From charles.parnot at gmail.com Sun Mar 1 00:33:25 2009 From: charles.parnot at gmail.com (Charles Parnot) Date: Sat, 28 Feb 2009 21:33:25 -0800 Subject: [Biococoa-dev] BCSequence class cluster? [Was Re: Introducing myself] In-Reply-To: <8F232061-3981-4E5F-95D1-E0C713AA117E@mac.com> References: <8F232061-3981-4E5F-95D1-E0C713AA117E@mac.com> Message-ID: <8327B7A4-A0D1-4854-8BD3-34CA3AC4672A@gmail.com> Hi Scott, Thanks for all the good points! > * I think the mutable sequence is useful. It isn't very common > though as typically sequence data is considered to be ground truth > but I think it will become more so as people start doing in silico > experimentation, asking "what if" questions when the sequence is > mutated. This can be tricky to handle efficiently, but maybe we > would want to design the interface around the biological, i.e. SNPs, > insertions, deletions, inversions, duplications, etc. Yes, a mutable sequence is definitely very useful. But an immutable sequence is also very useful. Knowning that a sequence does not change allows for many optimizations and makes thread-safety much easier. Thus, it is good to have both, which I supposed is anyway what you gave in mind. FWIW, if I had to choose to choose only 1, it would be the immutable class. But there is no reason to stick to just 1 class. NSString/NSMutableString, NSArray/NSMutableArray, NSDIcitonary/ NSMutableDictionary, etc... all exist for a reason :-) charles -- OpenMacGrid Help science move fast forward: http://www.macresearch.org/openmacgrid Charles Parnot charles.parnot at gmail.com From craig at batemanspace.com Sun Mar 1 13:13:43 2009 From: craig at batemanspace.com (Craig Bateman) Date: Sun, 1 Mar 2009 10:13:43 -0800 Subject: [Biococoa-dev] BCSequence class cluster? [Was Re: Introducing myself] In-Reply-To: <58C5486C-A170-4F59-BC36-4D2EE8F4F35A@gmail.com> References: <8F232061-3981-4E5F-95D1-E0C713AA117E@mac.com> <58C5486C-A170-4F59-BC36-4D2EE8F4F35A@gmail.com> Message-ID: Might it have been a wrapper around NSArray so that the macros in BCInternal.h could be used for array access rather than making users of the toolkit call "ugly" macros for array handling? These are the macros that use NSArray, NSSet, etc. functions on GnuStep, but the CFArray & CFSet functions on a mac. On Feb 28, 2009, at 10:38 AM, Koen van der Drift wrote: > > On Feb 28, 2009, at 12:51 PM, Scott Christley wrote: >> >> * I'm not very enamored with the BCSequenceArray class. I'm not >> sure how it is any better than just using a standard NSArray, I >> tried looking in the archives for discussion but didn't really find >> anything. However my guess is that BCSequenceArray would somehow >> provide additional sequence specific functionality? Personally, I >> don't really want to treat BCSequence objects in any special way. >> I think its best if users can include into standard collections >> (NSArray, NSDictionary, NSSet) instead of having to use specialized >> collections. Thoughts? > > I think I added it to be a replacement for NSArray. I cannot really > think what any additional functionality could have been, if I > remember I'll post it here. > > >> >> * Craig makes a good point about being able to do -sequenceWithId: >> to lookup a sequence. One issue to be aware of is that the id's in >> the FASTA files are not necessarily unique. In fact, the >> definition of the sequences often lie outside of the fasta file. >> Now if you download from NCBI then you have a good chance of >> getting unique id's, but take UCSC's goldenPath for example. If >> you download the human genome from there, the id just says chr1, >> chr2, etc. Mix and match with another organism and you can quickly >> forget which chr goes with whom. >> So from this perspective, we need to be careful not to rely upon >> the id's being unique. Typically id's are unique within a file, >> but this would really have to be a contract that the user enforces, >> it is not part of the FASTA format. > > This is why we added the BCAnnotation and BCFeature classes. Most > data formats have different labels for name, sequence, authors, etc. > I think the idea was to make our own definitions (BSSequenceName, > BCSequenceAuthor, etc), and let BCSequenceReader take care of > putting the right annotation and or feature in combination wth the > actual sequence. > > - Koen. > > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/biococoa-dev > > From koenvanderdrift at gmail.com Sun Mar 1 14:10:03 2009 From: koenvanderdrift at gmail.com (Koen van der Drift) Date: Sun, 1 Mar 2009 14:10:03 -0500 Subject: [Biococoa-dev] BCSequence class cluster? [Was Re: Introducing myself] In-Reply-To: References: <8F232061-3981-4E5F-95D1-E0C713AA117E@mac.com> <58C5486C-A170-4F59-BC36-4D2EE8F4F35A@gmail.com> Message-ID: On Mar 1, 2009, at 1:13 PM, Craig Bateman wrote: > Might it have been a wrapper around NSArray so that the macros in > BCInternal.h could be used for array access rather than making users > of the toolkit call "ugly" macros for array handling? These are the > macros that use NSArray, NSSet, etc. functions on GnuStep, but the > CFArray & CFSet functions on a mac. Yes, I just looked at the code and that seems about right. So instead of addObject, we just have a wrapper method addSequence, which is I guess just a more suiable name. I also saw I never finished the removeSequence, and my comment seems a bit cryptic too. Feel free to go ahead to add stuff. - Koen. 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