From a.griekspoor at nki.nl Thu Mar 2 06:10:37 2006 From: a.griekspoor at nki.nl (Alexander Griekspoor) Date: Thu, 2 Mar 2006 12:10:37 +0100 Subject: [Biococoa-dev] New goodies - BCStandaloneReader Message-ID: <376584F3-85F2-4E3D-A196-8C6C37DBE297@nki.nl> Hi guys, Long time, no activity unfortunately. Still there is some news. The last two weeks I've used my (very) few spare hours to fulfil some long standing promises, and updated our programs to bring them at least on par with OSX Tiger. For instance, we were so optimistic (read: stupid) to write on our website that we would release new versions of both EnzymeX and iRNAi "soon". That was 2 years ago ;-) Anyway, they're finished now (iRNAi 2 released today and EnzymeX 3 finishing up). In both of them I used some of Peter's "old" BioCocoa code to allow reading of most common sequence file formats, and I would like to share that with you guys. Perhaps Peter can give it a place on the BioCocoa CVS/SVN or post it on the BioCocoa webpage. I made a standalone version of the BCReader code, so that adding these 4 files is sufficient to add reading of all of the following formats to your app for free: - BEAST, - Clustal - DNA Strider - EMBL - Fasta - GCG-MSF - GCK (Gene Construction Kit) - GDE - Hennig86 - NCBI - NEXUS - NONA - PDB - Phylip - PIR - Plain/Raw - Swiss-Prot - TNT As you can see I've added the binary formats DNAStrider and Gene Construction Kit files (the latter using a bit of (very simple) reverse engineering ;-) Below is a snippet from iRNAi that shows you how to read a sequence file: - (IBAction)importSequence:(id)sender{ NSOpenPanel * oPanel = [NSOpenPanel openPanel]; [oPanel setAllowsMultipleSelection:NO]; [oPanel setResolvesAliases: YES]; [oPanel setCanChooseDirectories: NO]; [oPanel setCanChooseFiles: YES]; NSArray *fileTypes = [NSArray arrayWithObjects: @"text", @"TEXT", @"txt", @"TXT", @"fasta", @"FASTA", @"seq", @"SEQ", @"html", @"HTML", @"htm", @"HTM", @"rtf", @"RTF", @"rtfd", @"RTFD", @"gde", @"fas", @"nessig", @"pir", @"nona", @"phylip", @"nexus", @"GDE", @"FAS", @"NESSIG", @"PIR", @"NONA", @"PHYLIP", @"NEXUS", @"raw", @"clustal", @"pdb", @"embl", @"swissprot", @"NCBI", @"GCK", @"RAW", @"CLUSTAL", @"PDB", @"EMBL", @"SWISSPROT", @"ncbi", @"gck", @"aln", @"hen", @"fst", @"msf", @"nxs", @"non", @"phy", @"tnt", @"ALN", @"HEN", @"FST", @"MSF", @"NXS", @"NON", @"PHY", @"TNT", @"", NSFileTypeForHFSTypeCode('TEXT'), NSFileTypeForHFSTypeCode('TXT '), NSFileTypeForHFSTypeCode('text'), NSFileTypeForHFSTypeCode('xDNA'), NSFileTypeForHFSTypeCode('DNA '), NSFileTypeForHFSTypeCode('GCKc'), NSFileTypeForHFSTypeCode('GCKs'), NSFileTypeForHFSTypeCode('NUCL'), nil]; [oPanel beginSheetForDirectory: nil file: nil types: fileTypes modalForWindow: [NSApp mainWindow] modalDelegate: self didEndSelector: @selector (importPanelDidEnd:returnCode:contextInfo:) contextInfo: nil]; } - (void)importPanelDidEnd:(NSOpenPanel *)oPanel returnCode:(int) returnCode contextInfo:(void *)contextInfo{ if (returnCode == NSOKButton) { BCReader *reader = [[BCReader alloc]init]; NS_DURING NSDictionary *dict = [reader readFile: [[oPanel filenames] objectAtIndex: 0]]; // In the future it would be nice to present a dialog to the user // where he/she could choose which sequence to open in case the file // contains multiple sequences if([[dict objectForKey: @"items"] count] > 0) { NSString *name = [[dict objectForKey: @"items"]objectAtIndex: 0]; NSString *sequence = [[dict objectForKey: @"matrix"] objectForKey: name]; // do your stuff here with the obtained sequence... } NS_HANDLER NSBeep(); NSString *title = @"Error Reading File"; NSString *defaultButton = @"OK"; NSString *alternateButton = nil; NSString *otherButton = nil; NSString *message = @"iRNAi could not read the selected file, which might not be a sequence file or not of a format that EnzymeX does not support. Try converting it to plain text or fasta format. Alternatively, you can copy the sequence from its native application."; NSRunAlertPanel(title, message, defaultButton, alternateButton, otherButton); NS_ENDHANDLER [BCReader release]; } } The source code can be downloaded here: http://www.mekentosj.com/biococoa/BCStandaloneReader.zip Hey, but wait, that's not all! In 4Peaks I used James S. Derry's JSDTextView to display sequences in a TextView with linenumbers. James had received a lot of help from Koen, who basically figured out how to do all this. Unfortunately, in OSX 10.4 Tiger this textview shows a weird drawing bug so I had to go on the look out for alternatives. And guess what, Koen actually had posted some sample code himself as well, which was actually a much more elegant solution. So I used his KDTextView in 4Peaks. For iRNAi 2 and EnzymeX 3 I decided to pimp Koen's textview a bit more and added a number of interesting new features: - better support for printing - the mouse location and selections are shown using fancy semi- transparent overlays - added columnspacing support in the textcontainer class: instead of xxxxxxxxxxxxxxxxx now: xxxxx xxxxx xxxxx , without introducing spaces in the text, so copy/paste, drag and drop, selections etc all work without having to think about spacing. Check out iRNAi 2 for a demo (http://www.mekentosj.com/irnai ) It isn't completely ready yet to release it, but once I've finished EnzymeX 3, I'll post it and let you guys know. Thanks Koen for the excellent foundation! Enjoy! Cheers, Alex Ps. Peter kudos on the new stuff your doing and congratulations with Orbicule, it seems a very successful launch and although not so much biology, cool product you created!! Didn't have time to write you this before, but "petje af!" Are you now fulltime doing that? ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com 4Peaks - For Peaks, Four Peaks. 2004 Winner of the Apple Design Awards Best Mac OS X Student Product http://www.mekentosj.com/4peaks ********************************************************* From charles.parnot at gmail.com Thu Mar 2 20:04:57 2006 From: charles.parnot at gmail.com (Charles Parnot) Date: Thu, 2 Mar 2006 17:04:57 -0800 Subject: [Biococoa-dev] New goodies - BCStandaloneReader In-Reply-To: <376584F3-85F2-4E3D-A196-8C6C37DBE297@nki.nl> References: <376584F3-85F2-4E3D-A196-8C6C37DBE297@nki.nl> Message-ID: <1DABB1E4-D7B5-4E84-80A5-9827692E9870@gmail.com> Alex, this is great stuff, thanks! I have never liked gck, and now hates it. I am stuck with files I can only open, and not even copy/paste from using their demo version. Good job!! The text view looks great too! And EnzymeX 3.0 is coming sooooooon... good news ;-) charles On Mar 2, 2006, at 3:10 AM, Alexander Griekspoor wrote: > Hi guys, > > Long time, no activity unfortunately. Still there is some news. The > last two weeks I've used my (very) few spare hours to fulfil some > long standing promises, and updated our programs to bring them at > least on par with OSX Tiger. For instance, we were so optimistic > (read: stupid) to write on our website that we would release new > versions of both EnzymeX and iRNAi "soon". That was 2 years ago ;-) > Anyway, they're finished now (iRNAi 2 released today and EnzymeX 3 > finishing up). In both of them I used some of Peter's "old" > BioCocoa code to allow reading of most common sequence file > formats, and I would like to share that with you guys. Perhaps > Peter can give it a place on the BioCocoa CVS/SVN or post it on the > BioCocoa webpage. > I made a standalone version of the BCReader code, so that adding > these 4 files is sufficient to add reading of all of the following > formats to your app for free: > > - BEAST, > - Clustal > - DNA Strider > - EMBL > - Fasta > - GCG-MSF > - GCK (Gene Construction Kit) > - GDE > - Hennig86 > - NCBI > - NEXUS > - NONA > - PDB > - Phylip > - PIR > - Plain/Raw > - Swiss-Prot > - TNT > > As you can see I've added the binary formats DNAStrider and Gene > Construction Kit files (the latter using a bit of (very simple) > reverse engineering ;-) > Below is a snippet from iRNAi that shows you how to read a sequence > file: > > - (IBAction)importSequence:(id)sender{ > > NSOpenPanel * oPanel = [NSOpenPanel openPanel]; > [oPanel setAllowsMultipleSelection:NO]; > [oPanel setResolvesAliases: YES]; > [oPanel setCanChooseDirectories: NO]; > [oPanel setCanChooseFiles: YES]; > NSArray *fileTypes = [NSArray arrayWithObjects: @"text", > @"TEXT", @"txt", @"TXT", @"fasta", @"FASTA", @"seq", @"SEQ", > @"html", @"HTML", @"htm", @"HTM", @"rtf", @"RTF", @"rtfd", @"RTFD", > @"gde", @"fas", @"nessig", @"pir", @"nona", @"phylip", @"nexus", > @"GDE", @"FAS", @"NESSIG", @"PIR", @"NONA", @"PHYLIP", @"NEXUS", > @"raw", @"clustal", @"pdb", @"embl", @"swissprot", @"NCBI", @"GCK", > @"RAW", @"CLUSTAL", @"PDB", @"EMBL", @"SWISSPROT", @"ncbi", @"gck", > @"aln", @"hen", @"fst", @"msf", @"nxs", @"non", @"phy", @"tnt", > @"ALN", @"HEN", @"FST", @"MSF", @"NXS", @"NON", @"PHY", @"TNT", @"", > NSFileTypeForHFSTypeCode('TEXT'), NSFileTypeForHFSTypeCode('TXT > '), NSFileTypeForHFSTypeCode('text'), > NSFileTypeForHFSTypeCode('xDNA'), NSFileTypeForHFSTypeCode('DNA '), > NSFileTypeForHFSTypeCode('GCKc'), NSFileTypeForHFSTypeCode('GCKs'), > NSFileTypeForHFSTypeCode('NUCL'), nil]; > > [oPanel beginSheetForDirectory: nil > file: nil > types: fileTypes > modalForWindow: [NSApp mainWindow] > modalDelegate: self > didEndSelector: @selector > (importPanelDidEnd:returnCode:contextInfo:) > contextInfo: nil]; > } > > > - (void)importPanelDidEnd:(NSOpenPanel *)oPanel returnCode:(int) > returnCode contextInfo:(void *)contextInfo{ > > if (returnCode == NSOKButton) { > > BCReader *reader = [[BCReader alloc]init]; > > NS_DURING > > NSDictionary *dict = [reader readFile: [[oPanel filenames] > objectAtIndex: 0]]; > > // In the future it would be nice to present a dialog to the user > // where he/she could choose which sequence to open in case the > file > // contains multiple sequences > if([[dict objectForKey: @"items"] count] > 0) { > NSString *name = [[dict objectForKey: @"items"]objectAtIndex: 0]; > NSString *sequence = [[dict objectForKey: @"matrix"] > objectForKey: name]; > > // do your stuff here with the obtained sequence... > > } > > NS_HANDLER > NSBeep(); > NSString *title = @"Error Reading File"; > NSString *defaultButton = @"OK"; > NSString *alternateButton = nil; > NSString *otherButton = nil; > NSString *message = @"iRNAi could not read the selected file, > which might not be a sequence file or not of a format that EnzymeX > does not support. Try converting it to plain text or fasta format. > Alternatively, you can copy the sequence from its native > application."; > > NSRunAlertPanel(title, message, defaultButton, alternateButton, > otherButton); > NS_ENDHANDLER > > [BCReader release]; > } > } > > The source code can be downloaded here: > http://www.mekentosj.com/biococoa/BCStandaloneReader.zip > > > Hey, but wait, that's not all! > In 4Peaks I used James S. Derry's JSDTextView to display sequences > in a TextView with linenumbers. James had received a lot of help > from Koen, who basically figured out how to do all this. > Unfortunately, in OSX 10.4 Tiger this textview shows a weird > drawing bug so I had to go on the look out for alternatives. And > guess what, Koen actually had posted some sample code himself as > well, which was actually a much more elegant solution. So I used > his KDTextView in 4Peaks. > For iRNAi 2 and EnzymeX 3 I decided to pimp Koen's textview a bit > more and added a number of interesting new features: > - better support for printing > - the mouse location and selections are shown using fancy semi- > transparent overlays > - added columnspacing support in the textcontainer class: instead > of xxxxxxxxxxxxxxxxx now: xxxxx xxxxx xxxxx , without introducing > spaces in the text, so copy/paste, drag and drop, selections etc > all work without having to think about spacing. > > Check out iRNAi 2 for a demo (http://www.mekentosj.com/irnai ) > It isn't completely ready yet to release it, but once I've finished > EnzymeX 3, I'll post it and let you guys know. Thanks Koen for the > excellent foundation! > > Enjoy! > Cheers, > Alex > > > Ps. Peter kudos on the new stuff your doing and congratulations > with Orbicule, it seems a very successful launch and although not > so much biology, cool product you created!! Didn't have time to > write you this before, but "petje af!" Are you now fulltime doing > that? > > ********************************************************* > ** Alexander Griekspoor ** > ********************************************************* > The Netherlands Cancer Institute > Department of Tumorbiology (H4) > Plesmanlaan 121, 1066 CX, Amsterdam > Tel: + 31 20 - 512 2023 > Fax: + 31 20 - 512 2029 > AIM: mekentosj at mac.com > E-mail: a.griekspoor at nki.nl > Web: http://www.mekentosj.com > > 4Peaks - For Peaks, Four Peaks. > 2004 Winner of the Apple Design Awards > Best Mac OS X Student Product > http://www.mekentosj.com/4peaks > > ********************************************************* > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev -- Xgrid-at-Stanford Help science move fast forward: http://cmgm.stanford.edu/~cparnot/xgrid-stanford Charles Parnot charles.parnot at gmail.com From kvddrift at earthlink.net Thu Mar 2 20:21:56 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Thu, 2 Mar 2006 20:21:56 -0500 Subject: [Biococoa-dev] New goodies - BCStandaloneReader In-Reply-To: <376584F3-85F2-4E3D-A196-8C6C37DBE297@nki.nl> References: <376584F3-85F2-4E3D-A196-8C6C37DBE297@nki.nl> Message-ID: Hi Alex, Good news! The classes you submitted are a great extension of the current reader class, although it would fit BioCocoa better in the way the framework is currently setip, so that each method returns a BCSequenceArray instead of NSDictionary. I can go ahead this weekend and add it to BioCocoa in that form. Peter, did we switch to svn, or was that only an announcement that it is available? And thanks for the compliments of the textview, I'm glad it's of use in at least one other app that I know of. cheers, - Koen. From a.griekspoor at nki.nl Fri Mar 3 05:08:12 2006 From: a.griekspoor at nki.nl (Alexander Griekspoor) Date: Fri, 3 Mar 2006 11:08:12 +0100 Subject: [Biococoa-dev] New goodies - BCStandaloneReader In-Reply-To: References: <376584F3-85F2-4E3D-A196-8C6C37DBE297@nki.nl> Message-ID: <373106AD-1C8F-4143-BC48-0A9C6C97E1A1@nki.nl> Thanks Koen! > > Good news! The classes you submitted are a great extension of the > current reader class, although it would fit BioCocoa better in the > way the framework is currently setip, so that each method returns a > BCSequenceArray instead of NSDictionary. I can go ahead this > weekend and add it to BioCocoa in that form. Definitely, the reason to do it like this was to have a standalone, simple, version of the Reader classes only if you only need the simple file to string features. But yes, it would be great to have it use the BCSequence classes of course. The only real change I made was to make the app pass just the filename instead of the raw ASCII text of the file already extracted like in Peter's original implementation. The reason is the fact that I have now added to binary file formats, which need the filename, not the ASCII text. Anyway it's a better separation of code, with the app not having to care about anything else than the filepath, and the framework doing the rest. > > Peter, did we switch to svn, or was that only an announcement that > it is available? That was my reason to leave it up to you guys ;-) Still, it would perhaps be nice to give a place to the standalone reader classes as well on the server. > > And thanks for the compliments of the textview, I'm glad it's of > use in at least one other app that I know of. Great, in that case I can tell you that your user base tripled ;-) It's now used by 4Peaks, iRNAi, and EnzymeX ;-) Alex ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com 4Peaks - For Peaks, Four Peaks. 2004 Winner of the Apple Design Awards Best Mac OS X Student Product http://www.mekentosj.com/4peaks ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From peter.schols at bio.kuleuven.be Fri Mar 3 05:16:19 2006 From: peter.schols at bio.kuleuven.be (Peter Schols) Date: Fri, 3 Mar 2006 11:16:19 +0100 Subject: [Biococoa-dev] Re: New goodies - BCStandaloneReader In-Reply-To: <376584F3-85F2-4E3D-A196-8C6C37DBE297@nki.nl> References: <376584F3-85F2-4E3D-A196-8C6C37DBE297@nki.nl> Message-ID: Wow BioCocoa is back alive, that's great! Alex and Tom, first of all, congratulations on the new versions of iRNAi and EnzymeX 3 (almost)! The extended BCReader class is fantastic. I think everyone will agree with Koen's comment that we could easily incorporate this into the main BioCocoa project, just by switching to a BCSequenceArray (although I can understand why Alex did not change this for use in his apps). As far as I can see from the BCReader code, Alex did not only add the DNAStrider and GCK formats, he also incorporated my "GNUStep code" for reading Hennig, TNT, ... files, which is great as well ;-) I promised to do this almost a year ago, but still had not done it - shame on me... The KDTextView is awesome! It looks already very polished to me (I like the fancy overlays showing position and selection, those are brilliant). This is exactly what I need for a small in-house project I'm planning to do for my former lab. A bit on my own situation (feel free to skip this paragraph): I stopped working at the university of Leuven on January 1st 2006 and founded Orbicule, my own 'software company' (sounds too big because right now it's just me). I finally figured out that writing software and designing apps is really what I want to do. Right now, I'm working on consumer software such as Undercover (because I really like to do consumer software and because it's a good way to start the company) but I'm also planning to continue writing science-related applications such as iMap. And finally - to come back to BioCocoa - I'm planning to do some BioCocoa-work again. I will be presenting Undercover at the SoHo Apple store in NY later this month so things will be quite busy until then. Starting in April, I will have more time to work on BioCocoa. I have been thinking about BioCocoa and this is what I think we could do next: - First of all, we should move to SVN. I'm running my own in-house Subversion server on a Mac OS X machine for almost two years now and it is not even in the same league when compared to CVS. Moving to SVN would be great for several reasons (better support for binary files (nibs!), easier to create branches, great svnx front-end for Mac OS X, better Xcode integration, ...), and it will definitely encourage us to submit more to the repository. Since bioinformatics.org recently announced support for svn, I'm willing to move the project to svn. The only problem is that I can't login on the Bioinformatics.org homepage. I always get the not logged in error message. I have tried several things in 3 different browsers, but always the same error... could someone verify this with their account? - I have to enhance and cleanup my BLAST and Entrez classes and add them to BioCocoa. I have a working demo app in which you can do a BLAST query on the Net and get results in an NSTableView with only 3 lines of code. I'll need to incorporate more BLAST settings into this BLAST classes though to increase usefulness. - During some tests of the BLAST classes with ObjectAlloc (don't ask me why) I noticed what could be a memory leak in BCSequence. I was in a hurry back then (it was right before WWDC) but I'll do some more testing and see if it's still there ;-) - As Koen suggested, we should move the BCReader code into the main project and switch to BCSequenceArray. Koen proposed to do this and that would be great! I'm always willing to help. - Koen and Alex, any chance you will be donating the KDTextView to the project? - Later on, it would also be worth discussing CoreData and if/how we could use it in BC. These are just a few thoughts, I'm sure many of you have their own to- do lists and plans. Feel free to comment! Peter PS: If anybody is interested in a license key for Undercover, please drop me a line Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From a.griekspoor at nki.nl Fri Mar 3 05:29:57 2006 From: a.griekspoor at nki.nl (Alexander Griekspoor) Date: Fri, 3 Mar 2006 11:29:57 +0100 Subject: [Biococoa-dev] Re: New goodies - BCStandaloneReader In-Reply-To: References: <376584F3-85F2-4E3D-A196-8C6C37DBE297@nki.nl> Message-ID: <1E0C41F6-46B5-4EF5-8DD2-45E3B3234EAF@nki.nl> Hi Peter, Nice to hear you're doing so well! > Wow BioCocoa is back alive, that's great! Alive is a big word perhaps, still certainly good to hear there's still interest! > > Alex and Tom, first of all, congratulations on the new versions of > iRNAi and EnzymeX 3 (almost)! Haha, thanks! > The extended BCReader class is fantastic. I think everyone will > agree with Koen's comment that we could easily incorporate this > into the main BioCocoa project, just by switching to a > BCSequenceArray (although I can understand why Alex did not change > this for use in his apps). > As far as I can see from the BCReader code, Alex did not only add > the DNAStrider and GCK formats, he also incorporated my "GNUStep > code" for reading Hennig, TNT, ... files, which is great as well ;-) > I promised to do this almost a year ago, but still had not done it > - shame on me... Ho ho ho, I just copied those from the BioCocoa website (I was to lazy to look it up in the code), guess I have to be ashamed here.. > > The KDTextView is awesome! It looks already very polished to me (I > like the fancy overlays showing position and selection, those are > brilliant). This is exactly what I need for a small in-house > project I'm planning to do for my former lab. Good! > A bit on my own situation (feel free to skip this paragraph): I > stopped working at the university of Leuven on January 1st 2006 and > founded Orbicule, my own 'software company' (sounds too big because > right now it's just me). I finally figured out that writing > software and designing apps is really what I want to do. > Right now, I'm working on consumer software such as Undercover > (because I really like to do consumer software and because it's a > good way to start the company) but I'm also planning to continue > writing science-related applications such as iMap. And finally - to > come back to BioCocoa - I'm planning to do some BioCocoa-work > again. I will be presenting Undercover at the SoHo Apple store in > NY later this month so things will be quite busy until then. > Starting in April, I will have more time to work on BioCocoa. Very nice, I kind of made the same decision (software development rather than wetlab bio), but in a different way, I'm going to the European Bioinformatics Institute to a group who works on textmining... ;-) But great to hear that Orbicule goes so well, seems you have things organized very well, kudos! Also very cool the presentation in the SoHo store, be sure to share some pictures (and update your blog a bit more often, just nitpicking ;-) > > I have been thinking about BioCocoa and this is what I think we > could do next: > - First of all, we should move to SVN. > I'm running my own in-house Subversion server on a Mac OS X machine > for almost two years now and it is not even in the same league when > compared to CVS. Moving to SVN would be great for several reasons > (better support for binary files (nibs!), easier to create > branches, great svnx front-end for Mac OS X, better Xcode > integration, ...), and it will definitely encourage us to submit > more to the repository. Since bioinformatics.org recently announced > support for svn, I'm willing to move the project to svn. The only > problem is that I can't login on the Bioinformatics.org homepage. I > always get the not logged in error message. I have tried several > things in 3 different browsers, but always the same error... could > someone verify this with their account? Good plan, I don't have much experience here, but Charles is the king (at least in my world ;-).. Charles perhaps you also want to inform these guys on the project you're doing with Drew.. > > - I have to enhance and cleanup my BLAST and Entrez classes and > add them to BioCocoa. > I have a working demo app in which you can do a BLAST query on the > Net and get results in an NSTableView with only 3 lines of code. > I'll need to incorporate more BLAST settings into this BLAST > classes though to increase usefulness. That's awesome, I once had an idea for some BLAST app, which in the end wasn't feasible, but perhaps some code/ideas still can be used.. > > - During some tests of the BLAST classes with ObjectAlloc (don't > ask me why) I noticed what could be a memory leak in BCSequence. I > was in a hurry back then (it was right before WWDC) but I'll do > some more testing and see if it's still there ;-) > > - As Koen suggested, we should move the BCReader code into the main > project and switch to BCSequenceArray. Koen proposed to do this and > that would be great! I'm always willing to help. > > - Koen and Alex, any chance you will be donating the KDTextView to > the project? I promised that already, so yes. But first I want to finish EnzymeX for the simple reason that I will probably find bugs still in the Textview class that can be fixed first. For instance, I now added a unit property as it didn't make sense that the textview shows 166-182 (16bp) while I had 16 aminoacids selected ;-) > > - Later on, it would also be worth discussing CoreData and if/how > we could use it in BC. I still have to dive in that whole thing, soooon ;-) > > > PS: If anybody is interested in a license key for Undercover, > please drop me a line Definitely!! But I'm for sure willing to pay for it as well Peter, have been considering to buy a license already... > > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com iRNAi, do you? http://www.mekentosj.com/irnai ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.griekspoor at nki.nl Fri Mar 3 05:00:38 2006 From: a.griekspoor at nki.nl (Alexander Griekspoor) Date: Fri, 3 Mar 2006 11:00:38 +0100 Subject: [Biococoa-dev] New goodies - BCStandaloneReader In-Reply-To: <1DABB1E4-D7B5-4E84-80A5-9827692E9870@gmail.com> References: <376584F3-85F2-4E3D-A196-8C6C37DBE297@nki.nl> <1DABB1E4-D7B5-4E84-80A5-9827692E9870@gmail.com> Message-ID: <795F61C2-FBD6-4120-AAF9-2EF0946A7C48@nki.nl> > I have never liked gck, and now hates it. I am stuck with files I > can only open, and not even copy/paste from using their demo > version. Good job!! That was quite some fun to kind of reverse engineer actually, using hexedit it was quite easy to do. It turns out that GCK writes a small header of which the last int contains the size of the sequence. After that it's just reading all bytes after the header up to the size of the sequence using NSData. Easy does it, of course the fact that I don't care about all the other crap GCK writes into the file following that sequence (containing all annotations stuff etc) made life (very) easy... As far as I know, BioCocoa is now the only thing that can do something at all with GCK files.... > And EnzymeX 3.0 is coming sooooooon... good news ;-) Yeah, rub it in ;-) Cheers, Alex > > > On Mar 2, 2006, at 3:10 AM, Alexander Griekspoor wrote: > >> Hi guys, >> >> Long time, no activity unfortunately. Still there is some news. >> The last two weeks I've used my (very) few spare hours to fulfil >> some long standing promises, and updated our programs to bring >> them at least on par with OSX Tiger. For instance, we were so >> optimistic (read: stupid) to write on our website that we would >> release new versions of both EnzymeX and iRNAi "soon". That was 2 >> years ago ;-) >> Anyway, they're finished now (iRNAi 2 released today and EnzymeX 3 >> finishing up). In both of them I used some of Peter's "old" >> BioCocoa code to allow reading of most common sequence file >> formats, and I would like to share that with you guys. Perhaps >> Peter can give it a place on the BioCocoa CVS/SVN or post it on >> the BioCocoa webpage. >> I made a standalone version of the BCReader code, so that adding >> these 4 files is sufficient to add reading of all of the following >> formats to your app for free: >> >> - BEAST, >> - Clustal >> - DNA Strider >> - EMBL >> - Fasta >> - GCG-MSF >> - GCK (Gene Construction Kit) >> - GDE >> - Hennig86 >> - NCBI >> - NEXUS >> - NONA >> - PDB >> - Phylip >> - PIR >> - Plain/Raw >> - Swiss-Prot >> - TNT >> >> As you can see I've added the binary formats DNAStrider and Gene >> Construction Kit files (the latter using a bit of (very simple) >> reverse engineering ;-) >> Below is a snippet from iRNAi that shows you how to read a >> sequence file: >> >> - (IBAction)importSequence:(id)sender{ >> >> NSOpenPanel * oPanel = [NSOpenPanel openPanel]; >> [oPanel setAllowsMultipleSelection:NO]; >> [oPanel setResolvesAliases: YES]; >> [oPanel setCanChooseDirectories: NO]; >> [oPanel setCanChooseFiles: YES]; >> NSArray *fileTypes = [NSArray arrayWithObjects: @"text", >> @"TEXT", @"txt", @"TXT", @"fasta", @"FASTA", @"seq", @"SEQ", >> @"html", @"HTML", @"htm", @"HTM", @"rtf", @"RTF", @"rtfd", @"RTFD", >> @"gde", @"fas", @"nessig", @"pir", @"nona", @"phylip", @"nexus", >> @"GDE", @"FAS", @"NESSIG", @"PIR", @"NONA", @"PHYLIP", @"NEXUS", >> @"raw", @"clustal", @"pdb", @"embl", @"swissprot", @"NCBI", @"GCK", >> @"RAW", @"CLUSTAL", @"PDB", @"EMBL", @"SWISSPROT", @"ncbi", @"gck", >> @"aln", @"hen", @"fst", @"msf", @"nxs", @"non", @"phy", @"tnt", >> @"ALN", @"HEN", @"FST", @"MSF", @"NXS", @"NON", @"PHY", @"TNT", >> @"", >> NSFileTypeForHFSTypeCode('TEXT'), NSFileTypeForHFSTypeCode('TXT >> '), NSFileTypeForHFSTypeCode('text'), >> NSFileTypeForHFSTypeCode('xDNA'), NSFileTypeForHFSTypeCode('DNA '), >> NSFileTypeForHFSTypeCode('GCKc'), NSFileTypeForHFSTypeCode('GCKs'), >> NSFileTypeForHFSTypeCode('NUCL'), nil]; >> >> [oPanel beginSheetForDirectory: nil >> file: nil >> types: fileTypes >> modalForWindow: [NSApp mainWindow] >> modalDelegate: self >> didEndSelector: @selector >> (importPanelDidEnd:returnCode:contextInfo:) >> contextInfo: nil]; >> } >> >> >> - (void)importPanelDidEnd:(NSOpenPanel *)oPanel returnCode:(int) >> returnCode contextInfo:(void *)contextInfo{ >> >> if (returnCode == NSOKButton) { >> >> BCReader *reader = [[BCReader alloc]init]; >> >> NS_DURING >> >> NSDictionary *dict = [reader readFile: [[oPanel filenames] >> objectAtIndex: 0]]; >> >> // In the future it would be nice to present a dialog to the user >> // where he/she could choose which sequence to open in case the >> file >> // contains multiple sequences >> if([[dict objectForKey: @"items"] count] > 0) { >> NSString *name = [[dict objectForKey: @"items"]objectAtIndex: 0]; >> NSString *sequence = [[dict objectForKey: @"matrix"] >> objectForKey: name]; >> >> // do your stuff here with the obtained sequence... >> >> } >> >> NS_HANDLER >> NSBeep(); >> NSString *title = @"Error Reading File"; >> NSString *defaultButton = @"OK"; >> NSString *alternateButton = nil; >> NSString *otherButton = nil; >> NSString *message = @"iRNAi could not read the selected file, >> which might not be a sequence file or not of a format that EnzymeX >> does not support. Try converting it to plain text or fasta format. >> Alternatively, you can copy the sequence from its native >> application."; >> >> NSRunAlertPanel(title, message, defaultButton, >> alternateButton, otherButton); >> NS_ENDHANDLER >> >> [BCReader release]; >> } >> } >> >> The source code can be downloaded here: >> http://www.mekentosj.com/biococoa/BCStandaloneReader.zip >> >> >> Hey, but wait, that's not all! >> In 4Peaks I used James S. Derry's JSDTextView to display sequences >> in a TextView with linenumbers. James had received a lot of help >> from Koen, who basically figured out how to do all this. >> Unfortunately, in OSX 10.4 Tiger this textview shows a weird >> drawing bug so I had to go on the look out for alternatives. And >> guess what, Koen actually had posted some sample code himself as >> well, which was actually a much more elegant solution. So I used >> his KDTextView in 4Peaks. >> For iRNAi 2 and EnzymeX 3 I decided to pimp Koen's textview a bit >> more and added a number of interesting new features: >> - better support for printing >> - the mouse location and selections are shown using fancy semi- >> transparent overlays >> - added columnspacing support in the textcontainer class: instead >> of xxxxxxxxxxxxxxxxx now: xxxxx xxxxx xxxxx , without introducing >> spaces in the text, so copy/paste, drag and drop, selections etc >> all work without having to think about spacing. >> >> Check out iRNAi 2 for a demo (http://www.mekentosj.com/irnai ) >> It isn't completely ready yet to release it, but once I've >> finished EnzymeX 3, I'll post it and let you guys know. Thanks >> Koen for the excellent foundation! >> >> Enjoy! >> Cheers, >> Alex >> >> >> Ps. Peter kudos on the new stuff your doing and congratulations >> with Orbicule, it seems a very successful launch and although not >> so much biology, cool product you created!! Didn't have time to >> write you this before, but "petje af!" Are you now fulltime doing >> that? >> >> ********************************************************* >> ** Alexander Griekspoor ** >> ********************************************************* >> The Netherlands Cancer Institute >> Department of Tumorbiology (H4) >> Plesmanlaan 121, 1066 CX, Amsterdam >> Tel: + 31 20 - 512 2023 >> Fax: + 31 20 - 512 2029 >> AIM: mekentosj at mac.com >> E-mail: a.griekspoor at nki.nl >> Web: http://www.mekentosj.com >> >> 4Peaks - For Peaks, Four Peaks. >> 2004 Winner of the Apple Design Awards >> Best Mac OS X Student Product >> http://www.mekentosj.com/4peaks >> >> ********************************************************* >> >> _______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/biococoa-dev > > -- > Xgrid-at-Stanford > Help science move fast forward: > http://cmgm.stanford.edu/~cparnot/xgrid-stanford > > Charles Parnot > charles.parnot at gmail.com > > > > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com Windows is a 32-bit patch to a 16-bit shell for an 8-bit operating system, written for a 4-bit processor by a 2- bit company without 1 bit of sense. ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From peter.schols at bio.kuleuven.be Fri Mar 3 05:49:45 2006 From: peter.schols at bio.kuleuven.be (Peter Schols) Date: Fri, 3 Mar 2006 11:49:45 +0100 Subject: [Biococoa-dev] Re: New goodies - BCStandaloneReader In-Reply-To: <1E0C41F6-46B5-4EF5-8DD2-45E3B3234EAF@nki.nl> References: <376584F3-85F2-4E3D-A196-8C6C37DBE297@nki.nl> <1E0C41F6-46B5-4EF5-8DD2-45E3B3234EAF@nki.nl> Message-ID: <56E383DE-20C3-4C50-AD1F-1165BF8761E9@bio.kuleuven.be> Hi Alex, > Ho ho ho, I just copied those from the BioCocoa website (I was to > lazy to look it up in the code), guess I have to be ashamed here.. The version on the website was the GNUStep version indeed... you don't have to be ashamed at all, I'm glad it has finally been done ;-) > Very nice, I kind of made the same decision (software development > rather than wetlab bio), but in a different way, I'm going to the > European Bioinformatics Institute to a group who works on > textmining... Wow, great news! Congratulations! When are you moving to the UK? > ;-) But great to hear that Orbicule goes so well, seems you have > things organized very well, kudos! Also very cool the presentation > in the SoHo store, be sure to share some pictures (and update your > blog a bit more often, just nitpicking ;-) ;-))) I'll post some pictures... > Good plan, I don't have much experience here, but Charles is the > king (at least in my world ;-).. > Charles perhaps you also want to inform these guys on the project > you're doing with Drew.. I'm curious... > I promised that already, so yes. But first I want to finish EnzymeX > for the simple reason that I will probably find bugs still in the > Textview class that can be fixed first. For instance, I now added a > unit property as it didn't make sense that the textview shows > 166-182 (16bp) while I had 16 aminoacids selected ;-) Great! > Definitely!! But I'm for sure willing to pay for it as well Peter, > have been considering to buy a license already... A license key is on its way. peter Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From a.griekspoor at nki.nl Fri Mar 3 06:13:45 2006 From: a.griekspoor at nki.nl (a.griekspoor at nki.nl) Date: Fri, 3 Mar 2006 12:13:45 +0100 Subject: [Biococoa-dev] Re: New goodies - BCStandaloneReader Message-ID: <667464FDA2C81D4CA79D7F3B728D10E75A85EF@adsrv100.nki.nl> Peter, > Ho ho ho, I just copied those from the BioCocoa website (I was to > lazy to look it up in the code), guess I have to be ashamed here.. The version on the website was the GNUStep version indeed... you don't have to be ashamed at all, I'm glad it has finally been done ;-) Pfeww. > Very nice, I kind of made the same decision (software development > rather than wetlab bio), but in a different way, I'm going to the > European Bioinformatics Institute to a group who works on > textmining... Wow, great news! Congratulations! When are you moving to the UK? We hope around October, finance is sure for about 90%, so for me everything seems set, we still have to work hard to get the same thing done for Tania though.. > ;-) But great to hear that Orbicule goes so well, seems you have > things organized very well, kudos! Also very cool the presentation > in the SoHo store, be sure to share some pictures (and update your > blog a bit more often, just nitpicking ;-) ;-))) I'll post some pictures... Looking forward to that! > Definitely!! But I'm for sure willing to pay for it as well Peter, > have been considering to buy a license already... A license key is on its way. AWESOME! Enorm bedankt! Alex From kvddrift at earthlink.net Fri Mar 3 06:59:22 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Fri, 3 Mar 2006 06:59:22 -0500 Subject: [Biococoa-dev] Re: New goodies - BCStandaloneReader In-Reply-To: References: <376584F3-85F2-4E3D-A196-8C6C37DBE297@nki.nl> Message-ID: <989F659C-71B4-41F7-A65D-D0DB111ED455@earthlink.net> On Mar 3, 2006, at 5:16 AM, Peter Schols wrote: > > - Koen and Alex, any chance you will be donating the KDTextView to > the project? > Just a quick reaction before I run off to work. You can already d/l my code here: http://home.earthlink.net/~kvddrift/software/ linenumbers.tar.gz Alex made some nice additions, I like especially the cursor with the selection - very handy! Peter, I have no problems logging into bioinformatics.org. cheers, - Koen. From charles.parnot at gmail.com Fri Mar 3 16:27:43 2006 From: charles.parnot at gmail.com (Charles Parnot) Date: Fri, 3 Mar 2006 13:27:43 -0800 Subject: [Biococoa-dev] Re: New goodies - BCStandaloneReader In-Reply-To: References: <376584F3-85F2-4E3D-A196-8C6C37DBE297@nki.nl> Message-ID: Peter, nice to hear from you! Your new endeavour seems really exciting. Probably scary too. I am looking forward to your "living the life" post in a few months from now ;-) Undercover looks like a great idea. I got myself a copy to support your new venture... and, uh, well, because I want to use it! Btw, thanks for the link on your blog, next to the big stars like Wil Shipley and Mekentosj. Now, regarding BioCocoa, I have just one comment about the inclusion of Alex's code on the svn repository. Svn is really very nice for tags and branches, like you say. So I think it is very important that we add a tag with the version of Alex, used in real-life applications, as this should be an official release with a number, e.g. 1.5 (if 1.0 was the initial release... not sure?). We could even start a branch on it if more bugs are fixed later on this first version. I am proposing this, because it is always a good idea to have some stable official release, that people can rely on, and that we can go back to for testing. cheers, charles -- Xgrid-at-Stanford Help science move fast forward: http://cmgm.stanford.edu/~cparnot/xgrid-stanford Charles Parnot charles.parnot at gmail.com From info at orbicule.com Fri Mar 3 16:50:31 2006 From: info at orbicule.com (Peter Schols) Date: Fri, 3 Mar 2006 22:50:31 +0100 Subject: [Biococoa-dev] Re: New goodies - BCStandaloneReader In-Reply-To: References: <376584F3-85F2-4E3D-A196-8C6C37DBE297@nki.nl> Message-ID: <7FEAA4EA-2FAE-42AD-85FF-6896B056292A@orbicule.com> Hi Charles, Thanks for your support and enthusiasm! (although I would have been glad to send you a free license key -- I just did not want to post a key on the list as everyone will be able to see it in the archives). I'll make sure not to forget the "living the life" post within a few months... ;-) I fully agree with your idea to have a separate branch for Alex's code. It is very important indeed for a user of the framework to have a stable version while we work on the more 'experimental' stuff ;-) best wishes, peter On 03 Mar 2006, at 22:27, Charles Parnot wrote: > Peter, nice to hear from you! Your new endeavour seems really > exciting. Probably scary too. I am looking forward to your "living > the life" post in a few months from now ;-) > > Undercover looks like a great idea. I got myself a copy to support > your new venture... and, uh, well, because I want to use it! > > Btw, thanks for the link on your blog, next to the big stars like > Wil Shipley and Mekentosj. > > Now, regarding BioCocoa, I have just one comment about the > inclusion of Alex's code on the svn repository. Svn is really very > nice for tags and branches, like you say. So I think it is very > important that we add a tag with the version of Alex, used in real- > life applications, as this should be an official release with a > number, e.g. 1.5 (if 1.0 was the initial release... not sure?). We > could even start a branch on it if more bugs are fixed later on > this first version. I am proposing this, because it is always a > good idea to have some stable official release, that people can > rely on, and that we can go back to for testing. > > cheers, > > charles > > > > -- > Xgrid-at-Stanford > Help science move fast forward: > http://cmgm.stanford.edu/~cparnot/xgrid-stanford > > Charles Parnot > charles.parnot at gmail.com > > > > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > From charles.parnot at gmail.com Fri Mar 3 17:03:37 2006 From: charles.parnot at gmail.com (Charles Parnot) Date: Fri, 3 Mar 2006 14:03:37 -0800 Subject: [Biococoa-dev] Re: New goodies - BCStandaloneReader In-Reply-To: <7FEAA4EA-2FAE-42AD-85FF-6896B056292A@orbicule.com> References: <376584F3-85F2-4E3D-A196-8C6C37DBE297@nki.nl> <7FEAA4EA-2FAE-42AD-85FF-6896B056292A@orbicule.com> Message-ID: > Hi Charles, > > Thanks for your support and enthusiasm! (although I would have been > glad to send you a free license key -- I just did not want to post > a key on the list as everyone will be able to see it in the archives). > I'll make sure not to forget the "living the life" post within a > few months... ;-) > > I fully agree with your idea to have a separate branch for Alex's > code. It is very important indeed for a user of the framework to > have a stable version while we work on the more 'experimental' > stuff ;-) > > best wishes, > > peter I forgot to mention I love the name "Orbicule" and the logo looks great. The web site too. And while we are on it, the pictures of you and the mysterious eyes behind the powerbook too. I sent an email to the people I know in Stanford to let them know about Undercover, hopefully spreading the word a bit more... cheers, charles -- Xgrid-at-Stanford Help science move fast forward: http://cmgm.stanford.edu/~cparnot/xgrid-stanford Charles Parnot charles.parnot at gmail.com From mek at mekentosj.com Fri Mar 3 17:14:07 2006 From: mek at mekentosj.com (Alexander Griekspoor) Date: Fri, 3 Mar 2006 23:14:07 +0100 Subject: [Biococoa-dev] Re: New goodies - BCStandaloneReader In-Reply-To: References: <376584F3-85F2-4E3D-A196-8C6C37DBE297@nki.nl> Message-ID: > Btw, thanks for the link on your blog, next to the big stars like > Wil Shipley and Mekentosj. Yes, Peter thanks for sharing our site on your blog, next to the big stars like Wil Shipley. ;-) Thanks Charles, but that's too much credit. Cheers, Alex ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com LabAssistant - Get your life organized! http://www.mekentosj.com/labassistant ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From kvddrift at earthlink.net Fri Mar 3 17:12:11 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Fri, 3 Mar 2006 17:12:11 -0500 Subject: [Biococoa-dev] New goodies - BCStandaloneReader In-Reply-To: <376584F3-85F2-4E3D-A196-8C6C37DBE297@nki.nl> References: <376584F3-85F2-4E3D-A196-8C6C37DBE297@nki.nl> Message-ID: On Mar 2, 2006, at 6:10 AM, Alexander Griekspoor wrote: > NSString *message = @"iRNAi could not read the selected file, which > might not be a sequence file or not of a format that EnzymeX does > not support. Try converting it to plain text or fasta format. > Alternatively, you can copy the sequence from its native > application."; I'm sure this message is fixed in the released version ? ;-) - Koen. From a.griekspoor at nki.nl Sat Mar 4 04:38:44 2006 From: a.griekspoor at nki.nl (a.griekspoor at nki.nl) Date: Sat, 4 Mar 2006 10:38:44 +0100 Subject: [Biococoa-dev] New goodies - BCStandaloneReader Message-ID: <667464FDA2C81D4CA79D7F3B728D10E75A85F4@adsrv100.nki.nl> Haha, no it doesn't, so no we will see how well the BCReader works before people start sending this bug in (other than reading the code) ;-) Cheers, Alex -----Original Message----- From: Koen van der Drift [mailto:kvddrift at earthlink.net] Sent: Fri 3/3/2006 11:12 PM To: Alexander Griekspoor Cc: BioCocoa Mailinglist Subject: Re: [Biococoa-dev] New goodies - BCStandaloneReader On Mar 2, 2006, at 6:10 AM, Alexander Griekspoor wrote: > NSString *message = @"iRNAi could not read the selected file, which > might not be a sequence file or not of a format that EnzymeX does > not support. Try converting it to plain text or fasta format. > Alternatively, you can copy the sequence from its native > application."; I'm sure this message is fixed in the released version ? ;-) - Koen. From kvddrift at earthlink.net Sat Mar 4 10:09:28 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sat, 4 Mar 2006 10:09:28 -0500 Subject: [Biococoa-dev] Re: New goodies - BCStandaloneReader In-Reply-To: References: <376584F3-85F2-4E3D-A196-8C6C37DBE297@nki.nl> Message-ID: On Mar 3, 2006, at 5:16 AM, Peter Schols wrote: > I have been thinking about BioCocoa and this is what I think we > could do next: > - First of all, we should move to SVN. > I'm running my own in-house Subversion server on a Mac OS X machine > for almost two years now and it is not even in the same league when > compared to CVS. Moving to SVN would be great for several reasons > (better support for binary files (nibs!), easier to create > branches, great svnx front-end for Mac OS X, better Xcode > integration, ...), and it will definitely encourage us to submit > more to the repository. Since bioinformatics.org recently announced > support for svn, I'm willing to move the project to svn. The only > problem is that I can't login on the Bioinformatics.org homepage. I > always get the not logged in error message. I have tried several > things in 3 different browsers, but always the same error... could > someone verify this with their account? > > - I have to enhance and cleanup my BLAST and Entrez classes and > add them to BioCocoa. > I have a working demo app in which you can do a BLAST query on the > Net and get results in an NSTableView with only 3 lines of code. > I'll need to incorporate more BLAST settings into this BLAST > classes though to increase usefulness. > > - During some tests of the BLAST classes with ObjectAlloc (don't > ask me why) I noticed what could be a memory leak in BCSequence. I > was in a hurry back then (it was right before WWDC) but I'll do > some more testing and see if it's still there ;-) > > - As Koen suggested, we should move the BCReader code into the main > project and switch to BCSequenceArray. Koen proposed to do this and > that would be great! I'm always willing to help. > > - Koen and Alex, any chance you will be donating the KDTextView to > the project? > > - Later on, it would also be worth discussing CoreData and if/how > we could use it in BC. > > These are just a few thoughts, I'm sure many of you have their own > to-do lists and plans. Feel free to comment! Hi, I'm glad there is still some interest in pumping new life into BioCocoa. I have gone through a rough year personally and haven't had my mind on programming, but always had the feeling that BioCocoa shouldn't be left the way it is now. Here are some of my thoughts on the project. 1. Try to aim for a stable release as soon as possble 2. Move to svn 3. Review and address the TODO list in the project 4. Add new functionalities 5. Add more to BCAppKit 6. Promote BioCocoa. I recently found this website, http:// macresearch.org/, I strongly suggest we try to get an entry here, maybe for the next stable release. Also Peter and Alex, good luck with your new career moves - it all sounds very exciting. Alex when are you graduating? Happy Saturday! - Koen. From kvddrift at earthlink.net Sat Mar 4 15:36:09 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sat, 4 Mar 2006 15:36:09 -0500 Subject: [Biococoa-dev] New goodies - BCStandaloneReader In-Reply-To: <373106AD-1C8F-4143-BC48-0A9C6C97E1A1@nki.nl> References: <376584F3-85F2-4E3D-A196-8C6C37DBE297@nki.nl> <373106AD-1C8F-4143-BC48-0A9C6C97E1A1@nki.nl> Message-ID: On Mar 3, 2006, at 5:08 AM, Alexander Griekspoor wrote: > The only real change I made was to make the app pass just the > filename instead of the raw ASCII text of the file already > extracted like in Peter's original implementation. The reason is > the fact that I have now added to binary file formats, which need > the filename, not the ASCII text. Anyway it's a better separation > of code, with the app not having to care about anything else than > the filepath, and the framework doing the rest. Will this also work when using NSURLConnection to download a sequence from a website? As far as I can tell using NSURLConnection will return an NSData object from which an NSString can be retrieved. So maybe we should have both possibilities. - Koen. From a.griekspoor at nki.nl Sat Mar 4 15:44:52 2006 From: a.griekspoor at nki.nl (Alexander Griekspoor) Date: Sat, 4 Mar 2006 21:44:52 +0100 Subject: [Biococoa-dev] New goodies - BCStandaloneReader In-Reply-To: References: <376584F3-85F2-4E3D-A196-8C6C37DBE297@nki.nl> <373106AD-1C8F-4143-BC48-0A9C6C97E1A1@nki.nl> Message-ID: Hi Koen, No, the current version doesn't work with remote files, in fact a path (NSString) is passed, not an URL. So yes, there definitely is room for improvement there. Perhaps the best would be have indeed the string analysis code separated such that also fetched Data from remote locations can be fed... Cheers, Alex On 4-mrt-2006, at 21:36, Koen van der Drift wrote: > > On Mar 3, 2006, at 5:08 AM, Alexander Griekspoor wrote: > >> The only real change I made was to make the app pass just the >> filename instead of the raw ASCII text of the file already >> extracted like in Peter's original implementation. The reason is >> the fact that I have now added to binary file formats, which need >> the filename, not the ASCII text. Anyway it's a better separation >> of code, with the app not having to care about anything else than >> the filepath, and the framework doing the rest. > > Will this also work when using NSURLConnection to download a > sequence from a website? As far as I can tell using NSURLConnection > will return an NSData object from which an NSString can be > retrieved. So maybe we should have both possibilities. > > - Koen. > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > ************************************************************** ** Alexander Griekspoor ** ************************************************************** The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com MacOS X: The power of UNIX with the simplicity of the Mac *************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.griekspoor at nki.nl Sat Mar 4 15:45:52 2006 From: a.griekspoor at nki.nl (Alexander Griekspoor) Date: Sat, 4 Mar 2006 21:45:52 +0100 Subject: [Biococoa-dev] Re: New goodies - BCStandaloneReader In-Reply-To: References: <376584F3-85F2-4E3D-A196-8C6C37DBE297@nki.nl> Message-ID: <84E3E842-7046-4416-8EB2-874B0AEF57EF@nki.nl> > Alex when are you graduating? Working hard to get a date now, hopefully september, plus Tom and I hope to do it on the same day ;-) ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com Claiming that the Macintosh is inferior to Windows because most people use Windows, is like saying that all other restaurants serve food that is inferior to McDonalds ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From biococoa at bioworxx.com Sun Mar 5 14:57:29 2006 From: biococoa at bioworxx.com (Philipp Seibel) Date: Sun, 5 Mar 2006 20:57:29 +0100 Subject: [Biococoa-dev] Nice to see some activity Message-ID: Hey guys, i'm still alive as well :-). Nice to see you all on the list again. Everyone seems to be interested in an ongoing biococoa project. Thats nice to hear, i'm also interested to continue, but my spare time is very limited at the moment. I'm not programming very much cocoa the last few month, but i'm interested in some minor tasks to help you guys. @Alex & Tom: Very good job, i like the new versions of your apps. Btw: I'm still interested in the pictures from last year :-) Probably we can ichat sometime, would be nice to hear something from you. @Peter: Exciting news, i wish you all the best with your own company. I have to admit i haven't seen undercover so far, but i will have a look for sure. Looking forward to active discussions on the list :-) Phil From kvddrift at earthlink.net Sun Mar 5 17:14:20 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sun, 5 Mar 2006 17:14:20 -0500 Subject: [Biococoa-dev] Nice to see some activity In-Reply-To: References: Message-ID: On Mar 5, 2006, at 2:57 PM, Philipp Seibel wrote: > > i'm still alive as well :-). > Nice to see you all on the list again. Everyone seems to be > interested in an ongoing biococoa project. Thats nice to hear, i'm > also interested to continue, but my spare time is very limited at > the moment. I'm not programming very much cocoa the last few month, > but i'm interested in some minor tasks to help you guys. Hi Philip, Good to see that you are still interested! Don't worry about not having enough time right now. Regarding 'little tasks', maybe when we're up and running again, we can populate the TODO list with more items, so everyone can pick something that suits there availability. cheers, - Koen. From a.griekspoor at nki.nl Mon Mar 6 05:08:11 2006 From: a.griekspoor at nki.nl (Alexander Griekspoor) Date: Mon, 6 Mar 2006 11:08:11 +0100 Subject: [Biococoa-dev] More goodies!! Message-ID: Hi guys, With EnzymeX3 now in beta testing phase it's time to share the wealth... I've thrown together a very simple demo app showing the three goodies I would like to donate back to the BioCocoa project: - BCReader, the standalone BCReader classes for sequence file IO (original version Peter Schols) - EntrezController, a controller plus view for browsing and fetching NCBI's Entrez Database - KDTextView+, a custom NSTextView for displaying biological sequences (original version Koen van der Drift) Download and enjoy at: http://www.mekentosj.com/biococoa/ BCAppkit_Test.dmg Of course all feedback and bug reports are welcome (or not depending on how you interpret this sentence ;-) Also, coming back to Koen's remark. There are a few things I/we could do. First, it would be nice if it had these views mentioned as available on the website and the code given a place on the svn server. Second, we could perhaps post a small announcement (few lines) on cocoa-dev to notify other cocoa developers, also letting them know about BioCocoa again. Finally, we could compose a little message to MacResearch describing the BioCocoa project and also the availability of this code. Alternatively, I can inform them about it when we release the EnzymeX final version. I believe Tom spoke a few times with the guys behind MacResearch, so we could inform them directly.. Let me know what you guys think. Cheers, Alex ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com 4Peaks - For Peaks, Four Peaks. 2004 Winner of the Apple Design Awards Best Mac OS X Student Product http://www.mekentosj.com/4peaks ********************************************************* From mek at mekentosj.com Mon Mar 6 05:09:39 2006 From: mek at mekentosj.com (Alexander Griekspoor) Date: Mon, 6 Mar 2006 11:09:39 +0100 Subject: [Biococoa-dev] Nice to see some activity In-Reply-To: References: Message-ID: Hi Phil, Good to hear from you again! Yeah, we should definitely exchange the pictures from last year, forgot completely about it. Let's discuss it offline and we can setup an FTP account... Cheers, Alex On 5-mrt-2006, at 20:57, Philipp Seibel wrote: > Hey guys, > > i'm still alive as well :-). > Nice to see you all on the list again. Everyone seems to be > interested in an ongoing biococoa project. Thats nice to hear, i'm > also interested to continue, but my spare time is very limited at > the moment. I'm not programming very much cocoa the last few month, > but i'm interested in some minor tasks to help you guys. > > @Alex & Tom: Very good job, i like the new versions of your apps. > Btw: I'm still interested in the pictures from last year :-) > Probably we can ichat sometime, would be nice to hear something > from you. > > @Peter: Exciting news, i wish you all the best with your own > company. I have to admit i haven't seen undercover so far, but i > will have a look for sure. > > Looking forward to active discussions on the list :-) > > Phil > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com Windows vs Mac 65 million years ago, there were more dinosaurs than humans. Where are the dinosaurs now? ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From peter.schols at bio.kuleuven.be Mon Mar 6 07:33:17 2006 From: peter.schols at bio.kuleuven.be (Peter Schols) Date: Mon, 6 Mar 2006 13:33:17 +0100 Subject: [Biococoa-dev] More goodies!! In-Reply-To: References: Message-ID: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> Hi Alex and other listers, This BCAppkitTest works great and it will be a great addition to BioCocoa! Over the weekend, I have worked with the - very helpful - people at Bioinformatics.org to solve my login problems (it turned out to be a proxy issue that was caused by a bug on their end, they have been able to fix it). As a result, I am totally ready to start the subversion repository and do the initial import. The main question I have now is: how should we organise the repository and the BioCocoa website? There are several scenarios: 1. Checkout the latest version of the BioCocoa framework from CVS and use that as the initial import for SVN. Make the BCAppkitTest available as a download on our website (both source and compiled app) but wait to put it in the repository until it's adapted to use the classes in our own framework. 2. Checkout the latest version of the BioCocoa framework from CVS and use that as the initial import for SVN. Make a second repository (I think this is possible @ bioinformatics.org) and put BCAppkitTest in there. 3. Checkout the latest version of the BioCocoa framework from CVS, add the BCAppkitTest somewhere in the hierarchy of that same BioCocoa folder and check this hybrid framework in to one repository. I think I'd prefer solution number 1 (or 2) because - it seems a bit weird to have part of a framework that does not use the base classes available in the rest of the framework - it might confuse users of the framework - we should aim to integrate BCAppkitTest into BioCocoa asap, this won't be a huge undertaking Please let me know your preference and I would be glad to create the Subversion repository and send instructions on using it. I'd also be glad to update the website and make the BCAppkitTest available. Peter On 06 Mar 2006, at 11:08, Alexander Griekspoor wrote: > Hi guys, > > With EnzymeX3 now in beta testing phase it's time to share the > wealth... > I've thrown together a very simple demo app showing the three > goodies I would like to donate back to the BioCocoa project: > - BCReader, the standalone BCReader classes for sequence file IO > (original version Peter Schols) > - EntrezController, a controller plus view for browsing and > fetching NCBI's Entrez Database > - KDTextView+, a custom NSTextView for displaying biological > sequences (original version Koen van der Drift) > > Download and enjoy at: http://www.mekentosj.com/biococoa/ > BCAppkit_Test.dmg > Of course all feedback and bug reports are welcome (or not > depending on how you interpret this sentence ;-) > > Also, coming back to Koen's remark. There are a few things I/we > could do. > First, it would be nice if it had these views mentioned as > available on the website and the code given a place on the svn server. > Second, we could perhaps post a small announcement (few lines) on > cocoa-dev to notify other cocoa developers, also letting them know > about BioCocoa again. > Finally, we could compose a little message to MacResearch > describing the BioCocoa project and also the availability of this > code. > Alternatively, I can inform them about it when we release the > EnzymeX final version. I believe Tom spoke a few times with the > guys behind MacResearch, so we could inform them directly.. Let me > know what you guys think. > Cheers, > Alex > > > ********************************************************* > ** Alexander Griekspoor ** > ********************************************************* > The Netherlands Cancer Institute > Department of Tumorbiology (H4) > Plesmanlaan 121, 1066 CX, Amsterdam > Tel: + 31 20 - 512 2023 > Fax: + 31 20 - 512 2029 > AIM: mekentosj at mac.com > E-mail: a.griekspoor at nki.nl > Web: http://www.mekentosj.com > > 4Peaks - For Peaks, Four Peaks. > 2004 Winner of the Apple Design Awards > Best Mac OS X Student Product > http://www.mekentosj.com/4peaks > > ********************************************************* > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From a.griekspoor at nki.nl Mon Mar 6 07:40:50 2006 From: a.griekspoor at nki.nl (Alexander Griekspoor) Date: Mon, 6 Mar 2006 13:40:50 +0100 Subject: [Biococoa-dev] More goodies!! In-Reply-To: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> References: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> Message-ID: <03C7D5DA-B993-41F9-A227-4ED264EBA540@nki.nl> Good news! I totally agree, I would go for option 1 as well, post the code on the website and continue working on the new approach/classes. In principle we don't expect to change much on this Appkit test, all new developments should focus on the new classes and on getting the equivalent functionality of the BCAppkit-Test using these new base classes. Still, it's nice for people with legacy or minor requirements (just simple textview, text base sequences, etc) to have something really simple without having to use/learn the new approach, so they can download it from the website. Also, I think its time to update the BioCocoa website to represent this all. It should give a general introduction of who we are and what we aim. It should describe the current stable releases (BioCocoa 1.6 + "BCAppkitStandalone", with links to download etc It should describe our current plans on developing BioCocoa 2.0 -> give some ideaof what we want and info on how to join, access the svn server etc. After that it's time to send an email to MacResearch ;-) Cheers, Alex On 6-mrt-2006, at 13:33, Peter Schols wrote: > Hi Alex and other listers, > > This BCAppkitTest works great and it will be a great addition to > BioCocoa! > Over the weekend, I have worked with the - very helpful - people at > Bioinformatics.org to solve my login problems (it turned out to be > a proxy issue that was caused by a bug on their end, they have been > able to fix it). > As a result, I am totally ready to start the subversion repository > and do the initial import. > > The main question I have now is: how should we organise the > repository and the BioCocoa website? There are several scenarios: > > 1. Checkout the latest version of the BioCocoa framework from CVS > and use that as the initial import for SVN. Make the BCAppkitTest > available as a download on our website (both source and compiled > app) but wait to put it in the repository until it's adapted to use > the classes in our own framework. > > 2. Checkout the latest version of the BioCocoa framework from CVS > and use that as the initial import for SVN. Make a second > repository (I think this is possible @ bioinformatics.org) and put > BCAppkitTest in there. > > 3. Checkout the latest version of the BioCocoa framework from CVS, > add the BCAppkitTest somewhere in the hierarchy of that same > BioCocoa folder and check this hybrid framework in to one repository. > > > I think I'd prefer solution number 1 (or 2) because > - it seems a bit weird to have part of a framework that does not > use the base classes available in the rest of the framework > - it might confuse users of the framework > - we should aim to integrate BCAppkitTest into BioCocoa asap, this > won't be a huge undertaking > > Please let me know your preference and I would be glad to create > the Subversion repository and send instructions on using it. I'd > also be glad to update the website and make the BCAppkitTest > available. > > Peter > > > > On 06 Mar 2006, at 11:08, Alexander Griekspoor wrote: > >> Hi guys, >> >> With EnzymeX3 now in beta testing phase it's time to share the >> wealth... >> I've thrown together a very simple demo app showing the three >> goodies I would like to donate back to the BioCocoa project: >> - BCReader, the standalone BCReader classes for sequence file IO >> (original version Peter Schols) >> - EntrezController, a controller plus view for browsing and >> fetching NCBI's Entrez Database >> - KDTextView+, a custom NSTextView for displaying biological >> sequences (original version Koen van der Drift) >> >> Download and enjoy at: http://www.mekentosj.com/biococoa/ >> BCAppkit_Test.dmg >> Of course all feedback and bug reports are welcome (or not >> depending on how you interpret this sentence ;-) >> >> Also, coming back to Koen's remark. There are a few things I/we >> could do. >> First, it would be nice if it had these views mentioned as >> available on the website and the code given a place on the svn >> server. >> Second, we could perhaps post a small announcement (few lines) on >> cocoa-dev to notify other cocoa developers, also letting them know >> about BioCocoa again. >> Finally, we could compose a little message to MacResearch >> describing the BioCocoa project and also the availability of this >> code. >> Alternatively, I can inform them about it when we release the >> EnzymeX final version. I believe Tom spoke a few times with the >> guys behind MacResearch, so we could inform them directly.. Let me >> know what you guys think. >> Cheers, >> Alex >> >> >> ********************************************************* >> ** Alexander Griekspoor ** >> ********************************************************* >> The Netherlands Cancer Institute >> Department of Tumorbiology (H4) >> Plesmanlaan 121, 1066 CX, Amsterdam >> Tel: + 31 20 - 512 2023 >> Fax: + 31 20 - 512 2029 >> AIM: mekentosj at mac.com >> E-mail: a.griekspoor at nki.nl >> Web: http://www.mekentosj.com >> >> 4Peaks - For Peaks, Four Peaks. >> 2004 Winner of the Apple Design Awards >> Best Mac OS X Student Product >> http://www.mekentosj.com/4peaks >> >> ********************************************************* >> >> _______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/biococoa-dev >> > > > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com 4Peaks - For Peaks, Four Peaks. 2004 Winner of the Apple Design Awards Best Mac OS X Student Product http://www.mekentosj.com/4peaks ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.griekspoor at nki.nl Mon Mar 6 07:44:00 2006 From: a.griekspoor at nki.nl (Alexander Griekspoor) Date: Mon, 6 Mar 2006 13:44:00 +0100 Subject: [Biococoa-dev] More goodies!! In-Reply-To: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> References: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> Message-ID: Oh Peter, forgot to add... if you can make it look as good as the Orbicule website, then please go ahead! Very well done. Do you do all artwork youself? Website, undercover icon, intro movie of the registration app etc? I was impressed, time to submit undercover for the Design Awards I would say!! This time the silver cube, absolutely sure! Cheers, Alex On 6-mrt-2006, at 13:33, Peter Schols wrote: > Hi Alex and other listers, > > This BCAppkitTest works great and it will be a great addition to > BioCocoa! > Over the weekend, I have worked with the - very helpful - people at > Bioinformatics.org to solve my login problems (it turned out to be > a proxy issue that was caused by a bug on their end, they have been > able to fix it). > As a result, I am totally ready to start the subversion repository > and do the initial import. > > The main question I have now is: how should we organise the > repository and the BioCocoa website? There are several scenarios: > > 1. Checkout the latest version of the BioCocoa framework from CVS > and use that as the initial import for SVN. Make the BCAppkitTest > available as a download on our website (both source and compiled > app) but wait to put it in the repository until it's adapted to use > the classes in our own framework. > > 2. Checkout the latest version of the BioCocoa framework from CVS > and use that as the initial import for SVN. Make a second > repository (I think this is possible @ bioinformatics.org) and put > BCAppkitTest in there. > > 3. Checkout the latest version of the BioCocoa framework from CVS, > add the BCAppkitTest somewhere in the hierarchy of that same > BioCocoa folder and check this hybrid framework in to one repository. > > > I think I'd prefer solution number 1 (or 2) because > - it seems a bit weird to have part of a framework that does not > use the base classes available in the rest of the framework > - it might confuse users of the framework > - we should aim to integrate BCAppkitTest into BioCocoa asap, this > won't be a huge undertaking > > Please let me know your preference and I would be glad to create > the Subversion repository and send instructions on using it. I'd > also be glad to update the website and make the BCAppkitTest > available. > > Peter > > > > On 06 Mar 2006, at 11:08, Alexander Griekspoor wrote: > >> Hi guys, >> >> With EnzymeX3 now in beta testing phase it's time to share the >> wealth... >> I've thrown together a very simple demo app showing the three >> goodies I would like to donate back to the BioCocoa project: >> - BCReader, the standalone BCReader classes for sequence file IO >> (original version Peter Schols) >> - EntrezController, a controller plus view for browsing and >> fetching NCBI's Entrez Database >> - KDTextView+, a custom NSTextView for displaying biological >> sequences (original version Koen van der Drift) >> >> Download and enjoy at: http://www.mekentosj.com/biococoa/ >> BCAppkit_Test.dmg >> Of course all feedback and bug reports are welcome (or not >> depending on how you interpret this sentence ;-) >> >> Also, coming back to Koen's remark. There are a few things I/we >> could do. >> First, it would be nice if it had these views mentioned as >> available on the website and the code given a place on the svn >> server. >> Second, we could perhaps post a small announcement (few lines) on >> cocoa-dev to notify other cocoa developers, also letting them know >> about BioCocoa again. >> Finally, we could compose a little message to MacResearch >> describing the BioCocoa project and also the availability of this >> code. >> Alternatively, I can inform them about it when we release the >> EnzymeX final version. I believe Tom spoke a few times with the >> guys behind MacResearch, so we could inform them directly.. Let me >> know what you guys think. >> Cheers, >> Alex >> >> >> ********************************************************* >> ** Alexander Griekspoor ** >> ********************************************************* >> The Netherlands Cancer Institute >> Department of Tumorbiology (H4) >> Plesmanlaan 121, 1066 CX, Amsterdam >> Tel: + 31 20 - 512 2023 >> Fax: + 31 20 - 512 2029 >> AIM: mekentosj at mac.com >> E-mail: a.griekspoor at nki.nl >> Web: http://www.mekentosj.com >> >> 4Peaks - For Peaks, Four Peaks. >> 2004 Winner of the Apple Design Awards >> Best Mac OS X Student Product >> http://www.mekentosj.com/4peaks >> >> ********************************************************* >> >> _______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/biococoa-dev >> > > > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > *********************************** Mek (Alexander Griekspoor) MekenTosj.com Web: http://www.mekentosj.com Mail: mek at mekentosj.com *********************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From charles.parnot at gmail.com Mon Mar 6 12:49:02 2006 From: charles.parnot at gmail.com (Charles Parnot) Date: Mon, 6 Mar 2006 09:49:02 -0800 Subject: [Biococoa-dev] More goodies!! In-Reply-To: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> References: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> Message-ID: I don't think we need 2 repositories. Subversion is very convenient for branches and tags. I think Alex's final code should be included "as is" in the current svn directory, as a side project of BioCocoa, because this is usable-right-now tested code, just like BioCocoa 1.6 is. I would do the following structure in the repository, something close to the usual "recommanded" layout: BioCoao ...Trunk ...... ......[Checkout of the latest CVS repository] ...... ...Tags ......BioCocoa 1.6 <-- BCReader from Peter ......BioCocoa 1.7 <-- BCReader from Alex ......Goodies .........EntrezController 1.0 <--- From Alex .........KDTextView 1.0 <-- From Koen .........KDTextView 1.1 <-- From Alex ...Branches ......Goodies The "Goodies" directory could be named something else, like "Subprojects" or whatever you like, and might alternatively be moved to the root (under BioCocoa), and have its own Trunk, Tags and Branches. The "Branches" directory is empty right now, but might soon have a "BioCocoa 1.x" branch if we want to fix bugs / add features on the 1.7 version, and/or have a "Goodies/KDTextView 1.x" branch for the same reasons. Of course, the code for these should be merged in the BioCocoa Trunk as soon as possible too, and we probably don't want to generate too much code on the 1.x versions. Let's take advantage of super-easy management of Tags and Branches with Subversion... Just my 2 cents! charles On Mar 6, 2006, at 4:33 AM, Peter Schols wrote: > Hi Alex and other listers, > > This BCAppkitTest works great and it will be a great addition to > BioCocoa! > Over the weekend, I have worked with the - very helpful - people at > Bioinformatics.org to solve my login problems (it turned out to be > a proxy issue that was caused by a bug on their end, they have been > able to fix it). > As a result, I am totally ready to start the subversion repository > and do the initial import. > > The main question I have now is: how should we organise the > repository and the BioCocoa website? There are several scenarios: > > 1. Checkout the latest version of the BioCocoa framework from CVS > and use that as the initial import for SVN. Make the BCAppkitTest > available as a download on our website (both source and compiled > app) but wait to put it in the repository until it's adapted to use > the classes in our own framework. > > 2. Checkout the latest version of the BioCocoa framework from CVS > and use that as the initial import for SVN. Make a second > repository (I think this is possible @ bioinformatics.org) and put > BCAppkitTest in there. > > 3. Checkout the latest version of the BioCocoa framework from CVS, > add the BCAppkitTest somewhere in the hierarchy of that same > BioCocoa folder and check this hybrid framework in to one repository. > > > I think I'd prefer solution number 1 (or 2) because > - it seems a bit weird to have part of a framework that does not > use the base classes available in the rest of the framework > - it might confuse users of the framework > - we should aim to integrate BCAppkitTest into BioCocoa asap, this > won't be a huge undertaking > > Please let me know your preference and I would be glad to create > the Subversion repository and send instructions on using it. I'd > also be glad to update the website and make the BCAppkitTest > available. > > Peter > > > > On 06 Mar 2006, at 11:08, Alexander Griekspoor wrote: > >> Hi guys, >> >> With EnzymeX3 now in beta testing phase it's time to share the >> wealth... >> I've thrown together a very simple demo app showing the three >> goodies I would like to donate back to the BioCocoa project: >> - BCReader, the standalone BCReader classes for sequence file IO >> (original version Peter Schols) >> - EntrezController, a controller plus view for browsing and >> fetching NCBI's Entrez Database >> - KDTextView+, a custom NSTextView for displaying biological >> sequences (original version Koen van der Drift) >> >> Download and enjoy at: http://www.mekentosj.com/biococoa/ >> BCAppkit_Test.dmg >> Of course all feedback and bug reports are welcome (or not >> depending on how you interpret this sentence ;-) >> >> Also, coming back to Koen's remark. There are a few things I/we >> could do. >> First, it would be nice if it had these views mentioned as >> available on the website and the code given a place on the svn >> server. >> Second, we could perhaps post a small announcement (few lines) on >> cocoa-dev to notify other cocoa developers, also letting them know >> about BioCocoa again. >> Finally, we could compose a little message to MacResearch >> describing the BioCocoa project and also the availability of this >> code. >> Alternatively, I can inform them about it when we release the >> EnzymeX final version. I believe Tom spoke a few times with the >> guys behind MacResearch, so we could inform them directly.. Let me >> know what you guys think. >> Cheers, >> Alex >> >> >> ********************************************************* >> ** Alexander Griekspoor ** >> ********************************************************* >> The Netherlands Cancer Institute >> Department of Tumorbiology (H4) >> Plesmanlaan 121, 1066 CX, Amsterdam >> Tel: + 31 20 - 512 2023 >> Fax: + 31 20 - 512 2029 >> AIM: mekentosj at mac.com >> E-mail: a.griekspoor at nki.nl >> Web: http://www.mekentosj.com >> >> 4Peaks - For Peaks, Four Peaks. >> 2004 Winner of the Apple Design Awards >> Best Mac OS X Student Product >> http://www.mekentosj.com/4peaks >> >> ********************************************************* >> >> _______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/biococoa-dev >> > > > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev -- Xgrid-at-Stanford Help science move fast forward: http://cmgm.stanford.edu/~cparnot/xgrid-stanford Charles Parnot charles.parnot at gmail.com From peter.schols at bio.kuleuven.be Mon Mar 6 12:58:19 2006 From: peter.schols at bio.kuleuven.be (Peter Schols) Date: Mon, 6 Mar 2006 18:58:19 +0100 Subject: [Biococoa-dev] More goodies!! In-Reply-To: <03C7D5DA-B993-41F9-A227-4ED264EBA540@nki.nl> References: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> <03C7D5DA-B993-41F9-A227-4ED264EBA540@nki.nl> Message-ID: Alex, I fully agree. I wanted to start importing right now, but I can't seem to login to the CVS repository to checkout the latest version. Since I don't want to bother with CVS anymore, could someone send me a freshly checked out copy of the entire CVS repository (in a .zip archive if possible)? Thanks! Peter On 06 Mar 2006, at 13:40, Alexander Griekspoor wrote: > Good news! > > I totally agree, I would go for option 1 as well, post the code on > the website and continue working on the new approach/classes. > In principle we don't expect to change much on this Appkit test, > all new developments should focus on the new classes and on getting > the equivalent functionality of the BCAppkit-Test using these new > base classes. > > Still, it's nice for people with legacy or minor requirements (just > simple textview, text base sequences, etc) to have something really > simple without having to use/learn the new approach, so they can > download it from the website. > > Also, I think its time to update the BioCocoa website to represent > this all. > It should give a general introduction of who we are and what we aim. > It should describe the current stable releases (BioCocoa 1.6 + > "BCAppkitStandalone", with links to download etc > It should describe our current plans on developing BioCocoa 2.0 -> > give some ideaof what we want and info on how to join, access the > svn server etc. > After that it's time to send an email to MacResearch ;-) > > Cheers, > Alex > > > On 6-mrt-2006, at 13:33, Peter Schols wrote: > >> Hi Alex and other listers, >> >> This BCAppkitTest works great and it will be a great addition to >> BioCocoa! >> Over the weekend, I have worked with the - very helpful - people >> at Bioinformatics.org to solve my login problems (it turned out to >> be a proxy issue that was caused by a bug on their end, they have >> been able to fix it). >> As a result, I am totally ready to start the subversion repository >> and do the initial import. >> >> The main question I have now is: how should we organise the >> repository and the BioCocoa website? There are several scenarios: >> >> 1. Checkout the latest version of the BioCocoa framework from CVS >> and use that as the initial import for SVN. Make the BCAppkitTest >> available as a download on our website (both source and compiled >> app) but wait to put it in the repository until it's adapted to >> use the classes in our own framework. >> >> 2. Checkout the latest version of the BioCocoa framework from CVS >> and use that as the initial import for SVN. Make a second >> repository (I think this is possible @ bioinformatics.org) and put >> BCAppkitTest in there. >> >> 3. Checkout the latest version of the BioCocoa framework from CVS, >> add the BCAppkitTest somewhere in the hierarchy of that same >> BioCocoa folder and check this hybrid framework in to one repository. >> >> >> I think I'd prefer solution number 1 (or 2) because >> - it seems a bit weird to have part of a framework that does not >> use the base classes available in the rest of the framework >> - it might confuse users of the framework >> - we should aim to integrate BCAppkitTest into BioCocoa asap, this >> won't be a huge undertaking >> >> Please let me know your preference and I would be glad to create >> the Subversion repository and send instructions on using it. I'd >> also be glad to update the website and make the BCAppkitTest >> available. >> >> Peter >> >> >> >> On 06 Mar 2006, at 11:08, Alexander Griekspoor wrote: >> >>> Hi guys, >>> >>> With EnzymeX3 now in beta testing phase it's time to share the >>> wealth... >>> I've thrown together a very simple demo app showing the three >>> goodies I would like to donate back to the BioCocoa project: >>> - BCReader, the standalone BCReader classes for sequence file IO >>> (original version Peter Schols) >>> - EntrezController, a controller plus view for browsing and >>> fetching NCBI's Entrez Database >>> - KDTextView+, a custom NSTextView for displaying biological >>> sequences (original version Koen van der Drift) >>> >>> Download and enjoy at: http://www.mekentosj.com/biococoa/ >>> BCAppkit_Test.dmg >>> Of course all feedback and bug reports are welcome (or not >>> depending on how you interpret this sentence ;-) >>> >>> Also, coming back to Koen's remark. There are a few things I/we >>> could do. >>> First, it would be nice if it had these views mentioned as >>> available on the website and the code given a place on the svn >>> server. >>> Second, we could perhaps post a small announcement (few lines) on >>> cocoa-dev to notify other cocoa developers, also letting them >>> know about BioCocoa again. >>> Finally, we could compose a little message to MacResearch >>> describing the BioCocoa project and also the availability of this >>> code. >>> Alternatively, I can inform them about it when we release the >>> EnzymeX final version. I believe Tom spoke a few times with the >>> guys behind MacResearch, so we could inform them directly.. Let >>> me know what you guys think. >>> Cheers, >>> Alex >>> >>> >>> ********************************************************* >>> ** Alexander Griekspoor ** >>> ********************************************************* >>> The Netherlands Cancer Institute >>> Department of Tumorbiology (H4) >>> Plesmanlaan 121, 1066 CX, Amsterdam >>> Tel: + 31 20 - 512 2023 >>> Fax: + 31 20 - 512 2029 >>> AIM: mekentosj at mac.com >>> E-mail: a.griekspoor at nki.nl >>> Web: http://www.mekentosj.com >>> >>> 4Peaks - For Peaks, Four Peaks. >>> 2004 Winner of the Apple Design Awards >>> Best Mac OS X Student Product >>> http://www.mekentosj.com/4peaks >>> >>> ********************************************************* >>> >>> _______________________________________________ >>> Biococoa-dev mailing list >>> Biococoa-dev at bioinformatics.org >>> https://bioinformatics.org/mailman/listinfo/biococoa-dev >>> >> >> >> Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm >> >> _______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/biococoa-dev >> > > ********************************************************* > ** Alexander Griekspoor ** > ********************************************************* > The Netherlands Cancer Institute > Department of Tumorbiology (H4) > Plesmanlaan 121, 1066 CX, Amsterdam > Tel: + 31 20 - 512 2023 > Fax: + 31 20 - 512 2029 > AIM: mekentosj at mac.com > E-mail: a.griekspoor at nki.nl > Web: http://www.mekentosj.com > > 4Peaks - For Peaks, Four Peaks. > 2004 Winner of the Apple Design Awards > Best Mac OS X Student Product > http://www.mekentosj.com/4peaks > > ********************************************************* > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From peter.schols at bio.kuleuven.be Mon Mar 6 13:03:32 2006 From: peter.schols at bio.kuleuven.be (Peter Schols) Date: Mon, 6 Mar 2006 19:03:32 +0100 Subject: [Biococoa-dev] More goodies!! In-Reply-To: References: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> Message-ID: <2E39A5B3-EAFD-41F7-8A29-8ED09FB461DB@bio.kuleuven.be> Wow, thanks ;-) I did everything myself, except for the icon, which has been designed by Jasper Hauser who lives very close to you, Alex. Once I get the SVN repository ready, I'll spend some time with the BC website and see what I can do... ;-) peter On 06 Mar 2006, at 13:44, Alexander Griekspoor wrote: > Oh Peter, forgot to add... if you can make it look as good as the > Orbicule website, then please go ahead! > Very well done. Do you do all artwork youself? Website, undercover > icon, intro movie of the registration app etc? > I was impressed, time to submit undercover for the Design Awards I > would say!! This time the silver cube, absolutely sure! > Cheers, > Alex > > > On 6-mrt-2006, at 13:33, Peter Schols wrote: > >> Hi Alex and other listers, >> >> This BCAppkitTest works great and it will be a great addition to >> BioCocoa! >> Over the weekend, I have worked with the - very helpful - people >> at Bioinformatics.org to solve my login problems (it turned out to >> be a proxy issue that was caused by a bug on their end, they have >> been able to fix it). >> As a result, I am totally ready to start the subversion repository >> and do the initial import. >> >> The main question I have now is: how should we organise the >> repository and the BioCocoa website? There are several scenarios: >> >> 1. Checkout the latest version of the BioCocoa framework from CVS >> and use that as the initial import for SVN. Make the BCAppkitTest >> available as a download on our website (both source and compiled >> app) but wait to put it in the repository until it's adapted to >> use the classes in our own framework. >> >> 2. Checkout the latest version of the BioCocoa framework from CVS >> and use that as the initial import for SVN. Make a second >> repository (I think this is possible @ bioinformatics.org) and put >> BCAppkitTest in there. >> >> 3. Checkout the latest version of the BioCocoa framework from CVS, >> add the BCAppkitTest somewhere in the hierarchy of that same >> BioCocoa folder and check this hybrid framework in to one repository. >> >> >> I think I'd prefer solution number 1 (or 2) because >> - it seems a bit weird to have part of a framework that does not >> use the base classes available in the rest of the framework >> - it might confuse users of the framework >> - we should aim to integrate BCAppkitTest into BioCocoa asap, this >> won't be a huge undertaking >> >> Please let me know your preference and I would be glad to create >> the Subversion repository and send instructions on using it. I'd >> also be glad to update the website and make the BCAppkitTest >> available. >> >> Peter >> >> >> >> On 06 Mar 2006, at 11:08, Alexander Griekspoor wrote: >> >>> Hi guys, >>> >>> With EnzymeX3 now in beta testing phase it's time to share the >>> wealth... >>> I've thrown together a very simple demo app showing the three >>> goodies I would like to donate back to the BioCocoa project: >>> - BCReader, the standalone BCReader classes for sequence file IO >>> (original version Peter Schols) >>> - EntrezController, a controller plus view for browsing and >>> fetching NCBI's Entrez Database >>> - KDTextView+, a custom NSTextView for displaying biological >>> sequences (original version Koen van der Drift) >>> >>> Download and enjoy at: http://www.mekentosj.com/biococoa/ >>> BCAppkit_Test.dmg >>> Of course all feedback and bug reports are welcome (or not >>> depending on how you interpret this sentence ;-) >>> >>> Also, coming back to Koen's remark. There are a few things I/we >>> could do. >>> First, it would be nice if it had these views mentioned as >>> available on the website and the code given a place on the svn >>> server. >>> Second, we could perhaps post a small announcement (few lines) on >>> cocoa-dev to notify other cocoa developers, also letting them >>> know about BioCocoa again. >>> Finally, we could compose a little message to MacResearch >>> describing the BioCocoa project and also the availability of this >>> code. >>> Alternatively, I can inform them about it when we release the >>> EnzymeX final version. I believe Tom spoke a few times with the >>> guys behind MacResearch, so we could inform them directly.. Let >>> me know what you guys think. >>> Cheers, >>> Alex >>> >>> >>> ********************************************************* >>> ** Alexander Griekspoor ** >>> ********************************************************* >>> The Netherlands Cancer Institute >>> Department of Tumorbiology (H4) >>> Plesmanlaan 121, 1066 CX, Amsterdam >>> Tel: + 31 20 - 512 2023 >>> Fax: + 31 20 - 512 2029 >>> AIM: mekentosj at mac.com >>> E-mail: a.griekspoor at nki.nl >>> Web: http://www.mekentosj.com >>> >>> 4Peaks - For Peaks, Four Peaks. >>> 2004 Winner of the Apple Design Awards >>> Best Mac OS X Student Product >>> http://www.mekentosj.com/4peaks >>> >>> ********************************************************* >>> >>> _______________________________________________ >>> Biococoa-dev mailing list >>> Biococoa-dev at bioinformatics.org >>> https://bioinformatics.org/mailman/listinfo/biococoa-dev >>> >> >> >> Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm >> >> _______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/biococoa-dev >> > > *********************************** > Mek (Alexander Griekspoor) > MekenTosj.com > Web: http://www.mekentosj.com > Mail: mek at mekentosj.com > *********************************** > > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From peter.schols at bio.kuleuven.be Mon Mar 6 14:04:30 2006 From: peter.schols at bio.kuleuven.be (Peter Schols) Date: Mon, 6 Mar 2006 20:04:30 +0100 Subject: [Biococoa-dev] More goodies!! In-Reply-To: References: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> Message-ID: <35546CEE-7C11-4314-87A2-644FE49C08D8@bio.kuleuven.be> Hi Charles, If I get you right, you would prefer option 3, so you'd move the "AlexCode" to a separate folder in the trunk? I'm a bit confused... sorry Peter On 06 Mar 2006, at 18:49, Charles Parnot wrote: > I don't think we need 2 repositories. Subversion is very convenient > for branches and tags. I think Alex's final code should be included > "as is" in the current svn directory, as a side project of > BioCocoa, because this is usable-right-now tested code, just like > BioCocoa 1.6 is. I would do the following structure in the > repository, something close to the usual "recommanded" layout: > > BioCoao > ...Trunk > ...... > ......[Checkout of the latest CVS repository] > ...... > ...Tags > ......BioCocoa 1.6 <-- BCReader from Peter > ......BioCocoa 1.7 <-- BCReader from Alex > ......Goodies > .........EntrezController 1.0 <--- From Alex > .........KDTextView 1.0 <-- From Koen > .........KDTextView 1.1 <-- From Alex > ...Branches > ......Goodies > > > The "Goodies" directory could be named something else, like > "Subprojects" or whatever you like, and might alternatively be > moved to the root (under BioCocoa), and have its own Trunk, Tags > and Branches. > > The "Branches" directory is empty right now, but might soon have a > "BioCocoa 1.x" branch if we want to fix bugs / add features on the > 1.7 version, and/or have a "Goodies/KDTextView 1.x" branch for the > same reasons. Of course, the code for these should be merged in the > BioCocoa Trunk as soon as possible too, and we probably don't want > to generate too much code on the 1.x versions. > > Let's take advantage of super-easy management of Tags and Branches > with Subversion... Just my 2 cents! > > charles > > > On Mar 6, 2006, at 4:33 AM, Peter Schols wrote: > >> Hi Alex and other listers, >> >> This BCAppkitTest works great and it will be a great addition to >> BioCocoa! >> Over the weekend, I have worked with the - very helpful - people >> at Bioinformatics.org to solve my login problems (it turned out to >> be a proxy issue that was caused by a bug on their end, they have >> been able to fix it). >> As a result, I am totally ready to start the subversion repository >> and do the initial import. >> >> The main question I have now is: how should we organise the >> repository and the BioCocoa website? There are several scenarios: >> >> 1. Checkout the latest version of the BioCocoa framework from CVS >> and use that as the initial import for SVN. Make the BCAppkitTest >> available as a download on our website (both source and compiled >> app) but wait to put it in the repository until it's adapted to >> use the classes in our own framework. >> >> 2. Checkout the latest version of the BioCocoa framework from CVS >> and use that as the initial import for SVN. Make a second >> repository (I think this is possible @ bioinformatics.org) and put >> BCAppkitTest in there. >> >> 3. Checkout the latest version of the BioCocoa framework from CVS, >> add the BCAppkitTest somewhere in the hierarchy of that same >> BioCocoa folder and check this hybrid framework in to one repository. >> >> >> I think I'd prefer solution number 1 (or 2) because >> - it seems a bit weird to have part of a framework that does not >> use the base classes available in the rest of the framework >> - it might confuse users of the framework >> - we should aim to integrate BCAppkitTest into BioCocoa asap, this >> won't be a huge undertaking >> >> Please let me know your preference and I would be glad to create >> the Subversion repository and send instructions on using it. I'd >> also be glad to update the website and make the BCAppkitTest >> available. >> >> Peter >> >> >> >> On 06 Mar 2006, at 11:08, Alexander Griekspoor wrote: >> >>> Hi guys, >>> >>> With EnzymeX3 now in beta testing phase it's time to share the >>> wealth... >>> I've thrown together a very simple demo app showing the three >>> goodies I would like to donate back to the BioCocoa project: >>> - BCReader, the standalone BCReader classes for sequence file IO >>> (original version Peter Schols) >>> - EntrezController, a controller plus view for browsing and >>> fetching NCBI's Entrez Database >>> - KDTextView+, a custom NSTextView for displaying biological >>> sequences (original version Koen van der Drift) >>> >>> Download and enjoy at: http://www.mekentosj.com/biococoa/ >>> BCAppkit_Test.dmg >>> Of course all feedback and bug reports are welcome (or not >>> depending on how you interpret this sentence ;-) >>> >>> Also, coming back to Koen's remark. There are a few things I/we >>> could do. >>> First, it would be nice if it had these views mentioned as >>> available on the website and the code given a place on the svn >>> server. >>> Second, we could perhaps post a small announcement (few lines) on >>> cocoa-dev to notify other cocoa developers, also letting them >>> know about BioCocoa again. >>> Finally, we could compose a little message to MacResearch >>> describing the BioCocoa project and also the availability of this >>> code. >>> Alternatively, I can inform them about it when we release the >>> EnzymeX final version. I believe Tom spoke a few times with the >>> guys behind MacResearch, so we could inform them directly.. Let >>> me know what you guys think. >>> Cheers, >>> Alex >>> >>> >>> ********************************************************* >>> ** Alexander Griekspoor ** >>> ********************************************************* >>> The Netherlands Cancer Institute >>> Department of Tumorbiology (H4) >>> Plesmanlaan 121, 1066 CX, Amsterdam >>> Tel: + 31 20 - 512 2023 >>> Fax: + 31 20 - 512 2029 >>> AIM: mekentosj at mac.com >>> E-mail: a.griekspoor at nki.nl >>> Web: http://www.mekentosj.com >>> >>> 4Peaks - For Peaks, Four Peaks. >>> 2004 Winner of the Apple Design Awards >>> Best Mac OS X Student Product >>> http://www.mekentosj.com/4peaks >>> >>> ********************************************************* >>> >>> _______________________________________________ >>> Biococoa-dev mailing list >>> Biococoa-dev at bioinformatics.org >>> https://bioinformatics.org/mailman/listinfo/biococoa-dev >>> >> >> >> Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm >> >> _______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/biococoa-dev > > -- > Xgrid-at-Stanford > Help science move fast forward: > http://cmgm.stanford.edu/~cparnot/xgrid-stanford > > Charles Parnot > charles.parnot at gmail.com > > > > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From charles.parnot at gmail.com Mon Mar 6 14:54:40 2006 From: charles.parnot at gmail.com (Charles Parnot) Date: Mon, 6 Mar 2006 11:54:40 -0800 Subject: [Biococoa-dev] More goodies!! In-Reply-To: <35546CEE-7C11-4314-87A2-644FE49C08D8@bio.kuleuven.be> References: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> <35546CEE-7C11-4314-87A2-644FE49C08D8@bio.kuleuven.be> Message-ID: <95EBE6D2-6229-48FD-9492-6A9E9E76D384@gmail.com> > Hi Charles, > > If I get you right, you would prefer option 3, so you'd move the > "AlexCode" to a separate folder in the trunk? > I'm a bit confused... sorry > > Peter Well, actually, it seems like I do, though I did not really realize :-) My point is simply: Alex's code is being used in 1-3 "stable" applications, and will thus be tested and used quite a lot. Such code is very valuable and should be included "as is" in the repository. I realize now that you want to avoid "extra" code outside of the BioCocoa stuff. So, at least, BioCocoa 1.7 could be included. Including the other "goodies" may or may not make sense, and may or may not make things more confusing. However, maybe restricting it to a particular subdir in the Tags directory is still OK, as this is the place for "frozen" items. Starting branches with these is probably a very bad idea, and I would actually not include a BioCocoa/Branches/ Goodies directory, shame on me! All of this also depends how you can bundle things. If the new BCReader integrates well with BioCocoa 1.6, then we should definitely make a BioCocoa 1.7 with it. Regarding the other extras, we could bundle them with BioCocoa 1.7, or keep them separate (Goodies), or not include them. Again, if they can be bundled easily and transparently with it, then we should do it, so the good code is there on the repository. Alex, what do you think? In your email, you proposed: > Also, I think its time to update the BioCocoa website to represent > this all. > It should give a general introduction of who we are and what we aim. > It should describe the current stable releases (BioCocoa 1.6 + > "BCAppkitStandalone", with links to download etc > It should describe our current plans on developing BioCocoa 2.0 -> > give some ideaof what we want and info on how to join, access the > svn server etc. but did you mean to have BioCocoa 1.6 + "BCAppkitStandalone" available on the svn server? In the end, don't worry too much about what I say, Peter: do what you think is best. Anyway, we can always decide to add stuff later, and start with some minimal layout for now. charles > > > > On 06 Mar 2006, at 18:49, Charles Parnot wrote: > >> I don't think we need 2 repositories. Subversion is very >> convenient for branches and tags. I think Alex's final code should >> be included "as is" in the current svn directory, as a side >> project of BioCocoa, because this is usable-right-now tested code, >> just like BioCocoa 1.6 is. I would do the following structure in >> the repository, something close to the usual "recommanded" layout: >> >> BioCoao >> ...Trunk >> ...... >> ......[Checkout of the latest CVS repository] >> ...... >> ...Tags >> ......BioCocoa 1.6 <-- BCReader from Peter >> ......BioCocoa 1.7 <-- BCReader from Alex >> ......Goodies >> .........EntrezController 1.0 <--- From Alex >> .........KDTextView 1.0 <-- From Koen >> .........KDTextView 1.1 <-- From Alex >> ...Branches >> ......Goodies >> >> >> The "Goodies" directory could be named something else, like >> "Subprojects" or whatever you like, and might alternatively be >> moved to the root (under BioCocoa), and have its own Trunk, Tags >> and Branches. >> >> The "Branches" directory is empty right now, but might soon have a >> "BioCocoa 1.x" branch if we want to fix bugs / add features on the >> 1.7 version, and/or have a "Goodies/KDTextView 1.x" branch for the >> same reasons. Of course, the code for these should be merged in >> the BioCocoa Trunk as soon as possible too, and we probably don't >> want to generate too much code on the 1.x versions. >> >> Let's take advantage of super-easy management of Tags and Branches >> with Subversion... Just my 2 cents! >> >> charles >> >> >> On Mar 6, 2006, at 4:33 AM, Peter Schols wrote: >> >>> Hi Alex and other listers, >>> >>> This BCAppkitTest works great and it will be a great addition to >>> BioCocoa! >>> Over the weekend, I have worked with the - very helpful - people >>> at Bioinformatics.org to solve my login problems (it turned out >>> to be a proxy issue that was caused by a bug on their end, they >>> have been able to fix it). >>> As a result, I am totally ready to start the subversion >>> repository and do the initial import. >>> >>> The main question I have now is: how should we organise the >>> repository and the BioCocoa website? There are several scenarios: >>> >>> 1. Checkout the latest version of the BioCocoa framework from CVS >>> and use that as the initial import for SVN. Make the BCAppkitTest >>> available as a download on our website (both source and compiled >>> app) but wait to put it in the repository until it's adapted to >>> use the classes in our own framework. >>> >>> 2. Checkout the latest version of the BioCocoa framework from CVS >>> and use that as the initial import for SVN. Make a second >>> repository (I think this is possible @ bioinformatics.org) and >>> put BCAppkitTest in there. >>> >>> 3. Checkout the latest version of the BioCocoa framework from >>> CVS, add the BCAppkitTest somewhere in the hierarchy of that same >>> BioCocoa folder and check this hybrid framework in to one >>> repository. >>> >>> >>> I think I'd prefer solution number 1 (or 2) because >>> - it seems a bit weird to have part of a framework that does not >>> use the base classes available in the rest of the framework >>> - it might confuse users of the framework >>> - we should aim to integrate BCAppkitTest into BioCocoa asap, >>> this won't be a huge undertaking >>> >>> Please let me know your preference and I would be glad to create >>> the Subversion repository and send instructions on using it. I'd >>> also be glad to update the website and make the BCAppkitTest >>> available. >>> >>> Peter >>> >>> >>> >>> On 06 Mar 2006, at 11:08, Alexander Griekspoor wrote: >>> >>>> Hi guys, >>>> >>>> With EnzymeX3 now in beta testing phase it's time to share the >>>> wealth... >>>> I've thrown together a very simple demo app showing the three >>>> goodies I would like to donate back to the BioCocoa project: >>>> - BCReader, the standalone BCReader classes for sequence file >>>> IO (original version Peter Schols) >>>> - EntrezController, a controller plus view for browsing and >>>> fetching NCBI's Entrez Database >>>> - KDTextView+, a custom NSTextView for displaying biological >>>> sequences (original version Koen van der Drift) >>>> >>>> Download and enjoy at: http://www.mekentosj.com/biococoa/ >>>> BCAppkit_Test.dmg >>>> Of course all feedback and bug reports are welcome (or not >>>> depending on how you interpret this sentence ;-) >>>> >>>> Also, coming back to Koen's remark. There are a few things I/we >>>> could do. >>>> First, it would be nice if it had these views mentioned as >>>> available on the website and the code given a place on the svn >>>> server. >>>> Second, we could perhaps post a small announcement (few lines) >>>> on cocoa-dev to notify other cocoa developers, also letting them >>>> know about BioCocoa again. >>>> Finally, we could compose a little message to MacResearch >>>> describing the BioCocoa project and also the availability of >>>> this code. >>>> Alternatively, I can inform them about it when we release the >>>> EnzymeX final version. I believe Tom spoke a few times with the >>>> guys behind MacResearch, so we could inform them directly.. Let >>>> me know what you guys think. >>>> Cheers, >>>> Alex >>>> >>>> >>>> ********************************************************* >>>> ** Alexander Griekspoor ** >>>> ********************************************************* >>>> The Netherlands Cancer Institute >>>> Department of Tumorbiology (H4) >>>> Plesmanlaan 121, 1066 CX, Amsterdam >>>> Tel: + 31 20 - 512 2023 >>>> Fax: + 31 20 - 512 2029 >>>> AIM: mekentosj at mac.com >>>> E-mail: a.griekspoor at nki.nl >>>> Web: http://www.mekentosj.com >>>> >>>> 4Peaks - For Peaks, Four Peaks. >>>> 2004 Winner of the Apple Design Awards >>>> Best Mac OS X Student Product >>>> http://www.mekentosj.com/4peaks >>>> >>>> ********************************************************* >>>> >>>> _______________________________________________ >>>> Biococoa-dev mailing list >>>> Biococoa-dev at bioinformatics.org >>>> https://bioinformatics.org/mailman/listinfo/biococoa-dev >>>> >>> >>> >>> Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm >>> >>> _______________________________________________ >>> Biococoa-dev mailing list >>> Biococoa-dev at bioinformatics.org >>> https://bioinformatics.org/mailman/listinfo/biococoa-dev >> >> -- >> Xgrid-at-Stanford >> Help science move fast forward: >> http://cmgm.stanford.edu/~cparnot/xgrid-stanford >> >> Charles Parnot >> charles.parnot at gmail.com >> >> >> >> >> _______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/biococoa-dev >> > > > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm > -- Xgrid-at-Stanford Help science move fast forward: http://cmgm.stanford.edu/~cparnot/xgrid-stanford Charles Parnot charles.parnot at gmail.com From peter.schols at bio.kuleuven.be Mon Mar 6 15:23:30 2006 From: peter.schols at bio.kuleuven.be (Peter Schols) Date: Mon, 6 Mar 2006 21:23:30 +0100 Subject: [Biococoa-dev] Subversion proposal In-Reply-To: <95EBE6D2-6229-48FD-9492-6A9E9E76D384@gmail.com> References: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> <35546CEE-7C11-4314-87A2-644FE49C08D8@bio.kuleuven.be> <95EBE6D2-6229-48FD-9492-6A9E9E76D384@gmail.com> Message-ID: <84699BC8-AE0C-40DA-98F6-74C39966FE0A@bio.kuleuven.be> Hi Charles and Alex, I'm almost getting it... still a bit confused with all those names though ;-) To me, BioCocoa 1.7 == Alex's code == BCAppkitStandalone. At least to me these three items point to the same thing: the ready-to-use code that Alex announced yesterday. I think Charles has a point to include this code in the repository so we can easily improve it. Here is what I'm proposing now: - I checked out the latest CVS version (I finally got it to work, it seems like bioinformatics.org does not keep your account password in sync with your CVS password) - I removed all CVS folders (including those in bundles) - I upgraded the project to the latest version of Xcode (2.2) and built it to make sure it works - I removed the .pbproj file - I linked to the Mac OS X 10.3.9 SDK because I did not have any previous SDKs installed. I guess Mac OS X 10.3.9 should be a good minimum target by now. - I added a new folder to the root of the BioCocoa folder, on the same level of BCAppKit, ... This new folder is called BCStandalone (another new name ;-)) and contains all great code Alex has posted yesterday. I chose the name BCStandalone because it does not only contain AppKit code but also new reader classes which are more BCFoundation-like. As far as I can tell this structure is ready to be imported into our SVN rep. Please let me know if you all agree with this approach. Of course, we can always add new folders later. For now, the hierarchy would be: - Trunk - BC.icns - BCAppKit - BCFoundation - BCStandalone - BCStringDefinitions.h - BCStringDefinitions.m - BioCocoa_Prefix.h - BioCocoa.xcodeproj - Copying.txt - DeveloperDocs - Documentation - Examples - Info-BioCocoa.plist - main.c - Readme.txt - Resources - Tests - Tags still empty - Branches still empty cheers, peter PS: Now that I see this hierarchy, shouldn't we move the BCStringDefinitions files to the BCFoundation folder? And the BC.icns to the Resources folder, as well as the .plist file? That should keep the root nice and clean. On 06 Mar 2006, at 20:54, Charles Parnot wrote: >> Hi Charles, >> >> If I get you right, you would prefer option 3, so you'd move the >> "AlexCode" to a separate folder in the trunk? >> I'm a bit confused... sorry >> >> Peter > > Well, actually, it seems like I do, though I did not really > realize :-) > > My point is simply: Alex's code is being used in 1-3 "stable" > applications, and will thus be tested and used quite a lot. Such > code is very valuable and should be included "as is" in the > repository. I realize now that you want to avoid "extra" code > outside of the BioCocoa stuff. So, at least, BioCocoa 1.7 could be > included. Including the other "goodies" may or may not make sense, > and may or may not make things more confusing. However, maybe > restricting it to a particular subdir in the Tags directory is > still OK, as this is the place for "frozen" items. Starting > branches with these is probably a very bad idea, and I would > actually not include a BioCocoa/Branches/Goodies directory, shame > on me! > > All of this also depends how you can bundle things. If the new > BCReader integrates well with BioCocoa 1.6, then we should > definitely make a BioCocoa 1.7 with it. Regarding the other extras, > we could bundle them with BioCocoa 1.7, or keep them separate > (Goodies), or not include them. Again, if they can be bundled > easily and transparently with it, then we should do it, so the good > code is there on the repository. > > Alex, what do you think? In your email, you proposed: >> Also, I think its time to update the BioCocoa website to represent >> this all. >> It should give a general introduction of who we are and what we aim. >> It should describe the current stable releases (BioCocoa 1.6 + >> "BCAppkitStandalone", with links to download etc >> It should describe our current plans on developing BioCocoa 2.0 -> >> give some ideaof what we want and info on how to join, access the >> svn server etc. > > but did you mean to have BioCocoa 1.6 + "BCAppkitStandalone" > available on the svn server? > > In the end, don't worry too much about what I say, Peter: do what > you think is best. Anyway, we can always decide to add stuff later, > and start with some minimal layout for now. > > charles > > > > > > > >> >> >> >> On 06 Mar 2006, at 18:49, Charles Parnot wrote: >> >>> I don't think we need 2 repositories. Subversion is very >>> convenient for branches and tags. I think Alex's final code >>> should be included "as is" in the current svn directory, as a >>> side project of BioCocoa, because this is usable-right-now tested >>> code, just like BioCocoa 1.6 is. I would do the following >>> structure in the repository, something close to the usual >>> "recommanded" layout: >>> >>> BioCoao >>> ...Trunk >>> ...... >>> ......[Checkout of the latest CVS repository] >>> ...... >>> ...Tags >>> ......BioCocoa 1.6 <-- BCReader from Peter >>> ......BioCocoa 1.7 <-- BCReader from Alex >>> ......Goodies >>> .........EntrezController 1.0 <--- From Alex >>> .........KDTextView 1.0 <-- From Koen >>> .........KDTextView 1.1 <-- From Alex >>> ...Branches >>> ......Goodies >>> >>> >>> The "Goodies" directory could be named something else, like >>> "Subprojects" or whatever you like, and might alternatively be >>> moved to the root (under BioCocoa), and have its own Trunk, Tags >>> and Branches. >>> >>> The "Branches" directory is empty right now, but might soon have >>> a "BioCocoa 1.x" branch if we want to fix bugs / add features on >>> the 1.7 version, and/or have a "Goodies/KDTextView 1.x" branch >>> for the same reasons. Of course, the code for these should be >>> merged in the BioCocoa Trunk as soon as possible too, and we >>> probably don't want to generate too much code on the 1.x versions. >>> >>> Let's take advantage of super-easy management of Tags and >>> Branches with Subversion... Just my 2 cents! >>> >>> charles >>> >>> >>> On Mar 6, 2006, at 4:33 AM, Peter Schols wrote: >>> >>>> Hi Alex and other listers, >>>> >>>> This BCAppkitTest works great and it will be a great addition to >>>> BioCocoa! >>>> Over the weekend, I have worked with the - very helpful - people >>>> at Bioinformatics.org to solve my login problems (it turned out >>>> to be a proxy issue that was caused by a bug on their end, they >>>> have been able to fix it). >>>> As a result, I am totally ready to start the subversion >>>> repository and do the initial import. >>>> >>>> The main question I have now is: how should we organise the >>>> repository and the BioCocoa website? There are several scenarios: >>>> >>>> 1. Checkout the latest version of the BioCocoa framework from >>>> CVS and use that as the initial import for SVN. Make the >>>> BCAppkitTest available as a download on our website (both source >>>> and compiled app) but wait to put it in the repository until >>>> it's adapted to use the classes in our own framework. >>>> >>>> 2. Checkout the latest version of the BioCocoa framework from >>>> CVS and use that as the initial import for SVN. Make a second >>>> repository (I think this is possible @ bioinformatics.org) and >>>> put BCAppkitTest in there. >>>> >>>> 3. Checkout the latest version of the BioCocoa framework from >>>> CVS, add the BCAppkitTest somewhere in the hierarchy of that >>>> same BioCocoa folder and check this hybrid framework in to one >>>> repository. >>>> >>>> >>>> I think I'd prefer solution number 1 (or 2) because >>>> - it seems a bit weird to have part of a framework that does not >>>> use the base classes available in the rest of the framework >>>> - it might confuse users of the framework >>>> - we should aim to integrate BCAppkitTest into BioCocoa asap, >>>> this won't be a huge undertaking >>>> >>>> Please let me know your preference and I would be glad to create >>>> the Subversion repository and send instructions on using it. I'd >>>> also be glad to update the website and make the BCAppkitTest >>>> available. >>>> >>>> Peter >>>> >>>> >>>> >>>> On 06 Mar 2006, at 11:08, Alexander Griekspoor wrote: >>>> >>>>> Hi guys, >>>>> >>>>> With EnzymeX3 now in beta testing phase it's time to share the >>>>> wealth... >>>>> I've thrown together a very simple demo app showing the three >>>>> goodies I would like to donate back to the BioCocoa project: >>>>> - BCReader, the standalone BCReader classes for sequence file >>>>> IO (original version Peter Schols) >>>>> - EntrezController, a controller plus view for browsing and >>>>> fetching NCBI's Entrez Database >>>>> - KDTextView+, a custom NSTextView for displaying biological >>>>> sequences (original version Koen van der Drift) >>>>> >>>>> Download and enjoy at: http://www.mekentosj.com/biococoa/ >>>>> BCAppkit_Test.dmg >>>>> Of course all feedback and bug reports are welcome (or not >>>>> depending on how you interpret this sentence ;-) >>>>> >>>>> Also, coming back to Koen's remark. There are a few things I/we >>>>> could do. >>>>> First, it would be nice if it had these views mentioned as >>>>> available on the website and the code given a place on the svn >>>>> server. >>>>> Second, we could perhaps post a small announcement (few lines) >>>>> on cocoa-dev to notify other cocoa developers, also letting >>>>> them know about BioCocoa again. >>>>> Finally, we could compose a little message to MacResearch >>>>> describing the BioCocoa project and also the availability of >>>>> this code. >>>>> Alternatively, I can inform them about it when we release the >>>>> EnzymeX final version. I believe Tom spoke a few times with the >>>>> guys behind MacResearch, so we could inform them directly.. Let >>>>> me know what you guys think. >>>>> Cheers, >>>>> Alex >>>>> >>>>> >>>>> ********************************************************* >>>>> ** Alexander Griekspoor ** >>>>> ********************************************************* >>>>> The Netherlands Cancer Institute >>>>> Department of Tumorbiology (H4) >>>>> Plesmanlaan 121, 1066 CX, Amsterdam >>>>> Tel: + 31 20 - 512 2023 >>>>> Fax: + 31 20 - 512 2029 >>>>> AIM: mekentosj at mac.com >>>>> E-mail: a.griekspoor at nki.nl >>>>> Web: http://www.mekentosj.com >>>>> >>>>> 4Peaks - For Peaks, Four Peaks. >>>>> 2004 Winner of the Apple Design Awards >>>>> Best Mac OS X Student Product >>>>> http://www.mekentosj.com/4peaks >>>>> >>>>> ********************************************************* >>>>> >>>>> _______________________________________________ >>>>> Biococoa-dev mailing list >>>>> Biococoa-dev at bioinformatics.org >>>>> https://bioinformatics.org/mailman/listinfo/biococoa-dev >>>>> >>>> >>>> >>>> Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm >>>> >>>> _______________________________________________ >>>> Biococoa-dev mailing list >>>> Biococoa-dev at bioinformatics.org >>>> https://bioinformatics.org/mailman/listinfo/biococoa-dev >>> >>> -- >>> Xgrid-at-Stanford >>> Help science move fast forward: >>> http://cmgm.stanford.edu/~cparnot/xgrid-stanford >>> >>> Charles Parnot >>> charles.parnot at gmail.com >>> >>> >>> >>> >>> _______________________________________________ >>> Biococoa-dev mailing list >>> Biococoa-dev at bioinformatics.org >>> https://bioinformatics.org/mailman/listinfo/biococoa-dev >>> >> >> >> Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm >> > > -- > Xgrid-at-Stanford > Help science move fast forward: > http://cmgm.stanford.edu/~cparnot/xgrid-stanford > > Charles Parnot > charles.parnot at gmail.com > > > > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From james.balhoff at duke.edu Mon Mar 6 16:00:52 2006 From: james.balhoff at duke.edu (Jim Balhoff) Date: Mon, 6 Mar 2006 16:00:52 -0500 Subject: [Biococoa-dev] Nice to see some activity In-Reply-To: References: Message-ID: <60E85293-F5B0-4AAB-8006-412AF6EDC7CA@duke.edu> Hey guys, Since everyone is checking in I thought I would mention that I have been working on some objects for working with phylogenetic trees. Currently model objects for trees and nodes, as well as a tree view. Hopefully we can integrate them into BioCocoa at some point (I'll work on them a little more first). Good to hear from everybody! Jim ____________________________________________ James P. Balhoff National Evolutionary Synthesis Center Dept. of Biology Duke University Durham, NC 27708-0338 USA From charles.parnot at gmail.com Mon Mar 6 16:41:19 2006 From: charles.parnot at gmail.com (Charles Parnot) Date: Mon, 6 Mar 2006 13:41:19 -0800 Subject: [Biococoa-dev] Re: Subversion proposal In-Reply-To: <84699BC8-AE0C-40DA-98F6-74C39966FE0A@bio.kuleuven.be> References: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> <35546CEE-7C11-4314-87A2-644FE49C08D8@bio.kuleuven.be> <95EBE6D2-6229-48FD-9492-6A9E9E76D384@gmail.com> <84699BC8-AE0C-40DA-98F6-74C39966FE0A@bio.kuleuven.be> Message-ID: Sorry, I seem to spread confusion... I would not make BCStandalone part of the Trunk. Trunk should only contain the files that are actually really part of the Xcode project, otherwise that would be confusing. Also, BCStandalone is not conceptually code that belongs to the Trunk: it is not code that is being worked on for the next version of BioCocoa (instead, some of the code might be merged into the trunk). The trunk should only contains code for version 2.0. Alex's stuff definitely belongs to the "Tags" directory, as being a "frozen" version of some side project. I am not sure we should modify that independent code too much, but if we do, we would start a branch (Branch 1.x). But again, it is probably not something we should do. Instead, we would merge the useful code in the Trunk, where it belongs, and go from there (e.g KDTExtView --> svn copy into Trunk/BCAppKit/BCTExtView). I think the way a subversion layout is supposed to be organized is: * Trunk = only the latest version = BioCocoa future 2.0 * Tags = finished versions, one directory per version; for instance, "BioCocoa 1.6" should be one such directory; the contents of the "Tags" directory is never modified, only new directories added for each new version (this is just a convention, of course; the "Tags" directory does not magically prevent modifications; only by convention, you should never commit a new version of a file in the Tags directory) * Branches = if one wants to update an older version, a branch can be created; for instance, we may want a "BioCocoa 1.x" branch if we want to modify BioCocoa 1.6 and be able to commit changes, until it is stable and reaches "1.7"... at which point we use svn copy to add a directory to the "Tags". Just in case some of you don't know how svn works: making a svn-copy of a full directory does not create any files; it is merely creating an pointer to that version and not using any disk space. It is a very easy to create regular snapshots of the code as things go along, with numbers, e.g. "BioCocoa 2-beta1", "BioCocoa 2-beta2", "BioCocoa 2-beta3",... Besides that, your email makes sense. The other confusion I spread was that to me, BioCocoa 1.7 = version following BioCocoa 1.6, which should be your code updated with the new BCReader code, and maybe including Alex's AppKit stuff, all in the Tags directory. The bottom line is: somebody interested in using stable code, would go in the Tags, and pick which version she wants, and check out that version. Somebody interested in development would check out the Trunk and work on the latest version. Somebody interested in merging the 2 would check out both, and copy/paste codes between the 2. Or, in the case of KDTextView, use svn-copy to get the code from the BioCocoa 1.7 tag into the trunk, with its new name BCTextView. I hope I explained things better, this time! charles On Mar 6, 2006, at 12:23 PM, Peter Schols wrote: > Hi Charles and Alex, > > I'm almost getting it... still a bit confused with all those names > though ;-) > To me, BioCocoa 1.7 == Alex's code == BCAppkitStandalone. At least > to me these three items point to the same thing: the ready-to-use > code that Alex announced yesterday. > > I think Charles has a point to include this code in the repository > so we can easily improve it. Here is what I'm proposing now: > - I checked out the latest CVS version (I finally got it to work, > it seems like bioinformatics.org does not keep your account > password in sync with your CVS password) > - I removed all CVS folders (including those in bundles) > - I upgraded the project to the latest version of Xcode (2.2) and > built it to make sure it works > - I removed the .pbproj file > - I linked to the Mac OS X 10.3.9 SDK because I did not have any > previous SDKs installed. I guess Mac OS X 10.3.9 should be a good > minimum target by now. > - I added a new folder to the root of the BioCocoa folder, on the > same level of BCAppKit, ... This new folder is called BCStandalone > (another new name ;-)) and contains all great code Alex has posted > yesterday. I chose the name BCStandalone because it does not only > contain AppKit code but also new reader classes which are more > BCFoundation-like. > > As far as I can tell this structure is ready to be imported into > our SVN rep. Please let me know if you all agree with this approach. > Of course, we can always add new folders later. For now, the > hierarchy would be: > > - Trunk > - BC.icns > - BCAppKit > - BCFoundation > - BCStandalone > - BCStringDefinitions.h > - BCStringDefinitions.m > - BioCocoa_Prefix.h > - BioCocoa.xcodeproj > - Copying.txt > - DeveloperDocs > - Documentation > - Examples > - Info-BioCocoa.plist > - main.c > - Readme.txt > - Resources > - Tests > > - Tags > still empty > > - Branches > still empty > > cheers, > peter > > > PS: Now that I see this hierarchy, shouldn't we move the > BCStringDefinitions files to the BCFoundation folder? And the > BC.icns to the Resources folder, as well as the .plist file? That > should keep the root nice and clean. > > > On 06 Mar 2006, at 20:54, Charles Parnot wrote: > >>> Hi Charles, >>> >>> If I get you right, you would prefer option 3, so you'd move the >>> "AlexCode" to a separate folder in the trunk? >>> I'm a bit confused... sorry >>> >>> Peter >> >> Well, actually, it seems like I do, though I did not really >> realize :-) >> >> My point is simply: Alex's code is being used in 1-3 "stable" >> applications, and will thus be tested and used quite a lot. Such >> code is very valuable and should be included "as is" in the >> repository. I realize now that you want to avoid "extra" code >> outside of the BioCocoa stuff. So, at least, BioCocoa 1.7 could be >> included. Including the other "goodies" may or may not make sense, >> and may or may not make things more confusing. However, maybe >> restricting it to a particular subdir in the Tags directory is >> still OK, as this is the place for "frozen" items. Starting >> branches with these is probably a very bad idea, and I would >> actually not include a BioCocoa/Branches/Goodies directory, shame >> on me! >> >> All of this also depends how you can bundle things. If the new >> BCReader integrates well with BioCocoa 1.6, then we should >> definitely make a BioCocoa 1.7 with it. Regarding the other >> extras, we could bundle them with BioCocoa 1.7, or keep them >> separate (Goodies), or not include them. Again, if they can be >> bundled easily and transparently with it, then we should do it, so >> the good code is there on the repository. >> >> Alex, what do you think? In your email, you proposed: >>> Also, I think its time to update the BioCocoa website to >>> represent this all. >>> It should give a general introduction of who we are and what we aim. >>> It should describe the current stable releases (BioCocoa 1.6 + >>> "BCAppkitStandalone", with links to download etc >>> It should describe our current plans on developing BioCocoa 2.0 - >>> > give some ideaof what we want and info on how to join, access >>> the svn server etc. >> >> but did you mean to have BioCocoa 1.6 + "BCAppkitStandalone" >> available on the svn server? >> >> In the end, don't worry too much about what I say, Peter: do what >> you think is best. Anyway, we can always decide to add stuff >> later, and start with some minimal layout for now. >> >> charles >> >> >> >> >> >> >> >>> >>> >>> >>> On 06 Mar 2006, at 18:49, Charles Parnot wrote: >>> >>>> I don't think we need 2 repositories. Subversion is very >>>> convenient for branches and tags. I think Alex's final code >>>> should be included "as is" in the current svn directory, as a >>>> side project of BioCocoa, because this is usable-right-now >>>> tested code, just like BioCocoa 1.6 is. I would do the following >>>> structure in the repository, something close to the usual >>>> "recommanded" layout: >>>> >>>> BioCoao >>>> ...Trunk >>>> ...... >>>> ......[Checkout of the latest CVS repository] >>>> ...... >>>> ...Tags >>>> ......BioCocoa 1.6 <-- BCReader from Peter >>>> ......BioCocoa 1.7 <-- BCReader from Alex >>>> ......Goodies >>>> .........EntrezController 1.0 <--- From Alex >>>> .........KDTextView 1.0 <-- From Koen >>>> .........KDTextView 1.1 <-- From Alex >>>> ...Branches >>>> ......Goodies >>>> >>>> >>>> The "Goodies" directory could be named something else, like >>>> "Subprojects" or whatever you like, and might alternatively be >>>> moved to the root (under BioCocoa), and have its own Trunk, Tags >>>> and Branches. >>>> >>>> The "Branches" directory is empty right now, but might soon have >>>> a "BioCocoa 1.x" branch if we want to fix bugs / add features on >>>> the 1.7 version, and/or have a "Goodies/KDTextView 1.x" branch >>>> for the same reasons. Of course, the code for these should be >>>> merged in the BioCocoa Trunk as soon as possible too, and we >>>> probably don't want to generate too much code on the 1.x versions. >>>> >>>> Let's take advantage of super-easy management of Tags and >>>> Branches with Subversion... Just my 2 cents! >>>> >>>> charles >>>> >>>> >>>> On Mar 6, 2006, at 4:33 AM, Peter Schols wrote: >>>> >>>>> Hi Alex and other listers, >>>>> >>>>> This BCAppkitTest works great and it will be a great addition >>>>> to BioCocoa! >>>>> Over the weekend, I have worked with the - very helpful - >>>>> people at Bioinformatics.org to solve my login problems (it >>>>> turned out to be a proxy issue that was caused by a bug on >>>>> their end, they have been able to fix it). >>>>> As a result, I am totally ready to start the subversion >>>>> repository and do the initial import. >>>>> >>>>> The main question I have now is: how should we organise the >>>>> repository and the BioCocoa website? There are several scenarios: >>>>> >>>>> 1. Checkout the latest version of the BioCocoa framework from >>>>> CVS and use that as the initial import for SVN. Make the >>>>> BCAppkitTest available as a download on our website (both >>>>> source and compiled app) but wait to put it in the repository >>>>> until it's adapted to use the classes in our own framework. >>>>> >>>>> 2. Checkout the latest version of the BioCocoa framework from >>>>> CVS and use that as the initial import for SVN. Make a second >>>>> repository (I think this is possible @ bioinformatics.org) and >>>>> put BCAppkitTest in there. >>>>> >>>>> 3. Checkout the latest version of the BioCocoa framework from >>>>> CVS, add the BCAppkitTest somewhere in the hierarchy of that >>>>> same BioCocoa folder and check this hybrid framework in to one >>>>> repository. >>>>> >>>>> >>>>> I think I'd prefer solution number 1 (or 2) because >>>>> - it seems a bit weird to have part of a framework that does >>>>> not use the base classes available in the rest of the framework >>>>> - it might confuse users of the framework >>>>> - we should aim to integrate BCAppkitTest into BioCocoa asap, >>>>> this won't be a huge undertaking >>>>> >>>>> Please let me know your preference and I would be glad to >>>>> create the Subversion repository and send instructions on using >>>>> it. I'd also be glad to update the website and make the >>>>> BCAppkitTest available. >>>>> >>>>> Peter >>>>> >>>>> >>>>> >>>>> On 06 Mar 2006, at 11:08, Alexander Griekspoor wrote: >>>>> >>>>>> Hi guys, >>>>>> >>>>>> With EnzymeX3 now in beta testing phase it's time to share the >>>>>> wealth... >>>>>> I've thrown together a very simple demo app showing the three >>>>>> goodies I would like to donate back to the BioCocoa project: >>>>>> - BCReader, the standalone BCReader classes for sequence file >>>>>> IO (original version Peter Schols) >>>>>> - EntrezController, a controller plus view for browsing and >>>>>> fetching NCBI's Entrez Database >>>>>> - KDTextView+, a custom NSTextView for displaying biological >>>>>> sequences (original version Koen van der Drift) >>>>>> >>>>>> Download and enjoy at: http://www.mekentosj.com/biococoa/ >>>>>> BCAppkit_Test.dmg >>>>>> Of course all feedback and bug reports are welcome (or not >>>>>> depending on how you interpret this sentence ;-) >>>>>> >>>>>> Also, coming back to Koen's remark. There are a few things I/ >>>>>> we could do. >>>>>> First, it would be nice if it had these views mentioned as >>>>>> available on the website and the code given a place on the svn >>>>>> server. >>>>>> Second, we could perhaps post a small announcement (few lines) >>>>>> on cocoa-dev to notify other cocoa developers, also letting >>>>>> them know about BioCocoa again. >>>>>> Finally, we could compose a little message to MacResearch >>>>>> describing the BioCocoa project and also the availability of >>>>>> this code. >>>>>> Alternatively, I can inform them about it when we release the >>>>>> EnzymeX final version. I believe Tom spoke a few times with >>>>>> the guys behind MacResearch, so we could inform them >>>>>> directly.. Let me know what you guys think. >>>>>> Cheers, >>>>>> Alex >>>>>> >>>>>> >>>>>> ********************************************************* >>>>>> ** Alexander Griekspoor ** >>>>>> ********************************************************* >>>>>> The Netherlands Cancer Institute >>>>>> Department of Tumorbiology (H4) >>>>>> Plesmanlaan 121, 1066 CX, Amsterdam >>>>>> Tel: + 31 20 - 512 2023 >>>>>> Fax: + 31 20 - 512 2029 >>>>>> AIM: mekentosj at mac.com >>>>>> E-mail: a.griekspoor at nki.nl >>>>>> Web: http://www.mekentosj.com >>>>>> >>>>>> 4Peaks - For Peaks, Four Peaks. >>>>>> 2004 Winner of the Apple Design Awards >>>>>> Best Mac OS X Student Product >>>>>> http://www.mekentosj.com/4peaks >>>>>> >>>>>> ********************************************************* >>>>>> >>>>>> _______________________________________________ >>>>>> Biococoa-dev mailing list >>>>>> Biococoa-dev at bioinformatics.org >>>>>> https://bioinformatics.org/mailman/listinfo/biococoa-dev >>>>>> >>>>> >>>>> >>>>> Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm >>>>> >>>>> _______________________________________________ >>>>> Biococoa-dev mailing list >>>>> Biococoa-dev at bioinformatics.org >>>>> https://bioinformatics.org/mailman/listinfo/biococoa-dev >>>> >>>> -- >>>> Xgrid-at-Stanford >>>> Help science move fast forward: >>>> http://cmgm.stanford.edu/~cparnot/xgrid-stanford >>>> >>>> Charles Parnot >>>> charles.parnot at gmail.com >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Biococoa-dev mailing list >>>> Biococoa-dev at bioinformatics.org >>>> https://bioinformatics.org/mailman/listinfo/biococoa-dev >>>> >>> >>> >>> Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm >>> >> >> -- >> Xgrid-at-Stanford >> Help science move fast forward: >> http://cmgm.stanford.edu/~cparnot/xgrid-stanford >> >> Charles Parnot >> charles.parnot at gmail.com >> >> >> >> >> _______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/biococoa-dev >> > > > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm > -- Xgrid-at-Stanford Help science move fast forward: http://cmgm.stanford.edu/~cparnot/xgrid-stanford Charles Parnot charles.parnot at gmail.com From peter.schols at bio.kuleuven.be Mon Mar 6 16:45:43 2006 From: peter.schols at bio.kuleuven.be (Peter Schols) Date: Mon, 6 Mar 2006 22:45:43 +0100 Subject: [Biococoa-dev] Nice to see some activity In-Reply-To: <60E85293-F5B0-4AAB-8006-412AF6EDC7CA@duke.edu> References: <60E85293-F5B0-4AAB-8006-412AF6EDC7CA@duke.edu> Message-ID: Hi Jim, Good to hear from you! Those objects for working with phylogenetic trees would make a great addition to BC, and definitely one I'd use. peter On 06 Mar 2006, at 22:00, Jim Balhoff wrote: > Hey guys, > > Since everyone is checking in I thought I would mention that I have > been working on some objects for working with phylogenetic trees. > Currently model objects for trees and nodes, as well as a tree > view. Hopefully we can integrate them into BioCocoa at some point > (I'll work on them a little more first). > > Good to hear from everybody! > > Jim > > > > ____________________________________________ > James P. Balhoff > National Evolutionary Synthesis Center > Dept. of Biology > Duke University > Durham, NC 27708-0338 > USA > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From peter.schols at bio.kuleuven.be Mon Mar 6 17:06:01 2006 From: peter.schols at bio.kuleuven.be (Peter Schols) Date: Mon, 6 Mar 2006 23:06:01 +0100 Subject: [Biococoa-dev] Re: Subversion proposal In-Reply-To: References: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> <35546CEE-7C11-4314-87A2-644FE49C08D8@bio.kuleuven.be> <95EBE6D2-6229-48FD-9492-6A9E9E76D384@gmail.com> <84699BC8-AE0C-40DA-98F6-74C39966FE0A@bio.kuleuven.be> Message-ID: Hi Charles, I follow your explanation and I agree with the philosophy of having stable tags and a trunk which is work in progress. I see two problems though: - I always see tags as a snapshot of the trunk at a certain point in time. With this structure, we'd end up with a tag that has code which is not represented in the trunk (the code Alex has submitted). So it wouldn't be a snapshot at all. In itself, this might not be a major problem, it just seems very confusing to me (but that might be just my short-sighted view of version control ;-)). - The point of including Alex's code into the repository is to be able to easily work on it and improve it. If we'd make it a tag, we are no longer 'allowed' to modify it (unless we make new tags for every little change), defeating the purpose of putting it under version control (except for the fact that all code is contained in one download). With this approach, we could as well offer Alex's code as a download without checking it in. In both cases, the code would be virtually 'unchangeable' until we check it into the main trunk. Again, I'm definitely not a specialist and I think we could either include or exclude Alex's code from the repository, either choice is OK with me. The point I would like to make here is that if we include it, it should also be in the trunk (and we can then make a tag for the 1.7 release). Apologies if I'm missing something here. peter Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From kvddrift at earthlink.net Mon Mar 6 17:34:23 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Mon, 6 Mar 2006 17:34:23 -0500 Subject: [Biococoa-dev] Nice to see some activity In-Reply-To: <60E85293-F5B0-4AAB-8006-412AF6EDC7CA@duke.edu> References: <60E85293-F5B0-4AAB-8006-412AF6EDC7CA@duke.edu> Message-ID: <6D86BD49-1DBB-4A36-89CA-412A5BE7FA91@earthlink.net> On Mar 6, 2006, at 4:00 PM, Jim Balhoff wrote: > Good to hear from everybody! > > Jim > Hi Jim, So the Triangle still has a major input :) Do I still have bragging rights for Saturday's game? - Koen. From kvddrift at earthlink.net Mon Mar 6 17:42:36 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Mon, 6 Mar 2006 17:42:36 -0500 Subject: [Biococoa-dev] Subversion proposal In-Reply-To: <84699BC8-AE0C-40DA-98F6-74C39966FE0A@bio.kuleuven.be> References: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> <35546CEE-7C11-4314-87A2-644FE49C08D8@bio.kuleuven.be> <95EBE6D2-6229-48FD-9492-6A9E9E76D384@gmail.com> <84699BC8-AE0C-40DA-98F6-74C39966FE0A@bio.kuleuven.be> Message-ID: <7E6C2E16-C8F7-4AE7-86F5-5C43F7A34FBC@earthlink.net> Hi, Since everything is tagged in svn, I guess it doesn't really matter in what organization the files are entered into svn. Also in svn it is very easy to change/rename directories. What I am more concerned with is how everything works with Xcode. Which files are included into the project, only the latest? How are trunks handled when using Xcode? Can I switch between trunks, without exiting my Xcode project? Do we now make keep a separate project for the example apps? Currently they all are in the same project. But I understand from you guys input that the new demo from Alex is a separate project. Another svn comment: I believe that svn doesn't like paths with a space in it, so be aware where you put BioCocoa on your HD. cheers, - Koen. ps Peter, do you still need the zipped project in your mailbox? From charles.parnot at gmail.com Mon Mar 6 18:35:38 2006 From: charles.parnot at gmail.com (Charles Parnot) Date: Mon, 6 Mar 2006 15:35:38 -0800 Subject: [Biococoa-dev] Subversion proposal In-Reply-To: <7E6C2E16-C8F7-4AE7-86F5-5C43F7A34FBC@earthlink.net> References: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> <35546CEE-7C11-4314-87A2-644FE49C08D8@bio.kuleuven.be> <95EBE6D2-6229-48FD-9492-6A9E9E76D384@gmail.com> <84699BC8-AE0C-40DA-98F6-74C39966FE0A@bio.kuleuven.be> <7E6C2E16-C8F7-4AE7-86F5-5C43F7A34FBC@earthlink.net> Message-ID: <2F610CBC-06D7-4334-AACD-40B566FAE55C@gmail.com> Koen, thanks for that email. What you say is exactly true, and we should in fact decide if we want to create a separate project for Alex's code, this is the real bottom line. And I was arguing we should, but the option of having it available as a download is good enough for me. To answer your question: yes, you would need to check out 2 separate projects when working on the trunk and on a branch (btw, there is only one trunk, not several "trunks", but several branches; think of a tree ;-) ...). And it is actually not very hard to manage. You just want to make sure you know which version of the project is open when you work on the code! Xcode can get a bit confused with the builds, so you may have to do some clean-up. But this probably does not have to happen here anyway. charles > Hi, > > Since everything is tagged in svn, I guess it doesn't really matter > in what organization the files are entered into svn. Also in svn it > is very easy to change/rename directories. > > What I am more concerned with is how everything works with Xcode. > Which files are included into the project, only the latest? How are > trunks handled when using Xcode? Can I switch between trunks, > without exiting my Xcode project? Do we now make keep a separate > project for the example apps? Currently they all are in the same > project. But I understand from you guys input that the new demo > from Alex is a separate project. > > Another svn comment: I believe that svn doesn't like paths with a > space in it, so be aware where you put BioCocoa on your HD. > > cheers, > > - Koen. > > ps Peter, do you still need the zipped project in your mailbox? -- Xgrid-at-Stanford Help science move fast forward: http://cmgm.stanford.edu/~cparnot/xgrid-stanford Charles Parnot charles.parnot at gmail.com From kvddrift at earthlink.net Mon Mar 6 18:46:53 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Mon, 6 Mar 2006 18:46:53 -0500 Subject: [Biococoa-dev] Subversion proposal In-Reply-To: <2F610CBC-06D7-4334-AACD-40B566FAE55C@gmail.com> References: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> <35546CEE-7C11-4314-87A2-644FE49C08D8@bio.kuleuven.be> <95EBE6D2-6229-48FD-9492-6A9E9E76D384@gmail.com> <84699BC8-AE0C-40DA-98F6-74C39966FE0A@bio.kuleuven.be> <7E6C2E16-C8F7-4AE7-86F5-5C43F7A34FBC@earthlink.net> <2F610CBC-06D7-4334-AACD-40B566FAE55C@gmail.com> Message-ID: On Mar 6, 2006, at 6:35 PM, Charles Parnot wrote: > Koen, thanks for that email. What you say is exactly true, and we > should in fact decide if we want to create a separate project for > Alex's code, this is the real bottom line. And I was arguing we > should, but the option of having it available as a download is good > enough for me. I agree with you. I think the framework should be one standalone project. This is what other developers will use, and I don't think it should be 'polluted' with all kind of sample code. For that we should make separate projects for each example. Also we should make the headerdoc output to describe all the classes available on the website. And finally, can we please have a Mac OS X screenshot on the website? ;-) cheers, - Koen. From peter.schols at bio.kuleuven.be Tue Mar 7 03:47:49 2006 From: peter.schols at bio.kuleuven.be (Peter Schols) Date: Tue, 7 Mar 2006 09:47:49 +0100 Subject: [Biococoa-dev] Subversion proposal In-Reply-To: References: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> <35546CEE-7C11-4314-87A2-644FE49C08D8@bio.kuleuven.be> <95EBE6D2-6229-48FD-9492-6A9E9E76D384@gmail.com> <84699BC8-AE0C-40DA-98F6-74C39966FE0A@bio.kuleuven.be> <7E6C2E16-C8F7-4AE7-86F5-5C43F7A34FBC@earthlink.net> <2F610CBC-06D7-4334-AACD-40B566FAE55C@gmail.com> Message-ID: > I agree with you. I think the framework should be one standalone > project. This is what other developers will use, and I don't think > it should be 'polluted' with all kind of sample code. Who is talking about sample code? > And finally, can we please have a Mac OS X screenshot on the > website? ;-) As I posted before, the current website is atypical because it was created to accompany a manuscript (that had to be submitted to a Mac- hating crowd ;-)) Now that this emphasis on GNUStep / cross-platform things is no longer needed, I'd be glad to remove these ugly Windows screenshots. If you can't wait, feel free to do so yourself, the website is open- source too ;-)) peter Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From peter.schols at bio.kuleuven.be Tue Mar 7 03:48:42 2006 From: peter.schols at bio.kuleuven.be (Peter Schols) Date: Tue, 7 Mar 2006 09:48:42 +0100 Subject: [Biococoa-dev] Subversion proposal In-Reply-To: <7E6C2E16-C8F7-4AE7-86F5-5C43F7A34FBC@earthlink.net> References: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> <35546CEE-7C11-4314-87A2-644FE49C08D8@bio.kuleuven.be> <95EBE6D2-6229-48FD-9492-6A9E9E76D384@gmail.com> <84699BC8-AE0C-40DA-98F6-74C39966FE0A@bio.kuleuven.be> <7E6C2E16-C8F7-4AE7-86F5-5C43F7A34FBC@earthlink.net> Message-ID: <163D2E1F-3266-40CA-BA53-B13A0F515BF4@bio.kuleuven.be> > ps Peter, do you still need the zipped project in your mailbox? Koen, thanks for the offer, but I managed to get it off CVS Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From peter.schols at bio.kuleuven.be Tue Mar 7 03:55:56 2006 From: peter.schols at bio.kuleuven.be (Peter Schols) Date: Tue, 7 Mar 2006 09:55:56 +0100 Subject: [Biococoa-dev] Subversion proposal [correction] In-Reply-To: References: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> <35546CEE-7C11-4314-87A2-644FE49C08D8@bio.kuleuven.be> <95EBE6D2-6229-48FD-9492-6A9E9E76D384@gmail.com> <84699BC8-AE0C-40DA-98F6-74C39966FE0A@bio.kuleuven.be> <7E6C2E16-C8F7-4AE7-86F5-5C43F7A34FBC@earthlink.net> <2F610CBC-06D7-4334-AACD-40B566FAE55C@gmail.com> Message-ID: Oops, sorry. I had not read all BioCocoa-dev emails before replying... (got not enough sleep ;-)) I now understand what you are aiming at with the sample code, and I agree. We could indeed separate these into different Xcode projects. On the other hand, this might make it a bit more difficult to build these sample projects. On 07 Mar 2006, at 09:47, Peter Schols wrote: >> I agree with you. I think the framework should be one standalone >> project. This is what other developers will use, and I don't think >> it should be 'polluted' with all kind of sample code. > > Who is talking about sample code? > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From mek at mekentosj.com Tue Mar 7 04:15:46 2006 From: mek at mekentosj.com (Alexander Griekspoor) Date: Tue, 7 Mar 2006 10:15:46 +0100 Subject: [Biococoa-dev] Subversion proposal [correction] In-Reply-To: References: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> <35546CEE-7C11-4314-87A2-644FE49C08D8@bio.kuleuven.be> <95EBE6D2-6229-48FD-9492-6A9E9E76D384@gmail.com> <84699BC8-AE0C-40DA-98F6-74C39966FE0A@bio.kuleuven.be> <7E6C2E16-C8F7-4AE7-86F5-5C43F7A34FBC@earthlink.net> <2F610CBC-06D7-4334-AACD-40B566FAE55C@gmail.com> Message-ID: <4C50652A-98AD-400A-8F9F-16828E676F48@mekentosj.com> Hi guys, Hmmm, from "great stuff" to "polluting sample code" huh, thanks! So just to clear up things, what I did was add a new, standalone xcode project that serves as both source and sample code for 1 custom foundation and 2 view objects, hence a good name Peter. Now what I propose to do is the following: - update the website of BioCocoa ;-) - post a direct download link with 1) BioCocoa 1.6 and 2) the sample code I posted, and explain what it does. This because many people (including myself like to be able to just download a stable release as zip or dmg instead of having to svn it. Now about that SVN, why don't we indeed give both a place in a spot where it's clear those are final versions. This way someone who is browsing our SVN can find it somewhere. Finally its clear that indeed the trunk is what we work on. I don't think there's a need to have a BioCocoa 1.7 (say, a future classic BioCocoa project), nor a special development space for the KDTextView/ EntrezController classes. No, what I would do is the following: - The additional code in the BCReader class is merged with the new one, which focuses on working with the sequencearray objects (Koen started this already I believe). - The KDTextView is put in the BCAppkit directory, and should in theory also be enhanced to work with our native objects - The EntrezController likewise gets a place in the trunk in the approriate folder and should be "fixed" to return BioCocoa objects. That's all I think, and of course the website should also list these current developments, how to connect to CVS etc etc. By the way, to bring even another topic up, wasn't it BioInformatics who now also features a wiki for each project? Maybe we can transfer a lot of discussions we want to archive and things like the todo list to that, just like Drew and Charles have done for the RemoteActivity monitor: http://tb.chem.vu.nl/wiki/ index.php/Remote_Activity_Monitor Cheers, Alex Ps. Charles, did you get did the other toy I sent you? On 7-mrt-2006, at 9:55, Peter Schols wrote: > Oops, sorry. I had not read all BioCocoa-dev emails before > replying... (got not enough sleep ;-)) > I now understand what you are aiming at with the sample code, and I > agree. We could indeed separate these into different Xcode > projects. On the other hand, this might make it a bit more > difficult to build these sample projects. > > > On 07 Mar 2006, at 09:47, Peter Schols wrote: > >>> I agree with you. I think the framework should be one standalone >>> project. This is what other developers will use, and I don't >>> think it should be 'polluted' with all kind of sample code. >> >> Who is talking about sample code? >> > > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com LabAssistant - Get your life organized! http://www.mekentosj.com/labassistant ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From peter.schols at bio.kuleuven.be Tue Mar 7 04:48:33 2006 From: peter.schols at bio.kuleuven.be (Peter Schols) Date: Tue, 7 Mar 2006 10:48:33 +0100 Subject: [Biococoa-dev] Re: Subversion proposal In-Reply-To: <3DDF45FA-D864-4457-B7CB-AA25E5F1005E@gmail.com> References: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> <35546CEE-7C11-4314-87A2-644FE49C08D8@bio.kuleuven.be> <95EBE6D2-6229-48FD-9492-6A9E9E76D384@gmail.com> <84699BC8-AE0C-40DA-98F6-74C39966FE0A@bio.kuleuven.be> <3DDF45FA-D864-4457-B7CB-AA25E5F1005E@gmail.com> Message-ID: Hi Charles and other listers, We are getting there indeed! Your paragraph below summarizes exactly what I had in mind. Both ways are very similar indeed, and from the point of view of the "user" your approach might be better because the tag will only contain the relevant code (while with my approach it would contain all trunk code). So, I'll move the code Alex has written to a folder called 1.7 inside the Tags folder and remove it from the trunk. Does everyone agree on this? It still feels a bit strange, but given the schizophrenic nature of BioCocoa, this will be the best indeed. I hope we can quickly have our own code use our own foundation classes and move it all to the trunk. If I don't hear any indications against this approach, I'll create the repository later today, so we can all start working on the code ;-) Regarding the website: I agree it needs a major treatment, and I'm willing to do this, but I'm afraid it won't be before the end of the month. Orbicule takes away too much of my time right now.... If anyone thinks it should be done sooner, feel free to do so. You have "carte blanche". Peter > Totally agree: it should be in the trunk too and made compatible > with the rest of BioCocoa 2.0. So, maybe, what you are thinking > about is: add the unmodified code to the trunk, take a snapshot for > the Tags, and then start working on it as part of 2.0. If this is > what you nhave in mind, it is exactly what I think too, except I > put it the other way around: make a 1.7 tag to check-in the code, > and then copy that code in the trunk to work on it. The end result > is the same, so either way is good. Again, I just wanted to make > sure we have a place in the repository with unmodified alex's code, > and the Tags seems like the right place. > > I am so sorry I seem to be making things so complicated! > > charles > > -- > Xgrid-at-Stanford > Help science move fast forward: > http://cmgm.stanford.edu/~cparnot/xgrid-stanford > > Charles Parnot > charles.parnot at gmail.com > > > > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From peter.schols at bio.kuleuven.be Tue Mar 7 04:54:19 2006 From: peter.schols at bio.kuleuven.be (Peter Schols) Date: Tue, 7 Mar 2006 10:54:19 +0100 Subject: [Biococoa-dev] Subversion proposal [correction] In-Reply-To: <4C50652A-98AD-400A-8F9F-16828E676F48@mekentosj.com> References: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> <35546CEE-7C11-4314-87A2-644FE49C08D8@bio.kuleuven.be> <95EBE6D2-6229-48FD-9492-6A9E9E76D384@gmail.com> <84699BC8-AE0C-40DA-98F6-74C39966FE0A@bio.kuleuven.be> <7E6C2E16-C8F7-4AE7-86F5-5C43F7A34FBC@earthlink.net> <2F610CBC-06D7-4334-AACD-40B566FAE55C@gmail.com> <4C50652A-98AD-400A-8F9F-16828E676F48@mekentosj.com> Message-ID: <54B50F8C-6051-4D1B-A42A-61989A027EDB@bio.kuleuven.be> Hi Alex, I love the Wiki idea! It would be a great way to share the To-Do lists and code snippets indeed! BTW: didn't we have a BioCocoa wiki already? I seem to remember this vaguely (maybe it was just a dream ;-)). Regarding the SVN: see my previous post to the list. I think Charles' approach might be the best for our end users. Keep the trunk as it is now in CVS and have a tag with your code. People who want to use the framework just check out the latest tag (= your version) and they are all set. As you write, we should aim asap for a BioCocoa 2.0 that only uses our own foundation classes. cheers, peter On 07 Mar 2006, at 10:15, Alexander Griekspoor wrote: > Hi guys, > > Hmmm, from "great stuff" to "polluting sample code" huh, thanks! > So just to clear up things, what I did was add a new, standalone > xcode project that serves as both source and sample code for 1 > custom foundation and 2 view objects, hence a good name Peter. > Now what I propose to do is the following: > - update the website of BioCocoa ;-) > - post a direct download link with 1) BioCocoa 1.6 and 2) the > sample code I posted, and explain what it does. > This because many people (including myself like to be able to just > download a stable release as zip or dmg instead of having to svn it. > > Now about that SVN, why don't we indeed give both a place in a spot > where it's clear those are final versions. This way someone who is > browsing our SVN can find it somewhere. > Finally its clear that indeed the trunk is what we work on. I don't > think there's a need to have a BioCocoa 1.7 (say, a future classic > BioCocoa project), nor a special development space for the > KDTextView/EntrezController classes. No, what I would do is the > following: > - The additional code in the BCReader class is merged with the new > one, which focuses on working with the sequencearray objects (Koen > started this already I believe). > - The KDTextView is put in the BCAppkit directory, and should in > theory also be enhanced to work with our native objects > - The EntrezController likewise gets a place in the trunk in the > approriate folder and should be "fixed" to return BioCocoa objects. > > That's all I think, and of course the website should also list > these current developments, how to connect to CVS etc etc. > By the way, to bring even another topic up, wasn't it > BioInformatics who now also features a wiki for each project? > Maybe we can transfer a lot of discussions we want to archive and > things like the todo list to that, just like Drew and Charles have > done for the RemoteActivity monitor: http://tb.chem.vu.nl/wiki/ > index.php/Remote_Activity_Monitor > > Cheers, > Alex > > Ps. Charles, did you get did the other toy I sent you? > > > On 7-mrt-2006, at 9:55, Peter Schols wrote: > >> Oops, sorry. I had not read all BioCocoa-dev emails before >> replying... (got not enough sleep ;-)) >> I now understand what you are aiming at with the sample code, and >> I agree. We could indeed separate these into different Xcode >> projects. On the other hand, this might make it a bit more >> difficult to build these sample projects. >> >> >> On 07 Mar 2006, at 09:47, Peter Schols wrote: >> >>>> I agree with you. I think the framework should be one standalone >>>> project. This is what other developers will use, and I don't >>>> think it should be 'polluted' with all kind of sample code. >>> >>> Who is talking about sample code? >>> >> >> Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm >> >> _______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/biococoa-dev >> > > ********************************************************* > ** Alexander Griekspoor ** > ********************************************************* > The Netherlands Cancer Institute > Department of Tumorbiology (H4) > Plesmanlaan 121, 1066 CX, Amsterdam > Tel: + 31 20 - 512 2023 > Fax: + 31 20 - 512 2029 > AIM: mekentosj at mac.com > E-mail: a.griekspoor at nki.nl > Web: http://www.mekentosj.com > > LabAssistant - Get your life organized! > http://www.mekentosj.com/labassistant > > ********************************************************* > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From mek at mekentosj.com Tue Mar 7 04:57:46 2006 From: mek at mekentosj.com (Alexander Griekspoor) Date: Tue, 7 Mar 2006 10:57:46 +0100 Subject: [Biococoa-dev] Subversion proposal [correction] In-Reply-To: <54B50F8C-6051-4D1B-A42A-61989A027EDB@bio.kuleuven.be> References: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> <35546CEE-7C11-4314-87A2-644FE49C08D8@bio.kuleuven.be> <95EBE6D2-6229-48FD-9492-6A9E9E76D384@gmail.com> <84699BC8-AE0C-40DA-98F6-74C39966FE0A@bio.kuleuven.be> <7E6C2E16-C8F7-4AE7-86F5-5C43F7A34FBC@earthlink.net> <2F610CBC-06D7-4334-AACD-40B566FAE55C@gmail.com> <4C50652A-98AD-400A-8F9F-16828E676F48@mekentosj.com> <54B50F8C-6051-4D1B-A42A-61989A027EDB@bio.kuleuven.be> Message-ID: <6B188E8A-31D4-4EB1-9994-53B27FE5790F@mekentosj.com> Very good, just 2 remarks: - My version is not the last version of BioCocoa, it doesn't contain the code to write files, if that could be added, we would be set. - We should also transfer a copy of the views I added and the additional support for reading binary strider and GCK files to the trunk: >> The KDTextView is put in the BCAppkit directory, and should in >> theory also be enhanced to work with our native objects >> - The EntrezController likewise gets a place in the trunk in the >> approriate folder and should be "fixed" to return BioCocoa objects. Cheers, Alex On 7-mrt-2006, at 10:54, Peter Schols wrote: > Hi Alex, > > I love the Wiki idea! It would be a great way to share the To-Do > lists and code snippets indeed! BTW: didn't we have a BioCocoa wiki > already? I seem to remember this vaguely (maybe it was just a > dream ;-)). > > Regarding the SVN: see my previous post to the list. I think > Charles' approach might be the best for our end users. Keep the > trunk as it is now in CVS and have a tag with your code. People who > want to use the framework just check out the latest tag (= your > version) and they are all set. As you write, we should aim asap for > a BioCocoa 2.0 that only uses our own foundation classes. > > cheers, > peter > > > > On 07 Mar 2006, at 10:15, Alexander Griekspoor wrote: > >> Hi guys, >> >> Hmmm, from "great stuff" to "polluting sample code" huh, thanks! >> So just to clear up things, what I did was add a new, standalone >> xcode project that serves as both source and sample code for 1 >> custom foundation and 2 view objects, hence a good name Peter. >> Now what I propose to do is the following: >> - update the website of BioCocoa ;-) >> - post a direct download link with 1) BioCocoa 1.6 and 2) the >> sample code I posted, and explain what it does. >> This because many people (including myself like to be able to just >> download a stable release as zip or dmg instead of having to svn it. >> >> Now about that SVN, why don't we indeed give both a place in a >> spot where it's clear those are final versions. This way someone >> who is browsing our SVN can find it somewhere. >> Finally its clear that indeed the trunk is what we work on. I >> don't think there's a need to have a BioCocoa 1.7 (say, a future >> classic BioCocoa project), nor a special development space for the >> KDTextView/EntrezController classes. No, what I would do is the >> following: >> - The additional code in the BCReader class is merged with the new >> one, which focuses on working with the sequencearray objects (Koen >> started this already I believe). >> - The KDTextView is put in the BCAppkit directory, and should in >> theory also be enhanced to work with our native objects >> - The EntrezController likewise gets a place in the trunk in the >> approriate folder and should be "fixed" to return BioCocoa objects. >> >> That's all I think, and of course the website should also list >> these current developments, how to connect to CVS etc etc. >> By the way, to bring even another topic up, wasn't it >> BioInformatics who now also features a wiki for each project? >> Maybe we can transfer a lot of discussions we want to archive and >> things like the todo list to that, just like Drew and Charles have >> done for the RemoteActivity monitor: http://tb.chem.vu.nl/wiki/ >> index.php/Remote_Activity_Monitor >> >> Cheers, >> Alex >> >> Ps. Charles, did you get did the other toy I sent you? >> >> >> On 7-mrt-2006, at 9:55, Peter Schols wrote: >> >>> Oops, sorry. I had not read all BioCocoa-dev emails before >>> replying... (got not enough sleep ;-)) >>> I now understand what you are aiming at with the sample code, and >>> I agree. We could indeed separate these into different Xcode >>> projects. On the other hand, this might make it a bit more >>> difficult to build these sample projects. >>> >>> >>> On 07 Mar 2006, at 09:47, Peter Schols wrote: >>> >>>>> I agree with you. I think the framework should be one >>>>> standalone project. This is what other developers will use, and >>>>> I don't think it should be 'polluted' with all kind of sample >>>>> code. >>>> >>>> Who is talking about sample code? >>>> >>> >>> Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm >>> >>> _______________________________________________ >>> Biococoa-dev mailing list >>> Biococoa-dev at bioinformatics.org >>> https://bioinformatics.org/mailman/listinfo/biococoa-dev >>> >> >> ********************************************************* >> ** Alexander Griekspoor ** >> ********************************************************* >> The Netherlands Cancer Institute >> Department of Tumorbiology (H4) >> Plesmanlaan 121, 1066 CX, Amsterdam >> Tel: + 31 20 - 512 2023 >> Fax: + 31 20 - 512 2029 >> AIM: mekentosj at mac.com >> E-mail: a.griekspoor at nki.nl >> Web: http://www.mekentosj.com >> >> LabAssistant - Get your life organized! >> http://www.mekentosj.com/labassistant >> >> ********************************************************* >> > > > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com Windows is a 32-bit patch to a 16-bit shell for an 8-bit operating system, written for a 4-bit processor by a 2- bit company without 1 bit of sense. ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From mek at mekentosj.com Tue Mar 7 05:00:19 2006 From: mek at mekentosj.com (Alexander Griekspoor) Date: Tue, 7 Mar 2006 11:00:19 +0100 Subject: [Biococoa-dev] Subversion proposal [correction] In-Reply-To: <6B188E8A-31D4-4EB1-9994-53B27FE5790F@mekentosj.com> References: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> <35546CEE-7C11-4314-87A2-644FE49C08D8@bio.kuleuven.be> <95EBE6D2-6229-48FD-9492-6A9E9E76D384@gmail.com> <84699BC8-AE0C-40DA-98F6-74C39966FE0A@bio.kuleuven.be> <7E6C2E16-C8F7-4AE7-86F5-5C43F7A34FBC@earthlink.net> <2F610CBC-06D7-4334-AACD-40B566FAE55C@gmail.com> <4C50652A-98AD-400A-8F9F-16828E676F48@mekentosj.com> <54B50F8C-6051-4D1B-A42A-61989A027EDB@bio.kuleuven.be> <6B188E8A-31D4-4EB1-9994-53B27FE5790F@mekentosj.com> Message-ID: <1CE55FBF-4D63-407E-AE3F-3F49068B2651@mekentosj.com> About the wiki... found this in the archives: http://bioinformatics.org/forums/forum.php?forum_id=3940 Anyone wants to try to get it working? ALex On 7-mrt-2006, at 10:57, Alexander Griekspoor wrote: > Very good, just 2 remarks: > - My version is not the last version of BioCocoa, it doesn't > contain the code to write files, if that could be added, we would > be set. > - We should also transfer a copy of the views I added and the > additional support for reading binary strider and GCK files to the > trunk: >>> The KDTextView is put in the BCAppkit directory, and should in >>> theory also be enhanced to work with our native objects >>> - The EntrezController likewise gets a place in the trunk in the >>> approriate folder and should be "fixed" to return BioCocoa objects. > > Cheers, > Alex > > > On 7-mrt-2006, at 10:54, Peter Schols wrote: > >> Hi Alex, >> >> I love the Wiki idea! It would be a great way to share the To-Do >> lists and code snippets indeed! BTW: didn't we have a BioCocoa >> wiki already? I seem to remember this vaguely (maybe it was just a >> dream ;-)). >> >> Regarding the SVN: see my previous post to the list. I think >> Charles' approach might be the best for our end users. Keep the >> trunk as it is now in CVS and have a tag with your code. People >> who want to use the framework just check out the latest tag (= >> your version) and they are all set. As you write, we should aim >> asap for a BioCocoa 2.0 that only uses our own foundation classes. >> >> cheers, >> peter >> >> >> >> On 07 Mar 2006, at 10:15, Alexander Griekspoor wrote: >> >>> Hi guys, >>> >>> Hmmm, from "great stuff" to "polluting sample code" huh, thanks! >>> So just to clear up things, what I did was add a new, standalone >>> xcode project that serves as both source and sample code for 1 >>> custom foundation and 2 view objects, hence a good name Peter. >>> Now what I propose to do is the following: >>> - update the website of BioCocoa ;-) >>> - post a direct download link with 1) BioCocoa 1.6 and 2) the >>> sample code I posted, and explain what it does. >>> This because many people (including myself like to be able to >>> just download a stable release as zip or dmg instead of having to >>> svn it. >>> >>> Now about that SVN, why don't we indeed give both a place in a >>> spot where it's clear those are final versions. This way someone >>> who is browsing our SVN can find it somewhere. >>> Finally its clear that indeed the trunk is what we work on. I >>> don't think there's a need to have a BioCocoa 1.7 (say, a future >>> classic BioCocoa project), nor a special development space for >>> the KDTextView/EntrezController classes. No, what I would do is >>> the following: >>> - The additional code in the BCReader class is merged with the >>> new one, which focuses on working with the sequencearray objects >>> (Koen started this already I believe). >>> - The KDTextView is put in the BCAppkit directory, and should in >>> theory also be enhanced to work with our native objects >>> - The EntrezController likewise gets a place in the trunk in the >>> approriate folder and should be "fixed" to return BioCocoa objects. >>> >>> That's all I think, and of course the website should also list >>> these current developments, how to connect to CVS etc etc. >>> By the way, to bring even another topic up, wasn't it >>> BioInformatics who now also features a wiki for each project? >>> Maybe we can transfer a lot of discussions we want to archive and >>> things like the todo list to that, just like Drew and Charles >>> have done for the RemoteActivity monitor: http://tb.chem.vu.nl/ >>> wiki/index.php/Remote_Activity_Monitor >>> >>> Cheers, >>> Alex >>> >>> Ps. Charles, did you get did the other toy I sent you? >>> >>> >>> On 7-mrt-2006, at 9:55, Peter Schols wrote: >>> >>>> Oops, sorry. I had not read all BioCocoa-dev emails before >>>> replying... (got not enough sleep ;-)) >>>> I now understand what you are aiming at with the sample code, >>>> and I agree. We could indeed separate these into different Xcode >>>> projects. On the other hand, this might make it a bit more >>>> difficult to build these sample projects. >>>> >>>> >>>> On 07 Mar 2006, at 09:47, Peter Schols wrote: >>>> >>>>>> I agree with you. I think the framework should be one >>>>>> standalone project. This is what other developers will use, >>>>>> and I don't think it should be 'polluted' with all kind of >>>>>> sample code. >>>>> >>>>> Who is talking about sample code? >>>>> >>>> >>>> Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm >>>> >>>> _______________________________________________ >>>> Biococoa-dev mailing list >>>> Biococoa-dev at bioinformatics.org >>>> https://bioinformatics.org/mailman/listinfo/biococoa-dev >>>> >>> >>> ********************************************************* >>> ** Alexander Griekspoor ** >>> ********************************************************* >>> The Netherlands Cancer Institute >>> Department of Tumorbiology (H4) >>> Plesmanlaan 121, 1066 CX, Amsterdam >>> Tel: + 31 20 - 512 2023 >>> Fax: + 31 20 - 512 2029 >>> AIM: mekentosj at mac.com >>> E-mail: a.griekspoor at nki.nl >>> Web: http://www.mekentosj.com >>> >>> LabAssistant - Get your life organized! >>> http://www.mekentosj.com/labassistant >>> >>> ********************************************************* >>> >> >> >> Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm >> >> _______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/biococoa-dev >> > > ********************************************************* > ** Alexander Griekspoor ** > ********************************************************* > The Netherlands Cancer Institute > Department of Tumorbiology (H4) > Plesmanlaan 121, 1066 CX, Amsterdam > Tel: + 31 20 - 512 2023 > Fax: + 31 20 - 512 2029 > AIM: mekentosj at mac.com > E-mail: a.griekspoor at nki.nl > Web: http://www.mekentosj.com > > Windows is a 32-bit patch to a 16-bit shell for an 8-bit > operating system, written for a 4-bit processor by a 2- > bit company without 1 bit of sense. > > ********************************************************* > > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com LabAssistant - Get your life organized! http://www.mekentosj.com/labassistant ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From peter.schols at bio.kuleuven.be Tue Mar 7 05:54:35 2006 From: peter.schols at bio.kuleuven.be (Peter Schols) Date: Tue, 7 Mar 2006 11:54:35 +0100 Subject: [Biococoa-dev] Subversion proposal [correction] In-Reply-To: <6B188E8A-31D4-4EB1-9994-53B27FE5790F@mekentosj.com> References: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> <35546CEE-7C11-4314-87A2-644FE49C08D8@bio.kuleuven.be> <95EBE6D2-6229-48FD-9492-6A9E9E76D384@gmail.com> <84699BC8-AE0C-40DA-98F6-74C39966FE0A@bio.kuleuven.be> <7E6C2E16-C8F7-4AE7-86F5-5C43F7A34FBC@earthlink.net> <2F610CBC-06D7-4334-AACD-40B566FAE55C@gmail.com> <4C50652A-98AD-400A-8F9F-16828E676F48@mekentosj.com> <54B50F8C-6051-4D1B-A42A-61989A027EDB@bio.kuleuven.be> <6B188E8A-31D4-4EB1-9994-53B27FE5790F@mekentosj.com> Message-ID: <209A20B5-D25C-4062-8F78-4EA43372B090@bio.kuleuven.be> Hi Alex, > Very good, just 2 remarks: > - My version is not the last version of BioCocoa, it doesn't > contain the code to write files, if that could be added, we would > be set. That's right, that's why we will include BioCocoa 1.6 as another tag. People needing the BCCreator class could use that version from 1.6, or combine BCCreator with 1.7 (your code) > - We should also transfer a copy of the views I added and the > additional support for reading binary strider and GCK files to the > trunk: We should do this as soon as these parts use our own foundation classes, at least that's what Charles was saying and that's what I agreed upon. Otherwise it's becoming really confusing. Here is a summary of the discussion (from my point of view): Peter: let's put only the CVS code in the SVN repository and have Alex's code as a simple download Alex: I agree Charles: I don't agree, let's put Alex's code in SVN too Peter & Alex: OK let's do that, and let's put it in the trunk Charles: No, let's put Alex's code in a separate tag Peter: Is it good to have tags containing code that's not in the trunk? Charles: It's not ideal, but it might be the best solution Peter: OK I see why this is a good solution, so we'll put Alex's code (BioCocoa 1.7) and my code (BioCocoa 1.6) in two separate tags and keep the trunk for classes that use our own BCFoundation. and now the last line appears to be: Alex: let's put my code (or at least parts of it) in the trunk! I thought we finally agreed to put all non-BCSequence code into separate tags (= stable, usable versions) and put all other code in trunk (= what will be BioCocoa 2.0) peter Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From mek at mekentosj.com Tue Mar 7 06:03:58 2006 From: mek at mekentosj.com (Alexander Griekspoor) Date: Tue, 7 Mar 2006 12:03:58 +0100 Subject: [Biococoa-dev] Subversion proposal [correction] In-Reply-To: <209A20B5-D25C-4062-8F78-4EA43372B090@bio.kuleuven.be> References: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> <35546CEE-7C11-4314-87A2-644FE49C08D8@bio.kuleuven.be> <95EBE6D2-6229-48FD-9492-6A9E9E76D384@gmail.com> <84699BC8-AE0C-40DA-98F6-74C39966FE0A@bio.kuleuven.be> <7E6C2E16-C8F7-4AE7-86F5-5C43F7A34FBC@earthlink.net> <2F610CBC-06D7-4334-AACD-40B566FAE55C@gmail.com> <4C50652A-98AD-400A-8F9F-16828E676F48@mekentosj.com> <54B50F8C-6051-4D1B-A42A-61989A027EDB@bio.kuleuven.be> <6B188E8A-31D4-4EB1-9994-53B27FE5790F@mekentosj.com> <209A20B5-D25C-4062-8F78-4EA43372B090@bio.kuleuven.be> Message-ID: On 7-mrt-2006, at 11:54, Peter Schols wrote: > Alex: let's put my code (or at least parts of it) in the trunk! Yes, because the trunk is work in progress, one part of that is fixing the views such that they use our foundation classes So, no not the whole xcode file etc etc, but yes the KDTextView.m and h, and the EntrezController.m and h, and put a notice in the todo and comments in these source files that they do not yet work with the new classes. But at least someone can work on it.... Alex ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com Claiming that the Macintosh is inferior to Windows because most people use Windows, is like saying that all other restaurants serve food that is inferior to McDonalds ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From kvddrift at earthlink.net Tue Mar 7 06:28:38 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Tue, 7 Mar 2006 06:28:38 -0500 Subject: [Biococoa-dev] Subversion proposal [correction] In-Reply-To: <4C50652A-98AD-400A-8F9F-16828E676F48@mekentosj.com> References: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> <35546CEE-7C11-4314-87A2-644FE49C08D8@bio.kuleuven.be> <95EBE6D2-6229-48FD-9492-6A9E9E76D384@gmail.com> <84699BC8-AE0C-40DA-98F6-74C39966FE0A@bio.kuleuven.be> <7E6C2E16-C8F7-4AE7-86F5-5C43F7A34FBC@earthlink.net> <2F610CBC-06D7-4334-AACD-40B566FAE55C@gmail.com> <4C50652A-98AD-400A-8F9F-16828E676F48@mekentosj.com> Message-ID: On Mar 7, 2006, at 4:15 AM, Alexander Griekspoor wrote: > Hmmm, from "great stuff" to "polluting sample code" huh, thanks! Guys, I was kidding about the 'polluting'. What I meant was that I think we should have all the examples (Peptides, Translation, SequenceConverter) and your new AppKit demo separate from the framework. I > - The additional code in the BCReader class is merged with the new > one, which focuses on working with the sequencearray objects (Koen > started this already I believe). Yes, the 'updated' version is called BCSequenceReader. I propose that once the transition is over, we remove BCReader to prevent confusion. And we also should not forget to work on BCSequenceWriter. > - The KDTextView is put in the BCAppkit directory, and should in > theory also be enhanced to work with our native objects The original version is already there, and called BCSequenceView. > By the way, to bring even another topic up, wasn't it > BioInformatics who now also features a wiki for each project? A wiki sounds like a great plan. cheers, - Koen. From peter.schols at bio.kuleuven.be Tue Mar 7 08:31:17 2006 From: peter.schols at bio.kuleuven.be (Peter Schols) Date: Tue, 7 Mar 2006 14:31:17 +0100 Subject: [Biococoa-dev] Subversion proposal [correction] In-Reply-To: References: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> <35546CEE-7C11-4314-87A2-644FE49C08D8@bio.kuleuven.be> <95EBE6D2-6229-48FD-9492-6A9E9E76D384@gmail.com> <84699BC8-AE0C-40DA-98F6-74C39966FE0A@bio.kuleuven.be> <7E6C2E16-C8F7-4AE7-86F5-5C43F7A34FBC@earthlink.net> <2F610CBC-06D7-4334-AACD-40B566FAE55C@gmail.com> <4C50652A-98AD-400A-8F9F-16828E676F48@mekentosj.com> <54B50F8C-6051-4D1B-A42A-61989A027EDB@bio.kuleuven.be> <6B188E8A-31D4-4EB1-9994-53B27FE5790F@mekentosj.com> <209A20B5-D25C-4062-8F78-4EA43372B090@bio.kuleuven.be> Message-ID: <5E5353C3-17AE-43E9-BFA9-A0F239CFEF9B@bio.kuleuven.be> OK, I think we are almost ready now to do the initial import... sometimes I'm thinking that this entire SVN discussion has taken more time than just updating everything to use BCSequence ;-) peter On 07 Mar 2006, at 12:03, Alexander Griekspoor wrote: > On 7-mrt-2006, at 11:54, Peter Schols wrote: > >> Alex: let's put my code (or at least parts of it) in the trunk! > > Yes, because the trunk is work in progress, one part of that is > fixing the views such that they use our foundation classes > So, no not the whole xcode file etc etc, but yes the KDTextView.m > and h, and the EntrezController.m and h, and put a notice in the > todo and comments in these source files that they do not yet work > with the new classes. But at least someone can work on it.... > Alex > > > ********************************************************* > ** Alexander Griekspoor ** > ********************************************************* > The Netherlands Cancer Institute > Department of Tumorbiology (H4) > Plesmanlaan 121, 1066 CX, Amsterdam > Tel: + 31 20 - 512 2023 > Fax: + 31 20 - 512 2029 > AIM: mekentosj at mac.com > E-mail: a.griekspoor at nki.nl > Web: http://www.mekentosj.com > > Claiming that the Macintosh is inferior to Windows > because most people use Windows, is like saying > that all other restaurants serve food that is > inferior to McDonalds > > ********************************************************* > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From peter.schols at bio.kuleuven.be Tue Mar 7 08:32:27 2006 From: peter.schols at bio.kuleuven.be (Peter Schols) Date: Tue, 7 Mar 2006 14:32:27 +0100 Subject: [Biococoa-dev] Subversion proposal [correction] In-Reply-To: References: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> <35546CEE-7C11-4314-87A2-644FE49C08D8@bio.kuleuven.be> <95EBE6D2-6229-48FD-9492-6A9E9E76D384@gmail.com> <84699BC8-AE0C-40DA-98F6-74C39966FE0A@bio.kuleuven.be> <7E6C2E16-C8F7-4AE7-86F5-5C43F7A34FBC@earthlink.net> <2F610CBC-06D7-4334-AACD-40B566FAE55C@gmail.com> <4C50652A-98AD-400A-8F9F-16828E676F48@mekentosj.com> Message-ID: <316F89B4-DE90-4F83-9A48-5A6019A23EDB@bio.kuleuven.be> > Yes, the 'updated' version is called BCSequenceReader. I propose > that once the transition is over, we remove BCReader to prevent > confusion. And we also should not forget to work on BCSequenceWriter. Absolutely, let's get rid of BCReader and BCWriter asap! peter Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From peter.schols at bio.kuleuven.be Tue Mar 7 16:06:32 2006 From: peter.schols at bio.kuleuven.be (Peter Schols) Date: Tue, 7 Mar 2006 22:06:32 +0100 Subject: [Biococoa-dev] Initial Subversion import Message-ID: <481F27F2-B783-4204-9712-5831D4021AFE@bio.kuleuven.be> Dear all, I've done the cleanup, reorganisation and initial SVN import of the BioCocoa project. You can view the repository using the web interface at: http:// bioinformatics.org/websvn/ This web interface is quite interesting, it can be used to checkout a copy of the repository. You can even use RSS to subscribe to the repository or certain folders in it. What bothers me, is that all bioinformatics.org repositories seem to be shared. As a result, our initial import is revision 3. Fortunately, there is only one other SVN hosted project right now. Nonetheless, this approach seems less than desirable and I'd really like a separate repository for BioCocoa. I'll contact the Bioinformatics.org sysadmin for more information on this. Update: the SVN website says the following: "You may choose any place on the server (to which you have access) to create a Subversion repository and import your code. However, if you want the public to see and download your code via the Web interface, it has to be in the main repository, svnroot." So it seems that we either have our own, private repository, or that our repository is accesible through a web interface... I'll check this. In the meantime, feel free to check out the repository ;-)) Peter Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From kvddrift at earthlink.net Tue Mar 7 17:53:47 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Tue, 7 Mar 2006 17:53:47 -0500 Subject: [Biococoa-dev] Initial Subversion import In-Reply-To: <481F27F2-B783-4204-9712-5831D4021AFE@bio.kuleuven.be> References: <481F27F2-B783-4204-9712-5831D4021AFE@bio.kuleuven.be> Message-ID: <835582AF-29DB-4BDA-A76A-4AD649972E0B@earthlink.net> On Mar 7, 2006, at 4:06 PM, Peter Schols wrote: > In the meantime, feel free to check out the repository ;-)) > Cool - great work Peter! - Koen. From kvddrift at earthlink.net Tue Mar 7 17:53:26 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Tue, 7 Mar 2006 17:53:26 -0500 Subject: [Biococoa-dev] Subversion proposal In-Reply-To: References: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> <35546CEE-7C11-4314-87A2-644FE49C08D8@bio.kuleuven.be> <95EBE6D2-6229-48FD-9492-6A9E9E76D384@gmail.com> <84699BC8-AE0C-40DA-98F6-74C39966FE0A@bio.kuleuven.be> <7E6C2E16-C8F7-4AE7-86F5-5C43F7A34FBC@earthlink.net> <2F610CBC-06D7-4334-AACD-40B566FAE55C@gmail.com> Message-ID: On Mar 7, 2006, at 3:47 AM, Peter Schols wrote: > If you can't wait, feel free to do so yourself, the website is open- > source too ;-)) I will look into setting up the wiki page, so where can I access and edit the webfiles ? They are not in the source code tree. cheers, - Koen. From kvddrift at earthlink.net Tue Mar 7 21:29:25 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Tue, 7 Mar 2006 21:29:25 -0500 Subject: [Biococoa-dev] Initial Subversion import In-Reply-To: <481F27F2-B783-4204-9712-5831D4021AFE@bio.kuleuven.be> References: <481F27F2-B783-4204-9712-5831D4021AFE@bio.kuleuven.be> Message-ID: <52BA1374-14FF-471B-B9B4-FAE5FFCD4415@earthlink.net> On Mar 7, 2006, at 4:06 PM, Peter Schols wrote: > Dear all, > > I've done the cleanup, reorganisation and initial SVN import of the > BioCocoa project. > You can view the repository using the web interface at: http:// > bioinformatics.org/websvn/ > > This web interface is quite interesting, it can be used to checkout > a copy of the repository. You can even use RSS to subscribe to the > repository or certain folders in it. > What bothers me, is that all bioinformatics.org repositories seem > to be shared. As a result, our initial import is revision 3. > Fortunately, there is only one other SVN hosted project right now. > Nonetheless, this approach seems less than desirable and I'd really > like a separate repository for BioCocoa. I'll contact the > Bioinformatics.org sysadmin for more information on this. > > Update: the SVN website says the following: "You may choose any > place on the server (to which you have access) to create a > Subversion repository and import your code. However, if you want > the public to see and download your code via the Web interface, it > has to be in the main repository, svnroot." > So it seems that we either have our own, private repository, or > that our repository is accesible through a web interface... I'll > check this. > > In the meantime, feel free to check out the repository ;-)) No luck so far :( I followed the instructions from this page: http://bioinformatics.org/docs/svn/ but keep getting the following error: $ svn checkout svn+ssh://bioinformatics.org/svnroot/repository/biococoa svn: No repository found in 'svn+ssh://bioinformatics.org/svnroot/ repository/biococoa' Did I miss anything? cheers, - Koen. From james.balhoff at duke.edu Tue Mar 7 22:11:44 2006 From: james.balhoff at duke.edu (Jim Balhoff) Date: Tue, 7 Mar 2006 22:11:44 -0500 Subject: [Biococoa-dev] Nice to see some activity In-Reply-To: <6D86BD49-1DBB-4A36-89CA-412A5BE7FA91@earthlink.net> References: <60E85293-F5B0-4AAB-8006-412AF6EDC7CA@duke.edu> <6D86BD49-1DBB-4A36-89CA-412A5BE7FA91@earthlink.net> Message-ID: On Mar 6, 2006, at 5:34 PM, Koen van der Drift wrote: > Hi Jim, > > So the Triangle still has a major input :) > > Do I still have bragging rights for Saturday's game? > Looks like you do! (until the next game...) Although I have to admit I've never been to a Duke basketball game :-) Later, Jim ____________________________________________ James P. Balhoff National Evolutionary Synthesis Center Dept. of Biology Duke University Durham, NC 27708-0338 USA From info at orbicule.com Wed Mar 8 11:37:26 2006 From: info at orbicule.com (Peter Schols) Date: Wed, 8 Mar 2006 17:37:26 +0100 Subject: [Biococoa-dev] Fwd: SVN question References: <440E09AE.5080404@bioinformatics.org> Message-ID: <31ED32A5-2EE4-4E91-9B27-34FE47DCA638@orbicule.com> Dear all, I'm forwarding my correspondence with the very helpful guys at bioinformatics.org. Basically, we will have to create our own repository if we don't want to have the revision numbers mixed up. In that case, we'll also need to install WebSVN ourselves (see below). I'd definitely go for our own repository, so we will have to do a little bit more work ourselves. I'm willing to do this but I'm afraid I can't do this before the end of the month. In the meantime we can use the repository as is. If someone else feels challenged to create our own rep. and install webSVN on our account, I'd be glad to give you all information. Peter Begin forwarded message: > From: "J.W. Bizzaro" > Date: Tue 7 Mar 2006 23:31:10 GMT+01:00 > To: Peter Schols > Subject: Re: SVN question > > Yes, that's exactly right. The WebSVN can read only one > repository. But, if you choose to create your own repository > elsewhere on the system, you may install WebSVN in your project's > Web directory: > > http://websvn.tigris.org/ > > Cheers, > Jeff > > Peter Schols wrote: >> Hi Jeff, >> Thanks a lot (again!) It now works! >> One more question: I did the initial import and at the end, SVN >> told me I was at revision 3. I guess this is because I checked our >> project in to the root repository. >> If I understand this well, we could create our own rep. somewhere >> else on the server (so that all revisions are related to our own >> project) but then we can have no web access? >> Thanks! >> Peter >> On 07 Mar 2006, at 19:46, J.W. Bizzaro wrote: >>> Hi Peter, >>> >>> It should be working now. Please try it again. >>> >>> Jeff >>> >>> Peter Schols wrote: >>>> Hi Jeff, >>>> It's me again. >>>> When trying to do the initial SVN import of our repository, I'm >>>> getting the following error: >>>> Am I doing something wrong? >>>> Thanks! >>>> Peter >>> >>> --J.W. Bizzaro >>> Bioinformatics Organization, Inc. (Bioinformatics.Org) >>> E-mail: jeff at bioinformatics.org >>> Phone: +1 508 890 8600 >>> -- > > -- > J.W. Bizzaro > Bioinformatics Organization, Inc. (Bioinformatics.Org) > E-mail: jeff at bioinformatics.org > Phone: +1 508 890 8600 > -- From peter.schols at bio.kuleuven.be Wed Mar 8 11:26:32 2006 From: peter.schols at bio.kuleuven.be (Peter Schols) Date: Wed, 8 Mar 2006 17:26:32 +0100 Subject: [Biococoa-dev] Initial Subversion import In-Reply-To: <835582AF-29DB-4BDA-A76A-4AD649972E0B@earthlink.net> References: <481F27F2-B783-4204-9712-5831D4021AFE@bio.kuleuven.be> <835582AF-29DB-4BDA-A76A-4AD649972E0B@earthlink.net> Message-ID: Thanks! I'm glad we got it online. On 07 Mar 2006, at 23:53, Koen van der Drift wrote: > > On Mar 7, 2006, at 4:06 PM, Peter Schols wrote: > >> In the meantime, feel free to check out the repository ;-)) >> > > Cool - great work Peter! > > - Koen. > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From peter.schols at bio.kuleuven.be Wed Mar 8 11:26:14 2006 From: peter.schols at bio.kuleuven.be (Peter Schols) Date: Wed, 8 Mar 2006 17:26:14 +0100 Subject: [Biococoa-dev] Subversion proposal In-Reply-To: References: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> <35546CEE-7C11-4314-87A2-644FE49C08D8@bio.kuleuven.be> <95EBE6D2-6229-48FD-9492-6A9E9E76D384@gmail.com> <84699BC8-AE0C-40DA-98F6-74C39966FE0A@bio.kuleuven.be> <7E6C2E16-C8F7-4AE7-86F5-5C43F7A34FBC@earthlink.net> <2F610CBC-06D7-4334-AACD-40B566FAE55C@gmail.com> Message-ID: Hi Koen, All webfiles are in the public_html folder. You can access this folder by using SFTP with your bioinf. username and password. I hope you'll have permissions to access these files. I checked on the bioinf. website and there don't seem to be separate settings for FTP access, so I guess all group members can login. If not, please let me know. Peter On 07 Mar 2006, at 23:53, Koen van der Drift wrote: > > On Mar 7, 2006, at 3:47 AM, Peter Schols wrote: > >> If you can't wait, feel free to do so yourself, the website is >> open-source too ;-)) > > > I will look into setting up the wiki page, so where can I access > and edit the webfiles ? They are not in the source code tree. > > cheers, > > - Koen. > > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From peter.schols at bio.kuleuven.be Wed Mar 8 11:30:17 2006 From: peter.schols at bio.kuleuven.be (Peter Schols) Date: Wed, 8 Mar 2006 17:30:17 +0100 Subject: [Biococoa-dev] Initial Subversion import In-Reply-To: <52BA1374-14FF-471B-B9B4-FAE5FFCD4415@earthlink.net> References: <481F27F2-B783-4204-9712-5831D4021AFE@bio.kuleuven.be> <52BA1374-14FF-471B-B9B4-FAE5FFCD4415@earthlink.net> Message-ID: <2B63AE40-4AE2-4F35-8E2F-A2B6003D9F56@bio.kuleuven.be> Hi Koen, I received an email yesterday evening that they were working on the SVN server (and the server still seems to be down). I'm pasting the email below. Anyway, the BioCocoa SVN repos. still worked for five minutes ;-) ------------ Peter, We're going to set up a central place for people to create Subversion repositories. Please stand by while Subversion may go offline. Jeff ------------ On 08 Mar 2006, at 03:29, Koen van der Drift wrote: > > On Mar 7, 2006, at 4:06 PM, Peter Schols wrote: > >> Dear all, >> >> I've done the cleanup, reorganisation and initial SVN import of >> the BioCocoa project. >> You can view the repository using the web interface at: http:// >> bioinformatics.org/websvn/ >> >> This web interface is quite interesting, it can be used to >> checkout a copy of the repository. You can even use RSS to >> subscribe to the repository or certain folders in it. >> What bothers me, is that all bioinformatics.org repositories seem >> to be shared. As a result, our initial import is revision 3. >> Fortunately, there is only one other SVN hosted project right now. >> Nonetheless, this approach seems less than desirable and I'd >> really like a separate repository for BioCocoa. I'll contact the >> Bioinformatics.org sysadmin for more information on this. >> >> Update: the SVN website says the following: "You may choose any >> place on the server (to which you have access) to create a >> Subversion repository and import your code. However, if you want >> the public to see and download your code via the Web interface, it >> has to be in the main repository, svnroot." >> So it seems that we either have our own, private repository, or >> that our repository is accesible through a web interface... I'll >> check this. >> >> In the meantime, feel free to check out the repository ;-)) > > > No luck so far :( > > I followed the instructions from this page: > > http://bioinformatics.org/docs/svn/ > > but keep getting the following error: > > $ svn checkout svn+ssh://bioinformatics.org/svnroot/repository/ > biococoa > svn: No repository found in 'svn+ssh://bioinformatics.org/svnroot/ > repository/biococoa' > > > Did I miss anything? > > cheers, > > - Koen. > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From info at orbicule.com Wed Mar 8 11:40:45 2006 From: info at orbicule.com (Peter Schols) Date: Wed, 8 Mar 2006 17:40:45 +0100 Subject: [Biococoa-dev] Fwd: SVN question References: <440E1C78.2060206@bioinformatics.org> Message-ID: Hi guys, I'm sorry but the guys at bioinformatics.org changed their mind about the SVN repositories (so you can ignore my previous email). It seems that everyone will have to create their own repositories (the way it should be!). I'll look into this tomorrow when I hopefully have a bit more time and I'll move the repository to this new system. Peter Begin forwarded message: > From: "J.W. Bizzaro" > Date: Wed 8 Mar 2006 00:51:20 GMT+01:00 > To: Peter Schols > Cc: BiO SysAdmins > Subject: Re: SVN question > > Peter, > > Okay, we changed the system so that /svnroot is a directory in > which repositories can be created (by users in the svn group). > These repositories can only work with anonymous downloads and the > Web interface if the DB files belong to the group svn. You > therefore need to run the "newgrp svn" command before making a > repository. The new instructions appear here: > > http://bioinformatics.org/docs/svn/ > > (Your previous module was moved to the repository named "default". > We'll probably get rid of that repository, so please create your own.) > > Cheers, > Jeff > -- > J.W. Bizzaro > Bioinformatics Organization, Inc. (Bioinformatics.Org) > E-mail: jeff at bioinformatics.org > Phone: +1 508 890 8600 > -- From charles.parnot at gmail.com Wed Mar 8 13:30:54 2006 From: charles.parnot at gmail.com (Charles Parnot) Date: Wed, 8 Mar 2006 10:30:54 -0800 Subject: [Biococoa-dev] Initial Subversion import In-Reply-To: <2B63AE40-4AE2-4F35-8E2F-A2B6003D9F56@bio.kuleuven.be> References: <481F27F2-B783-4204-9712-5831D4021AFE@bio.kuleuven.be> <52BA1374-14FF-471B-B9B4-FAE5FFCD4415@earthlink.net> <2B63AE40-4AE2-4F35-8E2F-A2B6003D9F56@bio.kuleuven.be> Message-ID: I noticed their database was failing yesterday, with database corrupted. We had the same issue on a different project recently. It turned out using the BerkeleyDB format is not a good idea for multiple user access, as it get corrupted all the time. Hopefully, they realize that too! charles On Mar 8, 2006, at 8:30 AM, Peter Schols wrote: > Hi Koen, > > I received an email yesterday evening that they were working on the > SVN server (and the server still seems to be down). I'm pasting the > email below. Anyway, the BioCocoa SVN repos. still worked for five > minutes ;-) > > ------------ > Peter, > > We're going to set up a central place for people to create > Subversion repositories. Please stand by while Subversion may go > offline. > > Jeff > ------------ > > > > > On 08 Mar 2006, at 03:29, Koen van der Drift wrote: > >> >> On Mar 7, 2006, at 4:06 PM, Peter Schols wrote: >> >>> Dear all, >>> >>> I've done the cleanup, reorganisation and initial SVN import of >>> the BioCocoa project. >>> You can view the repository using the web interface at: http:// >>> bioinformatics.org/websvn/ >>> >>> This web interface is quite interesting, it can be used to >>> checkout a copy of the repository. You can even use RSS to >>> subscribe to the repository or certain folders in it. >>> What bothers me, is that all bioinformatics.org repositories seem >>> to be shared. As a result, our initial import is revision 3. >>> Fortunately, there is only one other SVN hosted project right >>> now. Nonetheless, this approach seems less than desirable and I'd >>> really like a separate repository for BioCocoa. I'll contact the >>> Bioinformatics.org sysadmin for more information on this. >>> >>> Update: the SVN website says the following: "You may choose any >>> place on the server (to which you have access) to create a >>> Subversion repository and import your code. However, if you want >>> the public to see and download your code via the Web interface, >>> it has to be in the main repository, svnroot." >>> So it seems that we either have our own, private repository, or >>> that our repository is accesible through a web interface... I'll >>> check this. >>> >>> In the meantime, feel free to check out the repository ;-)) >> >> >> No luck so far :( >> >> I followed the instructions from this page: >> >> http://bioinformatics.org/docs/svn/ >> >> but keep getting the following error: >> >> $ svn checkout svn+ssh://bioinformatics.org/svnroot/repository/ >> biococoa >> svn: No repository found in 'svn+ssh://bioinformatics.org/svnroot/ >> repository/biococoa' >> >> >> Did I miss anything? >> >> cheers, >> >> - Koen. >> _______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/biococoa-dev >> > > > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev -- Xgrid-at-Stanford Help science move fast forward: http://cmgm.stanford.edu/~cparnot/xgrid-stanford Charles Parnot charles.parnot at gmail.com From kvddrift at earthlink.net Wed Mar 8 19:53:54 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Wed, 8 Mar 2006 19:53:54 -0500 Subject: [Biococoa-dev] Subversion proposal In-Reply-To: References: <7AF18F6F-F51B-43DB-980C-8B91AB1077D1@bio.kuleuven.be> <35546CEE-7C11-4314-87A2-644FE49C08D8@bio.kuleuven.be> <95EBE6D2-6229-48FD-9492-6A9E9E76D384@gmail.com> <84699BC8-AE0C-40DA-98F6-74C39966FE0A@bio.kuleuven.be> <7E6C2E16-C8F7-4AE7-86F5-5C43F7A34FBC@earthlink.net> <2F610CBC-06D7-4334-AACD-40B566FAE55C@gmail.com> Message-ID: <077D4311-A321-4666-9BD9-BC9A70909531@earthlink.net> On Mar 8, 2006, at 11:26 AM, Peter Schols wrote: > All webfiles are in the public_html folder. You can access this > folder by using SFTP with your bioinf. username and password. > I hope you'll have permissions to access these files. I checked on > the bioinf. website and there don't seem to be separate settings > for FTP access, so I guess all group members can login. If not, > please let me know. Peter, When I sftp into bioinformatics.org, I don't see the public_html folder, so maybe only you have it? In any event, today I realized that the idea of a wiki is that it should be editable from within the website, so server access should not be neccessary. I will look into the wiki docs on bioinformatics.org how I can do this. cheers, - Koen. From kvddrift at earthlink.net Thu Mar 9 18:17:19 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Thu, 9 Mar 2006 18:17:19 -0500 Subject: [Biococoa-dev] Initial Subversion import In-Reply-To: References: <481F27F2-B783-4204-9712-5831D4021AFE@bio.kuleuven.be> <52BA1374-14FF-471B-B9B4-FAE5FFCD4415@earthlink.net> <2B63AE40-4AE2-4F35-8E2F-A2B6003D9F56@bio.kuleuven.be> Message-ID: <653414BD-97CA-4100-8364-2FEFFB06CD32@earthlink.net> Hi all, Just did a checkout, and it worked! Use this command: svn checkout svn+ssh://bioinformatics.org/svnroot/BioCocoa Later tonight, I will se how well it works with Xcode :) cheers, - Koen. From kvddrift at earthlink.net Thu Mar 9 20:27:42 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Thu, 9 Mar 2006 20:27:42 -0500 Subject: [Biococoa-dev] Initial Subversion import In-Reply-To: <653414BD-97CA-4100-8364-2FEFFB06CD32@earthlink.net> References: <481F27F2-B783-4204-9712-5831D4021AFE@bio.kuleuven.be> <52BA1374-14FF-471B-B9B4-FAE5FFCD4415@earthlink.net> <2B63AE40-4AE2-4F35-8E2F-A2B6003D9F56@bio.kuleuven.be> <653414BD-97CA-4100-8364-2FEFFB06CD32@earthlink.net> Message-ID: <90DFC120-BDB8-4E5C-A06B-BBCB30422A42@earthlink.net> > Later tonight, I will se how well it works with Xcode :) > Hooray! That works too. Just make sure that you set the path to your svn binary. It's not installed by default (at least I didn't have it) so I installed it with fink. In that case the path is /sw/bin/svn. I hop the project doesn't get confused when others have a different location for their svn/ I have done an initial import of the strider and gck formats into BCSequenceReader. I am not familiar with those formats, so have only added code to import the sequence itself. The comments still need to be added to what I called the 'annotationsArray' Feel free to have a look at it and see how the annotationsArray is used for other formats. - Koen. From james.balhoff at duke.edu Thu Mar 9 21:10:48 2006 From: james.balhoff at duke.edu (Jim Balhoff) Date: Thu, 9 Mar 2006 21:10:48 -0500 Subject: [Biococoa-dev] Initial Subversion import In-Reply-To: <90DFC120-BDB8-4E5C-A06B-BBCB30422A42@earthlink.net> References: <481F27F2-B783-4204-9712-5831D4021AFE@bio.kuleuven.be> <52BA1374-14FF-471B-B9B4-FAE5FFCD4415@earthlink.net> <2B63AE40-4AE2-4F35-8E2F-A2B6003D9F56@bio.kuleuven.be> <653414BD-97CA-4100-8364-2FEFFB06CD32@earthlink.net> <90DFC120-BDB8-4E5C-A06B-BBCB30422A42@earthlink.net> Message-ID: On Mar 9, 2006, at 8:27 PM, Koen van der Drift wrote: >> Later tonight, I will se how well it works with Xcode :) >> > > Hooray! That works too. Just make sure that you set the path to > your svn binary. It's not installed by default (at least I didn't > have it) so I installed it with fink. In that case the path is /sw/ > bin/svn. I hop the project doesn't get confused when others have a > different location for their svn/ > I just wanted to mention - I used the Xcode svn functionality for a while, but it always seemed a little shaky. These days I turn off version control in Xcode and use svnX instead: Jim From kvddrift at earthlink.net Thu Mar 9 21:20:26 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Thu, 9 Mar 2006 21:20:26 -0500 Subject: [Biococoa-dev] wiki Message-ID: <287495C7-7ADD-40A2-BBBF-7F2137BB757F@earthlink.net> Hi, I was looking into setting up the wiki page for BioCocoa, and have been in contact with Jeff from Bioinformatics.org about that. In contrast to the info on the nwes website, not every project already has a wiki setup by default. That would include us. There are actually a few ways to do it, and I wanted to check with you first before I proceed. Here's what he replied: [quote] It is possible to combine the wiki with the existing website, provided none of the file names conflict. You may also choose to do as one other project has done: create a second directory in public_html named "BioCocoa-wiki" for that purpose. And, of course, you may choose to completely replace the existing webpage with the wiki. [/quote] My preference would be to leave the current website for publicity purposes (screenshots, downloads, etc), and set up a wikipage for everything else. So that would be either option 1 or 2. Option 2 seems the most logical to me: http://bioinformatics.org/biococoa/wiki/ Let me know what you think and I can contact the admins from Bioinformatics.org to set up the wiki for us. I also forwarded him the concern from Charles for the svn and BerkeleyDB conflicts, here is his answer (actually a question): [quote] Regarding SVN/BerkeleyDB, we're noticing the "corruption problem". We think it's actually a DB locking problem and no corruption is actually occurring. We have a cron script check on the DBs because of this. Do you know if there is a replacement (planned) for Berkeley DB in SVN? [/quote] Let me know if any of you can answer that, cheers, - Koen. From peter.schols at bio.kuleuven.be Fri Mar 10 03:44:41 2006 From: peter.schols at bio.kuleuven.be (Peter Schols) Date: Fri, 10 Mar 2006 09:44:41 +0100 Subject: [Biococoa-dev] Initial Subversion import In-Reply-To: <653414BD-97CA-4100-8364-2FEFFB06CD32@earthlink.net> References: <481F27F2-B783-4204-9712-5831D4021AFE@bio.kuleuven.be> <52BA1374-14FF-471B-B9B4-FAE5FFCD4415@earthlink.net> <2B63AE40-4AE2-4F35-8E2F-A2B6003D9F56@bio.kuleuven.be> <653414BD-97CA-4100-8364-2FEFFB06CD32@earthlink.net> Message-ID: <6C9D4004-8849-4F84-84C6-4D07685E0821@bio.kuleuven.be> Dear All, Yesterday afternoon, I worked on setting up our new repository, testing it and making sure everything works as expected (WebSVN, RSS feeds, ...). When I was done, I was too tired/busy to post a notification to the list. But it seems this is no longer necessary as Koen already figured out how to check out the rep and even added new code, which is great. For those of you who haven't already tried it, here is a short summary of commands that might be useful: - To checkout the rep: svn checkout svn+ssh://bioinformatics.org/ svnroot/BioCocoa - More information on other SVN commands are at: http:// bioinformatics.org/docs/svn/ - If you are not familiar with SVN, the free O'Reilly book on SVN is excellent: http://svnbook.red-bean.com/ - Installing SVN on your Mac can best be done using the ready-made packages Martin Ott offers on his website: http:// www.codingmonkeys.de/mbo/articles/page/3 - As Jim mentioned, SVNX is an excellent, open-source Cocoa front end to SVN. I'm using it since version 0.8 or something like that, and it's really awesome. For me, it worked much better than Xcode's SVN support too. You can get it at: http://www.lachoseinteractive.net/en/ community/subversion/svnx/features/ - When using SVN with a front-end, (either SVNX or XCode), make sure to put your public key on the bioinformatics.org server (instructions are included in the DeveloperDocs). - The BioCocoa SVN RSS feed can be found at: feed:// bioinformatics.org/websvn/rss.php?repname=BioCocoa&path=% 2F&rev=0&sc=0&isdir=1 I hope these instructions are helpful (especially to new developers). Cheers, Peter On 10 Mar 2006, at 00:17, Koen van der Drift wrote: > Hi all, > > Just did a checkout, and it worked! > > Use this command: > > svn checkout svn+ssh://bioinformatics.org/svnroot/BioCocoa > > > Later tonight, I will se how well it works with Xcode :) > > cheers, > > - Koen. > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From peter.schols at bio.kuleuven.be Fri Mar 10 03:46:59 2006 From: peter.schols at bio.kuleuven.be (Peter Schols) Date: Fri, 10 Mar 2006 09:46:59 +0100 Subject: [Biococoa-dev] wiki In-Reply-To: <287495C7-7ADD-40A2-BBBF-7F2137BB757F@earthlink.net> References: <287495C7-7ADD-40A2-BBBF-7F2137BB757F@earthlink.net> Message-ID: <38E56740-ABE1-4647-A664-211F0D766D20@bio.kuleuven.be> > My preference would be to leave the current website for publicity > purposes (screenshots, downloads, etc), and set up a wikipage for > everything else. So that would be either option 1 or 2. Option 2 > seems the most logical to me: http://bioinformatics.org/biococoa/wiki/ I'd prefer option 2 too. peter Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From charles.parnot at gmail.com Fri Mar 10 13:02:11 2006 From: charles.parnot at gmail.com (Charles Parnot) Date: Fri, 10 Mar 2006 10:02:11 -0800 Subject: [Biococoa-dev] wiki In-Reply-To: <38E56740-ABE1-4647-A664-211F0D766D20@bio.kuleuven.be> References: <287495C7-7ADD-40A2-BBBF-7F2137BB757F@earthlink.net> <38E56740-ABE1-4647-A664-211F0D766D20@bio.kuleuven.be> Message-ID: same for me! charles On Mar 10, 2006, at 12:46 AM, Peter Schols wrote: >> My preference would be to leave the current website for publicity >> purposes (screenshots, downloads, etc), and set up a wikipage for >> everything else. So that would be either option 1 or 2. Option 2 >> seems the most logical to me: http://bioinformatics.org/biococoa/ >> wiki/ > > > I'd prefer option 2 too. > > peter > > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev -- Xgrid-at-Stanford Help science move fast forward: http://cmgm.stanford.edu/~cparnot/xgrid-stanford Charles Parnot charles.parnot at gmail.com From charles.parnot at gmail.com Fri Mar 10 13:19:55 2006 From: charles.parnot at gmail.com (Charles Parnot) Date: Fri, 10 Mar 2006 10:19:55 -0800 Subject: [Biococoa-dev] Initial Subversion import In-Reply-To: <6C9D4004-8849-4F84-84C6-4D07685E0821@bio.kuleuven.be> References: <481F27F2-B783-4204-9712-5831D4021AFE@bio.kuleuven.be> <52BA1374-14FF-471B-B9B4-FAE5FFCD4415@earthlink.net> <2B63AE40-4AE2-4F35-8E2F-A2B6003D9F56@bio.kuleuven.be> <653414BD-97CA-4100-8364-2FEFFB06CD32@earthlink.net> <6C9D4004-8849-4F84-84C6-4D07685E0821@bio.kuleuven.be> Message-ID: <3093195F-0B0E-4D03-8F7A-EEFBD96D3E7A@gmail.com> > Dear All, > > Yesterday afternoon, I worked on setting up our new repository, > testing it and making sure everything works as expected (WebSVN, > RSS feeds, ...). When I was done, I was too tired/busy to post a > notification to the list. But it seems this is no longer necessary > as Koen already figured out how to check out the rep and even added > new code, which is great. > > For those of you who haven't already tried it, here is a short > summary of commands that might be useful: > > - To checkout the rep: svn checkout svn+ssh://bioinformatics.org/ > svnroot/BioCocoa Is that for anonymous checkout? One has to add the username, if different from your username on your computer: username at bioinformatics.org/...... > - More information on other SVN commands are at: http:// > bioinformatics.org/docs/svn/ > - If you are not familiar with SVN, the free O'Reilly book on SVN > is excellent: http://svnbook.red-bean.com/ > > - Installing SVN on your Mac can best be done using the ready-made > packages Martin Ott offers on his website: http:// > www.codingmonkeys.de/mbo/articles/page/3 What version are you guys using? Just to troubleshoot a problem I have (see below). > - As Jim mentioned, SVNX is an excellent, open-source Cocoa front > end to SVN. I'm using it since version 0.8 or something like that, > and it's really awesome. For me, it worked much better than Xcode's > SVN support too. You can get it at: http:// > www.lachoseinteractive.net/en/community/subversion/svnx/features/ Same here. SvnX is much better than using Xcode. Xcode is limited to files loaded into the project, and I found it easier to have to separate apps for coding and versioning. Somehow, separating the 2 tasks made things easier to control. > - When using SVN with a front-end, (either SVNX or XCode), make > sure to put your public key on the bioinformatics.org server > (instructions are included in the DeveloperDocs). I have a funny thing happening: * ssh works fine with my key; I can ssh in without typing a password * svn+ssh does not seem to use the key thing; it asks for my password; actually, it asks 3 times, and I really have to enter the right password 3 times, so it is like every operation needs some authentication, and my authentication does not last. * as a result, I can't use svnX... only the CLI...argggHhh! I will try to setup a new fresh key, but if you guys had a idea of what is going on, let me know :-) > - The BioCocoa SVN RSS feed can be found at: feed:// > bioinformatics.org/websvn/rss.php?repname=BioCocoa&path=% > 2F&rev=0&sc=0&isdir=1 This is ultra-super-mega-cool charles -- Xgrid-at-Stanford Help science move fast forward: http://cmgm.stanford.edu/~cparnot/xgrid-stanford Charles Parnot charles.parnot at gmail.com From james.balhoff at duke.edu Fri Mar 10 13:29:16 2006 From: james.balhoff at duke.edu (Jim Balhoff) Date: Fri, 10 Mar 2006 13:29:16 -0500 Subject: [Biococoa-dev] Initial Subversion import In-Reply-To: <3093195F-0B0E-4D03-8F7A-EEFBD96D3E7A@gmail.com> References: <481F27F2-B783-4204-9712-5831D4021AFE@bio.kuleuven.be> <52BA1374-14FF-471B-B9B4-FAE5FFCD4415@earthlink.net> <2B63AE40-4AE2-4F35-8E2F-A2B6003D9F56@bio.kuleuven.be> <653414BD-97CA-4100-8364-2FEFFB06CD32@earthlink.net> <6C9D4004-8849-4F84-84C6-4D07685E0821@bio.kuleuven.be> <3093195F-0B0E-4D03-8F7A-EEFBD96D3E7A@gmail.com> Message-ID: <25CFAD57-DBD5-49D3-B948-ADF94045B808@duke.edu> On Mar 10, 2006, at 1:19 PM, Charles Parnot wrote: > I have a funny thing happening: > * ssh works fine with my key; I can ssh in without typing a password > * svn+ssh does not seem to use the key thing; it asks for my > password; actually, it asks 3 times, and I really have to enter the > right password 3 times, so it is like every operation needs some > authentication, and my authentication does not last. > * as a result, I can't use svnX... only the CLI...argggHhh! > > I will try to setup a new fresh key, but if you guys had a idea of > what is going on, let me know :-) > I'm not sure what the problem is, since it sounds like you made your key with a blank password. But if not, you can use the program SSHKeychain to ask for your password when a program like SvnX needs it. I use it all the time (I put a password on my key). From charles.parnot at gmail.com Fri Mar 10 13:34:35 2006 From: charles.parnot at gmail.com (Charles Parnot) Date: Fri, 10 Mar 2006 10:34:35 -0800 Subject: [Biococoa-dev] wiki In-Reply-To: <287495C7-7ADD-40A2-BBBF-7F2137BB757F@earthlink.net> References: <287495C7-7ADD-40A2-BBBF-7F2137BB757F@earthlink.net> Message-ID: > > [quote] > Regarding SVN/BerkeleyDB, we're noticing the "corruption problem". > We think it's actually a DB locking problem and no corruption is > actually occurring. We have a cron script check on the DBs because > of this. Do you know if there is a replacement (planned) for > Berkeley DB in SVN? > [/quote] > > Let me know if any of you can answer that, > > cheers, > > - Koen. There are 2 database formats: http://svnbook.red-bean.com/en/1.1/ch05.html#svn-ch-5-sect-1.3 From that reading, it seems FSFS might be a safer route, particularly now that it has been around for a while: "The only real argument against FSFS is its relative immaturity compared to Berkeley DB. It hasn't been used or stress-tested nearly as much, and so a lot of these assertions about speed and scalability are just that: assertions, based on good guesses. In theory, it promises a lower barrier to entry for new administrators and is less susceptible to problems. In practice, only time will tell." (and that was written at least a year ago; FSFS was introduced with svn 1.1) See also the table on that same page: -------------- next part -------------- A non-text attachment was scrubbed... Name: Picture 2.png Type: image/png Size: 14167 bytes Desc: not available URL: -------------- next part -------------- Finally, at the bottom of this page on cocoadev: http://www.cocoadev.com/index.pl?SubVersionServer "...I've tried having a repository with two users accessing it through svnserve (what I call virtual users, since they are not users on the actual system) and one (me) using ssh, and that went really bad. Technically it's possible to do, it's described here: http:// svnbook.red-bean.com/nightly/en/svn.serverconfig.multimethod.html, however, it doesn't quite work, even if you follow the steps precisely. The Berkeley DB databases (redundant acronym, I know) crashes constantly. I have read that if you use FSFS instead it works better, but I haven't tried it yet. So, my single most important advice is: use only one access method per repository...." And the same problem experienced on a project with Drew McCormack by Alex and me. BUT I AM NO EXPERT AT ALL ON THIS STUFF!!! Maybe a little bit of Google-ing would add sense to all this :-) charles -- Xgrid-at-Stanford Help science move fast forward: http://cmgm.stanford.edu/~cparnot/xgrid-stanford Charles Parnot charles.parnot at gmail.com From peter.schols at bio.kuleuven.be Fri Mar 10 18:17:17 2006 From: peter.schols at bio.kuleuven.be (Peter Schols) Date: Sat, 11 Mar 2006 00:17:17 +0100 Subject: [Biococoa-dev] Initial Subversion import In-Reply-To: <3093195F-0B0E-4D03-8F7A-EEFBD96D3E7A@gmail.com> References: <481F27F2-B783-4204-9712-5831D4021AFE@bio.kuleuven.be> <52BA1374-14FF-471B-B9B4-FAE5FFCD4415@earthlink.net> <2B63AE40-4AE2-4F35-8E2F-A2B6003D9F56@bio.kuleuven.be> <653414BD-97CA-4100-8364-2FEFFB06CD32@earthlink.net> <6C9D4004-8849-4F84-84C6-4D07685E0821@bio.kuleuven.be> <3093195F-0B0E-4D03-8F7A-EEFBD96D3E7A@gmail.com> Message-ID: <98867BA1-5727-4098-82B3-0305A0C00B1A@bio.kuleuven.be> Hi Charles, > Is that for anonymous checkout? > One has to add the username, if different from your username on > your computer: username at bioinformatics.org/...... Indeed, for me it would become: svn checkout svn+ssh:// peterschols at bioinformatics.org/svnroot/BioCocoa > What version are you guys using? Just to troubleshoot a problem I > have (see below). 1.2.3 > I have a funny thing happening: > * ssh works fine with my key; I can ssh in without typing a password > * svn+ssh does not seem to use the key thing; it asks for my > password; actually, it asks 3 times, and I really have to enter the > right password 3 times, so it is like every operation needs some > authentication, and my authentication does not last. I experienced the same problem, it went away after creating a new key. best, Peter Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From kvddrift at earthlink.net Fri Mar 10 20:31:20 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Fri, 10 Mar 2006 20:31:20 -0500 Subject: [Biococoa-dev] wiki In-Reply-To: References: <287495C7-7ADD-40A2-BBBF-7F2137BB757F@earthlink.net> <38E56740-ABE1-4647-A664-211F0D766D20@bio.kuleuven.be> Message-ID: <3D3E6823-80DD-4AA3-B2BD-2546D7505291@earthlink.net> On Mar 10, 2006, at 1:02 PM, Charles Parnot wrote: > same for me! That's three - I have notified Jeff, so let's see what happens. - Koen. From kvddrift at earthlink.net Fri Mar 10 20:41:49 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Fri, 10 Mar 2006 20:41:49 -0500 Subject: [Biococoa-dev] strider and gck format Message-ID: Hi, I am still a bit confused about the strider and gck formats. In his code, Alex uses the following snippet to determine if a file is one of both formats: - (NSDictionary *)readFile:(NSString *)textFile { NSMutableDictionary *theContents; NSString *lineBreak; // BINARY // Strider? if([NSHFSTypeOfFile(textFile) isEqualToString: @"'xDNA'"]){ theContents = (NSMutableDictionary*) [self readStriderFile:textFile]; // GCK? }else if([NSHFSTypeOfFile(textFile) isEqualToString: @"'GCKc'"] || [NSHFSTypeOfFile(textFile) isEqualToString: @"'GCKs'"]){ theContents = (NSMutableDictionary*) [self readGCKFile:textFile]; // TEXT }else { So it's based on the file type. However, looked on the net for some sample files to test the code, and found those, but almost none of them have the xDNA, GCKc, or GCKs extension. So those files will be skipped by the code. For all other formats we use a recognition string within the file, eg > for fasta or HEADER for PDB's. I think that is a better approach, since we are not dependent on file types but on file content. Is there a typical recognition string for these data formats that we can use for file recognition? If not, is there another way we can make sure we catch all Strider and/or GCK files? cheers, - Koen. From a.griekspoor at nki.nl Sat Mar 11 04:44:39 2006 From: a.griekspoor at nki.nl (Alexander Griekspoor) Date: Sat, 11 Mar 2006 10:44:39 +0100 Subject: [Biococoa-dev] strider and gck format In-Reply-To: References: Message-ID: Hi Koen, Both the GCK and the Strider files are inherited from the good old MacOS9 period. In those days you would identify files using a type/ creator code, and that's what I check for in this code. You will never see these 4 character codes unless you use a program like resedit, and they are not the same as file extensions, in fact under MacOS9 you would never use file extensions unless you wanted your Windows buddies to open your word file as well. So NSHFSTypeOfFile is not the same as [filepath pathExtension]. The problem is that both filetypes are in binary format compared to the other formats which are ASCII based. Trying to read in the file as a string with ascii encoding creates some garbage which is impossible to interpret, let alone determine the filetype from. So the options were to either read all files in as data and check if it would fit the header of either filetype, and try to make anything out of that (quite tricky!) or simply to the filetype check. As a result I changed the code to have it pass the filepath instead of the raw text to the reader class. It better isolates code (no more reading at all in the delegate class), but we sacrifice the possibility to work with remote files. Guess this could be easily added to through a readFileFromURL method. Now that I think of it, perhaps we should also check for the file extensions that are added to GCK files if you create them on the windows platform. I'm not sure if in those files the creator/type codes are added, I could check that on monday... Hope this clears things up? Alex On 11-mrt-2006, at 2:41, Koen van der Drift wrote: > Hi, > > I am still a bit confused about the strider and gck formats. In his > code, Alex uses the following snippet to determine if a file is one > of both formats: > > - (NSDictionary *)readFile:(NSString *)textFile > { > NSMutableDictionary *theContents; > NSString *lineBreak; > > // BINARY > // Strider? > if([NSHFSTypeOfFile(textFile) isEqualToString: @"'xDNA'"]){ > > theContents = (NSMutableDictionary*) [self > readStriderFile:textFile]; > > // GCK? > }else if([NSHFSTypeOfFile(textFile) isEqualToString: @"'GCKc'"] || > [NSHFSTypeOfFile(textFile) isEqualToString: @"'GCKs'"]){ > > theContents = (NSMutableDictionary*) [self readGCKFile:textFile]; > > // TEXT > }else { > > > So it's based on the file type. However, looked on the net for some > sample files to test the code, and found those, but almost none of > them have the xDNA, GCKc, or GCKs extension. So those files will be > skipped by the code. For all other formats we use a recognition > string within the file, eg > for fasta or HEADER for PDB's. I > think that is a better approach, since we are not dependent on file > types but on file content. > > Is there a typical recognition string for these data formats that > we can use for file recognition? If not, is there another way we > can make sure we catch all Strider and/or GCK files? > > cheers, > > - Koen. > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com iRNAi, do you? http://www.mekentosj.com/irnai ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From kvddrift at earthlink.net Sat Mar 11 07:14:33 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sat, 11 Mar 2006 07:14:33 -0500 Subject: [Biococoa-dev] strider and gck format In-Reply-To: References: Message-ID: <0F6F416B-16F2-4913-BB6E-96D7C710B727@earthlink.net> On Mar 11, 2006, at 4:44 AM, Alexander Griekspoor wrote: > Both the GCK and the Strider files are inherited from the good old > MacOS9 period. In those days you would identify files using a type/ > creator code, and that's what I check for in this code. You will > never see these 4 character codes unless you use a program like > resedit, and they are not the same as file extensions, in fact > under MacOS9 you would never use file extensions unless you wanted > your Windows buddies to open your word file as well. So > NSHFSTypeOfFile is not the same as [filepath pathExtension]. > The problem is that both filetypes are in binary format compared to > the other formats which are ASCII based. Trying to read in the file > as a string with ascii encoding creates some garbage which is > impossible to interpret, let alone determine the filetype from. So > the options were to either read all files in as data and check if > it would fit the header of either filetype, and try to make > anything out of that (quite tricky!) or simply to the filetype > check. As a result I changed the code to have it pass the filepath > instead of the raw text to the reader class. It better isolates > code (no more reading at all in the delegate class), but we > sacrifice the possibility to work with remote files. Guess this > could be easily added to through a readFileFromURL method. > Now that I think of it, perhaps we should also check for the file > extensions that are added to GCK files if you create them on the > windows platform. I'm not sure if in those files the creator/type > codes are added, I could check that on monday... > Hope this clears things up? Yes, thanks! I was trying to test your code in the framework using the Translation example. So I found some strider test file and read that in with the current code in Translation. The file works fine with your demo app. However in Translation it doesn't. Right now I use: BCSequenceArray *sequenceArray = [sequenceReader readFileUsingText: [[NSBundle mainBundle] pathForResource: @"Strider" ofType:@"seq"]]; But that doesn't work. Maybe that should be changed to: BCSequenceArray *sequenceArray = [sequenceReader readFileUsingPath: [[NSBundle mainBundle] pathForResource: @"Strider" ofType:@"seq"]]; I agree with you that passing the filepath is a better way of doing things. I will look into that this weekend. cheers, - Koen. From a.griekspoor at nki.nl Sat Mar 11 07:19:02 2006 From: a.griekspoor at nki.nl (Alexander Griekspoor) Date: Sat, 11 Mar 2006 13:19:02 +0100 Subject: [Biococoa-dev] strider and gck format In-Reply-To: <0F6F416B-16F2-4913-BB6E-96D7C710B727@earthlink.net> References: <0F6F416B-16F2-4913-BB6E-96D7C710B727@earthlink.net> Message-ID: Just to make sure, you can also export DNA strider files in a ascii format, I've attached a native file for you to test that is in the default binary format. Again, you can't use text, trying to read in a binary file as ascii text will destroy the header.. Cheers, Alex ? On 11-mrt-2006, at 13:14, Koen van der Drift wrote: > > On Mar 11, 2006, at 4:44 AM, Alexander Griekspoor wrote: > >> Both the GCK and the Strider files are inherited from the good old >> MacOS9 period. In those days you would identify files using a type/ >> creator code, and that's what I check for in this code. You will >> never see these 4 character codes unless you use a program like >> resedit, and they are not the same as file extensions, in fact >> under MacOS9 you would never use file extensions unless you wanted >> your Windows buddies to open your word file as well. So >> NSHFSTypeOfFile is not the same as [filepath pathExtension]. >> The problem is that both filetypes are in binary format compared >> to the other formats which are ASCII based. Trying to read in the >> file as a string with ascii encoding creates some garbage which is >> impossible to interpret, let alone determine the filetype from. So >> the options were to either read all files in as data and check if >> it would fit the header of either filetype, and try to make >> anything out of that (quite tricky!) or simply to the filetype >> check. As a result I changed the code to have it pass the filepath >> instead of the raw text to the reader class. It better isolates >> code (no more reading at all in the delegate class), but we >> sacrifice the possibility to work with remote files. Guess this >> could be easily added to through a readFileFromURL method. >> Now that I think of it, perhaps we should also check for the file >> extensions that are added to GCK files if you create them on the >> windows platform. I'm not sure if in those files the creator/type >> codes are added, I could check that on monday... >> Hope this clears things up? > > > Yes, thanks! I was trying to test your code in the framework using > the Translation example. So I found some strider test file and read > that in with the current code in Translation. The file works fine > with your demo app. However in Translation it doesn't. Right now I > use: > > BCSequenceArray *sequenceArray = [sequenceReader readFileUsingText: > [[NSBundle mainBundle] pathForResource: @"Strider" ofType:@"seq"]]; > > But that doesn't work. Maybe that should be changed to: > > BCSequenceArray *sequenceArray = [sequenceReader readFileUsingPath: > [[NSBundle mainBundle] pathForResource: @"Strider" ofType:@"seq"]]; > > > I agree with you that passing the filepath is a better way of doing > things. I will look into that this weekend. > > cheers, > > - Koen. > > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > *********************************** Mek (Alexander Griekspoor) MekenTosj.com Web: http://www.mekentosj.com Mail: mek at mekentosj.com *********************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Ubiquitin Type: application/octet-stream Size: 340 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From kvddrift at earthlink.net Sat Mar 11 20:22:58 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sat, 11 Mar 2006 20:22:58 -0500 Subject: [Biococoa-dev] wiki In-Reply-To: <3D3E6823-80DD-4AA3-B2BD-2546D7505291@earthlink.net> References: <287495C7-7ADD-40A2-BBBF-7F2137BB757F@earthlink.net> <38E56740-ABE1-4647-A664-211F0D766D20@bio.kuleuven.be> <3D3E6823-80DD-4AA3-B2BD-2546D7505291@earthlink.net> Message-ID: <349B8F0E-4747-4106-990C-E676711B6CF4@earthlink.net> Hi all, The wiki page is now in place and can be found at http:// bioinformatics.org/biococoa/wiki/ Right now the wiki page requires a password for editing and is Peter's full kuleuven.ac.be email address. However, I think we should change that (it's waaaay to long), and distribute the new password off-list. The password can be changed in the config file: /projects/home/peterschols/public_html/biococoa/wiki/local/config.php Unfortunately, only Peter has write access to that directory, so I was unable to change it. cheers, - Koen. From peter.schols at bio.kuleuven.be Sun Mar 12 05:10:15 2006 From: peter.schols at bio.kuleuven.be (Peter Schols) Date: Sun, 12 Mar 2006 11:10:15 +0100 Subject: [Biococoa-dev] wiki In-Reply-To: <349B8F0E-4747-4106-990C-E676711B6CF4@earthlink.net> References: <287495C7-7ADD-40A2-BBBF-7F2137BB757F@earthlink.net> <38E56740-ABE1-4647-A664-211F0D766D20@bio.kuleuven.be> <3D3E6823-80DD-4AA3-B2BD-2546D7505291@earthlink.net> <349B8F0E-4747-4106-990C-E676711B6CF4@earthlink.net> Message-ID: <2449A1D8-29EC-4EDD-A971-578665027E30@bio.kuleuven.be> Koen,kvddrift at earthlink.net This is great! Together with the switch to SVN, this will enable us to work much more efficiently. I have updated the password and I'll send it to everyone off-list. best wishes, peter On 12 Mar 2006, at 02:22, Koen van der Drift wrote: > Hi all, > > The wiki page is now in place and can be found at http:// > bioinformatics.org/biococoa/wiki/ > > Right now the wiki page requires a password for editing and is > Peter's full kuleuven.ac.be email address. However, I think we > should change that (it's waaaay to long), and distribute the new > password off-list. The password can be changed in the config file: > > /projects/home/peterschols/public_html/biococoa/wiki/local/config.php > > Unfortunately, only Peter has write access to that directory, so I > was unable to change it. > > > cheers, > > - Koen. > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From kvddrift at earthlink.net Sun Mar 12 08:52:28 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sun, 12 Mar 2006 08:52:28 -0500 Subject: [Biococoa-dev] strider and gck format In-Reply-To: References: <0F6F416B-16F2-4913-BB6E-96D7C710B727@earthlink.net> Message-ID: <5EB8E66C-937C-4076-AFBA-E7932D418096@earthlink.net> On Mar 11, 2006, at 7:19 AM, Alexander Griekspoor wrote: > Just to make sure, you can also export DNA strider files in a ascii > format, I've attached a native file for you to test that is in the > default binary format. > Again, you can't use text, trying to read in a binary file as ascii > text will destroy the header.. > Thanks Alex, I was struggling some more with the Translation demo to get your sample file to work. Apparently hard-coding the path as we do now is not a good approach (at least in my hands). So I was thinking to add your openPanel code to the Translation demo. Or even better, we could have an openPanel controller class in our BCAppKit that can be used in various programs. It could then also be used to get sequences using NSURL. Let me know what you guys think of this approach, so I can start working on that class (BCSequenceIOController seems like a useful name). I won't have much time today though, it's going to be > 25 ?C, so I don't feel like sitting behind my computer :) cheers, - Koen. From a.griekspoor at nki.nl Mon Mar 13 05:10:17 2006 From: a.griekspoor at nki.nl (Alexander Griekspoor) Date: Mon, 13 Mar 2006 11:10:17 +0100 Subject: [Biococoa-dev] strider and gck format In-Reply-To: <5EB8E66C-937C-4076-AFBA-E7932D418096@earthlink.net> References: <0F6F416B-16F2-4913-BB6E-96D7C710B727@earthlink.net> <5EB8E66C-937C-4076-AFBA-E7932D418096@earthlink.net> Message-ID: <4698C100-9C3E-4A1C-B228-1E6A088D51AF@nki.nl> Hi Koen, Indeed hard-coding a path isn't very elegant ;-) I'm not sure whether we need the sequenceIOcontroller though. I would let the app decide how to do the interface and obtain the file path/url, after that everything can be done in the reader/writer classes. The reason is that 1) interfaces can be very different (i.e. metal or not), 2) implementations can be very different. An an example, in iRNAi i use the code that I included in previous emails, in EnzymeX 3 I make use of the standard NSDocument routines. No need to do any panel at all, just subclassing the read/writeFileFromPath:ofType: methods, all the panel stuff is handled by NSDocument itself. It might even be nice to have one demo app use this approach and one the iRNAi type approach. Cheers, Alex On 12-mrt-2006, at 14:52, Koen van der Drift wrote: > > On Mar 11, 2006, at 7:19 AM, Alexander Griekspoor wrote: > >> Just to make sure, you can also export DNA strider files in a >> ascii format, I've attached a native file for you to test that is >> in the default binary format. >> Again, you can't use text, trying to read in a binary file as >> ascii text will destroy the header.. >> > > Thanks Alex, > > I was struggling some more with the Translation demo to get your > sample file to work. Apparently hard-coding the path as we do now > is not a good approach (at least in my hands). So I was thinking to > add your openPanel code to the Translation demo. Or even better, we > could have an openPanel controller class in our BCAppKit that can > be used in various programs. It could then also be used to get > sequences using NSURL. > > Let me know what you guys think of this approach, so I can start > working on that class (BCSequenceIOController seems like a useful > name). I won't have much time today though, it's going to be > 25 > ?C, so I don't feel like sitting behind my computer :) > > cheers, > > - Koen._______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com LabAssistant - Get your life organized! http://www.mekentosj.com/labassistant ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From kvddrift at earthlink.net Mon Mar 13 06:55:15 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Mon, 13 Mar 2006 06:55:15 -0500 Subject: [Biococoa-dev] strider and gck format In-Reply-To: <4698C100-9C3E-4A1C-B228-1E6A088D51AF@nki.nl> References: <0F6F416B-16F2-4913-BB6E-96D7C710B727@earthlink.net> <5EB8E66C-937C-4076-AFBA-E7932D418096@earthlink.net> <4698C100-9C3E-4A1C-B228-1E6A088D51AF@nki.nl> Message-ID: <7F9A6C87-7F6A-4154-AC2E-866679C6B892@earthlink.net> On Mar 13, 2006, at 5:10 AM, Alexander Griekspoor wrote: > Indeed hard-coding a path isn't very elegant ;-) I'm not sure > whether we need the sequenceIOcontroller though. > I would let the app decide how to do the interface and obtain the > file path/url, after that everything can be done in the reader/ > writer classes. > That indeed makes a lot of sense. I will add some open file code to the Translation demo. BTW, would it be an idea to merge all examples in one big demo app? - Koen. From a.griekspoor at nki.nl Mon Mar 13 08:55:21 2006 From: a.griekspoor at nki.nl (Alexander Griekspoor) Date: Mon, 13 Mar 2006 14:55:21 +0100 Subject: [Biococoa-dev] strider and gck format In-Reply-To: <7F9A6C87-7F6A-4154-AC2E-866679C6B892@earthlink.net> References: <0F6F416B-16F2-4913-BB6E-96D7C710B727@earthlink.net> <5EB8E66C-937C-4076-AFBA-E7932D418096@earthlink.net> <4698C100-9C3E-4A1C-B228-1E6A088D51AF@nki.nl> <7F9A6C87-7F6A-4154-AC2E-866679C6B892@earthlink.net> Message-ID: <803C21CB-B23C-41D3-BAAA-7FC62ABA7C78@nki.nl> > BTW, would it be an idea to merge all examples in one big demo app? That depends, sometimes it's nicer to have multiple smaller demos, 1st they are easier to grasp because they're smaller and more targeted to a specific problem, 2nd you can demonstrated different ways of doing things (like document vs non-document based apps). Imagine having to get the full code of iTunes an an example to do MP3 encoding.. On the other hand, if you want to have a full blown app building upon BioCocoa which could be the next DNA strider, then yes would be nice but not so much as sample code. Just my 2 cents, Alex ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com LabAssistant - Get your life organized! http://www.mekentosj.com/labassistant ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From kvddrift at earthlink.net Tue Mar 14 19:40:26 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Tue, 14 Mar 2006 19:40:26 -0500 Subject: [Biococoa-dev] Fwd: wiki page for BioCocoa project References: <44164CDF.60004@bioinformatics.org> Message-ID: <1444A472-0BAF-4A4F-B069-7470F799A58E@earthlink.net> Hi, We now have the opportunety to switch to FSFS for the svn database (see message below). If anyone thinks it is really beneficial, please let Peter know, so he can go ahead and make the switch. cheers, - Koen. Begin forwarded message: > From: "J.W. Bizzaro" > Date: March 13, 2006 11:55:59 PM EST > To: kvddrift at earthlink.net > Cc: Administration discussions about BiO admin at bioinformatics.org> > Subject: Re: wiki page for BioCocoa project > > Hi Koen, > > The system is currently capable of using FSFS. When creating a > repository, simply use the following option: > > $ svnadmin create --fs-type fsfs /path/to/repos > > This section explains it: > > http://svnbook.red-bean.com/en/1.1/ch05s02.html > > Since BioCocoa is currently using BerkeleyDB, you would have to > recreate your repository. You may want to do that before you make > many more changes :-) If you keep the BerkeleyDB, it will simply > "wedge" itself from time-to-time and have to be unwedged by our > checkup script (every 15 minutes). > > Cheers, > Jeff From kvddrift at earthlink.net Sat Mar 18 09:30:41 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sat, 18 Mar 2006 09:30:41 -0500 Subject: [Biococoa-dev] strider and gck format In-Reply-To: <803C21CB-B23C-41D3-BAAA-7FC62ABA7C78@nki.nl> References: <0F6F416B-16F2-4913-BB6E-96D7C710B727@earthlink.net> <5EB8E66C-937C-4076-AFBA-E7932D418096@earthlink.net> <4698C100-9C3E-4A1C-B228-1E6A088D51AF@nki.nl> <7F9A6C87-7F6A-4154-AC2E-866679C6B892@earthlink.net> <803C21CB-B23C-41D3-BAAA-7FC62ABA7C78@nki.nl> Message-ID: <2BB2D9B8-62A7-46B8-88FF-656FEF710F48@earthlink.net> Hi, I have just updated the Translation demo, and added the openPanel code from the BCAppDemo to import files. It now works with the strider format. Next is to merge KDTextView with BCSequenceView. - Koen. From kvddrift at earthlink.net Sat Mar 18 10:10:52 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sat, 18 Mar 2006 10:10:52 -0500 Subject: [Biococoa-dev] Fwd: wiki page for BioCocoa project In-Reply-To: <1444A472-0BAF-4A4F-B069-7470F799A58E@earthlink.net> References: <44164CDF.60004@bioinformatics.org> <1444A472-0BAF-4A4F-B069-7470F799A58E@earthlink.net> Message-ID: On Mar 14, 2006, at 7:40 PM, Koen van der Drift wrote: > Hi, > > We now have the opportunety to switch to FSFS for the svn database > (see message below). > > If anyone thinks it is really beneficial, please let Peter know, so > he can go ahead and make the switch. Peter, Could you switch the project to FSFS? I was doing some commits, got a BerkeleyDB error message from the svn server, and after that some of my earlier commits seemed to be undone. thanks, - Koen. From mek at mekentosj.com Sun Mar 19 05:57:41 2006 From: mek at mekentosj.com (Alexander Griekspoor) Date: Sun, 19 Mar 2006 11:57:41 +0100 Subject: [Biococoa-dev] strider and gck format In-Reply-To: <2BB2D9B8-62A7-46B8-88FF-656FEF710F48@earthlink.net> References: <0F6F416B-16F2-4913-BB6E-96D7C710B727@earthlink.net> <5EB8E66C-937C-4076-AFBA-E7932D418096@earthlink.net> <4698C100-9C3E-4A1C-B228-1E6A088D51AF@nki.nl> <7F9A6C87-7F6A-4154-AC2E-866679C6B892@earthlink.net> <803C21CB-B23C-41D3-BAAA-7FC62ABA7C78@nki.nl> <2BB2D9B8-62A7-46B8-88FF-656FEF710F48@earthlink.net> Message-ID: Great work Koen! Nice! Alex On 18-mrt-2006, at 15:30, Koen van der Drift wrote: > Hi, > > I have just updated the Translation demo, and added the openPanel > code from the BCAppDemo to import files. It now works with the > strider format. > > Next is to merge KDTextView with BCSequenceView. > > - Koen._______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com Windows is a 32-bit patch to a 16-bit shell for an 8-bit operating system, written for a 4-bit processor by a 2- bit company without 1 bit of sense. ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From kvddrift at earthlink.net Sun Mar 19 10:11:49 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sun, 19 Mar 2006 10:11:49 -0500 Subject: [Biococoa-dev] strider and gck format In-Reply-To: References: <0F6F416B-16F2-4913-BB6E-96D7C710B727@earthlink.net> <5EB8E66C-937C-4076-AFBA-E7932D418096@earthlink.net> <4698C100-9C3E-4A1C-B228-1E6A088D51AF@nki.nl> <7F9A6C87-7F6A-4154-AC2E-866679C6B892@earthlink.net> <803C21CB-B23C-41D3-BAAA-7FC62ABA7C78@nki.nl> <2BB2D9B8-62A7-46B8-88FF-656FEF710F48@earthlink.net> Message-ID: On Mar 19, 2006, at 5:57 AM, Alexander Griekspoor wrote: > Great work Koen! Nice! > Alex > > On 18-mrt-2006, at 15:30, Koen van der Drift wrote: > >> Hi, >> >> I have just updated the Translation demo, and added the openPanel >> code from the BCAppDemo to import files. It now works with the >> strider format. >> >> Next is to merge KDTextView with BCSequenceView. Alex, How can I control the number of symbols in the column view (in the KDTextView) ? It would be nice to make that variable, eg my preference would be to have 10 symbols in one column. You already added a method setColumnWidth, but I don't see anything similar for the number of symbols. We should also be careful that we don't hard- code the dimensions of the column (and the overlay), because the user may want to change the fonttype and -size. cheers, - Koen. From mek at mekentosj.com Sun Mar 19 11:08:48 2006 From: mek at mekentosj.com (Alexander Griekspoor) Date: Sun, 19 Mar 2006 17:08:48 +0100 Subject: [Biococoa-dev] strider and gck format In-Reply-To: References: <0F6F416B-16F2-4913-BB6E-96D7C710B727@earthlink.net> <5EB8E66C-937C-4076-AFBA-E7932D418096@earthlink.net> <4698C100-9C3E-4A1C-B228-1E6A088D51AF@nki.nl> <7F9A6C87-7F6A-4154-AC2E-866679C6B892@earthlink.net> <803C21CB-B23C-41D3-BAAA-7FC62ABA7C78@nki.nl> <2BB2D9B8-62A7-46B8-88FF-656FEF710F48@earthlink.net> Message-ID: <40CC6729-B52B-437D-A946-761B99A36A72@mekentosj.com> Hi Koen, The columnwidth parameter is exactly that, it's not the spacing, it determines the space for characters. The default of 90 matches exactly 10 courier 12 characters. Here's the awakefromnib stuff I use: [sequenceTextView setSelectedTextAttributes: [NSDictionary dictionaryWithObjectsAndKeys: [NSColor colorWithCalibratedRed: 178.0 / 255.0 green: 198.0 / 255.0 blue: 223.0 / 255.0 alpha: 1.0], NSBackgroundColorAttributeName, nil]]; [sequenceTextView setContinuousSpellCheckingEnabled: NO]; [sequenceTextView setFont: [NSFont fontWithName: @"Courier" size: 12.0]]; [sequenceTextView setUnit: @"bp"]; Now it would indeed by logical (and a future plan), that the columnwidth is not a property but is calculated based on the current font. Then the number of characters per column would be a nice property to add. This was outside the current scope for me though. One other thing, there seems to be a bug in the textview that if you have less than one row of text, you can't select any of the first 10 characters, if you would find the fix for this bug I would be very greatful! Cheers, Alex On 19-mrt-2006, at 16:11, Koen van der Drift wrote: > > On Mar 19, 2006, at 5:57 AM, Alexander Griekspoor wrote: > >> Great work Koen! Nice! >> Alex >> >> On 18-mrt-2006, at 15:30, Koen van der Drift wrote: >> >>> Hi, >>> >>> I have just updated the Translation demo, and added the openPanel >>> code from the BCAppDemo to import files. It now works with the >>> strider format. >>> >>> Next is to merge KDTextView with BCSequenceView. > > Alex, > > How can I control the number of symbols in the column view (in the > KDTextView) ? It would be nice to make that variable, eg my > preference would be to have 10 symbols in one column. You already > added a method setColumnWidth, but I don't see anything similar for > the number of symbols. We should also be careful that we don't hard- > code the dimensions of the column (and the overlay), because the > user may want to change the fonttype and -size. > > cheers, > > - Koen. > > *********************************** Mek (Alexander Griekspoor) MekenTosj.com Web: http://www.mekentosj.com Mail: mek at mekentosj.com *********************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From kvddrift at earthlink.net Sun Mar 19 18:34:55 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sun, 19 Mar 2006 18:34:55 -0500 Subject: [Biococoa-dev] strider and gck format In-Reply-To: <40CC6729-B52B-437D-A946-761B99A36A72@mekentosj.com> References: <0F6F416B-16F2-4913-BB6E-96D7C710B727@earthlink.net> <5EB8E66C-937C-4076-AFBA-E7932D418096@earthlink.net> <4698C100-9C3E-4A1C-B228-1E6A088D51AF@nki.nl> <7F9A6C87-7F6A-4154-AC2E-866679C6B892@earthlink.net> <803C21CB-B23C-41D3-BAAA-7FC62ABA7C78@nki.nl> <2BB2D9B8-62A7-46B8-88FF-656FEF710F48@earthlink.net> <40CC6729-B52B-437D-A946-761B99A36A72@mekentosj.com> Message-ID: Hi, One thing that the BCSequenceView will also need (or actually maybe its controller) is a method that checks whether what the user types is part of the symbolset of the sequence. If the controller does that, it's probably needed in a delegate method, such as - (BOOL)textView:(NSTextView *)aTextView shouldChangeTextInRange:(NSRange)affectedCharRange replacementString:(NSString *)replacementString And also a way to change every typed letter to uppercase/lowercase automagically. Alex, I will look into the bug - that is indeed very weird, and difficult to debug :( However, the fact that it only is for the first 10 characters, which is hardecoded in the default value of 90 for the columnwidth, could give a clue. cheers, - Koen. On Mar 19, 2006, at 11:08 AM, Alexander Griekspoor wrote: > Hi Koen, > > The columnwidth parameter is exactly that, it's not the spacing, it > determines the space for characters. The default of 90 matches > exactly 10 courier 12 characters. Here's the awakefromnib stuff I use: > > [sequenceTextView setSelectedTextAttributes: [NSDictionary > dictionaryWithObjectsAndKeys: [NSColor colorWithCalibratedRed: > 178.0 / 255.0 green: 198.0 / 255.0 blue: 223.0 / 255.0 alpha: 1.0], > NSBackgroundColorAttributeName, nil]]; > [sequenceTextView setContinuousSpellCheckingEnabled: NO]; > [sequenceTextView setFont: [NSFont fontWithName: @"Courier" size: > 12.0]]; > [sequenceTextView setUnit: @"bp"]; > > Now it would indeed by logical (and a future plan), that the > columnwidth is not a property but is calculated based on the > current font. Then the number of characters per column would be a > nice property to add. This was outside the current scope for me > though. > > One other thing, there seems to be a bug in the textview that if > you have less than one row of text, you can't select any of the > first 10 characters, if you would find the fix for this bug I would > be very greatful! > Cheers, > Alex > > > > On 19-mrt-2006, at 16:11, Koen van der Drift wrote: > >> >> On Mar 19, 2006, at 5:57 AM, Alexander Griekspoor wrote: >> >>> Great work Koen! Nice! >>> Alex >>> >>> On 18-mrt-2006, at 15:30, Koen van der Drift wrote: >>> >>>> Hi, >>>> >>>> I have just updated the Translation demo, and added the >>>> openPanel code from the BCAppDemo to import files. It now works >>>> with the strider format. >>>> >>>> Next is to merge KDTextView with BCSequenceView. >> >> Alex, >> >> How can I control the number of symbols in the column view (in the >> KDTextView) ? It would be nice to make that variable, eg my >> preference would be to have 10 symbols in one column. You already >> added a method setColumnWidth, but I don't see anything similar >> for the number of symbols. We should also be careful that we don't >> hard-code the dimensions of the column (and the overlay), because >> the user may want to change the fonttype and -size. >> >> cheers, >> >> - Koen. >> >> > > *********************************** > Mek (Alexander Griekspoor) > MekenTosj.com > Web: http://www.mekentosj.com > Mail: mek at mekentosj.com > *********************************** > > From kvddrift at earthlink.net Sun Mar 19 20:25:06 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sun, 19 Mar 2006 20:25:06 -0500 Subject: [Biococoa-dev] strider and gck format In-Reply-To: References: <0F6F416B-16F2-4913-BB6E-96D7C710B727@earthlink.net> <5EB8E66C-937C-4076-AFBA-E7932D418096@earthlink.net> <4698C100-9C3E-4A1C-B228-1E6A088D51AF@nki.nl> <7F9A6C87-7F6A-4154-AC2E-866679C6B892@earthlink.net> <803C21CB-B23C-41D3-BAAA-7FC62ABA7C78@nki.nl> <2BB2D9B8-62A7-46B8-88FF-656FEF710F48@earthlink.net> <40CC6729-B52B-437D-A946-761B99A36A72@mekentosj.com> Message-ID: <7521DE10-0A94-4CB3-B53F-132FCC50FBAF@earthlink.net> On Mar 19, 2006, at 6:34 PM, Koen van der Drift wrote: > One thing that the BCSequenceView will also need (or actually maybe > its controller) is a method that checks whether what the user types > is part of the symbolset of the sequence. If the controller does > that, it's probably needed in a delegate method, such as > > - (BOOL)textView:(NSTextView *)aTextView > shouldChangeTextInRange:(NSRange)affectedCharRange > replacementString:(NSString *)replacementString > > > And also a way to change every typed letter to uppercase/lowercase > automagically. Hmm, replying to myself here :) Another possibilty could be to make a formatter that takes care of these things. I will look into that, unless someone thinks that's a bad idea. cheers, - Koen. From mek at mekentosj.com Mon Mar 20 05:04:59 2006 From: mek at mekentosj.com (Alexander Griekspoor) Date: Mon, 20 Mar 2006 11:04:59 +0100 Subject: [Biococoa-dev] strider and gck format In-Reply-To: <7521DE10-0A94-4CB3-B53F-132FCC50FBAF@earthlink.net> References: <0F6F416B-16F2-4913-BB6E-96D7C710B727@earthlink.net> <5EB8E66C-937C-4076-AFBA-E7932D418096@earthlink.net> <4698C100-9C3E-4A1C-B228-1E6A088D51AF@nki.nl> <7F9A6C87-7F6A-4154-AC2E-866679C6B892@earthlink.net> <803C21CB-B23C-41D3-BAAA-7FC62ABA7C78@nki.nl> <2BB2D9B8-62A7-46B8-88FF-656FEF710F48@earthlink.net> <40CC6729-B52B-437D-A946-761B99A36A72@mekentosj.com> <7521DE10-0A94-4CB3-B53F-132FCC50FBAF@earthlink.net> Message-ID: <56E18C08-A882-4247-A775-FD5038FFD24C@mekentosj.com> Hi Koen, Indeed, I use a stripForeignCharacters method in EnzymeX and iRNAi, still have to move it to the shouldChangeTextinRange method (currently it is still invoked on the whole textStorage every time). It indeed also does the case conversion. I'm not sure if you can use a formatter in combination with a textview, I thought only with a textfield (update, just checked. setformatter: indeed only works with NSCell, but perhaps you could set it on the fieldeditor. probably also not, because that one is also of class NSText). Cheers, Alex - (void)stripForeignCharacters{ NSRange oldRange = [sequenceView selectedRange]; NSTextStorage* textstorage = [sequenceView textStorage]; NSString* strippedString = @""; NSString* oldString = [[textstorage string] uppercaseString]; NSMutableString* newString = [NSMutableString stringWithCapacity: [textstorage length]]; NSScanner* scanner = [NSScanner scannerWithString: oldString]; [scanner scanUpToCharactersFromSet: charSet intoString: nil]; while ( [scanner isAtEnd] == NO) { if(![scanner scanCharactersFromSet: charSet intoString: &strippedString]) continue; [newString appendString: strippedString]; if(![scanner scanUpToCharactersFromSet: charSet intoString: nil]) continue; } NSAttributedString* attstring = [[NSAttributedString alloc] initWithString: newString]; [textstorage setAttributedString: attstring]; [textstorage addAttribute: NSFontAttributeName value: [NSFont fontWithName: @"Courier" size: 12.0] range: NSMakeRange (0,[[textstorage mutableString] length])]; [attstring release]; if(oldRange.length == 0 && ([[textstorage mutableString] length] > oldRange.location)){ [sequenceView setSelectedRange: NSMakeRange (oldRange.location, 0)]; } [mainWindow makeFirstResponder: sequenceView]; } On 20-mrt-2006, at 2:25, Koen van der Drift wrote: > > On Mar 19, 2006, at 6:34 PM, Koen van der Drift wrote: > >> One thing that the BCSequenceView will also need (or actually >> maybe its controller) is a method that checks whether what the >> user types is part of the symbolset of the sequence. If the >> controller does that, it's probably needed in a delegate method, >> such as >> >> - (BOOL)textView:(NSTextView *)aTextView >> shouldChangeTextInRange:(NSRange)affectedCharRange >> replacementString:(NSString *)replacementString >> >> >> And also a way to change every typed letter to uppercase/lowercase >> automagically. > > > Hmm, replying to myself here :) Another possibilty could be to make > a formatter that takes care of these things. I will look into that, > unless someone thinks that's a bad idea. > > cheers, > > - Koen. > *********************************** Mek (Alexander Griekspoor) MekenTosj.com Web: http://www.mekentosj.com Mail: mek at mekentosj.com *********************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From kvddrift at earthlink.net Mon Mar 20 17:25:30 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Mon, 20 Mar 2006 17:25:30 -0500 Subject: [Biococoa-dev] strider and gck format In-Reply-To: <56E18C08-A882-4247-A775-FD5038FFD24C@mekentosj.com> References: <0F6F416B-16F2-4913-BB6E-96D7C710B727@earthlink.net> <5EB8E66C-937C-4076-AFBA-E7932D418096@earthlink.net> <4698C100-9C3E-4A1C-B228-1E6A088D51AF@nki.nl> <7F9A6C87-7F6A-4154-AC2E-866679C6B892@earthlink.net> <803C21CB-B23C-41D3-BAAA-7FC62ABA7C78@nki.nl> <2BB2D9B8-62A7-46B8-88FF-656FEF710F48@earthlink.net> <40CC6729-B52B-437D-A946-761B99A36A72@mekentosj.com> <7521DE10-0A94-4CB3-B53F-132FCC50FBAF@earthlink.net> <56E18C08-A882-4247-A775-FD5038FFD24C@mekentosj.com> Message-ID: <06646BD8-1144-4100-A87D-EA48849F40FC@earthlink.net> On Mar 20, 2006, at 5:04 AM, Alexander Griekspoor wrote: > 'm not sure if you can use a formatter in combination with a > textview, I thought only with a textfield (update, just checked. > setformatter: indeed only works with NSCell, but perhaps you could > set it on the fieldeditor. probably also not, because that one is > also of class NSText). Yep, I found that out a little bit after doing some more reading :( Anyway, with shouldChangeTextinRange it is very easy to do: - (BOOL)textView:(NSTextView *)aTextView shouldChangeTextInRange:(NSRange)affectedCharRange replacementString:(NSString *)replacementString { if ([[self protein] validateInput: replacementString]) { editedRange = affectedCharRange; [[self protein] changeSequenceStringInRange: editedRange withString: newString]; // this needs some more attention return YES; } return NO; } and in validateInput: - (BOOL)validateInput: (NSString *)aString { return [[self symbolSet] containsCharactersFromString: aString]; } - Koen. From kvddrift at earthlink.net Mon Mar 20 21:56:07 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Mon, 20 Mar 2006 21:56:07 -0500 Subject: [Biococoa-dev] translation demo Message-ID: Hi, I have updated the translation demo a bit more. It now includes symbol filtering, and is a bit more MVC aware. Because we do not have mutable sequences yet, a new sequence is created everytime the 'process' button is pressed. Please have a look and let me know what you think. - Koen. From mek at mekentosj.com Tue Mar 21 07:56:46 2006 From: mek at mekentosj.com (Alexander Griekspoor) Date: Tue, 21 Mar 2006 13:56:46 +0100 Subject: [Biococoa-dev] translation demo In-Reply-To: References: Message-ID: Hi Koen, I tried to checkout and build the project, first it did want to as some values were not defined, but second it seems that you haven't committed the project, the BCSequenceView isn't yet the new one... Alex On 21-mrt-2006, at 3:56, Koen van der Drift wrote: > Hi, > > I have updated the translation demo a bit more. It now includes > symbol filtering, and is a bit more MVC aware. Because we do not > have mutable sequences yet, a new sequence is created everytime the > 'process' button is pressed. Please have a look and let me know > what you think. > > - Koen. > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > *********************************** Mek (Alexander Griekspoor) MekenTosj.com Web: http://www.mekentosj.com Mail: mek at mekentosj.com *********************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From kvddrift at earthlink.net Tue Mar 21 17:11:25 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Tue, 21 Mar 2006 17:11:25 -0500 Subject: [Biococoa-dev] translation demo In-Reply-To: References: Message-ID: <0A5BD701-12B7-445C-9452-DAB0FD01F177@earthlink.net> Hi Alex, > I tried to checkout and build the project, first it did want to as > some values were not defined, but second it seems that you haven't > committed the project, the BCSequenceView isn't yet the new one... > That seems to be a Xcode-svn snafu. I will have a look later and see if I can use svnX to fix it. - Koen. From kvddrift at earthlink.net Tue Mar 21 17:24:51 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Tue, 21 Mar 2006 17:24:51 -0500 Subject: [Biococoa-dev] translation demo In-Reply-To: <0A5BD701-12B7-445C-9452-DAB0FD01F177@earthlink.net> References: <0A5BD701-12B7-445C-9452-DAB0FD01F177@earthlink.net> Message-ID: On Mar 21, 2006, at 5:11 PM, Koen van der Drift wrote: > >> I tried to checkout and build the project, first it did want to as >> some values were not defined, but second it seems that you haven't >> committed the project, the BCSequenceView isn't yet the new one... >> > > That seems to be a Xcode-svn snafu. I will have a look later and > see if I can use svnX to fix it. > Actually - I think it is more related to the BerkeleyDB-svn issue. I get a lot of error dialogs in Xcode. Peter, as suggested by Jeff, could you re-create the svn repository, using FSFS. I quote his earlier message: [quote] The system is currently capable of using FSFS. When creating a repository, simply use the following option: $ svnadmin create --fs-type fsfs /path/to/repos This section explains it: http://svnbook.red-bean.com/en/1.1/ch05s02.html Since BioCocoa is currently using BerkeleyDB, you would have to recreate your repository. You may want to do that before you make many more changes :-) If you keep the BerkeleyDB, it will simply "wedge" itself from time-to-time and have to be unwedged by our checkup script (every 15 minutes). [/quote] cheers, - Koen. From kvddrift at earthlink.net Tue Mar 21 18:17:08 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Tue, 21 Mar 2006 18:17:08 -0500 Subject: [Biococoa-dev] translation demo In-Reply-To: References: <0A5BD701-12B7-445C-9452-DAB0FD01F177@earthlink.net> Message-ID: Well well well, I was able to commit the new BCSequenceView, hopefully everything compiles and runs fine. I also just got a mail from Jeff from bioinformatics.org, who strongly recommended to move to FSFS. In case Peter is unable to do the switch, I will do it, I already asked him for more detailed instructions. watch this space for updates ;-) - Koen. From kvddrift at earthlink.net Tue Mar 21 21:46:11 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Tue, 21 Mar 2006 21:46:11 -0500 Subject: [Biococoa-dev] new svn repository Message-ID: Hi, We now have a new svn repository, using FSFS. Please check it out (no pun intended): svn checkout svn+ssh://bioinformatics.org/svnroot/BioCocoa Let me know if it works fine, so I can inform Jeff that he can delete the old version. cheers, - Koen. From mek at mekentosj.com Thu Mar 23 05:18:34 2006 From: mek at mekentosj.com (Alexander Griekspoor) Date: Thu, 23 Mar 2006 11:18:34 +0100 Subject: [Biococoa-dev] new svn repository In-Reply-To: References: Message-ID: Hi Koen, checkout went fine, I'll have a look at the demo later... Alex On 22-mrt-2006, at 3:46, Koen van der Drift wrote: > Hi, > > We now have a new svn repository, using FSFS. Please check it out > (no pun intended): > > svn checkout svn+ssh://bioinformatics.org/svnroot/BioCocoa > > > Let me know if it works fine, so I can inform Jeff that he can > delete the old version. > > > cheers, > > - Koen. > > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > *********************************** Mek (Alexander Griekspoor) MekenTosj.com Web: http://www.mekentosj.com Mail: mek at mekentosj.com *********************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From kvddrift at earthlink.net Thu Mar 23 21:03:33 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Thu, 23 Mar 2006 21:03:33 -0500 Subject: [Biococoa-dev] new svn repository In-Reply-To: References: Message-ID: <05183F17-080C-4827-B53A-D8E6759CC083@earthlink.net> On Mar 23, 2006, at 5:18 AM, Alexander Griekspoor wrote: > checkout went fine, I'll have a look at the demo later... > Alex, I just started converting the BCAppDemo, and have some questions for you. In the complement, etc methods, you use the following code: - (IBAction)complement:(id)sender{ NSString *replacement; NSTextStorage *ts = [sequenceTextView textStorage]; if([ts length] == 0){ NSBeep(); return; } NSRange sel = [sequenceTextView selectedRange]; if(sel.length > 0) { replacement = [[[ts attributedSubstringFromRange: sel] string] convertToComplement]; [ts replaceCharactersInRange: sel withString: replacement]; [sequenceTextView setSelectedRange: sel]; } else { replacement = [[ts string]convertToComplement]; [sequenceTextView setString: replacement]; } } 1. Why are you using textStorage and attributedstring, instead of just the string from the NSTextView? 2. If there is a selection, you seem to be just calculating the complement of that part, and leave the rest intact, is that correct? When using the BCSequence, I will probably use code similar to: BCSequence *original = [BCSequence initWithString: [sequenceTextView string]]; BCSequence *complement = [original complement]; [sequenceTextView setString: [complement sequenceString]]; However, I will wait for your comments about the selection range before I implement it. cheers, - Koen. From kvddrift at earthlink.net Thu Mar 23 21:27:47 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Thu, 23 Mar 2006 21:27:47 -0500 Subject: [Biococoa-dev] svn and NIB files Message-ID: <627E43DE-24D8-4FB3-96F9-73E178A0B3F3@earthlink.net> Hi, How can I update nib files with svn? I am using svnX, and want to update the MainMenu.nib from the BCDemoApp, but the English.proj in the working copy is not editable, so I cannot get to the nib files. Also in Xcode I cannot get it to work. thanks, - Koen. From kvddrift at earthlink.net Fri Mar 24 19:59:53 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Fri, 24 Mar 2006 19:59:53 -0500 Subject: [Biococoa-dev] svn and NIB files - solved In-Reply-To: <627E43DE-24D8-4FB3-96F9-73E178A0B3F3@earthlink.net> References: <627E43DE-24D8-4FB3-96F9-73E178A0B3F3@earthlink.net> Message-ID: <92D78B2C-7C15-4AAB-813F-CF32AE53682D@earthlink.net> On Mar 23, 2006, at 9:27 PM, Koen van der Drift wrote: > Hi, > > How can I update nib files with svn? I am using svnX, and want to > update the MainMenu.nib from the BCDemoApp, but the English.proj in > the working copy is not editable, so I cannot get to the nib files. > Also in Xcode I cannot get it to work. I think I solved that, please refresh and test the demoapp, it should now use the BCSequenceView in the .nib file. I also noted that in svnX I have to log into the repository using svn +ssh://bioinformatics.org/svnroot/BioCocoa, otherwise I don't have all write permissions. cheers, - Koen. From kvddrift at earthlink.net Sat Mar 25 05:48:58 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sat, 25 Mar 2006 05:48:58 -0500 Subject: [Biococoa-dev] strider and gck format In-Reply-To: <40CC6729-B52B-437D-A946-761B99A36A72@mekentosj.com> References: <0F6F416B-16F2-4913-BB6E-96D7C710B727@earthlink.net> <5EB8E66C-937C-4076-AFBA-E7932D418096@earthlink.net> <4698C100-9C3E-4A1C-B228-1E6A088D51AF@nki.nl> <7F9A6C87-7F6A-4154-AC2E-866679C6B892@earthlink.net> <803C21CB-B23C-41D3-BAAA-7FC62ABA7C78@nki.nl> <2BB2D9B8-62A7-46B8-88FF-656FEF710F48@earthlink.net> <40CC6729-B52B-437D-A946-761B99A36A72@mekentosj.com> Message-ID: <02110653-5CF5-4233-ADC9-8176E73855EB@earthlink.net> On Mar 19, 2006, at 11:08 AM, Alexander Griekspoor wrote: > One other thing, there seems to be a bug in the textview that if > you have less than one row of text, you can't select any of the > first 10 characters There is another bug probably related to this. If I doubleclick in a column, I expect only those 10 symbols to be selected (just as if it is a word in a sentence). However, the whole sequence gets selected. I am wondering if we should go back to inserting the whitespace approach. cheers, - Koen. From mek at mekentosj.com Sat Mar 25 06:22:06 2006 From: mek at mekentosj.com (Alexander Griekspoor) Date: Sat, 25 Mar 2006 12:22:06 +0100 Subject: [Biococoa-dev] strider and gck format In-Reply-To: <02110653-5CF5-4233-ADC9-8176E73855EB@earthlink.net> References: <0F6F416B-16F2-4913-BB6E-96D7C710B727@earthlink.net> <5EB8E66C-937C-4076-AFBA-E7932D418096@earthlink.net> <4698C100-9C3E-4A1C-B228-1E6A088D51AF@nki.nl> <7F9A6C87-7F6A-4154-AC2E-866679C6B892@earthlink.net> <803C21CB-B23C-41D3-BAAA-7FC62ABA7C78@nki.nl> <2BB2D9B8-62A7-46B8-88FF-656FEF710F48@earthlink.net> <40CC6729-B52B-437D-A946-761B99A36A72@mekentosj.com> <02110653-5CF5-4233-ADC9-8176E73855EB@earthlink.net> Message-ID: <769205AC-5236-4D05-B380-2E89424D5399@mekentosj.com> I don't think that is a bug. I guess that is a personal taste. I see the columns purely as a visual aid, but think a sequence is a continues stretch of characters, hence not separated by spaces. I think the whitespace approach is a hack, and this is more elegant but that's a personal opinion. It would definitely complicates working with the sequence a lot if you continuously have to take the spaces into account. The "1st 10 char selection" bug must be one that is to fix, and if we indeed want the word selection that is something that should be able to be relatively easily implemented using: - (NSRange) selectionRangeForProposedRange:(NSRange)proposedCharRange granularity: (NSSelectionGranularity)granularity (which we override anyway already). The granularity normal returns one (selectByCharacter), but two upon doubleclick (selectByWord) or three upon tripple click (by paragraph). ..and then I decided to just do it ;-) Here's the specific method, and now it selects the 10 nucleotides on which you doubleclick ;-) - (NSRange)selectionRangeForProposedRange:(NSRange)proposedCharRange granularity:(NSSelectionGranularity)granularity{ NSRange newCharRange; if(granularity == NSSelectByWord){ newCharRange.location = (proposedCharRange.location / 10) * 10; newCharRange.length = ((proposedCharRange.location + proposedCharRange.length) / 10 + 1) * 10 - newCharRange.location; // sanity checks if(newCharRange.location < 0){ newCharRange.length -= -newCharRange.location; newCharRange.location = 0; } if(newCharRange.location + newCharRange.length > [[self textStorage] length]){ newCharRange.length -= (newCharRange.location + newCharRange.length) - [[self textStorage]length]; } } else { newCharRange = [super selectionRangeForProposedRange:proposedCharRange granularity:granularity]; } //NSLog(@"%d -> old: %@ new: %@", granularity, NSStringFromRange (proposedCharRange), NSStringFromRange(newCharRange)); // DRAGGING SELECTION id delegate = [self delegate]; if ([delegate respondsToSelector:@selector (didDragSelectionInTextView:range:)]){ [delegate didDragSelectionInTextView: self range: newCharRange]; } // MAKE SURE THAT SELECTION IS REDRAWN DURING DRAG [self setNeedsDisplay: YES]; return newCharRange; } Now please please let's stay away from the whitespace hack, at least I will ;-) Only this one stupid bug to fix... I'll post that one on cocoa-dev. Cheers, Alex On 25-mrt-2006, at 11:48, Koen van der Drift wrote: > > On Mar 19, 2006, at 11:08 AM, Alexander Griekspoor wrote: > >> One other thing, there seems to be a bug in the textview that if >> you have less than one row of text, you can't select any of the >> first 10 characters > > There is another bug probably related to this. If I doubleclick in > a column, I expect only those 10 symbols to be selected (just as if > it is a word in a sentence). However, the whole sequence gets > selected. I am wondering if we should go back to inserting the > whitespace approach. > > cheers, > > - Koen. > ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com 4Peaks - For Peaks, Four Peaks. 2004 Winner of the Apple Design Awards Best Mac OS X Student Product http://www.mekentosj.com/4peaks ********************************************************* From mek at mekentosj.com Sat Mar 25 06:27:19 2006 From: mek at mekentosj.com (Alexander Griekspoor) Date: Sat, 25 Mar 2006 12:27:19 +0100 Subject: [Biococoa-dev] strider and gck format In-Reply-To: <769205AC-5236-4D05-B380-2E89424D5399@mekentosj.com> References: <0F6F416B-16F2-4913-BB6E-96D7C710B727@earthlink.net> <5EB8E66C-937C-4076-AFBA-E7932D418096@earthlink.net> <4698C100-9C3E-4A1C-B228-1E6A088D51AF@nki.nl> <7F9A6C87-7F6A-4154-AC2E-866679C6B892@earthlink.net> <803C21CB-B23C-41D3-BAAA-7FC62ABA7C78@nki.nl> <2BB2D9B8-62A7-46B8-88FF-656FEF710F48@earthlink.net> <40CC6729-B52B-437D-A946-761B99A36A72@mekentosj.com> <02110653-5CF5-4233-ADC9-8176E73855EB@earthlink.net> <769205AC-5236-4D05-B380-2E89424D5399@mekentosj.com> Message-ID: <088EBD68-5B52-4F15-B1F8-9359FFAFDDF0@mekentosj.com> Pretty cool actually, I just discovered that with the new implementation if you first doubleclick to select a 10 nucleotide "word" and then shift click somewhere else it will extend/crop the selection also per 10 nucleotides... Cheers, Alex On 25-mrt-2006, at 12:22, Alexander Griekspoor wrote: > I don't think that is a bug. I guess that is a personal taste. I > see the columns purely as a visual aid, but think a sequence is a > continues stretch of characters, hence not separated by spaces. I > think the whitespace approach is a hack, and this is more elegant > but that's a personal opinion. It would definitely complicates > working with the sequence a lot if you continuously have to take > the spaces into account. > The "1st 10 char selection" bug must be one that is to fix, and if > we indeed want the word selection that is something that should be > able to be relatively easily implemented using: - (NSRange) > selectionRangeForProposedRange:(NSRange)proposedCharRange > granularity:(NSSelectionGranularity)granularity > (which we override anyway already). The granularity normal returns > one (selectByCharacter), but two upon doubleclick (selectByWord) or > three upon tripple click (by paragraph). > > ..and then I decided to just do it ;-) > > Here's the specific method, and now it selects the 10 nucleotides > on which you doubleclick ;-) > > - (NSRange)selectionRangeForProposedRange:(NSRange) > proposedCharRange granularity:(NSSelectionGranularity)granularity{ > NSRange newCharRange; > if(granularity == NSSelectByWord){ > newCharRange.location = (proposedCharRange.location / 10) * 10; > newCharRange.length = ((proposedCharRange.location + > proposedCharRange.length) / 10 + 1) * 10 - newCharRange.location; > // sanity checks > if(newCharRange.location < 0){ > newCharRange.length -= -newCharRange.location; > newCharRange.location = 0; > } > if(newCharRange.location + newCharRange.length > [[self > textStorage]length]){ > newCharRange.length -= (newCharRange.location + > newCharRange.length) - [[self textStorage]length]; > } > } > else { > newCharRange = [super > selectionRangeForProposedRange:proposedCharRange > granularity:granularity]; > } > //NSLog(@"%d -> old: %@ new: %@", granularity, NSStringFromRange > (proposedCharRange), NSStringFromRange(newCharRange)); > > // DRAGGING SELECTION > id delegate = [self delegate]; > if ([delegate respondsToSelector:@selector > (didDragSelectionInTextView:range:)]){ > [delegate didDragSelectionInTextView: self range: newCharRange]; > } > > // MAKE SURE THAT SELECTION IS REDRAWN DURING DRAG > [self setNeedsDisplay: YES]; > return newCharRange; > } > > > Now please please let's stay away from the whitespace hack, at > least I will ;-) > Only this one stupid bug to fix... I'll post that one on cocoa-dev. > Cheers, > Alex > > > > On 25-mrt-2006, at 11:48, Koen van der Drift wrote: > >> >> On Mar 19, 2006, at 11:08 AM, Alexander Griekspoor wrote: >> >>> One other thing, there seems to be a bug in the textview that if >>> you have less than one row of text, you can't select any of the >>> first 10 characters >> >> There is another bug probably related to this. If I doubleclick in >> a column, I expect only those 10 symbols to be selected (just as >> if it is a word in a sentence). However, the whole sequence gets >> selected. I am wondering if we should go back to inserting the >> whitespace approach. >> >> cheers, >> >> - Koen. >> > > ********************************************************* > ** Alexander Griekspoor ** > ********************************************************* > The Netherlands Cancer Institute > Department of Tumorbiology (H4) > Plesmanlaan 121, 1066 CX, Amsterdam > Tel: + 31 20 - 512 2023 > Fax: + 31 20 - 512 2029 > AIM: mekentosj at mac.com > E-mail: a.griekspoor at nki.nl > Web: http://www.mekentosj.com > > 4Peaks - For Peaks, Four Peaks. > 2004 Winner of the Apple Design Awards > Best Mac OS X Student Product > http://www.mekentosj.com/4peaks > > ********************************************************* > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com Claiming that the Macintosh is inferior to Windows because most people use Windows, is like saying that all other restaurants serve food that is inferior to McDonalds ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From kvddrift at earthlink.net Sat Mar 25 07:49:40 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sat, 25 Mar 2006 07:49:40 -0500 Subject: [Biococoa-dev] strider and gck format In-Reply-To: <769205AC-5236-4D05-B380-2E89424D5399@mekentosj.com> References: <0F6F416B-16F2-4913-BB6E-96D7C710B727@earthlink.net> <5EB8E66C-937C-4076-AFBA-E7932D418096@earthlink.net> <4698C100-9C3E-4A1C-B228-1E6A088D51AF@nki.nl> <7F9A6C87-7F6A-4154-AC2E-866679C6B892@earthlink.net> <803C21CB-B23C-41D3-BAAA-7FC62ABA7C78@nki.nl> <2BB2D9B8-62A7-46B8-88FF-656FEF710F48@earthlink.net> <40CC6729-B52B-437D-A946-761B99A36A72@mekentosj.com> <02110653-5CF5-4233-ADC9-8176E73855EB@earthlink.net> <769205AC-5236-4D05-B380-2E89424D5399@mekentosj.com> Message-ID: <89032073-6240-41B1-8851-C133399EEC5C@earthlink.net> On Mar 25, 2006, at 6:22 AM, Alexander Griekspoor wrote: > ..and then I decided to just do it ;-) > > Here's the specific method, and now it selects the 10 nucleotides > on which you doubleclick ;-) > Great solution, Alex. Of course much better than the whitespace hack. One point though, it only works with Courier 10 pt. At least in your Entrez demo. I have committed the code, so you can see what I mean. Regarding the 1-10 selection bug, it may be related to our 'hack' to move the left margin to the right (kLEFT_MARGIN_WIDTH). - Koen. From kvddrift at earthlink.net Sat Mar 25 07:51:26 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sat, 25 Mar 2006 07:51:26 -0500 Subject: [Biococoa-dev] strider and gck format In-Reply-To: <088EBD68-5B52-4F15-B1F8-9359FFAFDDF0@mekentosj.com> References: <0F6F416B-16F2-4913-BB6E-96D7C710B727@earthlink.net> <5EB8E66C-937C-4076-AFBA-E7932D418096@earthlink.net> <4698C100-9C3E-4A1C-B228-1E6A088D51AF@nki.nl> <7F9A6C87-7F6A-4154-AC2E-866679C6B892@earthlink.net> <803C21CB-B23C-41D3-BAAA-7FC62ABA7C78@nki.nl> <2BB2D9B8-62A7-46B8-88FF-656FEF710F48@earthlink.net> <40CC6729-B52B-437D-A946-761B99A36A72@mekentosj.com> <02110653-5CF5-4233-ADC9-8176E73855EB@earthlink.net> <769205AC-5236-4D05-B380-2E89424D5399@mekentosj.com> <088EBD68-5B52-4F15-B1F8-9359FFAFDDF0@mekentosj.com> Message-ID: <73FC349D-F05D-4480-8463-87AD913AE889@earthlink.net> On Mar 25, 2006, at 6:27 AM, Alexander Griekspoor wrote: > Pretty cool actually, I just discovered that with the new > implementation if you first doubleclick to select a 10 nucleotide > "word" and then shift click somewhere else it will extend/crop the > selection also per 10 nucleotides... Now try option-dragging, you can select vertically :-) - Koen. From mek at mekentosj.com Sat Mar 25 10:35:34 2006 From: mek at mekentosj.com (Alexander Griekspoor) Date: Sat, 25 Mar 2006 16:35:34 +0100 Subject: [Biococoa-dev] strider and gck format In-Reply-To: <89032073-6240-41B1-8851-C133399EEC5C@earthlink.net> References: <0F6F416B-16F2-4913-BB6E-96D7C710B727@earthlink.net> <5EB8E66C-937C-4076-AFBA-E7932D418096@earthlink.net> <4698C100-9C3E-4A1C-B228-1E6A088D51AF@nki.nl> <7F9A6C87-7F6A-4154-AC2E-866679C6B892@earthlink.net> <803C21CB-B23C-41D3-BAAA-7FC62ABA7C78@nki.nl> <2BB2D9B8-62A7-46B8-88FF-656FEF710F48@earthlink.net> <40CC6729-B52B-437D-A946-761B99A36A72@mekentosj.com> <02110653-5CF5-4233-ADC9-8176E73855EB@earthlink.net> <769205AC-5236-4D05-B380-2E89424D5399@mekentosj.com> <89032073-6240-41B1-8851-C133399EEC5C@earthlink.net> Message-ID: <0EB25A5B-E1F1-4EBC-9509-A4678B5C0DD0@mekentosj.com> Yes I know, and I only use 10pt courier in my apps for that reason ;-) No seriously, this comes down to an extension of the view that I would like to see in the future. I think the view should have three properties accessors - the font (which it already has of course, although we should make sure you can only set one font for the whole textview) - the numbers of characters per column - the column spacing Based on the first two we should then calculate the columnwidth dynamically, and the numbers_of_characters_per_column property can be used in the select by word range calculations. > > Regarding the 1-10 selection bug, it may be related to our 'hack' > to move the left margin to the right (kLEFT_MARGIN_WIDTH). Hmm, I actually thought of the columnwidth because the problems are limited to exactly a column. This is the email I try to post to the cocoa-dev list for a couple of times already (it contains some more info, also see the picture), but no success yet... ******** Hi all, I ran in this weird bug and you guys are my last resort.. For a new DNA analysis program I subclassed Koen van der Drift's excellent NSTextView linenumbering variant and modified the textcontainer such that it automagically adds spaces between every 10th character. I did this by overriding in NSTextContainer (see below). This works beautifully except for this single strange behaviour where text is not selected if A) there are more than 10 characters (is one column) present B there's not more than 1 line of text. Trying to select the first 10 characters is not possible and a reverse selection started at for instance char 20 back will stop always at character 11. If the textview does not contain more than 9 characters selection goes fine in the first column! So does it when the textview contains more than one line of text! In other words, I cannot select the 10 characters in the first column for some reason. I've illustrated the problem in this screenshot: http:// www.mekentosj.com/temporary/textview_problem.jpg Any solution / clue where to start looking would be enormously appreciated. Last bug standing before a release... Cheers, Alex - (NSRect)lineFragmentRectForProposedRect:(NSRect)proposedRect sweepDirection:(NSLineSweepDirection)sweepDirection movementDirection:(NSLineMovementDirection)movementDirection remainingRect:(NSRect *)remainingRect { // create space for the linenumber margin if(proposedRect.origin.x <= 0.0) proposedRect.origin.x = kLEFT_MARGIN_WIDTH; // set the width of a column of text proposedRect.size.width = columnWidth; // make sure we nicely break after a full column if (proposedRect.origin.x + 2 * columnWidth - 20.0 >= [self containerSize].width) *remainingRect = NSZeroRect; else { remainingRect->origin.x = proposedRect.origin.x + columnWidth - 10.0; remainingRect->origin.y = proposedRect.origin.y; remainingRect->size.width = [self containerSize].width - proposedRect.origin.x + columnWidth - 10.0; remainingRect->size.height = proposedRect.size.height; } return proposedRect; } ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com Windows is a 32-bit patch to a 16-bit shell for an 8-bit operating system, written for a 4-bit processor by a 2- bit company without 1 bit of sense. ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From kvddrift at earthlink.net Sat Mar 25 11:11:03 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sat, 25 Mar 2006 11:11:03 -0500 Subject: [Biococoa-dev] strider and gck format In-Reply-To: <0EB25A5B-E1F1-4EBC-9509-A4678B5C0DD0@mekentosj.com> References: <0F6F416B-16F2-4913-BB6E-96D7C710B727@earthlink.net> <5EB8E66C-937C-4076-AFBA-E7932D418096@earthlink.net> <4698C100-9C3E-4A1C-B228-1E6A088D51AF@nki.nl> <7F9A6C87-7F6A-4154-AC2E-866679C6B892@earthlink.net> <803C21CB-B23C-41D3-BAAA-7FC62ABA7C78@nki.nl> <2BB2D9B8-62A7-46B8-88FF-656FEF710F48@earthlink.net> <40CC6729-B52B-437D-A946-761B99A36A72@mekentosj.com> <02110653-5CF5-4233-ADC9-8176E73855EB@earthlink.net> <769205AC-5236-4D05-B380-2E89424D5399@mekentosj.com> <89032073-6240-41B1-8851-C133399EEC5C@earthlink.net> <0EB25A5B-E1F1-4EBC-9509-A4678B5C0DD0@mekentosj.com> Message-ID: On Mar 25, 2006, at 10:35 AM, Alexander Griekspoor wrote: > Yes I know, and I only use 10pt courier in my apps for that reason ;-) > No seriously, this comes down to an extension of the view that I > would like to see in the future. I think the view should have three > properties accessors > - the font (which it already has of course, although we should make > sure you can only set one font for the whole textview) > - the numbers of characters per column > - the column spacing Sounds good. > Based on the first two we should then calculate the columnwidth > dynamically, and the numbers_of_characters_per_column property can > be used in the select by word range calculations. >> >> Regarding the 1-10 selection bug, it may be related to our 'hack' >> to move the left margin to the right (kLEFT_MARGIN_WIDTH). > Hmm, I actually thought of the columnwidth because the problems are > limited to exactly a column. That's possible too :) Somewhere I have a feeling that we may need to subclass the layoutmanager, instead of the textcontainer, though. For my linenumber code it works well with the textcontainer subclass, however, for biological sequences that require more advanced layouts, including the columns, it may not be sufficient. This may also help to draw annotations, lines, markers, etc. I will look a bit more into this this weekend. > This is the email I try to post to the cocoa-dev list for a couple > of times already (it contains some more info, also see the > picture), but no success yet... > I haven't seen any mails from cocodev in a couple of hours, I guess their mailing listserver has some hiccups. - Koen. From mek at mekentosj.com Sat Mar 25 11:17:54 2006 From: mek at mekentosj.com (Alexander Griekspoor) Date: Sat, 25 Mar 2006 17:17:54 +0100 Subject: [Biococoa-dev] strider and gck format In-Reply-To: References: <0F6F416B-16F2-4913-BB6E-96D7C710B727@earthlink.net> <5EB8E66C-937C-4076-AFBA-E7932D418096@earthlink.net> <4698C100-9C3E-4A1C-B228-1E6A088D51AF@nki.nl> <7F9A6C87-7F6A-4154-AC2E-866679C6B892@earthlink.net> <803C21CB-B23C-41D3-BAAA-7FC62ABA7C78@nki.nl> <2BB2D9B8-62A7-46B8-88FF-656FEF710F48@earthlink.net> <40CC6729-B52B-437D-A946-761B99A36A72@mekentosj.com> <02110653-5CF5-4233-ADC9-8176E73855EB@earthlink.net> <769205AC-5236-4D05-B380-2E89424D5399@mekentosj.com> <89032073-6240-41B1-8851-C133399EEC5C@earthlink.net> <0EB25A5B-E1F1-4EBC-9509-A4678B5C0DD0@mekentosj.com> Message-ID: > Somewhere I have a feeling that we may need to subclass the > layoutmanager, instead of the textcontainer, though. For my > linenumber code it works well with the textcontainer subclass, > however, for biological sequences that require more advanced > layouts, including the columns, it may not be sufficient. This may > also help to draw annotations, lines, markers, etc. I will look a > bit more into this this weekend. Yes, I got that idea too, still, everything works perfectly except for this minor issue. So I hope to not have to do that. Also, if you think about it, the textcontainer is the place to be also for things like annotations and stuff, the layoutmanager does the layout but it is the role of the textcontainer to tell where. Also, the textcontainer is quite light weight and still relatively basic, so nice to subclass. The layoutmanager is a monster in terms of complexity. > > > I haven't seen any mails from cocodev in a couple of hours, I guess > their mailing listserver has some hiccups. Aha, that explains a lot... Cheers, Alex ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com LabAssistant - Get your life organized! http://www.mekentosj.com/labassistant ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From kvddrift at earthlink.net Sat Mar 25 11:36:01 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sat, 25 Mar 2006 11:36:01 -0500 Subject: [Biococoa-dev] strider and gck format In-Reply-To: References: <0F6F416B-16F2-4913-BB6E-96D7C710B727@earthlink.net> <5EB8E66C-937C-4076-AFBA-E7932D418096@earthlink.net> <4698C100-9C3E-4A1C-B228-1E6A088D51AF@nki.nl> <7F9A6C87-7F6A-4154-AC2E-866679C6B892@earthlink.net> <803C21CB-B23C-41D3-BAAA-7FC62ABA7C78@nki.nl> <2BB2D9B8-62A7-46B8-88FF-656FEF710F48@earthlink.net> <40CC6729-B52B-437D-A946-761B99A36A72@mekentosj.com> <02110653-5CF5-4233-ADC9-8176E73855EB@earthlink.net> <769205AC-5236-4D05-B380-2E89424D5399@mekentosj.com> <89032073-6240-41B1-8851-C133399EEC5C@earthlink.net> <0EB25A5B-E1F1-4EBC-9509-A4678B5C0DD0@mekentosj.com> Message-ID: <2DDA1579-6D8A-456F-9B21-892149544EE8@earthlink.net> On Mar 25, 2006, at 11:17 AM, Alexander Griekspoor wrote: > The layoutmanager is a monster in terms of complexity. That's why I never looked into it :D - Koen. From kvddrift at earthlink.net Sat Mar 25 23:06:53 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sat, 25 Mar 2006 23:06:53 -0500 Subject: [Biococoa-dev] strider and gck format In-Reply-To: <0EB25A5B-E1F1-4EBC-9509-A4678B5C0DD0@mekentosj.com> References: <0F6F416B-16F2-4913-BB6E-96D7C710B727@earthlink.net> <5EB8E66C-937C-4076-AFBA-E7932D418096@earthlink.net> <4698C100-9C3E-4A1C-B228-1E6A088D51AF@nki.nl> <7F9A6C87-7F6A-4154-AC2E-866679C6B892@earthlink.net> <803C21CB-B23C-41D3-BAAA-7FC62ABA7C78@nki.nl> <2BB2D9B8-62A7-46B8-88FF-656FEF710F48@earthlink.net> <40CC6729-B52B-437D-A946-761B99A36A72@mekentosj.com> <02110653-5CF5-4233-ADC9-8176E73855EB@earthlink.net> <769205AC-5236-4D05-B380-2E89424D5399@mekentosj.com> <89032073-6240-41B1-8851-C133399EEC5C@earthlink.net> <0EB25A5B-E1F1-4EBC-9509-A4678B5C0DD0@mekentosj.com> Message-ID: <9936D0CC-3AAE-43AE-91E5-7461ACC7D3C4@earthlink.net> On Mar 25, 2006, at 10:35 AM, Alexander Griekspoor wrote: > - (NSRect)lineFragmentRectForProposedRect:(NSRect)proposedRect > sweepDirection:(NSLineSweepDirection)sweepDirection > movementDirection:(NSLineMovementDirection)movementDirection > remainingRect:(NSRect *)remainingRect > { > // create space for the linenumber margin > if(proposedRect.origin.x <= 0.0) > proposedRect.origin.x = kLEFT_MARGIN_WIDTH; > > // set the width of a column of text > proposedRect.size.width = columnWidth; > > // make sure we nicely break after a full column > if (proposedRect.origin.x + 2 * columnWidth - 20.0 >= [self > containerSize].width) *remainingRect = NSZeroRect; > else { > remainingRect->origin.x = proposedRect.origin.x + > columnWidth - 10.0; > remainingRect->origin.y = proposedRect.origin.y; > remainingRect->size.width = [self containerSize].width - > proposedRect.origin.x + columnWidth - 10.0; > remainingRect->size.height = proposedRect.size.height; > } > > return proposedRect; > } > More people seem to have had problems with that code, see http:// www.cocoabuilder.com/archive/message/cocoa/2003/5/1/4403 (hmm, that code looks very familiar ;-) It was even suggested it is a system bug, but that was posted 3 years ago, so I would expect it to be fixed already. - Koen. From mek at mekentosj.com Sun Mar 26 03:56:14 2006 From: mek at mekentosj.com (Alexander Griekspoor) Date: Sun, 26 Mar 2006 10:56:14 +0200 Subject: [Biococoa-dev] strider and gck format In-Reply-To: <9936D0CC-3AAE-43AE-91E5-7461ACC7D3C4@earthlink.net> References: <0F6F416B-16F2-4913-BB6E-96D7C710B727@earthlink.net> <5EB8E66C-937C-4076-AFBA-E7932D418096@earthlink.net> <4698C100-9C3E-4A1C-B228-1E6A088D51AF@nki.nl> <7F9A6C87-7F6A-4154-AC2E-866679C6B892@earthlink.net> <803C21CB-B23C-41D3-BAAA-7FC62ABA7C78@nki.nl> <2BB2D9B8-62A7-46B8-88FF-656FEF710F48@earthlink.net> <40CC6729-B52B-437D-A946-761B99A36A72@mekentosj.com> <02110653-5CF5-4233-ADC9-8176E73855EB@earthlink.net> <769205AC-5236-4D05-B380-2E89424D5399@mekentosj.com> <89032073-6240-41B1-8851-C133399EEC5C@earthlink.net> <0EB25A5B-E1F1-4EBC-9509-A4678B5C0DD0@mekentosj.com> <9936D0CC-3AAE-43AE-91E5-7461ACC7D3C4@earthlink.net> Message-ID: It certainly is familiar, still I did not took it from any samplecode, so guess I reinvented the wheel ;-) Anyway, I don't see the problems he describes where lines start to shift, they probably fixed that... Cheers, Alex On 26-mrt-2006, at 6:06, Koen van der Drift wrote: > > On Mar 25, 2006, at 10:35 AM, Alexander Griekspoor wrote: > >> - (NSRect)lineFragmentRectForProposedRect:(NSRect)proposedRect >> sweepDirection:(NSLineSweepDirection)sweepDirection >> movementDirection:(NSLineMovementDirection)movementDirection >> remainingRect:(NSRect *)remainingRect >> { >> // create space for the linenumber margin >> if(proposedRect.origin.x <= 0.0) >> proposedRect.origin.x = kLEFT_MARGIN_WIDTH; >> >> // set the width of a column of text >> proposedRect.size.width = columnWidth; >> >> // make sure we nicely break after a full column >> if (proposedRect.origin.x + 2 * columnWidth - 20.0 >= [self >> containerSize].width) *remainingRect = NSZeroRect; >> else { >> remainingRect->origin.x = proposedRect.origin.x + >> columnWidth - 10.0; >> remainingRect->origin.y = proposedRect.origin.y; >> remainingRect->size.width = [self containerSize].width - >> proposedRect.origin.x + columnWidth - 10.0; >> remainingRect->size.height = proposedRect.size.height; >> } >> >> return proposedRect; >> } >> > > > More people seem to have had problems with that code, see http:// > www.cocoabuilder.com/archive/message/cocoa/2003/5/1/4403 (hmm, that > code looks very familiar ;-) It was even suggested it is a system > bug, but that was posted 3 years ago, so I would expect it to be > fixed already. > > - Koen. > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com The requirements said: Windows 2000 or better. So I got a Macintosh. ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.griekspoor at nki.nl Mon Mar 27 06:13:47 2006 From: a.griekspoor at nki.nl (Alexander Griekspoor) Date: Mon, 27 Mar 2006 13:13:47 +0200 Subject: [Biococoa-dev] Fwd: Re : Strange Selection Behavior when using a custom NSTextContainer References: Message-ID: First I thought it was my message which finally arrived on the cocoa- dev list, turns out someone else has exactly the same problem as we do! See the mail below, perhaps it helps solving this nasty bug... Alex Begin forwarded message: > From: Alexander Griekspoor > Date: 27 maart 2006 13:01:32 GMT+02:00 > To: ernfrid at gmail.com > Subject: Re : Strange Selection Behavior when using a custom > NSTextContainer > > Hi David, > > I have exactly the same problem, well slightly different, but at > first I thought your message was mine. I am trying to post the > message below to apple's cocoa-dev but it seems they are offline. > Here is a copy, > perhaps we can together find out what goes wrong... If you have > found the solution already I would love to hear. Many thanks! > Cheers, > Alex > PS. I'm not a member of Omni's mailinglist, could you post my > message for the record and also for others to help us out? > > > ******* > Weird bug with selection in Textview with custom textcontainer > > > Hi all, > > I ran in this weird bug and you guys are my last resort.. > For a new DNA analysis program I subclassed Koen van der Drift's > excellent NSTextView linenumbering variant and modified the > textcontainer such that it automagically adds spaces between every > 10th character. I did this by overriding in NSTextContainer (see > below). > > This works beautifully except for this single strange behaviour > where text is not selected if > A) there are more than 10 characters (is one column) present > B there's not more than 1 line of text. > > Trying to select the first 10 characters is not possible and a > reverse selection started at for instance char 20 back will stop > always at character 11. If the textview does not contain more than > 9 characters selection goes fine in the first column! So does it > when the textview contains more than one line of text! > > In other words, I cannot select the 10 characters in the first > column for some reason. > I've illustrated the problem in this screenshot: http:// > www.mekentosj.com/temporary/textview_problem.jpg > > Any solution / clue where to start looking would be enormously > appreciated. Last bug standing before a release... > Cheers, > Alex > > - (NSRect)lineFragmentRectForProposedRect:(NSRect)proposedRect > sweepDirection:(NSLineSweepDirection)sweepDirection > movementDirection:(NSLineMovementDirection)movementDirection > remainingRect:(NSRect *)remainingRect > { > // create space for the linenumber margin > if(proposedRect.origin.x <= 0.0) > proposedRect.origin.x = kLEFT_MARGIN_WIDTH; > > // set the width of a column of text > proposedRect.size.width = columnWidth; > > // make sure we nicely break after a full column > if (proposedRect.origin.x + 2 * columnWidth - 20.0 >= [self > containerSize].width) *remainingRect = NSZeroRect; > else { > remainingRect->origin.x = proposedRect.origin.x + > columnWidth - 10.0; > remainingRect->origin.y = proposedRect.origin.y; > remainingRect->size.width = [self containerSize].width - > proposedRect.origin.x + columnWidth - 10.0; > remainingRect->size.height = proposedRect.size.height; > } > > return proposedRect; > } > > > > > > I'm using a custom NSTextContainer which breaks each line of the text > view into columns of ten characters. I noticed that when there is only > one line in the container, but there is text displayed outside of the > first column, clicking in the that first column moves the cursor to > the beginning of the second column instead of to its appropriate > insertion point in the first column. I can move the cursor using the > arrow keys into the first column, but even if the cursor is in the > first column, clicking on that column sends the cursor back to > beginning of the second column. If, however, there is only text in the > first column or there is more than one line, clicking in the first > column results in normal positioning of the cursor. I'm stumped. I > played around with overriding containsPoint: and clicks in the first > column were returned as being part of the container as they should be. > I also used a subclass of NSTextView to check what NSTextView was > returning for the selection function and found it was returning the > incorrect insertion point. If I comment out my > lineFragmentRectForProposedRect function then there is no problem with > moving the cursor back to the first ten characters with the mouse. I > should also mention I set the line fragment padding to zero and > changing this has no effect on this behavior. Here is the code I'm > using. columnWidth is the length of each column and gapWidth is the > space between each column. Anyone have any ideas about what I'm doing > wrong? I apologize for the long post but I believe it was necessary. > > Thanks > > David Larson > > - (NSRect)lineFragmentRectForProposedRect:(NSRect)proposedRect > sweepDirection:(NSLineSweepDirection)sweepDirection > movementDirection:(NSLineMovementDirection)movementDirection > remainingRect:(NSRect *)remainingRect > { > if((sweepDirection != NSLineSweepRight) ||( movementDirection != > NSLineMovesDown)) { > //check to make sure standard linesweep and movement direction > are correct > return NSZeroRect; > } > else { > //this code grabbed off of the CocoaBuilder webarchives from a Marco > Binder post. Minor modifications to include gap size were included > //Also modified the code to force a new line when the edge of the > container is reached > //Comments are mine > > //set the width to the column width > //note that this assumes that the rect starts at the beginning of > a column > > proposedRect.size.width = columnWidth; > > if (proposedRect.origin.x+columnWidth >= [self > containerSize].width) { > proposedRect.origin.x = 0; //if we can't fit the complete rect into > the rest of the line, reset the line manually > proposedRect.origin.y += proposedRect.size.height; > } > > remainingRect->origin.x = > proposedRect.origin.x+columnWidth+gapWidth; //move remaining rect > origin to the next column start > remainingRect->origin.y = proposedRect.origin.y; > remainingRect->size.width = [self containerSize].width - > proposedRect.origin.x - columnWidth-gapWidth; //size equals remaining > screen space minus the column and gap > remainingRect->size.height = proposedRect.size.height; > } > > return proposedRect; > } > > *********************************** > Mek (Alexander Griekspoor) > MekenTosj.com > Web: http://www.mekentosj.com > Mail: mek at mekentosj.com > *********************************** > > ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com Claiming that the Macintosh is inferior to Windows because most people use Windows, is like saying that all other restaurants serve food that is inferior to McDonalds ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From kvddrift at earthlink.net Mon Mar 27 07:08:27 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Mon, 27 Mar 2006 07:08:27 -0500 Subject: [Biococoa-dev] Re: Re : Strange Selection Behavior when using a custom NSTextContainer In-Reply-To: References: Message-ID: <9F633DB8-26FC-417F-B42E-260CFDF5A433@earthlink.net> One way to debug this would to be able to draw a rect around the various NSRects during the calculations. However, AFAICT that can only be done from within drawView, and I have no clue how to access these rects from the textContainer (except the container itself). cheers, - Koen. On Mar 27, 2006, at 6:13 AM, Alexander Griekspoor wrote: > First I thought it was my message which finally arrived on the > cocoa-dev list, turns out someone else has exactly the same problem > as we do! > See the mail below, perhaps it helps solving this nasty bug... > Alex > > Begin forwarded message: > >> From: Alexander Griekspoor >> Date: 27 maart 2006 13:01:32 GMT+02:00 >> To: ernfrid at gmail.com >> Subject: Re : Strange Selection Behavior when using a custom >> NSTextContainer >> >> Hi David, >> >> I have exactly the same problem, well slightly different, but at >> first I thought your message was mine. I am trying to post the >> message below to apple's cocoa-dev but it seems they are offline. >> Here is a copy, >> perhaps we can together find out what goes wrong... If you have >> found the solution already I would love to hear. Many thanks! >> Cheers, >> Alex >> PS. I'm not a member of Omni's mailinglist, could you post my >> message for the record and also for others to help us out? >> >> >> ******* >> Weird bug with selection in Textview with custom textcontainer >> >> >> Hi all, >> >> I ran in this weird bug and you guys are my last resort.. >> For a new DNA analysis program I subclassed Koen van der Drift's >> excellent NSTextView linenumbering variant and modified the >> textcontainer such that it automagically adds spaces between every >> 10th character. I did this by overriding in NSTextContainer (see >> below). >> >> This works beautifully except for this single strange behaviour >> where text is not selected if >> A) there are more than 10 characters (is one column) present >> B there's not more than 1 line of text. >> >> Trying to select the first 10 characters is not possible and a >> reverse selection started at for instance char 20 back will stop >> always at character 11. If the textview does not contain more than >> 9 characters selection goes fine in the first column! So does it >> when the textview contains more than one line of text! >> >> In other words, I cannot select the 10 characters in the first >> column for some reason. >> I've illustrated the problem in this screenshot: http:// >> www.mekentosj.com/temporary/textview_problem.jpg >> >> Any solution / clue where to start looking would be enormously >> appreciated. Last bug standing before a release... >> Cheers, >> Alex >> >> - (NSRect)lineFragmentRectForProposedRect:(NSRect)proposedRect >> sweepDirection:(NSLineSweepDirection)sweepDirection >> movementDirection:(NSLineMovementDirection)movementDirection >> remainingRect:(NSRect *)remainingRect >> { >> // create space for the linenumber margin >> if(proposedRect.origin.x <= 0.0) >> proposedRect.origin.x = kLEFT_MARGIN_WIDTH; >> >> // set the width of a column of text >> proposedRect.size.width = columnWidth; >> >> // make sure we nicely break after a full column >> if (proposedRect.origin.x + 2 * columnWidth - 20.0 >= [self >> containerSize].width) *remainingRect = NSZeroRect; >> else { >> remainingRect->origin.x = proposedRect.origin.x + >> columnWidth - 10.0; >> remainingRect->origin.y = proposedRect.origin.y; >> remainingRect->size.width = [self containerSize].width - >> proposedRect.origin.x + columnWidth - 10.0; >> remainingRect->size.height = proposedRect.size.height; >> } >> >> return proposedRect; >> } >> >> >> >> >> >> I'm using a custom NSTextContainer which breaks each line of the text >> view into columns of ten characters. I noticed that when there is >> only >> one line in the container, but there is text displayed outside of the >> first column, clicking in the that first column moves the cursor to >> the beginning of the second column instead of to its appropriate >> insertion point in the first column. I can move the cursor using the >> arrow keys into the first column, but even if the cursor is in the >> first column, clicking on that column sends the cursor back to >> beginning of the second column. If, however, there is only text in >> the >> first column or there is more than one line, clicking in the first >> column results in normal positioning of the cursor. I'm stumped. I >> played around with overriding containsPoint: and clicks in the first >> column were returned as being part of the container as they should >> be. >> I also used a subclass of NSTextView to check what NSTextView was >> returning for the selection function and found it was returning the >> incorrect insertion point. If I comment out my >> lineFragmentRectForProposedRect function then there is no problem >> with >> moving the cursor back to the first ten characters with the mouse. I >> should also mention I set the line fragment padding to zero and >> changing this has no effect on this behavior. Here is the code I'm >> using. columnWidth is the length of each column and gapWidth is the >> space between each column. Anyone have any ideas about what I'm doing >> wrong? I apologize for the long post but I believe it was necessary. >> >> Thanks >> >> David Larson >> >> - (NSRect)lineFragmentRectForProposedRect:(NSRect)proposedRect >> sweepDirection:(NSLineSweepDirection)sweepDirection >> movementDirection:(NSLineMovementDirection)movementDirection >> remainingRect:(NSRect *)remainingRect >> { >> if((sweepDirection != NSLineSweepRight) ||( movementDirection != >> NSLineMovesDown)) { >> //check to make sure standard linesweep and movement direction >> are correct >> return NSZeroRect; >> } >> else { >> //this code grabbed off of the CocoaBuilder webarchives from a >> Marco >> Binder post. Minor modifications to include gap size were included >> //Also modified the code to force a new line when the edge of the >> container is reached >> //Comments are mine >> >> //set the width to the column width >> //note that this assumes that the rect starts at the beginning >> of a column >> >> proposedRect.size.width = columnWidth; >> >> if (proposedRect.origin.x+columnWidth >= [self >> containerSize].width) { >> proposedRect.origin.x = 0; //if we can't fit the complete rect >> into >> the rest of the line, reset the line manually >> proposedRect.origin.y += proposedRect.size.height; >> } >> >> remainingRect->origin.x = >> proposedRect.origin.x+columnWidth+gapWidth; //move remaining rect >> origin to the next column start >> remainingRect->origin.y = proposedRect.origin.y; >> remainingRect->size.width = [self containerSize].width - >> proposedRect.origin.x - columnWidth-gapWidth; //size equals remaining >> screen space minus the column and gap >> remainingRect->size.height = proposedRect.size.height; >> } >> >> return proposedRect; >> } >> >> *********************************** >> Mek (Alexander Griekspoor) >> MekenTosj.com >> Web: http://www.mekentosj.com >> Mail: mek at mekentosj.com >> *********************************** >> >> > > ********************************************************* > ** Alexander Griekspoor ** > ********************************************************* > The Netherlands Cancer Institute > Department of Tumorbiology (H4) > Plesmanlaan 121, 1066 CX, Amsterdam > Tel: + 31 20 - 512 2023 > Fax: + 31 20 - 512 2029 > AIM: mekentosj at mac.com > E-mail: a.griekspoor at nki.nl > Web: http://www.mekentosj.com > > Claiming that the Macintosh is inferior to Windows > because most people use Windows, is like saying > that all other restaurants serve food that is > inferior to McDonalds > > ********************************************************* > From a.griekspoor at nki.nl Mon Mar 27 08:03:16 2006 From: a.griekspoor at nki.nl (Alexander Griekspoor) Date: Mon, 27 Mar 2006 15:03:16 +0200 Subject: [Biococoa-dev] Re: Re : Strange Selection Behavior when using a custom NSTextContainer In-Reply-To: <9F633DB8-26FC-417F-B42E-260CFDF5A433@earthlink.net> References: <9F633DB8-26FC-417F-B42E-260CFDF5A433@earthlink.net> Message-ID: But the problem seems to be in the selection, not in drawing... Alex On 27-mrt-2006, at 14:08, Koen van der Drift wrote: > One way to debug this would to be able to draw a rect around the > various NSRects during the calculations. However, AFAICT that can > only be done from within drawView, and I have no clue how to access > these rects from the textContainer (except the container itself). > > cheers, > > - Koen. > > > > On Mar 27, 2006, at 6:13 AM, Alexander Griekspoor wrote: > >> First I thought it was my message which finally arrived on the >> cocoa-dev list, turns out someone else has exactly the same >> problem as we do! >> See the mail below, perhaps it helps solving this nasty bug... >> Alex >> >> Begin forwarded message: >> >>> From: Alexander Griekspoor >>> Date: 27 maart 2006 13:01:32 GMT+02:00 >>> To: ernfrid at gmail.com >>> Subject: Re : Strange Selection Behavior when using a custom >>> NSTextContainer >>> >>> Hi David, >>> >>> I have exactly the same problem, well slightly different, but at >>> first I thought your message was mine. I am trying to post the >>> message below to apple's cocoa-dev but it seems they are offline. >>> Here is a copy, >>> perhaps we can together find out what goes wrong... If you have >>> found the solution already I would love to hear. Many thanks! >>> Cheers, >>> Alex >>> PS. I'm not a member of Omni's mailinglist, could you post my >>> message for the record and also for others to help us out? >>> >>> >>> ******* >>> Weird bug with selection in Textview with custom textcontainer >>> >>> >>> Hi all, >>> >>> I ran in this weird bug and you guys are my last resort.. >>> For a new DNA analysis program I subclassed Koen van der Drift's >>> excellent NSTextView linenumbering variant and modified the >>> textcontainer such that it automagically adds spaces between >>> every 10th character. I did this by overriding in NSTextContainer >>> (see below). >>> >>> This works beautifully except for this single strange behaviour >>> where text is not selected if >>> A) there are more than 10 characters (is one column) present >>> B there's not more than 1 line of text. >>> >>> Trying to select the first 10 characters is not possible and a >>> reverse selection started at for instance char 20 back will stop >>> always at character 11. If the textview does not contain more >>> than 9 characters selection goes fine in the first column! So >>> does it when the textview contains more than one line of text! >>> >>> In other words, I cannot select the 10 characters in the first >>> column for some reason. >>> I've illustrated the problem in this screenshot: http:// >>> www.mekentosj.com/temporary/textview_problem.jpg >>> >>> Any solution / clue where to start looking would be enormously >>> appreciated. Last bug standing before a release... >>> Cheers, >>> Alex >>> >>> - (NSRect)lineFragmentRectForProposedRect:(NSRect)proposedRect >>> sweepDirection:(NSLineSweepDirection)sweepDirection >>> movementDirection:(NSLineMovementDirection)movementDirection >>> remainingRect:(NSRect *)remainingRect >>> { >>> // create space for the linenumber margin >>> if(proposedRect.origin.x <= 0.0) >>> proposedRect.origin.x = kLEFT_MARGIN_WIDTH; >>> >>> // set the width of a column of text >>> proposedRect.size.width = columnWidth; >>> >>> // make sure we nicely break after a full column >>> if (proposedRect.origin.x + 2 * columnWidth - 20.0 >= [self >>> containerSize].width) *remainingRect = NSZeroRect; >>> else { >>> remainingRect->origin.x = proposedRect.origin.x + >>> columnWidth - 10.0; >>> remainingRect->origin.y = proposedRect.origin.y; >>> remainingRect->size.width = [self containerSize].width - >>> proposedRect.origin.x + columnWidth - 10.0; >>> remainingRect->size.height = proposedRect.size.height; >>> } >>> >>> return proposedRect; >>> } >>> >>> >>> >>> >>> >>> I'm using a custom NSTextContainer which breaks each line of the >>> text >>> view into columns of ten characters. I noticed that when there is >>> only >>> one line in the container, but there is text displayed outside of >>> the >>> first column, clicking in the that first column moves the cursor to >>> the beginning of the second column instead of to its appropriate >>> insertion point in the first column. I can move the cursor using the >>> arrow keys into the first column, but even if the cursor is in the >>> first column, clicking on that column sends the cursor back to >>> beginning of the second column. If, however, there is only text >>> in the >>> first column or there is more than one line, clicking in the first >>> column results in normal positioning of the cursor. I'm stumped. I >>> played around with overriding containsPoint: and clicks in the first >>> column were returned as being part of the container as they >>> should be. >>> I also used a subclass of NSTextView to check what NSTextView was >>> returning for the selection function and found it was returning the >>> incorrect insertion point. If I comment out my >>> lineFragmentRectForProposedRect function then there is no problem >>> with >>> moving the cursor back to the first ten characters with the mouse. I >>> should also mention I set the line fragment padding to zero and >>> changing this has no effect on this behavior. Here is the code I'm >>> using. columnWidth is the length of each column and gapWidth is the >>> space between each column. Anyone have any ideas about what I'm >>> doing >>> wrong? I apologize for the long post but I believe it was necessary. >>> >>> Thanks >>> >>> David Larson >>> >>> - (NSRect)lineFragmentRectForProposedRect:(NSRect)proposedRect >>> sweepDirection:(NSLineSweepDirection)sweepDirection >>> movementDirection:(NSLineMovementDirection)movementDirection >>> remainingRect:(NSRect *)remainingRect >>> { >>> if((sweepDirection != NSLineSweepRight) ||( movementDirection != >>> NSLineMovesDown)) { >>> //check to make sure standard linesweep and movement direction >>> are correct >>> return NSZeroRect; >>> } >>> else { >>> //this code grabbed off of the CocoaBuilder webarchives from a >>> Marco >>> Binder post. Minor modifications to include gap size were included >>> //Also modified the code to force a new line when the edge of the >>> container is reached >>> //Comments are mine >>> >>> //set the width to the column width >>> //note that this assumes that the rect starts at the beginning >>> of a column >>> >>> proposedRect.size.width = columnWidth; >>> >>> if (proposedRect.origin.x+columnWidth >= [self >>> containerSize].width) { >>> proposedRect.origin.x = 0; //if we can't fit the complete rect >>> into >>> the rest of the line, reset the line manually >>> proposedRect.origin.y += proposedRect.size.height; >>> } >>> >>> remainingRect->origin.x = >>> proposedRect.origin.x+columnWidth+gapWidth; //move remaining rect >>> origin to the next column start >>> remainingRect->origin.y = proposedRect.origin.y; >>> remainingRect->size.width = [self containerSize].width - >>> proposedRect.origin.x - columnWidth-gapWidth; //size equals >>> remaining >>> screen space minus the column and gap >>> remainingRect->size.height = proposedRect.size.height; >>> } >>> >>> return proposedRect; >>> } >>> >>> *********************************** >>> Mek (Alexander Griekspoor) >>> MekenTosj.com >>> Web: http://www.mekentosj.com >>> Mail: mek at mekentosj.com >>> *********************************** >>> >>> >> >> ********************************************************* >> ** Alexander Griekspoor ** >> ********************************************************* >> The Netherlands Cancer Institute >> Department of Tumorbiology (H4) >> Plesmanlaan 121, 1066 CX, Amsterdam >> Tel: + 31 20 - 512 2023 >> Fax: + 31 20 - 512 2029 >> AIM: mekentosj at mac.com >> E-mail: a.griekspoor at nki.nl >> Web: http://www.mekentosj.com >> >> Claiming that the Macintosh is inferior to Windows >> because most people use Windows, is like saying >> that all other restaurants serve food that is >> inferior to McDonalds >> >> ********************************************************* >> > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com Claiming that the Macintosh is inferior to Windows because most people use Windows, is like saying that all other restaurants serve food that is inferior to McDonalds ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From kvddrift at earthlink.net Tue Mar 28 19:21:38 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Tue, 28 Mar 2006 19:21:38 -0500 Subject: [Biococoa-dev] Re: Re : Strange Selection Behavior when using a custom NSTextContainer In-Reply-To: References: <9F633DB8-26FC-417F-B42E-260CFDF5A433@earthlink.net> Message-ID: <2450A7CE-BFDD-4522-9FFF-5BA928F50ADA@earthlink.net> On Mar 27, 2006, at 8:03 AM, Alexander Griekspoor wrote: > But the problem seems to be in the selection, not in drawing... That's true, but I think the selection gets it wrong because of whatever happens in lineFragmentRectForProposedRect. If you let that method return the value of the super instead of proposedRect, you will just get one column, but the selection is fine. BTW, I am amazed how little info and knowledge is available about this method. Do you want me to post it on the omni list as well? cheers, - Koen. From kvddrift at earthlink.net Tue Mar 28 21:09:06 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Tue, 28 Mar 2006 21:09:06 -0500 Subject: [Biococoa-dev] Re: Re : Strange Selection Behavior when using a custom NSTextContainer In-Reply-To: <2450A7CE-BFDD-4522-9FFF-5BA928F50ADA@earthlink.net> References: <9F633DB8-26FC-417F-B42E-260CFDF5A433@earthlink.net> <2450A7CE-BFDD-4522-9FFF-5BA928F50ADA@earthlink.net> Message-ID: <05413D09-253B-4392-82BE-BF9AB7449AB9@earthlink.net> On Mar 28, 2006, at 7:21 PM, Koen van der Drift wrote: > > On Mar 27, 2006, at 8:03 AM, Alexander Griekspoor wrote: > >> But the problem seems to be in the selection, not in drawing... > > That's true, but I think the selection gets it wrong because of > whatever happens in lineFragmentRectForProposedRect. If you let > that method return the value of the super instead of proposedRect, > you will just get one column, but the selection is fine. > > BTW, I am amazed how little info and knowledge is available about > this method. Do you want me to post it on the omni list as well? Some more debugging (and that's it for today ;-) makes the NSLayoutManager's functions boundingRectForGlyphRange: and glyphIndexForPoint: also very suspicious. These functions return the wrong value for the the charindex, thus resulting in a wrong value to be shown (or not at all). - Koen. From a.griekspoor at nki.nl Fri Mar 31 02:56:28 2006 From: a.griekspoor at nki.nl (Alexander Griekspoor) Date: Fri, 31 Mar 2006 09:56:28 +0200 Subject: [Biococoa-dev] [ANN] EnzymeX3 Message-ID: <022825CB-803D-40DC-A0B1-15BE7FDCDF86@nki.nl> Hi Guys, Just to let you know that Tom and I have released EnzymeX 3, the second app that uses the BioCocoa standalone reader to read sequence files. Check it out at mekentosj.com! Cheers, Alex ****************************** Announcement: EnzymeX 3 - To cut or not to cut, no longer a question! Amsterdam, March 31st 2006 Mek & Tosj like to announce a completely rewritten version of one their most popular programs, EnzymeX. EnzymeX has become a favorite tool of many molecular biologists using a mac. It is a program developed to help them determine which restriction enzymes they should use to cut their DNA of interest. In addition, it gives all the specific properties of these enzymes to make sure that every digestion is a success. One of the most requested features people wanted to see in EnzymeX was the ability to load their DNA of interest and analyze where exactly the different enzymes would cut. Sure there are other programs that can do this, but why do they have to look like coming straight from the 1980's or from another platform? Now the long wait is over and we have finally created a DNA sequence editor that brings all those features and the look and feel you can expect to come with a true MacOSX program. New in EnzymeX 3: What is not? We have completely redesigned the program, too many new things too mention. Here are a few a the main new features: - Support of many DNA sequence formats through the BioCocoa core - Direct download of sequences from NCBI's Entrez DNA database - Finding of Open Reading Frames and translation from DNA to Protein - Enzyme Restriction maps - Smart Quick Search, with Motifs searches - Mini enzyme inspector showing all the enzyme info you ever need - EnzymeX plugin architecture for custom extensions - And much much more... You can find more information about EnzymeX at: http:// www.mekentosj.com/enzymex Download EnzymeX directly from: http://www.mekentosj.com/enzymex/ enzymex.dmg Mek & Tosj are Alexander Griekspoor and Tom Groothuis, two phD students at the 4th floor of the Netherlands Cancer Institute. Headed by the characteristic professor Sjaak Neefjes, we are doing cell biological research studying the immune system and cellular transport. To make our lives a little bit less complicated, we wrote LabAssistant, a tool to organize scientific experiments, notes, reminders, etc. (http://www.mekentosj.com/labassistant), and iRNAi, a program to easily find an generate the building blocks for a technique called RNA interference. With our latest and most popular program 4Peaks we won the Apple Design Award for best MacOSX student project in 2004. Today we have released a complete new version of our popular program for molecular biologists: EnzymeX 3 Sincerly, Mek & Tosj Alexander Griekspoor Tom Groothuis ******************************************************** ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 E-mail: a.griekspoor at nki.nl AIM: mekentosj at mac.com Web: http://www.mekentosj.com EnzymeX - To cut or not to cut http://www.mekentosj.com/enzymex ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From peter.schols at bio.kuleuven.be Fri Mar 31 03:20:58 2006 From: peter.schols at bio.kuleuven.be (Peter Schols) Date: Fri, 31 Mar 2006 10:20:58 +0200 Subject: [Biococoa-dev] [ANN] EnzymeX3 In-Reply-To: <022825CB-803D-40DC-A0B1-15BE7FDCDF86@nki.nl> References: <022825CB-803D-40DC-A0B1-15BE7FDCDF86@nki.nl> Message-ID: The best got even better... Congratulations to Alex and Tom for this great release! My personal favorite is the virtual digest, but the entire app is a poster child for Mac OS X. Wow! And of course I'm happy to see BioCocoa included. Keep up the great work! Peter On 31 Mar 2006, at 09:56, Alexander Griekspoor wrote: > Hi Guys, > > Just to let you know that Tom and I have released EnzymeX 3, the > second app that uses the BioCocoa standalone reader to read > sequence files. > Check it out at mekentosj.com! > Cheers, > Alex > > ****************************** > Announcement: EnzymeX 3 - To cut or not to cut, no longer a question! > > Amsterdam, March 31st 2006 > > Mek & Tosj like to announce a completely rewritten version of one > their most popular programs, EnzymeX. EnzymeX has become a favorite > tool of many molecular biologists using a mac. It is a program > developed to help them determine which restriction enzymes they > should use to cut their DNA of interest. In addition, it gives all > the specific properties of these enzymes to make sure that every > digestion is a success. > One of the most requested features people wanted to see in EnzymeX > was the ability to load their DNA of interest and analyze where > exactly the different enzymes would cut. Sure there are other > programs that can do this, but why do they have to look like coming > straight from the 1980's or from another platform? Now the long > wait is over and we have finally created a DNA sequence editor that > brings all those features and the look and feel you can expect to > come with a true MacOSX program. > > New in EnzymeX 3: > What is not? We have completely redesigned the program, too many > new things too mention. > Here are a few a the main new features: > - Support of many DNA sequence formats through the BioCocoa core > - Direct download of sequences from NCBI's Entrez DNA database > - Finding of Open Reading Frames and translation from DNA to > Protein > - Enzyme Restriction maps > - Smart Quick Search, with Motifs searches > - Mini enzyme inspector showing all the enzyme info you ever need > - EnzymeX plugin architecture for custom extensions > - And much much more... > > You can find more information about EnzymeX at: http:// > www.mekentosj.com/enzymex > Download EnzymeX directly from: http://www.mekentosj.com/enzymex/ > enzymex.dmg > > Mek & Tosj are Alexander Griekspoor and Tom Groothuis, two phD > students at the 4th floor of the Netherlands Cancer Institute. > Headed by the characteristic professor Sjaak Neefjes, we are doing > cell biological research studying the immune system and cellular > transport. To make our lives a little bit less complicated, we > wrote LabAssistant, a tool to organize scientific experiments, > notes, reminders, etc. (http://www.mekentosj.com/labassistant), and > iRNAi, a program to easily find an generate the building blocks for > a technique called RNA interference. With our latest and most > popular program 4Peaks we won the Apple Design Award for best > MacOSX student project in 2004. > Today we have released a complete new version of our popular > program for molecular biologists: EnzymeX 3 > > Sincerly, > Mek & Tosj > > Alexander Griekspoor > Tom Groothuis > ******************************************************** > ** Alexander Griekspoor ** > ********************************************************* > The Netherlands Cancer Institute > Department of Tumorbiology (H4) > Plesmanlaan 121, 1066 CX, Amsterdam > Tel: + 31 20 - 512 2023 > Fax: + 31 20 - 512 2029 > E-mail: a.griekspoor at nki.nl > AIM: mekentosj at mac.com > Web: http://www.mekentosj.com > > EnzymeX - To cut or not to cut > http://www.mekentosj.com/enzymex > > ********************************************************* > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From a.griekspoor at nki.nl Fri Mar 31 03:29:01 2006 From: a.griekspoor at nki.nl (Alexander Griekspoor) Date: Fri, 31 Mar 2006 10:29:01 +0200 Subject: [Biococoa-dev] [ANN] EnzymeX3 In-Reply-To: References: <022825CB-803D-40DC-A0B1-15BE7FDCDF86@nki.nl> Message-ID: <38270361-85D9-4602-AB2D-A3A69915DC3B@nki.nl> Thanks Peter! I see it as a nice advertisement of BioCocoa, and of course in the future its foundation can become the new BioCocoa. If there are aspects/code snippets you would like to see shared for use in BioCocoa I'm happy to consider that.. Cheers, Alex On 31-mrt-2006, at 10:20, Peter Schols wrote: > The best got even better... > Congratulations to Alex and Tom for this great release! My personal > favorite is the virtual digest, but the entire app is a poster > child for Mac OS X. Wow! > > And of course I'm happy to see BioCocoa included. > Keep up the great work! > > Peter > > > On 31 Mar 2006, at 09:56, Alexander Griekspoor wrote: > >> Hi Guys, >> >> Just to let you know that Tom and I have released EnzymeX 3, the >> second app that uses the BioCocoa standalone reader to read >> sequence files. >> Check it out at mekentosj.com! >> Cheers, >> Alex >> >> ****************************** >> Announcement: EnzymeX 3 - To cut or not to cut, no longer a question! >> >> Amsterdam, March 31st 2006 >> >> Mek & Tosj like to announce a completely rewritten version of one >> their most popular programs, EnzymeX. EnzymeX has become a >> favorite tool of many molecular biologists using a mac. It is a >> program developed to help them determine which restriction enzymes >> they should use to cut their DNA of interest. In addition, it >> gives all the specific properties of these enzymes to make sure >> that every digestion is a success. >> One of the most requested features people wanted to see in EnzymeX >> was the ability to load their DNA of interest and analyze where >> exactly the different enzymes would cut. Sure there are other >> programs that can do this, but why do they have to look like >> coming straight from the 1980's or from another platform? Now the >> long wait is over and we have finally created a DNA sequence >> editor that brings all those features and the look and feel you >> can expect to come with a true MacOSX program. >> >> New in EnzymeX 3: >> What is not? We have completely redesigned the program, too many >> new things too mention. >> Here are a few a the main new features: >> - Support of many DNA sequence formats through the BioCocoa core >> - Direct download of sequences from NCBI's Entrez DNA database >> - Finding of Open Reading Frames and translation from DNA to >> Protein >> - Enzyme Restriction maps >> - Smart Quick Search, with Motifs searches >> - Mini enzyme inspector showing all the enzyme info you ever >> need >> - EnzymeX plugin architecture for custom extensions >> - And much much more... >> >> You can find more information about EnzymeX at: http:// >> www.mekentosj.com/enzymex >> Download EnzymeX directly from: http://www.mekentosj.com/enzymex/ >> enzymex.dmg >> >> Mek & Tosj are Alexander Griekspoor and Tom Groothuis, two phD >> students at the 4th floor of the Netherlands Cancer Institute. >> Headed by the characteristic professor Sjaak Neefjes, we are doing >> cell biological research studying the immune system and cellular >> transport. To make our lives a little bit less complicated, we >> wrote LabAssistant, a tool to organize scientific experiments, >> notes, reminders, etc. (http://www.mekentosj.com/labassistant), >> and iRNAi, a program to easily find an generate the building >> blocks for a technique called RNA interference. With our latest >> and most popular program 4Peaks we won the Apple Design Award for >> best MacOSX student project in 2004. >> Today we have released a complete new version of our popular >> program for molecular biologists: EnzymeX 3 >> >> Sincerly, >> Mek & Tosj >> >> Alexander Griekspoor >> Tom Groothuis >> ******************************************************** >> ** Alexander Griekspoor ** >> ********************************************************* >> The Netherlands Cancer Institute >> Department of Tumorbiology (H4) >> Plesmanlaan 121, 1066 CX, Amsterdam >> Tel: + 31 20 - 512 2023 >> Fax: + 31 20 - 512 2029 >> E-mail: a.griekspoor at nki.nl >> AIM: mekentosj at mac.com >> Web: http://www.mekentosj.com >> >> EnzymeX - To cut or not to cut >> http://www.mekentosj.com/enzymex >> >> ********************************************************* >> >> _______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/biococoa-dev > > > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com LabAssistant - Get your life organized! http://www.mekentosj.com/labassistant ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From kvddrift at earthlink.net Fri Mar 31 09:52:01 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Fri, 31 Mar 2006 09:52:01 -0500 Subject: [Biococoa-dev] [ANN] EnzymeX3 In-Reply-To: <022825CB-803D-40DC-A0B1-15BE7FDCDF86@nki.nl> References: <022825CB-803D-40DC-A0B1-15BE7FDCDF86@nki.nl> Message-ID: <482BE0FE-B184-43B0-AEB4-067D3891F939@earthlink.net> On Mar 31, 2006, at 2:56 AM, Alexander Griekspoor wrote: > Just to let you know that Tom and I have released EnzymeX 3, the > second app that uses the BioCocoa standalone reader to read > sequence files. > Check it out at mekentosj.com! > Nice job guys. Also a good press here: http://www.macnn.com/articles/ 06/03/31/enzymex.v3.released/, which mentions the 'BioCocoa core' :) - Koen. From kvddrift at earthlink.net Fri Mar 31 11:11:48 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Fri, 31 Mar 2006 11:11:48 -0500 Subject: [Biococoa-dev] [ANN] EnzymeX3 In-Reply-To: <022825CB-803D-40DC-A0B1-15BE7FDCDF86@nki.nl> References: <022825CB-803D-40DC-A0B1-15BE7FDCDF86@nki.nl> Message-ID: Hi Alex, Did you make some improvements/changes in the KDTextView in EnzymeX? I noticed that in your app the line numbers are drawn as they should. However, in the translation demo, the linenumbers actually draw the number of columns. Somehow the view thinks that every column is a new line. I went back to the original KDTextView+ that you use in the Entrez demo app, because I thought I had changed something while debugging the sequenceView. However, even in that original view I get this behaviour. I will be gone all weekend, so have no time to look into this right now. cheers, - Koen.