Issue 3763: why no CosLifeCycle::LifeCycleObject for BioSequence ? (biomolecular-ftf) Source: (Mr. Philip Lijnzaad, p.lijnzaad@med.uu.nl) Nature: Uncategorized Issue Severity: Summary: CosLifeCycle::LifeCycleObject, but BioSequence itself does not ? Was this deemed to present too much constraints on BioSequence ? The problem that Fabien Campagne <campagne@inka.mssm.edu> notes with this is that a client of BioSequences can only call remove() on one of the sub-classes, not on an un-extended BioSequence itself, nor on a different sub-class that does not have a remove() operation (or maybe has it under a different name or whatever). He thinks this is bad design because without remove(), the client loose the option of trying to be cooperative in the resource management of the server. I have to agree on this point. Or is inheriting from LifeCycleObject not there mainly of remove() ? In that case, why the asymmetry between BioSequence and it's sub-class. Resolution: accepted Revised Text: Add LifeCycleObject dependence to Figure 2-9. Add a single sentence paragraph just before BioSequence IDL in section 2.1.9. BioSequence inherits from CosLifeCycle:LifeCycleObject. Add dependence in BioSequence IDL in section 2.1.9. Remove LifeCycleObject dependence in Figure 2-10. Remove LifeCycleObject sentence just before NucleotideSequence IDL in section 2.1.10. Remove LifeCycleObject dependence in IDL for NucleotideSequence in section 2.1.10. Remove LifeCycleObject sentence just before AminoAcidSequence IDL in section 2.1.10. Remove LifeCycleObject dependence in IDL for AminoAcidSequence in section 2.1.10. Change IDL in section C.1. Actions taken: July 21, 2000: received issue May 24, 2001: closed issue Discussion: End of Annotations:===== Date: Fri, 21 Jul 2000 17:53:28 +0100 (BST) Message-Id: <200007211653.e6LGrSA08278@o2-3.ebi.ac.uk> X-Authentication-Warning: o2-3.ebi.ac.uk: lijnzaad set sender to lijnzaad@ebi.ac.uk using -f From: Philip Lijnzaad To: biomolecular-ftf@omg.org Subject: why no CosLifeCycle::LifeCycleObject for BioSequence ? Reply-to: lijnzaad@ebi.ac.uk Content-Type: text X-UIDL: 2+&e9TFC!!ciE!!V2W!! Dear all, can anyone remember why NucleotideSequence and AminoAcidSequence inherit from CosLifeCycle::LifeCycleObject, but BioSequence itself does not ? Was this deemed to present too much constraints on BioSequence ? The problem that Fabien Campagne notes with this is that a client of BioSequences can only call remove() on one of the sub-classes, not on an un-extended BioSequence itself, nor on a different sub-class that does not have a remove() operation (or maybe has it under a different name or whatever). He thinks this is bad design because without remove(), the client loose the option of trying to be cooperative in the resource management of the server. I have to agree on this point. Or is inheriting from LifeCycleObject not there mainly of remove() ? In that case, why the asymmetry between BioSequence and it's sub-class. Cheers, Philip -- When C++ is your hammer, everything looks like a thumb. (Steven Haflich) ----------------------------------------------------------------------------- Philip Lijnzaad, lijnzaad@ebi.ac.uk \ European Bioinformatics Institute,rm A2-24 +44 (0)1223 49 4639 / Wellcome Trust Genome Campus, Hinxton +44 (0)1223 49 4468 (fax) \ Cambridgeshire CB10 1SD, GREAT BRITAIN PGP fingerprint: E1 03 BF 80 94 61 B6 FC 50 3D 1F 64 40 75 FB 53 From: "Dickson, Mike" To: "'lijnzaad@ebi.ac.uk'" , biomolecular-ftf@omg.org Subject: RE: why no CosLifeCycle::LifeCycleObject for BioSequence ? Date: Fri, 21 Jul 2000 13:37:53 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) Content-Type: text/plain; charset="iso-8859-1" X-UIDL: CB?e9aa"e9W+n!!57f!! I very much agree with Philip on this one. My recollection was that we were treating BioSequence as a kind of lightweight, abstract class defining common BioSeq behaviour. In reality, people will make objects of that type and so having the LifeCycle operations factored to that level makes sense (and seems like better design anyway). Mike > -----Original Message----- > From: Philip Lijnzaad [mailto:lijnzaad@ebi.ac.uk] > Sent: Friday, July 21, 2000 12:53 PM > To: biomolecular-ftf@omg.org > Subject: why no CosLifeCycle::LifeCycleObject for BioSequence ? > > > Dear all, > > can anyone remember why NucleotideSequence and > AminoAcidSequence inherit from > CosLifeCycle::LifeCycleObject, but BioSequence itself does not ? > > Was this deemed to present too much constraints on BioSequence ? > > The problem that Fabien Campagne > notes with this is > that a client of BioSequences can only call remove() on one of the > sub-classes, not on an un-extended BioSequence itself, nor on > a different > sub-class that does not have a remove() operation (or maybe > has it under a > different name or whatever). > > He thinks this is bad design because without remove(), the > client loose the > option of trying to be cooperative in the resource management of the > server. I have to agree on this point. > > Or is inheriting from LifeCycleObject not there mainly of > remove() ? In that > case, why the asymmetry between BioSequence and it's sub-class. > > > Cheers, > > > Philip > -- > When C++ is your hammer, everything looks like a thumb. > (Steven Haflich) > -------------------------------------------------------------- > --------------- > Philip Lijnzaad, lijnzaad@ebi.ac.uk \ European Bioinformatics > Institute,rm A2-24 > +44 (0)1223 49 4639 / Wellcome Trust Genome > Campus, Hinxton > +44 (0)1223 49 4468 (fax) \ Cambridgeshire CB10 > 1SD, GREAT BRITAIN > PGP fingerprint: E1 03 BF 80 94 61 B6 FC 50 3D 1F 64 40 75 FB 53 > 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 3763: why no CosLifeCycle::LifeCycleObject for BioSequence ? Resolution: Add LifeCycleObject dependence to Figure 2-9. Add a single sentence paragraph just before BioSequence IDL in section 2.1.9. BioSequence inherits from CosLifeCycle:LifeCycleObject. Add dependence in BioSequence IDL in section 2.1.9. Remove LifeCycleObject dependence in Figure 2-10. Remove LifeCycleObject sentence just before NucleotideSequence IDL in section 2.1.10. Remove LifeCycleObject dependence in IDL for NucleotideSequence in section 2.1.10. Remove LifeCycleObject sentence just before AminoAcidSequence IDL in section 2.1.10. Remove LifeCycleObject dependence in IDL for AminoAcidSequence in section 2.1.10. Change IDL in section C.1.