Issue 3874: add an Identifier to SeqRegion (biomolecular-ftf) Source: SciTegic Inc. (Scott Markel, Ph.D., smarkel@scitegic.com smarkel@san.rr.com) Nature: Uncategorized Issue Severity: Significant Summary: Please add an Identifier to SeqRegion so that a CompositeSeqRegion can span multiple BioSequences. Resolution: accepted Revised Text: Add "sequence Identifier" to the SeqRegion paragraph on p. 2-6 (section 2.1.5). Add "public Identifier id;" to the IDL on the bottom of the same page. Add a description block describing the ID as a sequence ID on p. 2-7. Update the IDL in appendix C.1. Actions taken: September 25, 2000: received issue May 24, 2001: closed issue Discussion: End of Annotations:===== From: webmaster@omg.org Message-Id: <200009251856.e8PIuMC04845@emerald.omg.org> Date: 25 Sep 2000 14:58:54 -0400 To: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Subject: Issue/Bug Report Content-Type: Text/html; charset=windows-1252 X-UIDL: Organization: NetGenics, Inc. X-Mailer: Mozilla 4.75 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: BSA FTF Subject: Re: issue 3874 -- Biomolecular FTF issue References: <4.2.0.58.20000928143542.04fdc320@emerald.omg.org> Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii X-UIDL: 2TB!!Zn=e9dld!!*>,!! Juergen Boldt wrote: > > This is issue # 3874 (Scott Markel, smarkel@netgenics.com ) > > add an Identifier to SeqRegion > > Please add an Identifier to SeqRegion so that a CompositeSeqRegion can span > multiple BioSequences. Proposed resolution: Add "sequence Identifier" to the SeqRegion paragraph on p. 2-6 (section 2.1.5). Add "public Identifier id;" to the IDL on the bottom of the same page. Add a description block describing the ID as a sequence ID on p. 2-7. Update the IDL in appendix C.1. Scott -- Scott Markel, Ph.D. NetGenics, Inc. smarkel@netgenics.com 4350 Executive Drive Tel: 858 455 5223 Suite 260 FAX: 858 455 1388 San Diego, CA 92121 Date: Tue, 17 Oct 2000 16:16:08 -0700 From: Scott Markel Organization: NetGenics, Inc. X-Mailer: Mozilla 4.75 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: BSA FTF Subject: [OMG-BSA] proposed resolutions #3 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii X-UIDL: ZGd!!Y64e9e!gd9$Z6!! Here's a third batch of proposed resolutions. Based on email traffic there seems to be a consensus on the proposals. In a few cases the consensus is 2 of 3. In most cases it's 2 of 2. I'm not reproducing the entire text of the individual issues. You can find that at http://cgi.omg.org/issues/biomolecular-ftf.html. This message is *not* a vote. I plan to send out a message kicking off a vote probably on Friday. The timing depends on the responses to this message. Scott ======================================================================== Issue 3870: typedef sequence IntervalList; is missing from the spec Proposed resolution: No change. CompositeSeqRegion already has this behavior. ------------------------------------------------------------------------ Issue 3871: IntervalList get_gaps(in AlignmentElement element, in Interval the_interval Proposed resolution: Add CompositeSeqRegion get_gaps(in string key, in Interval the_interval) raises(ElementNotInAlignment, IntervalOutOfBounds); to the Alignment interface (section 2.1.15, IDL change on p. 2-43 and method block on p. 2-46). Update the IDL in appendix C.1. The coordinates of a gap would be those of the original sequence; gaps of length 0 are not allowed. A start == 0 would be before the first nucleotide/aminoacid; a start = N is a gap between nucleotides/aminoacids N and N+1 (so start = sequence.length would be after the last). ------------------------------------------------------------------------ Issue 3872: Separate the Alignment interface into more managable pieces Proposed resolution: No change. ------------------------------------------------------------------------ Issue 3874: add an Identifier to SeqRegion Proposed resolution: Add "sequence Identifier" to the SeqRegion paragraph on p. 2-6 (section 2.1.5). Add "public Identifier id;" to the IDL on the bottom of the same page. Add a description block describing the ID as a sequence ID on p. 2-7. Update the IDL in appendix C.1. ------------------------------------------------------------------------ Issue 3875: inheritance in annotation iterators Proposed resolution: Add the following to the single sentence description in section 2.1.7 (p. 2-15) SeqAnnotationIterator is not used directly in this specification, but is provided as a convenience for vendor-specific IDL extensions and future OMG specifications where a collection of Annotations contains only SeqAnnotations. SeqAnnotationIterator is an optional interface. In addition, add SeqAnnotationIterator to the list of optional interfaces in section 1.1 (p. 1-1). ------------------------------------------------------------------------ Issue 3924: octet iterator Proposed resolution: Out of scope. ------------------------------------------------------------------------ Issue 3962: clarification of strand_type and CompositeSeqRegions Proposed resolution: Add the following to the first paragraph under CompositeSeqRegion (section 2.1.5, p. 2-7) and to region_operator's description (section 2.1.5, p. 2-8). All CompositeSeqRegions are expected to be translated in a depth-first traversal, along each node of the tree represented by the CompositeSeqRegions. This includes those nodes that have region_operator equal to JOIN or ORDER. Add the following to the descriptions of BioSequence's seq_interval() (section 2.1.9, p. 2-24) and NucleotideSequence's translate_seq_region() (section 2.1.10, p. 2-30). If the StrandType is minus, the string returned should be taken as reverse-complemented. Add the following to the description of NucleotideSequence's reverse_complement_interval() (section 2.1.10, p. 2-28). If the StrandType is minus, the string returned should be taken as reverse-complemented. This will result in a no-op, i.e., the strand_type leads to reverse-complementing, which is then reverse-complementing due to the semantics of the method, resulting in the same string that would be returned from seq_interval(). ------------------------------------------------------------------------ Issue 3963: clarification of SeqRegionOperator.ORDER Proposed resolution: Add the following to the description of the enum SeqRegionOperator's ORDER value (section 2.1.5, p. 2-8). Typically, it is used to represent a discontinuous region to which a descriptive annotation pertains. ------------------------------------------------------------------------ Issue 3964: OutOfBounds exceptions for circular sequences if start = 0 Proposed resolution: Add text similar to the following (BioSequence and Interval replaced by derived types, as appropriate) to the descriptions of * IntervalOutOfBounds (section 2.1.9, p. 2-21) * SeqRegionOutOfBounds (section 2.1.9, p. 2-21) * SeqAnnotationOutOfBounds (section 2.1.23, p. 2-63) and to the exceptions of * BioSequence's seq_interval() (section 2.1.9, p. 2-24) * NucleotideSequence's reverse_complement_interval() (section * 2.1.10, p. 2-28) * NucleotideSequence's translate_seq_region() (section 2.1.10, p. 2-30) Raises IntervalOutOfBounds if the Interval's start is less than 1 or if its start+length-1 is greater than the length of the BioSequence. If a BioSequence represents circular DNA, then this exception should be raised if the Interval's start is less than 1 or greater than the length of the BioSequence, or if its length is greater than the length of the BioSequence. ------------------------------------------------------------------------ Issue 3965: add BioSequence.get_annotations_by_name()? Proposed resolution: Out of scope. ------------------------------------------------------------------------ -- Scott Markel, Ph.D. NetGenics, Inc. smarkel@netgenics.com 4350 Executive Drive Tel: 858 455 5223 Suite 260 FAX: 858 455 1388 San Diego, CA 92121