Issue 3811: section 2.1.9 (p. 2-25) 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. 2-25) BioSequence The descriptions for both get_annotations() and num_annotations() need to be made more precise. Change Only the SeqAnnotations that overlap seq_region will be returned. to Only the SeqAnnotations that overlap seq_region and have compatible StrandTypes will be returned. Add the following tables. BioSequence Type Valid StrandTypes BioSequence STRAND_NOT_KNOWN NucleotideSequence STRAND_NOT_KNOWN,STRAND_PLUS,STRAND_MINUS, STRAND_BOTH AminoAcidSequence STRAND_NOT_APPLICABLE StrandType Matching StrandTypes STRAND_NOT_KNOWN STRAND_NOT_KNOWN, STRAND_PLUS, STRAND_MINUS, STRAND_BOTH STRAND_NOT_APPLICABLE STRAND_NOT_APPLICABLE STRAND_PLUS STRAND_NOT_KNOWN, STRAND_PLUS, STRAND_BOTH STRAND_MINUS STRAND_NOT_KNOWN, STRAND_MINUS, STRAND_BOTH STRAND_BOTH STRAND_NOT_KNOWN, STRAND_PLUS, STRAND_MINUS, STRAND_BOTH Resolution: accepted Revised Text: Change the descriptions for both get_annotations() and num_annotations() from Only the SeqAnnotations that overlap seq_region will be returned. to Only the SeqAnnotations that overlap seq_region and have compatible StrandTypes will be returned. Add the following tables. BioSequence Type Valid StrandTypes BioSequence STRAND_NOT_KNOWN NucleotideSequence STRAND_NOT_KNOWN, STRAND_PLUS, STRAND_MINUS, STRAND_BOTH AminoAcidSequence STRAND_NOT_APPLICABLE StrandType Matching StrandTypes STRAND_NOT_KNOWN STRAND_NOT_KNOWN, STRAND_PLUS, STRAND_MINUS, STRAND_BOTH STRAND_NOT_APPLICABLE STRAND_NOT_APPLICABLE STRAND_PLUS STRAND_NOT_KNOWN, STRAND_PLUS, STRAND_BOTH STRAND_MINUS STRAND_NOT_KNOWN, STRAND_MINUS, STRAND_BOTH STRAND_BOTH STRAND_NOT_KNOWN, STRAND_PLUS, STRAND_MINUS, STRAND_BOTH 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 Organization: NetGenics, Inc. X-Mailer: Mozilla 4.73 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: BSA FTF Subject: BSA issues Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii X-UIDL: ,9D!!)j)e9)gL!!f^W!! Here are a few more BSA issues. Most are small changes to the text and involve no IDL changes. section 2.1.9 (p. 2-25) BioSequence The descriptions for both get_annotations() and num_annotations() need to be made more precise. Change Only the SeqAnnotations that overlap seq_region will be returned. to Only the SeqAnnotations that overlap seq_region and have compatible StrandTypes will be returned. Add the following tables. BioSequence Type Valid StrandTypes BioSequence STRAND_NOT_KNOWN NucleotideSequence STRAND_NOT_KNOWN,STRAND_PLUS,STRAND_MINUS, STRAND_BOTH AminoAcidSequence STRAND_NOT_APPLICABLE StrandType Matching StrandTypes STRAND_NOT_KNOWN STRAND_NOT_KNOWN, STRAND_PLUS, STRAND_MINUS, STRAND_BOTH STRAND_NOT_APPLICABLE STRAND_NOT_APPLICABLE STRAND_PLUS STRAND_NOT_KNOWN, STRAND_PLUS, STRAND_BOTH STRAND_MINUS STRAND_NOT_KNOWN, STRAND_MINUS, STRAND_BOTH STRAND_BOTH STRAND_NOT_KNOWN, STRAND_PLUS, STRAND_MINUS, STRAND_BOTH Date: Tue, 19 Sep 2000 20:21:40 -0700 From: Scott Markel Organization: NetGenics, Inc. X-Mailer: Mozilla 4.73 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: BSA FTF Subject: [OMG-BSA] proposed resolutions for some issues Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii X-UIDL: W9!e9QLE!!'Okd9>SPe9 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 3811: section 2.1.9 (p. 2-25) BioSequence Resolution: Change the descriptions for both get_annotations() and num_annotations() from Only the SeqAnnotations that overlap seq_region will be returned. to Only the SeqAnnotations that overlap seq_region and have compatible StrandTypes will be returned. Add the following tables. BioSequence Type Valid StrandTypes BioSequence STRAND_NOT_KNOWN NucleotideSequence STRAND_NOT_KNOWN,STRAND_PLUS,STRAND_MINUS, STRAND_BOTH AminoAcidSequence STRAND_NOT_APPLICABLE StrandType Matching StrandTypes STRAND_NOT_KNOWN STRAND_NOT_KNOWN, STRAND_PLUS, STRAND_MINUS, STRAND_BOTH STRAND_NOT_APPLICABLE STRAND_NOT_APPLICABLE STRAND_PLUS STRAND_NOT_KNOWN, STRAND_PLUS, STRAND_BOTH STRAND_MINUS STRAND_NOT_KNOWN, STRAND_MINUS, STRAND_BOTH STRAND_BOTH STRAND_NOT_KNOWN, STRAND_PLUS, STRAND_MINUS, STRAND_BOTH