel <smarkel@netgenics.com>
Organization: NetGenics, Inc.
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To: BSA FTF <biomolecular-ftf@omg.org>
Subject: [OMG-BSA] proposed resolutions for some issues
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In accordance with the consensus at last week's FTF meeting, here are
the proposed resolutions for the issues that were considered
straightforward.  Note that as some multi-issue issues are split
apart,
some of those may also fall into this category.

I'm not reproducing the entire text of the individual issues.  You can
find that at http://cgi.omg.org/issues/biomolecular-ftf.html.  Issues
can
be reported online at http://www.omg.org/technology/issuesform.htm.

This message is *not* a vote.  I just want to make sure these
particular
issues are as straightforward as some of us thought last week.  Please
let me know if you disagree.  Actually it would be nice to know if you
agree, too. :)  If there's been no response by early next week (Philip
is out until then), I'll send out a message kicking off a vote.  If
there
are responses, hopefully we'll get the resolutions resolved and still
vote on these issues next week.

Scott

Issue 3810: section 2.1.9 (p. 2-24) BioSequence

Resolution: Add SeqRegionInvalid to the IDL for seq_interval().  Add

  Raise SeqRegionInvalid if interval is a SeqRegion and has an
  incorrect
  StrandType or SeqRegionOperator.

to the exception row in the description box.  Change the IDL in C.1.
-