From Valentine at hall-mark.us Wed Apr 1 05:06:50 2009 From: Valentine at hall-mark.us (hallmark.com) Date: Wed, 01 Apr 2009 09:06:50 +0000 Subject: [Biococoa-dev] ***SPAM*** You've received A Hallmark Valentine-Card! Message-ID: An HTML attachment was scrubbed... URL: From Valentine at hall-mark.us Wed Apr 1 01:43:07 2009 From: Valentine at hall-mark.us (hallmark.com) Date: Wed, 01 Apr 2009 07:43:07 +0200 Subject: [Biococoa-dev] ***SPAM*** You've received A Hallmark Valentine-Card! Message-ID: An HTML attachment was scrubbed... URL: From stschiff80 at googlemail.com Wed Apr 1 06:05:00 2009 From: stschiff80 at googlemail.com (Stephan) Date: Wed, 1 Apr 2009 12:05:00 +0200 Subject: [Biococoa-dev] read Fasta File with gap symbols Message-ID: <01C0B30B-4F42-425E-8F38-A4FB1FAFC6F9@googlemail.com> Hi, I am new to BioCocoa and was wondering whether there is a way of parsing FASTA files that contain alignment-information, i.e. they include sequences with the gap-symbol "-". Right now, if I parse the file, the gaps are filtered out. Any sugguestions? Best, Stephan From schristley at mac.com Wed Apr 1 14:21:32 2009 From: schristley at mac.com (Scott Christley) Date: Wed, 01 Apr 2009 11:21:32 -0700 Subject: [Biococoa-dev] read Fasta File with gap symbols In-Reply-To: <01C0B30B-4F42-425E-8F38-A4FB1FAFC6F9@googlemail.com> References: <01C0B30B-4F42-425E-8F38-A4FB1FAFC6F9@googlemail.com> Message-ID: Hello Stephan, Yes this is an issue. BioCocoa attempts to determine the sequence type by looking at the symbols, once it makes a decision it strips any unknown symbols, of course it can make a wrong decision or more likely in your case, it considers the gap symbol as unknown. Unfortunately there isn't a direct workaround unless you are willing to make a modification to the BioCocoa source code, there are just a few lines you can comment out in BCSequence.m that will skip. I think BioCocoa probably needs to be changed so that it doesn't modify the sequence data at all, and the user is responsible for initiating a sequence type check and/or filtering. cheers Scott On Apr 1, 2009, at 3:05 AM, Stephan wrote: > Hi, > > I am new to BioCocoa and was wondering whether there is a way of > parsing FASTA files that contain alignment-information, i.e. they > include sequences with the gap-symbol "-". > Right now, if I parse the file, the gaps are filtered out. > > Any sugguestions? > > Best, > Stephan > > > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/biococoa-dev From stschiff80 at googlemail.com Wed Apr 1 15:10:12 2009 From: stschiff80 at googlemail.com (Stephan) Date: Wed, 1 Apr 2009 21:10:12 +0200 Subject: [Biococoa-dev] read Fasta File with gap symbols In-Reply-To: References: <01C0B30B-4F42-425E-8F38-A4FB1FAFC6F9@googlemail.com> Message-ID: Hi Scott, Thank you for answering. In fact I looked through the code and found a workaround in the BioCocoa Source Code. One more question: The newest version of BioCocoa is not Mac OS X Tiger compatible... is that right? Actually, I wanted to ask how active the community is right now... I might be able to contribute something to the project. I am working in the bioinformatics field and just digging into Cocoa (coming from C++ and python). How easy/hard is it to get a developer account? Also I could help updating the webpage or writing some more tutorials... Best, Stephan Am 01.04.2009 um 20:21 schrieb Scott Christley: > Hello Stephan, > > Yes this is an issue. BioCocoa attempts to determine the sequence > type by looking at the symbols, once it makes a decision it strips > any unknown symbols, of course it can make a wrong decision or more > likely in your case, it considers the gap symbol as unknown. > > Unfortunately there isn't a direct workaround unless you are > willing to make a modification to the BioCocoa source code, there > are just a few lines you can comment out in BCSequence.m that will > skip. > > I think BioCocoa probably needs to be changed so that it doesn't > modify the sequence data at all, and the user is responsible for > initiating a sequence type check and/or filtering. > > cheers > Scott > > On Apr 1, 2009, at 3:05 AM, Stephan wrote: > >> Hi, >> >> I am new to BioCocoa and was wondering whether there is a way of >> parsing FASTA files that contain alignment-information, i.e. they >> include sequences with the gap-symbol "-". >> Right now, if I parse the file, the gaps are filtered out. >> >> Any sugguestions? >> >> Best, >> Stephan >> >> >> >> _______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/biococoa-dev > From schristley at mac.com Wed Apr 1 15:34:48 2009 From: schristley at mac.com (Scott Christley) Date: Wed, 01 Apr 2009 12:34:48 -0700 Subject: [Biococoa-dev] read Fasta File with gap symbols In-Reply-To: References: <01C0B30B-4F42-425E-8F38-A4FB1FAFC6F9@googlemail.com> Message-ID: <106233E8-D076-46AD-9B53-66CC352DCB42@mac.com> On Apr 1, 2009, at 12:10 PM, Stephan wrote: > Hi Scott, > > Thank you for answering. > In fact I looked through the code and found a workaround in the > BioCocoa Source Code. Ok, cool, I imagine you commented out some code? I think a more permanent correct fix shouldn't be too difficult to implement. > One more question: The newest version of BioCocoa is not Mac OS X > Tiger compatible... is that right? I don't think there is anything preventing it, i.e. we are not using any Leopard specific functionality, it just may be how the current Xcode project settings are defined. You might give it a try. > Actually, I wanted to ask how active the community is right now... I > might be able to contribute something to the project. I am working > in the bioinformatics field and just digging into Cocoa (coming from > C++ and python). How easy/hard is it to get a developer account? > Also I could help updating the webpage or writing some more > tutorials... Well, there was a flurry of activity in the beginning, before I joined the project, but most people have moved on to other projects, though many continue to lurk on the mailing list. But no truthfully there really isn't much activity. I too work in bioinformatics, and I love ObjC, so BioCocoa is perfect for me to place my code where others can use; however I spend about 80% of my time doing research and only 20% coding, so my contributions come in spurts. One thing I would like for BioCocoa is not for it to just re-implement much of what is in (say) bioperl or biopython, ok reading sequence files is fine, but some good analysis algorithms or data structures would help set BioCocoa apart. But really that is my preference, any contributions are welcome, and getting a developer account is easy. What area of bioinformatics do you work in? cheers Scott From craig.bateman at gmail.com Wed Apr 1 20:19:14 2009 From: craig.bateman at gmail.com (Craig Bateman) Date: Wed, 1 Apr 2009 17:19:14 -0700 Subject: [Biococoa-dev] read Fasta File with gap symbols In-Reply-To: References: <01C0B30B-4F42-425E-8F38-A4FB1FAFC6F9@googlemail.com> Message-ID: I was going to recommend (or at least ask permission) to omit that very code while I'm working on the file-based vs memory-based sequence classes. Unfortunately, things have been very crazy at work for the last 2 months, so I haven't had the time I'd like to work on this. I only have skeletons of the new BCSequence class cluster together, but I was not finding an easy way to filter the file-based sequences like the memory-based ones are at init time. Omitting that code from the library is a breaking change... So it's probably not going to be well-received by any end-users. I have not heard back from Peter Schols regarding repository access. I would really like to branch the source and check-in on a regular basis. Is there anyone else that can grant this access? If not to the trunk, at least to a branched folder? On Wed, Apr 1, 2009 at 11:21 AM, Scott Christley wrote: > Hello Stephan, > > Yes this is an issue. BioCocoa attempts to determine the sequence type by > looking at the symbols, once it makes a decision it strips any unknown > symbols, of course it can make a wrong decision or more likely in your case, > it considers the gap symbol as unknown. > > Unfortunately there isn't a direct workaround unless you are willing to > make a modification to the BioCocoa source code, there are just a few lines > you can comment out in BCSequence.m that will skip. > > I think BioCocoa probably needs to be changed so that it doesn't modify the > sequence data at all, and the user is responsible for initiating a sequence > type check and/or filtering. > > cheers > Scott > > > On Apr 1, 2009, at 3:05 AM, Stephan wrote: > > Hi, >> >> I am new to BioCocoa and was wondering whether there is a way of parsing >> FASTA files that contain alignment-information, i.e. they include sequences >> with the gap-symbol "-". >> Right now, if I parse the file, the gaps are filtered out. >> >> Any sugguestions? >> >> Best, >> Stephan >> >> >> >> _______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/biococoa-dev >> > > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/biococoa-dev > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From schristley at mac.com Wed Apr 1 20:43:52 2009 From: schristley at mac.com (Scott Christley) Date: Wed, 01 Apr 2009 17:43:52 -0700 Subject: [Biococoa-dev] read Fasta File with gap symbols In-Reply-To: References: <01C0B30B-4F42-425E-8F38-A4FB1FAFC6F9@googlemail.com> Message-ID: On Apr 1, 2009, at 5:19 PM, Craig Bateman wrote: > I was going to recommend (or at least ask permission) to omit that > very code while I'm working on the file-based vs memory-based > sequence classes. Unfortunately, things have been very crazy at > work for the last 2 months, so I haven't had the time I'd like to > work on this. I only have skeletons of the new BCSequence class > cluster together, but I was not finding an easy way to filter the > file-based sequences like the memory-based ones are at init time. > Omitting that code from the library is a breaking change... So it's > probably not going to be well-received by any end-users. Yes, it doesn't seem reasonable to filter file-based sequences. It's a bit unclear to me why blindly removing symbols is considered acceptable behavior in the first place. I can see from a contract standpoint, the SymbolSet guarantees to algorithms working on the sequence, that they will only see a particular set of symbols, this is useful. However, the idea of "guessing" a symbol set then removing symbols which doesn't conform, doesn't make much sense to me, especially with how simplistic the "guessing" code is. What seems more reasonable is that you don't guess, you scan the sequence and construct a symbol set, if that symbol set matches a standard one, great, otherwise you have a unique symbol set that goes with that sequence. > I have not heard back from Peter Schols regarding repository > access. I would really like to branch the source and check-in on a > regular basis. Is there anyone else that can grant this access? If > not to the trunk, at least to a branched folder? I have admin access; if you give me your bioinformatics.org account name then I can add you to the project. Yes please, check in what you have done, a branch is fine too if your work is in an intermediate state. Scott From koenvanderdrift at gmail.com Wed Apr 1 22:45:17 2009 From: koenvanderdrift at gmail.com (Koen van der Drift) Date: Wed, 1 Apr 2009 22:45:17 -0400 Subject: [Biococoa-dev] read Fasta File with gap symbols In-Reply-To: References: <01C0B30B-4F42-425E-8F38-A4FB1FAFC6F9@googlemail.com> Message-ID: On Apr 1, 2009, at 8:43 PM, Scott Christley wrote: > Yes, it doesn't seem reasonable to filter file-based sequences. > It's a bit unclear to me why blindly removing symbols is considered > acceptable behavior in the first place. I suspect that's a 'work in progress' leftover :) One possible solution could also be to use a symbolset that takes into account gaps. - Koen. From stschiff80 at googlemail.com Thu Apr 2 03:28:22 2009 From: stschiff80 at googlemail.com (Stephan) Date: Thu, 2 Apr 2009 09:28:22 +0200 Subject: [Biococoa-dev] Fwd: read Fasta File with gap symbols References: Message-ID: Oops, forgot to add the mailing-list as recipient. Anfang der weitergeleiteten E-Mail: > Von: Stephan > Datum: 2. April 2009 09:26:50 MESZ > An: Scott Christley > Betreff: Re: [Biococoa-dev] read Fasta File with gap symbols > > > Am 01.04.2009 um 21:34 schrieb Scott Christley: > >> >> On Apr 1, 2009, at 12:10 PM, Stephan wrote: >> >>> Hi Scott, >>> >>> Thank you for answering. >>> In fact I looked through the code and found a workaround in the >>> BioCocoa Source Code. >> >> Ok, cool, I imagine you commented out some code? I think a more >> permanent correct fix shouldn't be too difficult to implement. >> > No, I actually just added the gap-character to lines 200 and 209 of > BCSymbolSet.m. That is the definition of the dnaSymbolSet and the > dnaStrictSymbolSet. I tried some more stuff before, such as > defining my own symbolset and pushing it as parameter to the > BCSequenceReader. I figured, however, as you guys already pointed > out, we need something more general to change there, and this > workaround was quick :-) > > >> >>> One more question: The newest version of BioCocoa is not Mac OS X >>> Tiger compatible... is that right? >> >> I don't think there is anything preventing it, i.e. we are not >> using any Leopard specific functionality, it just may be how the >> current Xcode project settings are defined. You might give it a try. > > Well, it seems there are some errors. So on Tiger, first of all I > had to modify the settings (the "architectures"-variable). When I > then tried to compile, I have errors occurring in line 126 of > BCUtilStrings.m. It does not understand the NSUIntger-type... I > dont know why that is, I have been coding in Cocoa too recently. > When I hacked around this by changing those lines to "unsigned int" > or something, there were other mistakes. The BioCocoa-2.0 - branch > does not have that issue. Any hints? > >> >> >>> Actually, I wanted to ask how active the community is right >>> now... I might be able to contribute something to the project. I >>> am working in the bioinformatics field and just digging into >>> Cocoa (coming from C++ and python). How easy/hard is it to get a >>> developer account? Also I could help updating the webpage or >>> writing some more tutorials... >> >> Well, there was a flurry of activity in the beginning, before I >> joined the project, but most people have moved on to other >> projects, though many continue to lurk on the mailing list. But >> no truthfully there really isn't much activity. I too work in >> bioinformatics, and I love ObjC, so BioCocoa is perfect for me to >> place my code where others can use; however I spend about 80% of >> my time doing research and only 20% coding, so my contributions >> come in spurts. > Right, 80% - 20% is about the same for me. > >> >> One thing I would like for BioCocoa is not for it to just re- >> implement much of what is in (say) bioperl or biopython, ok >> reading sequence files is fine, but some good analysis algorithms >> or data structures would help set BioCocoa apart. But really that >> is my preference, any contributions are welcome, and getting a >> developer account is easy. What area of bioinformatics do you >> work in? > > I am actually a theoretical physicist, but I am doing my PhD in > BioPhysics and currently working on Population genetics and - > genomics. I am developing code for both simulation programs and > data analysis tools. > > cheers, > Stephan > >> >> cheers >> Scott >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stschiff80 at googlemail.com Thu Apr 2 03:35:59 2009 From: stschiff80 at googlemail.com (Stephan) Date: Thu, 2 Apr 2009 09:35:59 +0200 Subject: [Biococoa-dev] read Fasta File with gap symbols In-Reply-To: <106233E8-D076-46AD-9B53-66CC352DCB42@mac.com> References: <01C0B30B-4F42-425E-8F38-A4FB1FAFC6F9@googlemail.com> <106233E8-D076-46AD-9B53-66CC352DCB42@mac.com> Message-ID: Am 01.04.2009 um 21:34 schrieb Scott Christley: > > On Apr 1, 2009, at 12:10 PM, Stephan wrote: > >> Hi Scott, >> >> Thank you for answering. >> In fact I looked through the code and found a workaround in the >> BioCocoa Source Code. > > Ok, cool, I imagine you commented out some code? I think a more > permanent correct fix shouldn't be too difficult to implement. > > >> One more question: The newest version of BioCocoa is not Mac OS X >> Tiger compatible... is that right? > > I don't think there is anything preventing it, i.e. we are not > using any Leopard specific functionality, it just may be how the > current Xcode project settings are defined. You might give it a try. > I found the problem. The newest BioCocoa trunk needs the Mac OS X 10.5 SDK. Stuff like NSUInteger from the Foundation-framework is not defined in previous SDKs... too bad, seems like I really have to upgrade my MacBook to Leopard then... > >> Actually, I wanted to ask how active the community is right now... >> I might be able to contribute something to the project. I am >> working in the bioinformatics field and just digging into Cocoa >> (coming from C++ and python). How easy/hard is it to get a >> developer account? Also I could help updating the webpage or >> writing some more tutorials... > > Well, there was a flurry of activity in the beginning, before I > joined the project, but most people have moved on to other > projects, though many continue to lurk on the mailing list. But no > truthfully there really isn't much activity. I too work in > bioinformatics, and I love ObjC, so BioCocoa is perfect for me to > place my code where others can use; however I spend about 80% of my > time doing research and only 20% coding, so my contributions come > in spurts. > > One thing I would like for BioCocoa is not for it to just re- > implement much of what is in (say) bioperl or biopython, ok reading > sequence files is fine, but some good analysis algorithms or data > structures would help set BioCocoa apart. But really that is my > preference, any contributions are welcome, and getting a developer > account is easy. What area of bioinformatics do you work in? > > cheers > Scott > From koenvanderdrift at gmail.com Thu Apr 2 07:41:28 2009 From: koenvanderdrift at gmail.com (Koen van der Drift) Date: Thu, 2 Apr 2009 07:41:28 -0400 Subject: [Biococoa-dev] read Fasta File with gap symbols In-Reply-To: References: <01C0B30B-4F42-425E-8F38-A4FB1FAFC6F9@googlemail.com> <106233E8-D076-46AD-9B53-66CC352DCB42@mac.com> Message-ID: <5cba6b9f0904020441n14d8223bu704f795a4526bef3@mail.gmail.com> > I found the problem. The newest BioCocoa trunk needs the Mac OS X 10.5 SDK. > Stuff like NSUInteger from the Foundation-framework is not defined in > previous SDKs... too bad, seems like I really have to upgrade my MacBook to > Leopard then... Hmm, that's not good, BioCocoa should be backward compatible at least one OS. Where is this NSUInteger used, can it be replaced by something else? - Koen. From mekentosj at gmail.com Thu Apr 2 07:44:48 2009 From: mekentosj at gmail.com (Alexander Griekspoor) Date: Thu, 2 Apr 2009 12:44:48 +0100 Subject: [Biococoa-dev] read Fasta File with gap symbols In-Reply-To: <5cba6b9f0904020441n14d8223bu704f795a4526bef3@mail.gmail.com> References: <01C0B30B-4F42-425E-8F38-A4FB1FAFC6F9@googlemail.com> <106233E8-D076-46AD-9B53-66CC352DCB42@mac.com> <5cba6b9f0904020441n14d8223bu704f795a4526bef3@mail.gmail.com> Message-ID: <8f2fa3f0904020444s3652b36apf634dd5acd176347@mail.gmail.com> Instead of trying to remove it, the alternative is to simply add: #ifndef NSInteger typedef int NSInteger; #endif #ifndef NSUInteger typedef unsigned int NSUInteger; #endif #ifndef CGFloat typedef float CGFloat; #endif On Thu, Apr 2, 2009 at 12:41 PM, Koen van der Drift wrote: >> I found the problem. The newest BioCocoa trunk needs the Mac OS X 10.5 SDK. >> Stuff like NSUInteger from the Foundation-framework is not defined in >> previous SDKs... too bad, seems like I really have to upgrade my MacBook to >> Leopard then... > > Hmm, that's not good, BioCocoa should be backward compatible at least > one OS. Where is this NSUInteger used, can it be replaced by something > else? > > - Koen. > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/biococoa-dev > > __________________________________________________ > D O T E A S Y - "Join the web hosting revolution!" > ? ? ? ? ? ? http://www.doteasy.com > -- **************************************************** ** Alexander Griekspoor PhD ** **************************************************** mekentosj.com Papers - Your Personal Library of Science 2007 Winner of the Apple Design Awards Best Mac OS X Scientific Solution http://www.mekentosj.com/papers **************************************************** From schristley at mac.com Thu Apr 2 14:52:15 2009 From: schristley at mac.com (Scott Christley) Date: Thu, 02 Apr 2009 11:52:15 -0700 Subject: [Biococoa-dev] read Fasta File with gap symbols In-Reply-To: References: <01C0B30B-4F42-425E-8F38-A4FB1FAFC6F9@googlemail.com> <106233E8-D076-46AD-9B53-66CC352DCB42@mac.com> Message-ID: <1092207A-6850-453C-B5FD-B3D9FB0C3A7E@mac.com> On Apr 2, 2009, at 12:35 AM, Stephan wrote: > I found the problem. The newest BioCocoa trunk needs the Mac OS X > 10.5 SDK. Stuff like NSUInteger from the Foundation-framework is not > defined in previous SDKs... too bad, seems like I really have to > upgrade my MacBook to Leopard then... Okay, yeah, that triggered a memory cell. With Leopard, Cocoa goes 64- bit so they introduced these NSUInteger types to manage quad-fat compilation. Alexander's typedefs should do the trick, can you try? Add the typedefs to the BCInternal.h file, then have BCUtilStrings.m include BCInternal.h if it isn't already. thanks Scott From stschiff80 at googlemail.com Fri Apr 3 04:24:09 2009 From: stschiff80 at googlemail.com (Stephan) Date: Fri, 3 Apr 2009 10:24:09 +0200 Subject: [Biococoa-dev] read Fasta File with gap symbols In-Reply-To: <8f2fa3f0904020444s3652b36apf634dd5acd176347@mail.gmail.com> References: <01C0B30B-4F42-425E-8F38-A4FB1FAFC6F9@googlemail.com> <106233E8-D076-46AD-9B53-66CC352DCB42@mac.com> <5cba6b9f0904020441n14d8223bu704f795a4526bef3@mail.gmail.com> <8f2fa3f0904020444s3652b36apf634dd5acd176347@mail.gmail.com> Message-ID: Hi Alexander... the typdefs worked. Thanks for this very nice solution! I put them into BCInternal.h as Scott suggested. I dont have an account on the svn repo, so can't upload that. Stephan Am 02.04.2009 um 13:44 schrieb Alexander Griekspoor: > Instead of trying to remove it, the alternative is to simply add: > > #ifndef NSInteger > typedef int NSInteger; > #endif > > #ifndef NSUInteger > typedef unsigned int NSUInteger; > #endif > > #ifndef CGFloat > typedef float CGFloat; > #endif > > > > On Thu, Apr 2, 2009 at 12:41 PM, Koen van der Drift > wrote: >>> I found the problem. The newest BioCocoa trunk needs the Mac OS X >>> 10.5 SDK. >>> Stuff like NSUInteger from the Foundation-framework is not defined >>> in >>> previous SDKs... too bad, seems like I really have to upgrade my >>> MacBook to >>> Leopard then... >> >> Hmm, that's not good, BioCocoa should be backward compatible at least >> one OS. Where is this NSUInteger used, can it be replaced by >> something >> else? >> >> - Koen. >> >> _______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/biococoa-dev >> >> __________________________________________________ >> D O T E A S Y - "Join the web hosting revolution!" >> http://www.doteasy.com >> > > > > -- > > **************************************************** > ** Alexander Griekspoor PhD ** > **************************************************** > mekentosj.com > > Papers - Your Personal Library of Science > 2007 Winner of the Apple Design Awards > Best Mac OS X Scientific Solution > http://www.mekentosj.com/papers > **************************************************** From stschiff80 at googlemail.com Fri Apr 3 06:26:48 2009 From: stschiff80 at googlemail.com (Stephan) Date: Fri, 3 Apr 2009 12:26:48 +0200 Subject: [Biococoa-dev] CachedSequenceFile Message-ID: <971E363E-8323-4E7E-B93B-94C7C3969087@googlemail.com> Hi, I am just looking through the implementation of BCCachedSequenceFile. It seems to be not ready yet, and the last modifications according to the svn log are from 2007... any further plans on that? Stephan From stschiff80 at googlemail.com Fri Apr 3 08:06:40 2009 From: stschiff80 at googlemail.com (Stephan) Date: Fri, 3 Apr 2009 14:06:40 +0200 Subject: [Biococoa-dev] Fwd: CachedSequenceFile References: <971E363E-8323-4E7E-B93B-94C7C3969087@googlemail.com> Message-ID: <072985D1-E061-4C3E-A2D2-F4C5F9B3B2A7@googlemail.com> Ah, I was confused. The inferface of BCCachedFastFile does not include the symbol-method-declarations. But they are actually overriden in the implementation. Is that on purpose? I didn't even know it's possible to override a method just in the implementation, without declaring it in the inferface... Stephan Anfang der weitergeleiteten E-Mail: > Von: Stephan > Datum: 3. April 2009 12:26:48 MESZ > An: biococoa-dev at bioinformatics.org > Betreff: CachedSequenceFile > > Hi, > > I am just looking through the implementation of > BCCachedSequenceFile. It seems to be not ready yet, and the last > modifications according to the svn log are from 2007... any further > plans on that? > > Stephan > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From postmaster at esox.it Sat Apr 18 16:35:06 2009 From: postmaster at esox.it (postmaster at esox.it) Date: Sat, 18 Apr 2009 22:35:06 +0200 Subject: [Biococoa-dev] Notifica sullo stato del recapito (Errore) Message-ID: Notifica sullo stato del recapito generata automaticamente. Recapito non riuscito per i seguenti destinatari. biococchi at esox.it -------------- next part -------------- An embedded message was scrubbed... From: VIAGRA ? Official Site Subject: RE: SALE 70% OFF on Pfizer! Date: 18 Apr 2009 22:35:06 +0200 Size: 5130 URL: From jeedward at yahoo.com Sun Apr 19 11:52:01 2009 From: jeedward at yahoo.com (John Edward) Date: Sun, 19 Apr 2009 08:52:01 -0700 (PDT) Subject: [Biococoa-dev] Extended draft paper submission: BCBGC-09 call for papers Message-ID: <376236.59661.qm@web45901.mail.sp1.yahoo.com> Extended draft paper submission: BCBGC-09 call for papers ? This Extended Call for Papers for the 2009 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09) (website: http://www.PromoteResearch.org ) is for those who didn't get a chance to submit the papers for the earlier call for papers. The papers received and accepted in response to this extended call for papers will be included in the final version of the respective conference proceedings. These proceedings will be either ready by the time of the conference (i.e., they will be available during the conference) or soon after the conference (before the end of August 2009), based how fast the proceedings can be prepared. Note: If you have already submitted a paper (whether accepted or rejected or currently under review) for MULTICONF-09, please DO NOT submit that paper again to this extended call for papers. IMPORTANT DATES: Draft paper submission date: May 11, 2009 Acceptance/rejection decision: May 21, 2009 Camera ready paper and copyright and pre-registration due: May 28, 2009 Conference dates: July 13-16, 2009 ? ? BCBGC-09 will be held during July 13-16 2009 in Orlando, FL, USA. The conference will take place at the same time and venue where several other international conferences are taking place. The other conferences include: ????????? International Conference on Artificial Intelligence and Pattern Recognition (AIPR-09) ????????? International Conference on Automation, Robotics and Control Systems (ARCS-09) ????????? International Conference on Enterprise Information Systems and Web Technologies (EISWT-09) ????????? International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-09) ????????? International Conference on Information Security and Privacy (ISP-09) ????????? International Conference on Recent Advances in Information Technology and Applications (RAITA-09) ????????? International Conference on Software Engineering Theory and Practice (SETP-09) ????????? International Conference on Theory and Applications of Computational Science (TACS-09) ????????? International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-09) ? The website http://www.PromoteResearch.org contains more details. ? Sincerely John Edward Publicity committee -------------- next part -------------- An HTML attachment was scrubbed... URL: