From thasso at minet.uni-jena.de Wed Aug 1 13:19:01 2007 From: thasso at minet.uni-jena.de (Thasso Griebel) Date: Wed, 1 Aug 2007 19:19:01 +0200 Subject: [Biojava-dev] phylo code Message-ID: <1EA22A3D-107C-455B-98A6-EFD4FEF77CCE@minet.uni-jena.de> hi, i recently explored the phylogeny code base in biojava. I am currently working on a phylogeny framework similar to mesquite (http://www.bio.informatik.uni-jena.de/epos) and i would like to add some functionality using biojava (the sequence stuff and the nexus parser). I saw the PhyloSOC07 page ( http://biojava.org/wiki/ BioJava:PhyloSOC07 ) and i might be able to help out with some of the methods, so is there a way to contribute ? Or is this closed to participants of the google summer of code ? I have code for n-consensus and adams consensus methods and some possible extensions for UPGMA (provide other distance computations, i.e wpgma, sigle linkage and complete linkage) and NJ ( outgroup and rooting support ). As our research groups has a focus on supertree construction, we have java implementations for several graph based supertree methods (aho's build, mincut, modified mincut, ranked tree, ancestral build). Regards, Thasso -- Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer Bioinformatik Office 3426--http://bio.informatik.uni-jena.de--Institut fuer Informatik Phone +49 (0)3641 9-46454-----------Friedrich-Schiller-Universitaet Jena Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, Germany From holland at ebi.ac.uk Wed Aug 1 14:03:29 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Wed, 1 Aug 2007 19:03:29 +0100 (BST) Subject: [Biojava-dev] phylo code In-Reply-To: <1EA22A3D-107C-455B-98A6-EFD4FEF77CCE@minet.uni-jena.de> References: <1EA22A3D-107C-455B-98A6-EFD4FEF77CCE@minet.uni-jena.de> Message-ID: <48008.80.42.98.32.1185991409.squirrel@webmail.ebi.ac.uk> Hi Thasso. Thanks for your interest! We always welcome all contributions of code and documentation to the BioJava project. Our GSOC project is well under way and has a plan as you have already noticed. The items on that plan are what was agreed with our student, Boh Yun Lee, and will be implemented by the time that GSOC is over (early September) - or at least, most of them will, and any that aren't will be flagged as such. If you have suggestions to make about code already committed, we would welcome them. Such feedback is a necessary part of the development cycle. Likewise we would welcome contributions of code not already mentioned as being planned on the GSOC pages. However, if your existing code implements something that is on the to-do list on the GSOC page, then the best thing would be to hang on till the end of the GSOC project then contribute any items that did not get implemented. cheers, Richard On Wed, August 1, 2007 6:19 pm, Thasso Griebel wrote: > hi, > > i recently explored the phylogeny code base in biojava. I am > currently working on a phylogeny framework similar to mesquite > (http://www.bio.informatik.uni-jena.de/epos) and i would like to add > some functionality using biojava (the sequence stuff and the nexus > parser). > > I saw the PhyloSOC07 page ( http://biojava.org/wiki/ > BioJava:PhyloSOC07 ) and i might be able to help out with some of the > methods, so is there a way to contribute ? Or is this closed to > participants of the google summer of code ? > > I have code for n-consensus and adams consensus methods and some > possible extensions for UPGMA (provide other distance computations, > i.e wpgma, sigle linkage and complete linkage) and NJ ( outgroup and > rooting support ). As our research groups has a focus on supertree > construction, we have java implementations for several graph based > supertree methods (aho's build, mincut, modified mincut, ranked tree, > ancestral build). > > > Regards, > > Thasso > > -- > Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer Bioinformatik > Office 3426--http://bio.informatik.uni-jena.de--Institut fuer Informatik > Phone +49 (0)3641 9-46454-----------Friedrich-Schiller-Universitaet Jena > Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, Germany > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > -- Richard Holland BioMart (http://www.biomart.org/) EMBL-EBI Hinxton, Cambridgeshire CB10 1SD, UK From thasso at minet.uni-jena.de Mon Aug 6 12:45:35 2007 From: thasso at minet.uni-jena.de (Thasso Griebel) Date: Mon, 6 Aug 2007 18:45:35 +0200 Subject: [Biojava-dev] phylo code In-Reply-To: <48008.80.42.98.32.1185991409.squirrel@webmail.ebi.ac.uk> References: <1EA22A3D-107C-455B-98A6-EFD4FEF77CCE@minet.uni-jena.de> <48008.80.42.98.32.1185991409.squirrel@webmail.ebi.ac.uk> Message-ID: <846222BD-73C8-4CE7-8CB1-E2249A25256D@minet.uni-jena.de> Hi, thanks for the fast answer. So, I would really like to contribute to the BioJava Phylogeny Package, but I will wait until the GSOC project is finished and I am back from my vacation ;) For now, I just took a look on the io package, especially the three classes concerning phylip io. Some personal feeling about the naming. I wouldn't mention "fire" and "events" in the documentation and rename PHYLIPFileListener to something else, i.e. PHYLIPFileHandler. For me, this was irritating. I started looking for a fireXXX method immediately and automatically started thinking about the EventDispatchingThread and synchronization. As far as I see, this is a direct handler delegate, the parser delegates some method calls to a given handler callback method, no events are fired (there is not even an Event class that could be fired) and no event dispatching is involved. Also, the io seem to focus on the output of alignment. What about trees and distance/character matrices ? And a really important point is the name handling. The method private static String formatSequenceLabel(String label) in PHYLIPFileFormat simply cuts names that are longer than 10 characters. I know that phylip has this stupid limitation. But cutting will not work in a lot of cases. If just two sequence names are identical over the first ten characters, the resulting phylip file is corrupted and can not be used by most of the phylip executables. Maybe the handler can do a renaming and keep track of the map. Then one can use the parser to write some phylip file, start a phylip method on that file, read in the results and do an automatic remapping of the names ? I also wanted to take a look on the tree model. Is this already in the CVS ? I found biojava-live/src/org/biojavax/bio/phylo/tree, but it was empty ? regards, thasso On 01.08.2007, at 20:03, Richard Holland wrote: > Hi Thasso. > > Thanks for your interest! We always welcome all contributions of > code and > documentation to the BioJava project. > > Our GSOC project is well under way and has a plan as you have already > noticed. The items on that plan are what was agreed with our > student, Boh > Yun Lee, and will be implemented by the time that GSOC is over (early > September) - or at least, most of them will, and any that aren't > will be > flagged as such. > > If you have suggestions to make about code already committed, we would > welcome them. Such feedback is a necessary part of the development > cycle. > Likewise we would welcome contributions of code not already > mentioned as > being planned on the GSOC pages. > > However, if your existing code implements something that is on the > to-do > list on the GSOC page, then the best thing would be to hang on till > the > end of the GSOC project then contribute any items that did not get > implemented. > > cheers, > Richard > > On Wed, August 1, 2007 6:19 pm, Thasso Griebel wrote: >> hi, >> >> i recently explored the phylogeny code base in biojava. I am >> currently working on a phylogeny framework similar to mesquite >> (http://www.bio.informatik.uni-jena.de/epos) and i would like to add >> some functionality using biojava (the sequence stuff and the nexus >> parser). >> >> I saw the PhyloSOC07 page ( http://biojava.org/wiki/ >> BioJava:PhyloSOC07 ) and i might be able to help out with some of the >> methods, so is there a way to contribute ? Or is this closed to >> participants of the google summer of code ? >> >> I have code for n-consensus and adams consensus methods and some >> possible extensions for UPGMA (provide other distance computations, >> i.e wpgma, sigle linkage and complete linkage) and NJ ( outgroup and >> rooting support ). As our research groups has a focus on supertree >> construction, we have java implementations for several graph based >> supertree methods (aho's build, mincut, modified mincut, ranked tree, >> ancestral build). >> >> >> Regards, >> >> Thasso >> >> -- >> Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer >> Bioinformatik >> Office 3426--http://bio.informatik.uni-jena.de--Institut fuer >> Informatik >> Phone +49 (0)3641 9-46454-----------Friedrich-Schiller- >> Universitaet Jena >> Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, >> Germany >> >> >> >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> > > > -- > Richard Holland > BioMart (http://www.biomart.org/) > EMBL-EBI > Hinxton, Cambridgeshire CB10 1SD, UK -- Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer Bioinformatik Office 3426--http://bio.informatik.uni-jena.de--Institut fuer Informatik Phone +49 (0)3641 9-46454-----------Friedrich-Schiller-Universitaet Jena Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, Germany From holland at ebi.ac.uk Tue Aug 7 03:48:05 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Tue, 07 Aug 2007 08:48:05 +0100 Subject: [Biojava-dev] phylo code In-Reply-To: <846222BD-73C8-4CE7-8CB1-E2249A25256D@minet.uni-jena.de> References: <1EA22A3D-107C-455B-98A6-EFD4FEF77CCE@minet.uni-jena.de> <48008.80.42.98.32.1185991409.squirrel@webmail.ebi.ac.uk> <846222BD-73C8-4CE7-8CB1-E2249A25256D@minet.uni-jena.de> Message-ID: <46B823B5.1010401@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Thanks for your feedback Thasso. The fire/events thing is certainly a misnomer - guilty as charged (I wrote the code...) - but I suppose I wasn't expecting the naming to matter much. I'll bear that in mind for future code. We can't really change the existing interfaces now as they've been released and it is not nice to users for us to change public interfaces that might already be in use. The PHYLIP format handler was written by Jim Balhoff. Jim - do you have any responses to Thasso's comments about the output options? I like the sound of your PHYLIP short-name map. You could definitely go ahead and contribute an update which implemented that. (Don't forget to make your code clear the map between one file and the next!) The tree model never materialised in the end. We chose instead to use the external JGraphT package to represent our trees. The exact way in which this is done will be documented by Boh-Yun as part of the GSOC project. cheers, Richard Thasso Griebel wrote: > Hi, > > thanks for the fast answer. > > So, I would really like to contribute to the BioJava Phylogeny > Package, but I will wait until the GSOC project is finished and I am > back from my vacation ;) For now, I just took a look on the io > package, especially the three classes concerning phylip io. > Some personal feeling about the naming. > I wouldn't mention "fire" and "events" in the documentation and > rename PHYLIPFileListener to something else, i.e. PHYLIPFileHandler. > For me, this was irritating. I started looking for a fireXXX method > immediately and automatically started thinking about the > EventDispatchingThread and synchronization. As far as I see, this is > a direct handler delegate, the parser delegates some method calls to > a given handler callback method, no events are fired (there is not > even an Event class that could be fired) and no event dispatching is > involved. > Also, the io seem to focus on the output of alignment. What about > trees and distance/character matrices ? > And a really important point is the name handling. The method > > private static String formatSequenceLabel(String label) > > in PHYLIPFileFormat simply cuts names that are longer than 10 > characters. I know that phylip has this stupid limitation. But > cutting will not work in a lot of cases. If just two sequence names > are identical over the first ten characters, the resulting phylip > file is corrupted and can not be used by most of the phylip > executables. Maybe the handler can do a renaming and keep track of > the map. Then one can use the parser to write some phylip file, start > a phylip method on that file, read in the results and do an automatic > remapping of the names ? > > I also wanted to take a look on the tree model. Is this already in > the CVS ? I found biojava-live/src/org/biojavax/bio/phylo/tree, but > it was empty ? > > regards, > > thasso > > > > On 01.08.2007, at 20:03, Richard Holland wrote: > >> Hi Thasso. >> >> Thanks for your interest! We always welcome all contributions of >> code and >> documentation to the BioJava project. >> >> Our GSOC project is well under way and has a plan as you have already >> noticed. The items on that plan are what was agreed with our >> student, Boh >> Yun Lee, and will be implemented by the time that GSOC is over (early >> September) - or at least, most of them will, and any that aren't >> will be >> flagged as such. >> >> If you have suggestions to make about code already committed, we would >> welcome them. Such feedback is a necessary part of the development >> cycle. >> Likewise we would welcome contributions of code not already >> mentioned as >> being planned on the GSOC pages. >> >> However, if your existing code implements something that is on the >> to-do >> list on the GSOC page, then the best thing would be to hang on till >> the >> end of the GSOC project then contribute any items that did not get >> implemented. >> >> cheers, >> Richard >> >> On Wed, August 1, 2007 6:19 pm, Thasso Griebel wrote: >>> hi, >>> >>> i recently explored the phylogeny code base in biojava. I am >>> currently working on a phylogeny framework similar to mesquite >>> (http://www.bio.informatik.uni-jena.de/epos) and i would like to add >>> some functionality using biojava (the sequence stuff and the nexus >>> parser). >>> >>> I saw the PhyloSOC07 page ( http://biojava.org/wiki/ >>> BioJava:PhyloSOC07 ) and i might be able to help out with some of the >>> methods, so is there a way to contribute ? Or is this closed to >>> participants of the google summer of code ? >>> >>> I have code for n-consensus and adams consensus methods and some >>> possible extensions for UPGMA (provide other distance computations, >>> i.e wpgma, sigle linkage and complete linkage) and NJ ( outgroup and >>> rooting support ). As our research groups has a focus on supertree >>> construction, we have java implementations for several graph based >>> supertree methods (aho's build, mincut, modified mincut, ranked tree, >>> ancestral build). >>> >>> >>> Regards, >>> >>> Thasso >>> >>> -- >>> Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer >>> Bioinformatik >>> Office 3426--http://bio.informatik.uni-jena.de--Institut fuer >>> Informatik >>> Phone +49 (0)3641 9-46454-----------Friedrich-Schiller- >>> Universitaet Jena >>> Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, >>> Germany >>> >>> >>> >>> _______________________________________________ >>> biojava-dev mailing list >>> biojava-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >>> >> >> -- >> Richard Holland >> BioMart (http://www.biomart.org/) >> EMBL-EBI >> Hinxton, Cambridgeshire CB10 1SD, UK > > -- > Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer Bioinformatik > Office 3426--http://bio.informatik.uni-jena.de--Institut fuer Informatik > Phone +49 (0)3641 9-46454-----------Friedrich-Schiller-Universitaet Jena > Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, Germany > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGuCO04C5LeMEKA/QRAritAJ0eFpRIQ7YP/NROSfoToo/+4aTfEwCfbFUU Hbne6alMOuzmr8CxX/hqsfs= =U4gJ -----END PGP SIGNATURE----- From thasso at minet.uni-jena.de Tue Aug 7 04:29:08 2007 From: thasso at minet.uni-jena.de (Thasso Griebel) Date: Tue, 7 Aug 2007 10:29:08 +0200 Subject: [Biojava-dev] phylo code In-Reply-To: <46B823B5.1010401@ebi.ac.uk> References: <1EA22A3D-107C-455B-98A6-EFD4FEF77CCE@minet.uni-jena.de> <48008.80.42.98.32.1185991409.squirrel@webmail.ebi.ac.uk> <846222BD-73C8-4CE7-8CB1-E2249A25256D@minet.uni-jena.de> <46B823B5.1010401@ebi.ac.uk> Message-ID: Hi, On the fire/event thing. You are right, it is not a good idea to change this if the code is already released. But maybe a little helper class with some static methods ( like IOTools ) would help. Something like PhylipIO.readTree(File) or PhylipIO.readAlignment (File) might do the job, the interfaces do not have to change and when it avoids direct contact with the parser implementation as long as standard phylip dataypes are concerned. And, as far as I see, this would follow the main path IO is done in BioJava. I can ( and will ) definitely work on the short-name map, but this has to wait at least 5 week as I am going on vacation ( yeah, 5 weeks without a computer nearby !!!). But currently I am really interested in a good phylip parser, so I will work on that. One thing about JGraphT. I used and use that a lot when doing phylogenetics, and its a great library. But you might consider adding a little interface structure on top at some point to decouple the the usage from the library. This would allow BioJava compatible tree implementations without the need of JGraphT. JGraphT is great for all the simple, and even the complex jobs, but for me there is one little drawback. You can fill in every Object as a graph vertex, which is great, but this makes the underlying implementation rather complex. I do not remember exactly, but I think they use a large set of HashMap structures and some complex mapping mechanism to build up a graph. There are situations where this makes it hard to extend. For example, for one of our supertree algorithm implementations we needed a MultiGraph, a graph with different edge types, and it was a real pain to add that to the library without reimplementing JGraphT's Graph interface completely. I think a Tree interface structure on top would be simple and easy and might be really helpful at some point. regards, thasso On 07.08.2007, at 09:48, Richard Holland wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Thanks for your feedback Thasso. > > The fire/events thing is certainly a misnomer - guilty as charged (I > wrote the code...) - but I suppose I wasn't expecting the naming to > matter much. I'll bear that in mind for future code. We can't really > change the existing interfaces now as they've been released and it is > not nice to users for us to change public interfaces that might > already > be in use. > > The PHYLIP format handler was written by Jim Balhoff. Jim - do you > have > any responses to Thasso's comments about the output options? > > I like the sound of your PHYLIP short-name map. You could > definitely go > ahead and contribute an update which implemented that. (Don't > forget to > make your code clear the map between one file and the next!) > > The tree model never materialised in the end. We chose instead to use > the external JGraphT package to represent our trees. The exact way in > which this is done will be documented by Boh-Yun as part of the GSOC > project. > > cheers, > Richard > > > Thasso Griebel wrote: >> Hi, >> >> thanks for the fast answer. >> >> So, I would really like to contribute to the BioJava Phylogeny >> Package, but I will wait until the GSOC project is finished and I am >> back from my vacation ;) For now, I just took a look on the io >> package, especially the three classes concerning phylip io. >> Some personal feeling about the naming. >> I wouldn't mention "fire" and "events" in the documentation and >> rename PHYLIPFileListener to something else, i.e. PHYLIPFileHandler. >> For me, this was irritating. I started looking for a fireXXX method >> immediately and automatically started thinking about the >> EventDispatchingThread and synchronization. As far as I see, this is >> a direct handler delegate, the parser delegates some method calls to >> a given handler callback method, no events are fired (there is not >> even an Event class that could be fired) and no event dispatching is >> involved. >> Also, the io seem to focus on the output of alignment. What about >> trees and distance/character matrices ? >> And a really important point is the name handling. The method >> >> private static String formatSequenceLabel(String label) >> >> in PHYLIPFileFormat simply cuts names that are longer than 10 >> characters. I know that phylip has this stupid limitation. But >> cutting will not work in a lot of cases. If just two sequence names >> are identical over the first ten characters, the resulting phylip >> file is corrupted and can not be used by most of the phylip >> executables. Maybe the handler can do a renaming and keep track of >> the map. Then one can use the parser to write some phylip file, start >> a phylip method on that file, read in the results and do an automatic >> remapping of the names ? >> >> I also wanted to take a look on the tree model. Is this already in >> the CVS ? I found biojava-live/src/org/biojavax/bio/phylo/tree, but >> it was empty ? >> >> regards, >> >> thasso >> >> >> >> On 01.08.2007, at 20:03, Richard Holland wrote: >> >>> Hi Thasso. >>> >>> Thanks for your interest! We always welcome all contributions of >>> code and >>> documentation to the BioJava project. >>> >>> Our GSOC project is well under way and has a plan as you have >>> already >>> noticed. The items on that plan are what was agreed with our >>> student, Boh >>> Yun Lee, and will be implemented by the time that GSOC is over >>> (early >>> September) - or at least, most of them will, and any that aren't >>> will be >>> flagged as such. >>> >>> If you have suggestions to make about code already committed, we >>> would >>> welcome them. Such feedback is a necessary part of the development >>> cycle. >>> Likewise we would welcome contributions of code not already >>> mentioned as >>> being planned on the GSOC pages. >>> >>> However, if your existing code implements something that is on the >>> to-do >>> list on the GSOC page, then the best thing would be to hang on till >>> the >>> end of the GSOC project then contribute any items that did not get >>> implemented. >>> >>> cheers, >>> Richard >>> >>> On Wed, August 1, 2007 6:19 pm, Thasso Griebel wrote: >>>> hi, >>>> >>>> i recently explored the phylogeny code base in biojava. I am >>>> currently working on a phylogeny framework similar to mesquite >>>> (http://www.bio.informatik.uni-jena.de/epos) and i would like to >>>> add >>>> some functionality using biojava (the sequence stuff and the nexus >>>> parser). >>>> >>>> I saw the PhyloSOC07 page ( http://biojava.org/wiki/ >>>> BioJava:PhyloSOC07 ) and i might be able to help out with some >>>> of the >>>> methods, so is there a way to contribute ? Or is this closed to >>>> participants of the google summer of code ? >>>> >>>> I have code for n-consensus and adams consensus methods and some >>>> possible extensions for UPGMA (provide other distance computations, >>>> i.e wpgma, sigle linkage and complete linkage) and NJ ( outgroup >>>> and >>>> rooting support ). As our research groups has a focus on supertree >>>> construction, we have java implementations for several graph based >>>> supertree methods (aho's build, mincut, modified mincut, ranked >>>> tree, >>>> ancestral build). >>>> >>>> >>>> Regards, >>>> >>>> Thasso >>>> >>>> -- >>>> Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer >>>> Bioinformatik >>>> Office 3426--http://bio.informatik.uni-jena.de--Institut fuer >>>> Informatik >>>> Phone +49 (0)3641 9-46454-----------Friedrich-Schiller- >>>> Universitaet Jena >>>> Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, >>>> Germany >>>> >>>> >>>> >>>> _______________________________________________ >>>> biojava-dev mailing list >>>> biojava-dev at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >>>> >>> >>> -- >>> Richard Holland >>> BioMart (http://www.biomart.org/) >>> EMBL-EBI >>> Hinxton, Cambridgeshire CB10 1SD, UK >> >> -- >> Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer >> Bioinformatik >> Office 3426--http://bio.informatik.uni-jena.de--Institut fuer >> Informatik >> Phone +49 (0)3641 9-46454-----------Friedrich-Schiller- >> Universitaet Jena >> Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, >> Germany >> >> >> >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.2.2 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iD8DBQFGuCO04C5LeMEKA/QRAritAJ0eFpRIQ7YP/NROSfoToo/+4aTfEwCfbFUU > Hbne6alMOuzmr8CxX/hqsfs= > =U4gJ > -----END PGP SIGNATURE----- -- Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer Bioinformatik Office 3426--http://bio.informatik.uni-jena.de--Institut fuer Informatik Phone +49 (0)3641 9-46454-----------Friedrich-Schiller-Universitaet Jena Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, Germany From james.balhoff at duke.edu Tue Aug 7 10:34:44 2007 From: james.balhoff at duke.edu (Jim Balhoff) Date: Tue, 7 Aug 2007 10:34:44 -0400 Subject: [Biojava-dev] phylo code In-Reply-To: <46B823B5.1010401@ebi.ac.uk> References: <1EA22A3D-107C-455B-98A6-EFD4FEF77CCE@minet.uni-jena.de> <48008.80.42.98.32.1185991409.squirrel@webmail.ebi.ac.uk> <846222BD-73C8-4CE7-8CB1-E2249A25256D@minet.uni-jena.de> <46B823B5.1010401@ebi.ac.uk> Message-ID: Hi Richard and Thasso, On Aug 7, 2007, at 3:48 AM, Richard Holland wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Thanks for your feedback Thasso. > > The fire/events thing is certainly a misnomer - guilty as charged (I > wrote the code...) - but I suppose I wasn't expecting the naming to > matter much. I'll bear that in mind for future code. We can't really > change the existing interfaces now as they've been released and it is > not nice to users for us to change public interfaces that might > already > be in use. > > The PHYLIP format handler was written by Jim Balhoff. Jim - do you > have > any responses to Thasso's comments about the output options? I think it would be great to have import and export classes for PHYLIP trees and distance matrices. The current code handles only alignments. The other data would be in separate files, and so not part of this parser. > I like the sound of your PHYLIP short-name map. You could > definitely go > ahead and contribute an update which implemented that. (Don't > forget to > make your code clear the map between one file and the next!) Yes, I think the the map is a great idea. The first edition of the PHYLIP parser was simple and strictly stuck to the format specification. The map would be a great way to transparently use longer names when running PHYLIP behind the scenes. If the user is actually exporting a PHYLIP formatted alignment to disk, it might be nice to have a few options for what should happen - the current truncation method could be one option, another might be to simply put in the long name and put a space before the sequence starts (not strictly PHYLIP, but it is a simple alignment format recognized by some programs), another might be to raise an exception or otherwise alert if sequence names are too long. Another enhancement to the PHYLIP classes would be to let the developer specify interleaved or sequential alignment format for import and export (and for both the length of the lines for export). Right now I think there are some possible files which will not be parsed correctly - probably a sequential style file with newlines within the sequences (if a "sequential" alignment has no newlines, it is equivalent to "interleaved"). Or instead of specifying interleaved or sequential, figure out how to detect them reliably. Here are the examples: Best regards, Jim ____________________________________________ James P. Balhoff, Ph.D. National Evolutionary Synthesis Center 2024 West Main St., Suite A200 Durham, NC 27705 USA From simpleyrx at 163.com Tue Aug 7 21:24:37 2007 From: simpleyrx at 163.com (simpleyrx) Date: Wed, 8 Aug 2007 09:24:37 +0800 (CST) Subject: [Biojava-dev] Reply:biojava-dev Digest, Vol 54, Issue 1 In-Reply-To: References: Message-ID: <620113805.735311186536277307.JavaMail.coremail@bj163app105.163.com> Dear sir, Thank you for your message for biojava. I am very interested in it. I am a graduate student of China Agriculture University and my major is bioinformatics. I would like to know that if I can join in developing biojava ? student simple ??2007-08-07??biojava-dev-request at lists.open-bio.org ?????? Send biojava-dev mailing list submissions to biojava-dev at lists.open-bio.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.open-bio.org/mailman/listinfo/biojava-dev or, via email, send a message with subject or body 'help' to biojava-dev-request at lists.open-bio.org You can reach the person managing the list at biojava-dev-owner at lists.open-bio.org When replying, please edit your Subject line so it is more specific than "Re: Contents of biojava-dev digest..." Today's Topics: 1. phylo code (Thasso Griebel) 2. Re: phylo code (Richard Holland) 3. Re: phylo code (Thasso Griebel) 4. Re: phylo code (Richard Holland) 5. Re: phylo code (Thasso Griebel) ---------------------------------------------------------------------- Message: 1 Date: Wed, 1 Aug 2007 19:19:01 +0200 From: Thasso Griebel Subject: [Biojava-dev] phylo code To: biojava-dev at biojava.org Message-ID: <1EA22A3D-107C-455B-98A6-EFD4FEF77CCE at minet.uni-jena.de> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed hi, i recently explored the phylogeny code base in biojava. I am currently working on a phylogeny framework similar to mesquite (http://www.bio.informatik.uni-jena.de/epos) and i would like to add some functionality using biojava (the sequence stuff and the nexus parser). I saw the PhyloSOC07 page ( http://biojava.org/wiki/ BioJava:PhyloSOC07 ) and i might be able to help out with some of the methods, so is there a way to contribute ? Or is this closed to participants of the google summer of code ? I have code for n-consensus and adams consensus methods and some possible extensions for UPGMA (provide other distance computations, i.e wpgma, sigle linkage and complete linkage) and NJ ( outgroup and rooting support ). As our research groups has a focus on supertree construction, we have java implementations for several graph based supertree methods (aho's build, mincut, modified mincut, ranked tree, ancestral build). Regards, Thasso -- Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer Bioinformatik Office 3426--http://bio.informatik.uni-jena.de--Institut fuer Informatik Phone +49 (0)3641 9-46454-----------Friedrich-Schiller-Universitaet Jena Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, Germany ------------------------------ Message: 2 Date: Wed, 1 Aug 2007 19:03:29 +0100 (BST) From: "Richard Holland" Subject: Re: [Biojava-dev] phylo code To: "Thasso Griebel" Cc: biojava-dev at biojava.org Message-ID: <48008.80.42.98.32.1185991409.squirrel at webmail.ebi.ac.uk> Content-Type: text/plain;charset=iso-8859-1 Hi Thasso. Thanks for your interest! We always welcome all contributions of code and documentation to the BioJava project. Our GSOC project is well under way and has a plan as you have already noticed. The items on that plan are what was agreed with our student, Boh Yun Lee, and will be implemented by the time that GSOC is over (early September) - or at least, most of them will, and any that aren't will be flagged as such. If you have suggestions to make about code already committed, we would welcome them. Such feedback is a necessary part of the development cycle. Likewise we would welcome contributions of code not already mentioned as being planned on the GSOC pages. However, if your existing code implements something that is on the to-do list on the GSOC page, then the best thing would be to hang on till the end of the GSOC project then contribute any items that did not get implemented. cheers, Richard On Wed, August 1, 2007 6:19 pm, Thasso Griebel wrote: > hi, > > i recently explored the phylogeny code base in biojava. I am > currently working on a phylogeny framework similar to mesquite > (http://www.bio.informatik.uni-jena.de/epos) and i would like to add > some functionality using biojava (the sequence stuff and the nexus > parser). > > I saw the PhyloSOC07 page ( http://biojava.org/wiki/ > BioJava:PhyloSOC07 ) and i might be able to help out with some of the > methods, so is there a way to contribute ? Or is this closed to > participants of the google summer of code ? > > I have code for n-consensus and adams consensus methods and some > possible extensions for UPGMA (provide other distance computations, > i.e wpgma, sigle linkage and complete linkage) and NJ ( outgroup and > rooting support ). As our research groups has a focus on supertree > construction, we have java implementations for several graph based > supertree methods (aho's build, mincut, modified mincut, ranked tree, > ancestral build). > > > Regards, > > Thasso > > -- > Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer Bioinformatik > Office 3426--http://bio.informatik.uni-jena.de--Institut fuer Informatik > Phone +49 (0)3641 9-46454-----------Friedrich-Schiller-Universitaet Jena > Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, Germany > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > -- Richard Holland BioMart (http://www.biomart.org/) EMBL-EBI Hinxton, Cambridgeshire CB10 1SD, UK ------------------------------ Message: 3 Date: Mon, 6 Aug 2007 18:45:35 +0200 From: Thasso Griebel Subject: Re: [Biojava-dev] phylo code To: Richard Holland Cc: biojava-dev at biojava.org Message-ID: <846222BD-73C8-4CE7-8CB1-E2249A25256D at minet.uni-jena.de> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Hi, thanks for the fast answer. So, I would really like to contribute to the BioJava Phylogeny Package, but I will wait until the GSOC project is finished and I am back from my vacation ;) For now, I just took a look on the io package, especially the three classes concerning phylip io. Some personal feeling about the naming. I wouldn't mention "fire" and "events" in the documentation and rename PHYLIPFileListener to something else, i.e. PHYLIPFileHandler. For me, this was irritating. I started looking for a fireXXX method immediately and automatically started thinking about the EventDispatchingThread and synchronization. As far as I see, this is a direct handler delegate, the parser delegates some method calls to a given handler callback method, no events are fired (there is not even an Event class that could be fired) and no event dispatching is involved. Also, the io seem to focus on the output of alignment. What about trees and distance/character matrices ? And a really important point is the name handling. The method private static String formatSequenceLabel(String label) in PHYLIPFileFormat simply cuts names that are longer than 10 characters. I know that phylip has this stupid limitation. But cutting will not work in a lot of cases. If just two sequence names are identical over the first ten characters, the resulting phylip file is corrupted and can not be used by most of the phylip executables. Maybe the handler can do a renaming and keep track of the map. Then one can use the parser to write some phylip file, start a phylip method on that file, read in the results and do an automatic remapping of the names ? I also wanted to take a look on the tree model. Is this already in the CVS ? I found biojava-live/src/org/biojavax/bio/phylo/tree, but it was empty ? regards, thasso On 01.08.2007, at 20:03, Richard Holland wrote: > Hi Thasso. > > Thanks for your interest! We always welcome all contributions of > code and > documentation to the BioJava project. > > Our GSOC project is well under way and has a plan as you have already > noticed. The items on that plan are what was agreed with our > student, Boh > Yun Lee, and will be implemented by the time that GSOC is over (early > September) - or at least, most of them will, and any that aren't > will be > flagged as such. > > If you have suggestions to make about code already committed, we would > welcome them. Such feedback is a necessary part of the development > cycle. > Likewise we would welcome contributions of code not already > mentioned as > being planned on the GSOC pages. > > However, if your existing code implements something that is on the > to-do > list on the GSOC page, then the best thing would be to hang on till > the > end of the GSOC project then contribute any items that did not get > implemented. > > cheers, > Richard > > On Wed, August 1, 2007 6:19 pm, Thasso Griebel wrote: >> hi, >> >> i recently explored the phylogeny code base in biojava. I am >> currently working on a phylogeny framework similar to mesquite >> (http://www.bio.informatik.uni-jena.de/epos) and i would like to add >> some functionality using biojava (the sequence stuff and the nexus >> parser). >> >> I saw the PhyloSOC07 page ( http://biojava.org/wiki/ >> BioJava:PhyloSOC07 ) and i might be able to help out with some of the >> methods, so is there a way to contribute ? Or is this closed to >> participants of the google summer of code ? >> >> I have code for n-consensus and adams consensus methods and some >> possible extensions for UPGMA (provide other distance computations, >> i.e wpgma, sigle linkage and complete linkage) and NJ ( outgroup and >> rooting support ). As our research groups has a focus on supertree >> construction, we have java implementations for several graph based >> supertree methods (aho's build, mincut, modified mincut, ranked tree, >> ancestral build). >> >> >> Regards, >> >> Thasso >> >> -- >> Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer >> Bioinformatik >> Office 3426--http://bio.informatik.uni-jena.de--Institut fuer >> Informatik >> Phone +49 (0)3641 9-46454-----------Friedrich-Schiller- >> Universitaet Jena >> Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, >> Germany >> >> >> >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> > > > -- > Richard Holland > BioMart (http://www.biomart.org/) > EMBL-EBI > Hinxton, Cambridgeshire CB10 1SD, UK -- Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer Bioinformatik Office 3426--http://bio.informatik.uni-jena.de--Institut fuer Informatik Phone +49 (0)3641 9-46454-----------Friedrich-Schiller-Universitaet Jena Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, Germany ------------------------------ Message: 4 Date: Tue, 07 Aug 2007 08:48:05 +0100 From: Richard Holland Subject: Re: [Biojava-dev] phylo code To: Thasso Griebel Cc: biojava-dev at biojava.org Message-ID: <46B823B5.1010401 at ebi.ac.uk> Content-Type: text/plain; charset=ISO-8859-1 -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Thanks for your feedback Thasso. The fire/events thing is certainly a misnomer - guilty as charged (I wrote the code...) - but I suppose I wasn't expecting the naming to matter much. I'll bear that in mind for future code. We can't really change the existing interfaces now as they've been released and it is not nice to users for us to change public interfaces that might already be in use. The PHYLIP format handler was written by Jim Balhoff. Jim - do you have any responses to Thasso's comments about the output options? I like the sound of your PHYLIP short-name map. You could definitely go ahead and contribute an update which implemented that. (Don't forget to make your code clear the map between one file and the next!) The tree model never materialised in the end. We chose instead to use the external JGraphT package to represent our trees. The exact way in which this is done will be documented by Boh-Yun as part of the GSOC project. cheers, Richard Thasso Griebel wrote: > Hi, > > thanks for the fast answer. > > So, I would really like to contribute to the BioJava Phylogeny > Package, but I will wait until the GSOC project is finished and I am > back from my vacation ;) For now, I just took a look on the io > package, especially the three classes concerning phylip io. > Some personal feeling about the naming. > I wouldn't mention "fire" and "events" in the documentation and > rename PHYLIPFileListener to something else, i.e. PHYLIPFileHandler. > For me, this was irritating. I started looking for a fireXXX method > immediately and automatically started thinking about the > EventDispatchingThread and synchronization. As far as I see, this is > a direct handler delegate, the parser delegates some method calls to > a given handler callback method, no events are fired (there is not > even an Event class that could be fired) and no event dispatching is > involved. > Also, the io seem to focus on the output of alignment. What about > trees and distance/character matrices ? > And a really important point is the name handling. The method > > private static String formatSequenceLabel(String label) > > in PHYLIPFileFormat simply cuts names that are longer than 10 > characters. I know that phylip has this stupid limitation. But > cutting will not work in a lot of cases. If just two sequence names > are identical over the first ten characters, the resulting phylip > file is corrupted and can not be used by most of the phylip > executables. Maybe the handler can do a renaming and keep track of > the map. Then one can use the parser to write some phylip file, start > a phylip method on that file, read in the results and do an automatic > remapping of the names ? > > I also wanted to take a look on the tree model. Is this already in > the CVS ? I found biojava-live/src/org/biojavax/bio/phylo/tree, but > it was empty ? > > regards, > > thasso > > > > On 01.08.2007, at 20:03, Richard Holland wrote: > >> Hi Thasso. >> >> Thanks for your interest! We always welcome all contributions of >> code and >> documentation to the BioJava project. >> >> Our GSOC project is well under way and has a plan as you have already >> noticed. The items on that plan are what was agreed with our >> student, Boh >> Yun Lee, and will be implemented by the time that GSOC is over (early >> September) - or at least, most of them will, and any that aren't >> will be >> flagged as such. >> >> If you have suggestions to make about code already committed, we would >> welcome them. Such feedback is a necessary part of the development >> cycle. >> Likewise we would welcome contributions of code not already >> mentioned as >> being planned on the GSOC pages. >> >> However, if your existing code implements something that is on the >> to-do >> list on the GSOC page, then the best thing would be to hang on till >> the >> end of the GSOC project then contribute any items that did not get >> implemented. >> >> cheers, >> Richard >> >> On Wed, August 1, 2007 6:19 pm, Thasso Griebel wrote: >>> hi, >>> >>> i recently explored the phylogeny code base in biojava. I am >>> currently working on a phylogeny framework similar to mesquite >>> (http://www.bio.informatik.uni-jena.de/epos) and i would like to add >>> some functionality using biojava (the sequence stuff and the nexus >>> parser). >>> >>> I saw the PhyloSOC07 page ( http://biojava.org/wiki/ >>> BioJava:PhyloSOC07 ) and i might be able to help out with some of the >>> methods, so is there a way to contribute ? Or is this closed to >>> participants of the google summer of code ? >>> >>> I have code for n-consensus and adams consensus methods and some >>> possible extensions for UPGMA (provide other distance computations, >>> i.e wpgma, sigle linkage and complete linkage) and NJ ( outgroup and >>> rooting support ). As our research groups has a focus on supertree >>> construction, we have java implementations for several graph based >>> supertree methods (aho's build, mincut, modified mincut, ranked tree, >>> ancestral build). >>> >>> >>> Regards, >>> >>> Thasso >>> >>> -- >>> Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer >>> Bioinformatik >>> Office 3426--http://bio.informatik.uni-jena.de--Institut fuer >>> Informatik >>> Phone +49 (0)3641 9-46454-----------Friedrich-Schiller- >>> Universitaet Jena >>> Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, >>> Germany >>> >>> >>> >>> _______________________________________________ >>> biojava-dev mailing list >>> biojava-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >>> >> >> -- >> Richard Holland >> BioMart (http://www.biomart.org/) >> EMBL-EBI >> Hinxton, Cambridgeshire CB10 1SD, UK > > -- > Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer Bioinformatik > Office 3426--http://bio.informatik.uni-jena.de--Institut fuer Informatik > Phone +49 (0)3641 9-46454-----------Friedrich-Schiller-Universitaet Jena > Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, Germany > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGuCO04C5LeMEKA/QRAritAJ0eFpRIQ7YP/NROSfoToo/+4aTfEwCfbFUU Hbne6alMOuzmr8CxX/hqsfs= =U4gJ -----END PGP SIGNATURE----- ------------------------------ Message: 5 Date: Tue, 7 Aug 2007 10:29:08 +0200 From: Thasso Griebel Subject: Re: [Biojava-dev] phylo code To: Richard Holland Cc: biojava-dev at biojava.org Message-ID: Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Hi, On the fire/event thing. You are right, it is not a good idea to change this if the code is already released. But maybe a little helper class with some static methods ( like IOTools ) would help. Something like PhylipIO.readTree(File) or PhylipIO.readAlignment (File) might do the job, the interfaces do not have to change and when it avoids direct contact with the parser implementation as long as standard phylip dataypes are concerned. And, as far as I see, this would follow the main path IO is done in BioJava. I can ( and will ) definitely work on the short-name map, but this has to wait at least 5 week as I am going on vacation ( yeah, 5 weeks without a computer nearby !!!). But currently I am really interested in a good phylip parser, so I will work on that. One thing about JGraphT. I used and use that a lot when doing phylogenetics, and its a great library. But you might consider adding a little interface structure on top at some point to decouple the the usage from the library. This would allow BioJava compatible tree implementations without the need of JGraphT. JGraphT is great for all the simple, and even the complex jobs, but for me there is one little drawback. You can fill in every Object as a graph vertex, which is great, but this makes the underlying implementation rather complex. I do not remember exactly, but I think they use a large set of HashMap structures and some complex mapping mechanism to build up a graph. There are situations where this makes it hard to extend. For example, for one of our supertree algorithm implementations we needed a MultiGraph, a graph with different edge types, and it was a real pain to add that to the library without reimplementing JGraphT's Graph interface completely. I think a Tree interface structure on top would be simple and easy and might be really helpful at some point. regards, thasso On 07.08.2007, at 09:48, Richard Holland wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Thanks for your feedback Thasso. > > The fire/events thing is certainly a misnomer - guilty as charged (I > wrote the code...) - but I suppose I wasn't expecting the naming to > matter much. I'll bear that in mind for future code. We can't really > change the existing interfaces now as they've been released and it is > not nice to users for us to change public interfaces that might > already > be in use. > > The PHYLIP format handler was written by Jim Balhoff. Jim - do you > have > any responses to Thasso's comments about the output options? > > I like the sound of your PHYLIP short-name map. You could > definitely go > ahead and contribute an update which implemented that. (Don't > forget to > make your code clear the map between one file and the next!) > > The tree model never materialised in the end. We chose instead to use > the external JGraphT package to represent our trees. The exact way in > which this is done will be documented by Boh-Yun as part of the GSOC > project. > > cheers, > Richard > > > Thasso Griebel wrote: >> Hi, >> >> thanks for the fast answer. >> >> So, I would really like to contribute to the BioJava Phylogeny >> Package, but I will wait until the GSOC project is finished and I am >> back from my vacation ;) For now, I just took a look on the io >> package, especially the three classes concerning phylip io. >> Some personal feeling about the naming. >> I wouldn't mention "fire" and "events" in the documentation and >> rename PHYLIPFileListener to something else, i.e. PHYLIPFileHandler. >> For me, this was irritating. I started looking for a fireXXX method >> immediately and automatically started thinking about the >> EventDispatchingThread and synchronization. As far as I see, this is >> a direct handler delegate, the parser delegates some method calls to >> a given handler callback method, no events are fired (there is not >> even an Event class that could be fired) and no event dispatching is >> involved. >> Also, the io seem to focus on the output of alignment. What about >> trees and distance/character matrices ? >> And a really important point is the name handling. The method >> >> private static String formatSequenceLabel(String label) >> >> in PHYLIPFileFormat simply cuts names that are longer than 10 >> characters. I know that phylip has this stupid limitation. But >> cutting will not work in a lot of cases. If just two sequence names >> are identical over the first ten characters, the resulting phylip >> file is corrupted and can not be used by most of the phylip >> executables. Maybe the handler can do a renaming and keep track of >> the map. Then one can use the parser to write some phylip file, start >> a phylip method on that file, read in the results and do an automatic >> remapping of the names ? >> >> I also wanted to take a look on the tree model. Is this already in >> the CVS ? I found biojava-live/src/org/biojavax/bio/phylo/tree, but >> it was empty ? >> >> regards, >> >> thasso >> >> >> >> On 01.08.2007, at 20:03, Richard Holland wrote: >> >>> Hi Thasso. >>> >>> Thanks for your interest! We always welcome all contributions of >>> code and >>> documentation to the BioJava project. >>> >>> Our GSOC project is well under way and has a plan as you have >>> already >>> noticed. The items on that plan are what was agreed with our >>> student, Boh >>> Yun Lee, and will be implemented by the time that GSOC is over >>> (early >>> September) - or at least, most of them will, and any that aren't >>> will be >>> flagged as such. >>> >>> If you have suggestions to make about code already committed, we >>> would >>> welcome them. Such feedback is a necessary part of the development >>> cycle. >>> Likewise we would welcome contributions of code not already >>> mentioned as >>> being planned on the GSOC pages. >>> >>> However, if your existing code implements something that is on the >>> to-do >>> list on the GSOC page, then the best thing would be to hang on till >>> the >>> end of the GSOC project then contribute any items that did not get >>> implemented. >>> >>> cheers, >>> Richard >>> >>> On Wed, August 1, 2007 6:19 pm, Thasso Griebel wrote: >>>> hi, >>>> >>>> i recently explored the phylogeny code base in biojava. I am >>>> currently working on a phylogeny framework similar to mesquite >>>> (http://www.bio.informatik.uni-jena.de/epos) and i would like to >>>> add >>>> some functionality using biojava (the sequence stuff and the nexus >>>> parser). >>>> >>>> I saw the PhyloSOC07 page ( http://biojava.org/wiki/ >>>> BioJava:PhyloSOC07 ) and i might be able to help out with some >>>> of the >>>> methods, so is there a way to contribute ? Or is this closed to >>>> participants of the google summer of code ? >>>> >>>> I have code for n-consensus and adams consensus methods and some >>>> possible extensions for UPGMA (provide other distance computations, >>>> i.e wpgma, sigle linkage and complete linkage) and NJ ( outgroup >>>> and >>>> rooting support ). As our research groups has a focus on supertree >>>> construction, we have java implementations for several graph based >>>> supertree methods (aho's build, mincut, modified mincut, ranked >>>> tree, >>>> ancestral build). >>>> >>>> >>>> Regards, >>>> >>>> Thasso >>>> >>>> -- >>>> Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer >>>> Bioinformatik >>>> Office 3426--http://bio.informatik.uni-jena.de--Institut fuer >>>> Informatik >>>> Phone +49 (0)3641 9-46454-----------Friedrich-Schiller- >>>> Universitaet Jena >>>> Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, >>>> Germany >>>> >>>> >>>> >>>> _______________________________________________ >>>> biojava-dev mailing list >>>> biojava-dev at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >>>> >>> >>> -- >>> Richard Holland >>> BioMart (http://www.biomart.org/) >>> EMBL-EBI >>> Hinxton, Cambridgeshire CB10 1SD, UK >> >> -- >> Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer >> Bioinformatik >> Office 3426--http://bio.informatik.uni-jena.de--Institut fuer >> Informatik >> Phone +49 (0)3641 9-46454-----------Friedrich-Schiller- >> Universitaet Jena >> Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, >> Germany >> >> >> >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.2.2 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iD8DBQFGuCO04C5LeMEKA/QRAritAJ0eFpRIQ7YP/NROSfoToo/+4aTfEwCfbFUU > Hbne6alMOuzmr8CxX/hqsfs= > =U4gJ > -----END PGP SIGNATURE----- -- Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer Bioinformatik Office 3426--http://bio.informatik.uni-jena.de--Institut fuer Informatik Phone +49 (0)3641 9-46454-----------Friedrich-Schiller-Universitaet Jena Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, Germany ------------------------------ _______________________________________________ biojava-dev mailing list biojava-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-dev End of biojava-dev Digest, Vol 54, Issue 1 ****************************************** From simpleyrx at 163.com Tue Aug 7 21:38:03 2007 From: simpleyrx at 163.com (simpleyrx) Date: Wed, 8 Aug 2007 09:38:03 +0800 (CST) Subject: [Biojava-dev] could I join in developing biojava ? Message-ID: <1941424432.747191186537083813.JavaMail.coremail@bj163app105.163.com> Dear sir, Thank you for your message for biojava. I am very interested in it. I am a graduate student of China Agriculture University and my major is bioinformatics and I love java programming. I would like to know that if I can join in developing biojava ? student simple From holland at ebi.ac.uk Wed Aug 8 03:40:38 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Wed, 08 Aug 2007 08:40:38 +0100 Subject: [Biojava-dev] could I join in developing biojava ? In-Reply-To: <1941424432.747191186537083813.JavaMail.coremail@bj163app105.163.com> References: <1941424432.747191186537083813.JavaMail.coremail@bj163app105.163.com> Message-ID: <46B97376.5040902@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi there. We welcome all contributions. You can read about existing capabilities on the BioJava website, then if you identify any areas which need improving you can contact this mailing list with your ideas and/or code. Someone will then check that the idea and/or code works, and make the appropriate changes. I look forward to seeing your suggestions on this list! The website is: http://www.biojava.org/ cheers, Richard simpleyrx wrote: > Dear sir, > > Thank you for your message for biojava. I am very interested in it. > I am a graduate student of China Agriculture University and my major is bioinformatics and I love java programming. I would like to know that if I can join in developing biojava ? > > > > student simple > > > ------------------------------------------------------------------------ > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGuXN14C5LeMEKA/QRAuUBAJ9UTaq0nmn4RU37juqQEduyP0pZawCfQb2I OpQScyV3G3Y0NHRY/NZm75U= =Xv6y -----END PGP SIGNATURE----- From Robin.Emig at pioneer.com Fri Aug 10 18:43:38 2007 From: Robin.Emig at pioneer.com (Emig, Robin) Date: Fri, 10 Aug 2007 15:43:38 -0700 Subject: [Biojava-dev] RichSequence output without namespace In-Reply-To: <4694896A.9050707@ebi.ac.uk> References: <4694896A.9050707@ebi.ac.uk> Message-ID: Is there anyway to use RichSequence.IOTools.writeFasta to output just the sequence name as the name and nothing else? Ie >SeqName Aatg Vs >Namespace|Seqname|SeqName Or >|Seqname|Seqname Thanks -Robin This communication is for use by the intended recipient and contains information that may be Privileged, confidential or copyrighted under applicable law. If you are not the intended recipient, you are hereby formally notified that any use, copying or distribution of this e-mail, in whole or in part, is strictly prohibited. Please notify the sender by return e-mail and delete this e-mail from your system. Unless explicitly and conspicuously designated as "E-Contract Intended", this e-mail does not constitute a contract offer, a contract amendment, or an acceptance of a contract offer. This e-mail does not constitute a consent to the use of sender's contact information for direct marketing purposes or for transfers of data to third parties. Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean http://www.DuPont.com/corp/email_disclaimer.html From markjschreiber at gmail.com Fri Aug 10 23:51:18 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Sat, 11 Aug 2007 11:51:18 +0800 Subject: [Biojava-dev] RichSequence output without namespace In-Reply-To: References: <4694896A.9050707@ebi.ac.uk> Message-ID: <93b45ca50708102051r24bbe45ct57284447cdedd2b1@mail.gmail.com> Hi Robin - RichSequenceIOTools.writeFasta uses the FastaFormat object to construct the sequence name. It might be worth extending FastaFormat to add methods that let you modify what is output in the name line. If you do it would probably be worth checking in to the CVS. You could then look at providing an overloaded writeFasta method that allows you to configure the output. - Mark On 8/11/07, Emig, Robin wrote: > Is there anyway to use RichSequence.IOTools.writeFasta to output just > the sequence name as the name and nothing else? > Ie > >SeqName > Aatg > > Vs > > >Namespace|Seqname|SeqName > Or > >|Seqname|Seqname > > > Thanks > -Robin > > This communication is for use by the intended recipient and contains > information that may be Privileged, confidential or copyrighted under > applicable law. If you are not the intended recipient, you are hereby > formally notified that any use, copying or distribution of this e-mail, > in whole or in part, is strictly prohibited. Please notify the sender by > return e-mail and delete this e-mail from your system. Unless explicitly > and conspicuously designated as "E-Contract Intended", this e-mail does > not constitute a contract offer, a contract amendment, or an acceptance > of a contract offer. This e-mail does not constitute a consent to the > use of sender's contact information for direct marketing purposes or for > transfers of data to third parties. > > Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean > > http://www.DuPont.com/corp/email_disclaimer.html > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From yp_riverol at yahoo.com Wed Aug 22 21:23:16 2007 From: yp_riverol at yahoo.com (yasset perez riverol) Date: Wed, 22 Aug 2007 20:23:16 -0500 (CDT) Subject: [Biojava-dev] Problem With Isoelectric point Message-ID: <799294.30713.qm@web37909.mail.mud.yahoo.com> Hi, I have a problem when I execute the Isoelectrc Point calculation for this peptides: ALLIDLPV FDIYAGTPV SVLLMSAEI PTGDTTGYLANPEEV I all the case I receive this error : Error, the peptide probably contains only positive or negative charges. Well I try to calculate the isoelectric Point for all the peptides with de Expasy Calculator and I obtained: ALLIDLPV: Theoretical pI: 3.80 Molecular weight (average): 853.07 FDIYAGTPV: Theoretical pI: 3.80 Molecular weight (average): 982.10 SVLLMSAEI: Theoretical pI: 4.00 Molecular weight (average): 962.17 PTGDTTGYLANPEEV: Theoretical pI: 3.57 Molecular weight (average): 1563.64 My code is this: OBioSeq = ProteinTools.createProtein(Sequence); IsoelectricPointCalc OBioIsoc = new IsoelectricPointCalc(); double dIsoelec = 0.0; dIsoelec = OBioIsoc.getPI(OBioSeq,true,true); Thanks in advance Centen of Molecular Biology. Havana University Cuba. __________________________________________________ Correo Yahoo! Espacio para todos tus mensajes, antivirus y antispam ?gratis! Reg?strate ya - http://correo.espanol.yahoo.com/ From yp_riverol at yahoo.com Mon Aug 27 09:45:16 2007 From: yp_riverol at yahoo.com (yasset perez riverol) Date: Mon, 27 Aug 2007 08:45:16 -0500 (CDT) Subject: [Biojava-dev] Retention Time Calculations In-Reply-To: <50890.74.232.148.95.1188111871.squirrel@webmail.cc.gatech.edu> Message-ID: <644850.61203.qm@web37909.mail.mud.yahoo.com> Hi all, I will try to compute the retention time for a peptide, but in biojava do not exist this kind of function, but in other bio-packages as InsilicoSpectro (Perl), these functions are implemented. Any help with this topic? Thank in advance Yasset. __________________________________________________ Correo Yahoo! Espacio para todos tus mensajes, antivirus y antispam ?gratis! Reg?strate ya - http://correo.espanol.yahoo.com/ From ap3 at sanger.ac.uk Tue Aug 28 11:42:55 2007 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Tue, 28 Aug 2007 16:42:55 +0100 Subject: [Biojava-dev] cruisecontrol Message-ID: Hi biojava - devs, would you be interested in getting CruiseControl running for BioJava? It would allow us to * provide nightly builds of biojava, * run unit test in regular intervals, * get a notification email sent to biojava-dev if the CVS does not build http://cruisecontrol.sourceforge.net/ If there is interest for this I will set it up, Andreas ----------------------------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK +44 (0) 1223 49 6891 ----------------------------------------------------------------------- -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From markjschreiber at gmail.com Tue Aug 28 20:16:06 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Wed, 29 Aug 2007 08:16:06 +0800 Subject: [Biojava-dev] cruisecontrol In-Reply-To: References: Message-ID: <93b45ca50708281716x3c2cadc9me9cb0b00b52647a2@mail.gmail.com> Sounds good. Thomas had a script running off his home machine a while ago for nightly builds which I have missed since he stopped running it. Notifications of failed tests would be good too. - Mark On 8/28/07, Andreas Prlic wrote: > Hi biojava - devs, > > would you be interested in getting CruiseControl running for BioJava? > > It would allow us to > > * provide nightly builds of biojava, > * run unit test in regular intervals, > * get a notification email sent to biojava-dev if the CVS does not build > > http://cruisecontrol.sourceforge.net/ > > If there is interest for this I will set it up, > > Andreas > > ----------------------------------------------------------------------- > > Andreas Prlic Wellcome Trust Sanger Institute > Hinxton, Cambridge CB10 1SA, UK > +44 (0) 1223 49 6891 > > ----------------------------------------------------------------------- > > > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a > company registered in England with number 2742969, whose registered > office is 215 Euston Road, London, NW1 2BE. > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From thasso at minet.uni-jena.de Wed Aug 1 17:19:01 2007 From: thasso at minet.uni-jena.de (Thasso Griebel) Date: Wed, 1 Aug 2007 19:19:01 +0200 Subject: [Biojava-dev] phylo code Message-ID: <1EA22A3D-107C-455B-98A6-EFD4FEF77CCE@minet.uni-jena.de> hi, i recently explored the phylogeny code base in biojava. I am currently working on a phylogeny framework similar to mesquite (http://www.bio.informatik.uni-jena.de/epos) and i would like to add some functionality using biojava (the sequence stuff and the nexus parser). I saw the PhyloSOC07 page ( http://biojava.org/wiki/ BioJava:PhyloSOC07 ) and i might be able to help out with some of the methods, so is there a way to contribute ? Or is this closed to participants of the google summer of code ? I have code for n-consensus and adams consensus methods and some possible extensions for UPGMA (provide other distance computations, i.e wpgma, sigle linkage and complete linkage) and NJ ( outgroup and rooting support ). As our research groups has a focus on supertree construction, we have java implementations for several graph based supertree methods (aho's build, mincut, modified mincut, ranked tree, ancestral build). Regards, Thasso -- Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer Bioinformatik Office 3426--http://bio.informatik.uni-jena.de--Institut fuer Informatik Phone +49 (0)3641 9-46454-----------Friedrich-Schiller-Universitaet Jena Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, Germany From holland at ebi.ac.uk Wed Aug 1 18:03:29 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Wed, 1 Aug 2007 19:03:29 +0100 (BST) Subject: [Biojava-dev] phylo code In-Reply-To: <1EA22A3D-107C-455B-98A6-EFD4FEF77CCE@minet.uni-jena.de> References: <1EA22A3D-107C-455B-98A6-EFD4FEF77CCE@minet.uni-jena.de> Message-ID: <48008.80.42.98.32.1185991409.squirrel@webmail.ebi.ac.uk> Hi Thasso. Thanks for your interest! We always welcome all contributions of code and documentation to the BioJava project. Our GSOC project is well under way and has a plan as you have already noticed. The items on that plan are what was agreed with our student, Boh Yun Lee, and will be implemented by the time that GSOC is over (early September) - or at least, most of them will, and any that aren't will be flagged as such. If you have suggestions to make about code already committed, we would welcome them. Such feedback is a necessary part of the development cycle. Likewise we would welcome contributions of code not already mentioned as being planned on the GSOC pages. However, if your existing code implements something that is on the to-do list on the GSOC page, then the best thing would be to hang on till the end of the GSOC project then contribute any items that did not get implemented. cheers, Richard On Wed, August 1, 2007 6:19 pm, Thasso Griebel wrote: > hi, > > i recently explored the phylogeny code base in biojava. I am > currently working on a phylogeny framework similar to mesquite > (http://www.bio.informatik.uni-jena.de/epos) and i would like to add > some functionality using biojava (the sequence stuff and the nexus > parser). > > I saw the PhyloSOC07 page ( http://biojava.org/wiki/ > BioJava:PhyloSOC07 ) and i might be able to help out with some of the > methods, so is there a way to contribute ? Or is this closed to > participants of the google summer of code ? > > I have code for n-consensus and adams consensus methods and some > possible extensions for UPGMA (provide other distance computations, > i.e wpgma, sigle linkage and complete linkage) and NJ ( outgroup and > rooting support ). As our research groups has a focus on supertree > construction, we have java implementations for several graph based > supertree methods (aho's build, mincut, modified mincut, ranked tree, > ancestral build). > > > Regards, > > Thasso > > -- > Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer Bioinformatik > Office 3426--http://bio.informatik.uni-jena.de--Institut fuer Informatik > Phone +49 (0)3641 9-46454-----------Friedrich-Schiller-Universitaet Jena > Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, Germany > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > -- Richard Holland BioMart (http://www.biomart.org/) EMBL-EBI Hinxton, Cambridgeshire CB10 1SD, UK From thasso at minet.uni-jena.de Mon Aug 6 16:45:35 2007 From: thasso at minet.uni-jena.de (Thasso Griebel) Date: Mon, 6 Aug 2007 18:45:35 +0200 Subject: [Biojava-dev] phylo code In-Reply-To: <48008.80.42.98.32.1185991409.squirrel@webmail.ebi.ac.uk> References: <1EA22A3D-107C-455B-98A6-EFD4FEF77CCE@minet.uni-jena.de> <48008.80.42.98.32.1185991409.squirrel@webmail.ebi.ac.uk> Message-ID: <846222BD-73C8-4CE7-8CB1-E2249A25256D@minet.uni-jena.de> Hi, thanks for the fast answer. So, I would really like to contribute to the BioJava Phylogeny Package, but I will wait until the GSOC project is finished and I am back from my vacation ;) For now, I just took a look on the io package, especially the three classes concerning phylip io. Some personal feeling about the naming. I wouldn't mention "fire" and "events" in the documentation and rename PHYLIPFileListener to something else, i.e. PHYLIPFileHandler. For me, this was irritating. I started looking for a fireXXX method immediately and automatically started thinking about the EventDispatchingThread and synchronization. As far as I see, this is a direct handler delegate, the parser delegates some method calls to a given handler callback method, no events are fired (there is not even an Event class that could be fired) and no event dispatching is involved. Also, the io seem to focus on the output of alignment. What about trees and distance/character matrices ? And a really important point is the name handling. The method private static String formatSequenceLabel(String label) in PHYLIPFileFormat simply cuts names that are longer than 10 characters. I know that phylip has this stupid limitation. But cutting will not work in a lot of cases. If just two sequence names are identical over the first ten characters, the resulting phylip file is corrupted and can not be used by most of the phylip executables. Maybe the handler can do a renaming and keep track of the map. Then one can use the parser to write some phylip file, start a phylip method on that file, read in the results and do an automatic remapping of the names ? I also wanted to take a look on the tree model. Is this already in the CVS ? I found biojava-live/src/org/biojavax/bio/phylo/tree, but it was empty ? regards, thasso On 01.08.2007, at 20:03, Richard Holland wrote: > Hi Thasso. > > Thanks for your interest! We always welcome all contributions of > code and > documentation to the BioJava project. > > Our GSOC project is well under way and has a plan as you have already > noticed. The items on that plan are what was agreed with our > student, Boh > Yun Lee, and will be implemented by the time that GSOC is over (early > September) - or at least, most of them will, and any that aren't > will be > flagged as such. > > If you have suggestions to make about code already committed, we would > welcome them. Such feedback is a necessary part of the development > cycle. > Likewise we would welcome contributions of code not already > mentioned as > being planned on the GSOC pages. > > However, if your existing code implements something that is on the > to-do > list on the GSOC page, then the best thing would be to hang on till > the > end of the GSOC project then contribute any items that did not get > implemented. > > cheers, > Richard > > On Wed, August 1, 2007 6:19 pm, Thasso Griebel wrote: >> hi, >> >> i recently explored the phylogeny code base in biojava. I am >> currently working on a phylogeny framework similar to mesquite >> (http://www.bio.informatik.uni-jena.de/epos) and i would like to add >> some functionality using biojava (the sequence stuff and the nexus >> parser). >> >> I saw the PhyloSOC07 page ( http://biojava.org/wiki/ >> BioJava:PhyloSOC07 ) and i might be able to help out with some of the >> methods, so is there a way to contribute ? Or is this closed to >> participants of the google summer of code ? >> >> I have code for n-consensus and adams consensus methods and some >> possible extensions for UPGMA (provide other distance computations, >> i.e wpgma, sigle linkage and complete linkage) and NJ ( outgroup and >> rooting support ). As our research groups has a focus on supertree >> construction, we have java implementations for several graph based >> supertree methods (aho's build, mincut, modified mincut, ranked tree, >> ancestral build). >> >> >> Regards, >> >> Thasso >> >> -- >> Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer >> Bioinformatik >> Office 3426--http://bio.informatik.uni-jena.de--Institut fuer >> Informatik >> Phone +49 (0)3641 9-46454-----------Friedrich-Schiller- >> Universitaet Jena >> Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, >> Germany >> >> >> >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> > > > -- > Richard Holland > BioMart (http://www.biomart.org/) > EMBL-EBI > Hinxton, Cambridgeshire CB10 1SD, UK -- Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer Bioinformatik Office 3426--http://bio.informatik.uni-jena.de--Institut fuer Informatik Phone +49 (0)3641 9-46454-----------Friedrich-Schiller-Universitaet Jena Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, Germany From holland at ebi.ac.uk Tue Aug 7 07:48:05 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Tue, 07 Aug 2007 08:48:05 +0100 Subject: [Biojava-dev] phylo code In-Reply-To: <846222BD-73C8-4CE7-8CB1-E2249A25256D@minet.uni-jena.de> References: <1EA22A3D-107C-455B-98A6-EFD4FEF77CCE@minet.uni-jena.de> <48008.80.42.98.32.1185991409.squirrel@webmail.ebi.ac.uk> <846222BD-73C8-4CE7-8CB1-E2249A25256D@minet.uni-jena.de> Message-ID: <46B823B5.1010401@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Thanks for your feedback Thasso. The fire/events thing is certainly a misnomer - guilty as charged (I wrote the code...) - but I suppose I wasn't expecting the naming to matter much. I'll bear that in mind for future code. We can't really change the existing interfaces now as they've been released and it is not nice to users for us to change public interfaces that might already be in use. The PHYLIP format handler was written by Jim Balhoff. Jim - do you have any responses to Thasso's comments about the output options? I like the sound of your PHYLIP short-name map. You could definitely go ahead and contribute an update which implemented that. (Don't forget to make your code clear the map between one file and the next!) The tree model never materialised in the end. We chose instead to use the external JGraphT package to represent our trees. The exact way in which this is done will be documented by Boh-Yun as part of the GSOC project. cheers, Richard Thasso Griebel wrote: > Hi, > > thanks for the fast answer. > > So, I would really like to contribute to the BioJava Phylogeny > Package, but I will wait until the GSOC project is finished and I am > back from my vacation ;) For now, I just took a look on the io > package, especially the three classes concerning phylip io. > Some personal feeling about the naming. > I wouldn't mention "fire" and "events" in the documentation and > rename PHYLIPFileListener to something else, i.e. PHYLIPFileHandler. > For me, this was irritating. I started looking for a fireXXX method > immediately and automatically started thinking about the > EventDispatchingThread and synchronization. As far as I see, this is > a direct handler delegate, the parser delegates some method calls to > a given handler callback method, no events are fired (there is not > even an Event class that could be fired) and no event dispatching is > involved. > Also, the io seem to focus on the output of alignment. What about > trees and distance/character matrices ? > And a really important point is the name handling. The method > > private static String formatSequenceLabel(String label) > > in PHYLIPFileFormat simply cuts names that are longer than 10 > characters. I know that phylip has this stupid limitation. But > cutting will not work in a lot of cases. If just two sequence names > are identical over the first ten characters, the resulting phylip > file is corrupted and can not be used by most of the phylip > executables. Maybe the handler can do a renaming and keep track of > the map. Then one can use the parser to write some phylip file, start > a phylip method on that file, read in the results and do an automatic > remapping of the names ? > > I also wanted to take a look on the tree model. Is this already in > the CVS ? I found biojava-live/src/org/biojavax/bio/phylo/tree, but > it was empty ? > > regards, > > thasso > > > > On 01.08.2007, at 20:03, Richard Holland wrote: > >> Hi Thasso. >> >> Thanks for your interest! We always welcome all contributions of >> code and >> documentation to the BioJava project. >> >> Our GSOC project is well under way and has a plan as you have already >> noticed. The items on that plan are what was agreed with our >> student, Boh >> Yun Lee, and will be implemented by the time that GSOC is over (early >> September) - or at least, most of them will, and any that aren't >> will be >> flagged as such. >> >> If you have suggestions to make about code already committed, we would >> welcome them. Such feedback is a necessary part of the development >> cycle. >> Likewise we would welcome contributions of code not already >> mentioned as >> being planned on the GSOC pages. >> >> However, if your existing code implements something that is on the >> to-do >> list on the GSOC page, then the best thing would be to hang on till >> the >> end of the GSOC project then contribute any items that did not get >> implemented. >> >> cheers, >> Richard >> >> On Wed, August 1, 2007 6:19 pm, Thasso Griebel wrote: >>> hi, >>> >>> i recently explored the phylogeny code base in biojava. I am >>> currently working on a phylogeny framework similar to mesquite >>> (http://www.bio.informatik.uni-jena.de/epos) and i would like to add >>> some functionality using biojava (the sequence stuff and the nexus >>> parser). >>> >>> I saw the PhyloSOC07 page ( http://biojava.org/wiki/ >>> BioJava:PhyloSOC07 ) and i might be able to help out with some of the >>> methods, so is there a way to contribute ? Or is this closed to >>> participants of the google summer of code ? >>> >>> I have code for n-consensus and adams consensus methods and some >>> possible extensions for UPGMA (provide other distance computations, >>> i.e wpgma, sigle linkage and complete linkage) and NJ ( outgroup and >>> rooting support ). As our research groups has a focus on supertree >>> construction, we have java implementations for several graph based >>> supertree methods (aho's build, mincut, modified mincut, ranked tree, >>> ancestral build). >>> >>> >>> Regards, >>> >>> Thasso >>> >>> -- >>> Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer >>> Bioinformatik >>> Office 3426--http://bio.informatik.uni-jena.de--Institut fuer >>> Informatik >>> Phone +49 (0)3641 9-46454-----------Friedrich-Schiller- >>> Universitaet Jena >>> Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, >>> Germany >>> >>> >>> >>> _______________________________________________ >>> biojava-dev mailing list >>> biojava-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >>> >> >> -- >> Richard Holland >> BioMart (http://www.biomart.org/) >> EMBL-EBI >> Hinxton, Cambridgeshire CB10 1SD, UK > > -- > Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer Bioinformatik > Office 3426--http://bio.informatik.uni-jena.de--Institut fuer Informatik > Phone +49 (0)3641 9-46454-----------Friedrich-Schiller-Universitaet Jena > Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, Germany > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGuCO04C5LeMEKA/QRAritAJ0eFpRIQ7YP/NROSfoToo/+4aTfEwCfbFUU Hbne6alMOuzmr8CxX/hqsfs= =U4gJ -----END PGP SIGNATURE----- From thasso at minet.uni-jena.de Tue Aug 7 08:29:08 2007 From: thasso at minet.uni-jena.de (Thasso Griebel) Date: Tue, 7 Aug 2007 10:29:08 +0200 Subject: [Biojava-dev] phylo code In-Reply-To: <46B823B5.1010401@ebi.ac.uk> References: <1EA22A3D-107C-455B-98A6-EFD4FEF77CCE@minet.uni-jena.de> <48008.80.42.98.32.1185991409.squirrel@webmail.ebi.ac.uk> <846222BD-73C8-4CE7-8CB1-E2249A25256D@minet.uni-jena.de> <46B823B5.1010401@ebi.ac.uk> Message-ID: Hi, On the fire/event thing. You are right, it is not a good idea to change this if the code is already released. But maybe a little helper class with some static methods ( like IOTools ) would help. Something like PhylipIO.readTree(File) or PhylipIO.readAlignment (File) might do the job, the interfaces do not have to change and when it avoids direct contact with the parser implementation as long as standard phylip dataypes are concerned. And, as far as I see, this would follow the main path IO is done in BioJava. I can ( and will ) definitely work on the short-name map, but this has to wait at least 5 week as I am going on vacation ( yeah, 5 weeks without a computer nearby !!!). But currently I am really interested in a good phylip parser, so I will work on that. One thing about JGraphT. I used and use that a lot when doing phylogenetics, and its a great library. But you might consider adding a little interface structure on top at some point to decouple the the usage from the library. This would allow BioJava compatible tree implementations without the need of JGraphT. JGraphT is great for all the simple, and even the complex jobs, but for me there is one little drawback. You can fill in every Object as a graph vertex, which is great, but this makes the underlying implementation rather complex. I do not remember exactly, but I think they use a large set of HashMap structures and some complex mapping mechanism to build up a graph. There are situations where this makes it hard to extend. For example, for one of our supertree algorithm implementations we needed a MultiGraph, a graph with different edge types, and it was a real pain to add that to the library without reimplementing JGraphT's Graph interface completely. I think a Tree interface structure on top would be simple and easy and might be really helpful at some point. regards, thasso On 07.08.2007, at 09:48, Richard Holland wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Thanks for your feedback Thasso. > > The fire/events thing is certainly a misnomer - guilty as charged (I > wrote the code...) - but I suppose I wasn't expecting the naming to > matter much. I'll bear that in mind for future code. We can't really > change the existing interfaces now as they've been released and it is > not nice to users for us to change public interfaces that might > already > be in use. > > The PHYLIP format handler was written by Jim Balhoff. Jim - do you > have > any responses to Thasso's comments about the output options? > > I like the sound of your PHYLIP short-name map. You could > definitely go > ahead and contribute an update which implemented that. (Don't > forget to > make your code clear the map between one file and the next!) > > The tree model never materialised in the end. We chose instead to use > the external JGraphT package to represent our trees. The exact way in > which this is done will be documented by Boh-Yun as part of the GSOC > project. > > cheers, > Richard > > > Thasso Griebel wrote: >> Hi, >> >> thanks for the fast answer. >> >> So, I would really like to contribute to the BioJava Phylogeny >> Package, but I will wait until the GSOC project is finished and I am >> back from my vacation ;) For now, I just took a look on the io >> package, especially the three classes concerning phylip io. >> Some personal feeling about the naming. >> I wouldn't mention "fire" and "events" in the documentation and >> rename PHYLIPFileListener to something else, i.e. PHYLIPFileHandler. >> For me, this was irritating. I started looking for a fireXXX method >> immediately and automatically started thinking about the >> EventDispatchingThread and synchronization. As far as I see, this is >> a direct handler delegate, the parser delegates some method calls to >> a given handler callback method, no events are fired (there is not >> even an Event class that could be fired) and no event dispatching is >> involved. >> Also, the io seem to focus on the output of alignment. What about >> trees and distance/character matrices ? >> And a really important point is the name handling. The method >> >> private static String formatSequenceLabel(String label) >> >> in PHYLIPFileFormat simply cuts names that are longer than 10 >> characters. I know that phylip has this stupid limitation. But >> cutting will not work in a lot of cases. If just two sequence names >> are identical over the first ten characters, the resulting phylip >> file is corrupted and can not be used by most of the phylip >> executables. Maybe the handler can do a renaming and keep track of >> the map. Then one can use the parser to write some phylip file, start >> a phylip method on that file, read in the results and do an automatic >> remapping of the names ? >> >> I also wanted to take a look on the tree model. Is this already in >> the CVS ? I found biojava-live/src/org/biojavax/bio/phylo/tree, but >> it was empty ? >> >> regards, >> >> thasso >> >> >> >> On 01.08.2007, at 20:03, Richard Holland wrote: >> >>> Hi Thasso. >>> >>> Thanks for your interest! We always welcome all contributions of >>> code and >>> documentation to the BioJava project. >>> >>> Our GSOC project is well under way and has a plan as you have >>> already >>> noticed. The items on that plan are what was agreed with our >>> student, Boh >>> Yun Lee, and will be implemented by the time that GSOC is over >>> (early >>> September) - or at least, most of them will, and any that aren't >>> will be >>> flagged as such. >>> >>> If you have suggestions to make about code already committed, we >>> would >>> welcome them. Such feedback is a necessary part of the development >>> cycle. >>> Likewise we would welcome contributions of code not already >>> mentioned as >>> being planned on the GSOC pages. >>> >>> However, if your existing code implements something that is on the >>> to-do >>> list on the GSOC page, then the best thing would be to hang on till >>> the >>> end of the GSOC project then contribute any items that did not get >>> implemented. >>> >>> cheers, >>> Richard >>> >>> On Wed, August 1, 2007 6:19 pm, Thasso Griebel wrote: >>>> hi, >>>> >>>> i recently explored the phylogeny code base in biojava. I am >>>> currently working on a phylogeny framework similar to mesquite >>>> (http://www.bio.informatik.uni-jena.de/epos) and i would like to >>>> add >>>> some functionality using biojava (the sequence stuff and the nexus >>>> parser). >>>> >>>> I saw the PhyloSOC07 page ( http://biojava.org/wiki/ >>>> BioJava:PhyloSOC07 ) and i might be able to help out with some >>>> of the >>>> methods, so is there a way to contribute ? Or is this closed to >>>> participants of the google summer of code ? >>>> >>>> I have code for n-consensus and adams consensus methods and some >>>> possible extensions for UPGMA (provide other distance computations, >>>> i.e wpgma, sigle linkage and complete linkage) and NJ ( outgroup >>>> and >>>> rooting support ). As our research groups has a focus on supertree >>>> construction, we have java implementations for several graph based >>>> supertree methods (aho's build, mincut, modified mincut, ranked >>>> tree, >>>> ancestral build). >>>> >>>> >>>> Regards, >>>> >>>> Thasso >>>> >>>> -- >>>> Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer >>>> Bioinformatik >>>> Office 3426--http://bio.informatik.uni-jena.de--Institut fuer >>>> Informatik >>>> Phone +49 (0)3641 9-46454-----------Friedrich-Schiller- >>>> Universitaet Jena >>>> Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, >>>> Germany >>>> >>>> >>>> >>>> _______________________________________________ >>>> biojava-dev mailing list >>>> biojava-dev at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >>>> >>> >>> -- >>> Richard Holland >>> BioMart (http://www.biomart.org/) >>> EMBL-EBI >>> Hinxton, Cambridgeshire CB10 1SD, UK >> >> -- >> Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer >> Bioinformatik >> Office 3426--http://bio.informatik.uni-jena.de--Institut fuer >> Informatik >> Phone +49 (0)3641 9-46454-----------Friedrich-Schiller- >> Universitaet Jena >> Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, >> Germany >> >> >> >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.2.2 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iD8DBQFGuCO04C5LeMEKA/QRAritAJ0eFpRIQ7YP/NROSfoToo/+4aTfEwCfbFUU > Hbne6alMOuzmr8CxX/hqsfs= > =U4gJ > -----END PGP SIGNATURE----- -- Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer Bioinformatik Office 3426--http://bio.informatik.uni-jena.de--Institut fuer Informatik Phone +49 (0)3641 9-46454-----------Friedrich-Schiller-Universitaet Jena Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, Germany From james.balhoff at duke.edu Tue Aug 7 14:34:44 2007 From: james.balhoff at duke.edu (Jim Balhoff) Date: Tue, 7 Aug 2007 10:34:44 -0400 Subject: [Biojava-dev] phylo code In-Reply-To: <46B823B5.1010401@ebi.ac.uk> References: <1EA22A3D-107C-455B-98A6-EFD4FEF77CCE@minet.uni-jena.de> <48008.80.42.98.32.1185991409.squirrel@webmail.ebi.ac.uk> <846222BD-73C8-4CE7-8CB1-E2249A25256D@minet.uni-jena.de> <46B823B5.1010401@ebi.ac.uk> Message-ID: Hi Richard and Thasso, On Aug 7, 2007, at 3:48 AM, Richard Holland wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Thanks for your feedback Thasso. > > The fire/events thing is certainly a misnomer - guilty as charged (I > wrote the code...) - but I suppose I wasn't expecting the naming to > matter much. I'll bear that in mind for future code. We can't really > change the existing interfaces now as they've been released and it is > not nice to users for us to change public interfaces that might > already > be in use. > > The PHYLIP format handler was written by Jim Balhoff. Jim - do you > have > any responses to Thasso's comments about the output options? I think it would be great to have import and export classes for PHYLIP trees and distance matrices. The current code handles only alignments. The other data would be in separate files, and so not part of this parser. > I like the sound of your PHYLIP short-name map. You could > definitely go > ahead and contribute an update which implemented that. (Don't > forget to > make your code clear the map between one file and the next!) Yes, I think the the map is a great idea. The first edition of the PHYLIP parser was simple and strictly stuck to the format specification. The map would be a great way to transparently use longer names when running PHYLIP behind the scenes. If the user is actually exporting a PHYLIP formatted alignment to disk, it might be nice to have a few options for what should happen - the current truncation method could be one option, another might be to simply put in the long name and put a space before the sequence starts (not strictly PHYLIP, but it is a simple alignment format recognized by some programs), another might be to raise an exception or otherwise alert if sequence names are too long. Another enhancement to the PHYLIP classes would be to let the developer specify interleaved or sequential alignment format for import and export (and for both the length of the lines for export). Right now I think there are some possible files which will not be parsed correctly - probably a sequential style file with newlines within the sequences (if a "sequential" alignment has no newlines, it is equivalent to "interleaved"). Or instead of specifying interleaved or sequential, figure out how to detect them reliably. Here are the examples: Best regards, Jim ____________________________________________ James P. Balhoff, Ph.D. National Evolutionary Synthesis Center 2024 West Main St., Suite A200 Durham, NC 27705 USA From simpleyrx at 163.com Wed Aug 8 01:24:37 2007 From: simpleyrx at 163.com (simpleyrx) Date: Wed, 8 Aug 2007 09:24:37 +0800 (CST) Subject: [Biojava-dev] Reply:biojava-dev Digest, Vol 54, Issue 1 In-Reply-To: References: Message-ID: <620113805.735311186536277307.JavaMail.coremail@bj163app105.163.com> Dear sir, Thank you for your message for biojava. I am very interested in it. I am a graduate student of China Agriculture University and my major is bioinformatics. I would like to know that if I can join in developing biojava ? student simple ?2007-08-07?biojava-dev-request at lists.open-bio.org ??? Send biojava-dev mailing list submissions to biojava-dev at lists.open-bio.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.open-bio.org/mailman/listinfo/biojava-dev or, via email, send a message with subject or body 'help' to biojava-dev-request at lists.open-bio.org You can reach the person managing the list at biojava-dev-owner at lists.open-bio.org When replying, please edit your Subject line so it is more specific than "Re: Contents of biojava-dev digest..." Today's Topics: 1. phylo code (Thasso Griebel) 2. Re: phylo code (Richard Holland) 3. Re: phylo code (Thasso Griebel) 4. Re: phylo code (Richard Holland) 5. Re: phylo code (Thasso Griebel) ---------------------------------------------------------------------- Message: 1 Date: Wed, 1 Aug 2007 19:19:01 +0200 From: Thasso Griebel Subject: [Biojava-dev] phylo code To: biojava-dev at biojava.org Message-ID: <1EA22A3D-107C-455B-98A6-EFD4FEF77CCE at minet.uni-jena.de> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed hi, i recently explored the phylogeny code base in biojava. I am currently working on a phylogeny framework similar to mesquite (http://www.bio.informatik.uni-jena.de/epos) and i would like to add some functionality using biojava (the sequence stuff and the nexus parser). I saw the PhyloSOC07 page ( http://biojava.org/wiki/ BioJava:PhyloSOC07 ) and i might be able to help out with some of the methods, so is there a way to contribute ? Or is this closed to participants of the google summer of code ? I have code for n-consensus and adams consensus methods and some possible extensions for UPGMA (provide other distance computations, i.e wpgma, sigle linkage and complete linkage) and NJ ( outgroup and rooting support ). As our research groups has a focus on supertree construction, we have java implementations for several graph based supertree methods (aho's build, mincut, modified mincut, ranked tree, ancestral build). Regards, Thasso -- Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer Bioinformatik Office 3426--http://bio.informatik.uni-jena.de--Institut fuer Informatik Phone +49 (0)3641 9-46454-----------Friedrich-Schiller-Universitaet Jena Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, Germany ------------------------------ Message: 2 Date: Wed, 1 Aug 2007 19:03:29 +0100 (BST) From: "Richard Holland" Subject: Re: [Biojava-dev] phylo code To: "Thasso Griebel" Cc: biojava-dev at biojava.org Message-ID: <48008.80.42.98.32.1185991409.squirrel at webmail.ebi.ac.uk> Content-Type: text/plain;charset=iso-8859-1 Hi Thasso. Thanks for your interest! We always welcome all contributions of code and documentation to the BioJava project. Our GSOC project is well under way and has a plan as you have already noticed. The items on that plan are what was agreed with our student, Boh Yun Lee, and will be implemented by the time that GSOC is over (early September) - or at least, most of them will, and any that aren't will be flagged as such. If you have suggestions to make about code already committed, we would welcome them. Such feedback is a necessary part of the development cycle. Likewise we would welcome contributions of code not already mentioned as being planned on the GSOC pages. However, if your existing code implements something that is on the to-do list on the GSOC page, then the best thing would be to hang on till the end of the GSOC project then contribute any items that did not get implemented. cheers, Richard On Wed, August 1, 2007 6:19 pm, Thasso Griebel wrote: > hi, > > i recently explored the phylogeny code base in biojava. I am > currently working on a phylogeny framework similar to mesquite > (http://www.bio.informatik.uni-jena.de/epos) and i would like to add > some functionality using biojava (the sequence stuff and the nexus > parser). > > I saw the PhyloSOC07 page ( http://biojava.org/wiki/ > BioJava:PhyloSOC07 ) and i might be able to help out with some of the > methods, so is there a way to contribute ? Or is this closed to > participants of the google summer of code ? > > I have code for n-consensus and adams consensus methods and some > possible extensions for UPGMA (provide other distance computations, > i.e wpgma, sigle linkage and complete linkage) and NJ ( outgroup and > rooting support ). As our research groups has a focus on supertree > construction, we have java implementations for several graph based > supertree methods (aho's build, mincut, modified mincut, ranked tree, > ancestral build). > > > Regards, > > Thasso > > -- > Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer Bioinformatik > Office 3426--http://bio.informatik.uni-jena.de--Institut fuer Informatik > Phone +49 (0)3641 9-46454-----------Friedrich-Schiller-Universitaet Jena > Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, Germany > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > -- Richard Holland BioMart (http://www.biomart.org/) EMBL-EBI Hinxton, Cambridgeshire CB10 1SD, UK ------------------------------ Message: 3 Date: Mon, 6 Aug 2007 18:45:35 +0200 From: Thasso Griebel Subject: Re: [Biojava-dev] phylo code To: Richard Holland Cc: biojava-dev at biojava.org Message-ID: <846222BD-73C8-4CE7-8CB1-E2249A25256D at minet.uni-jena.de> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Hi, thanks for the fast answer. So, I would really like to contribute to the BioJava Phylogeny Package, but I will wait until the GSOC project is finished and I am back from my vacation ;) For now, I just took a look on the io package, especially the three classes concerning phylip io. Some personal feeling about the naming. I wouldn't mention "fire" and "events" in the documentation and rename PHYLIPFileListener to something else, i.e. PHYLIPFileHandler. For me, this was irritating. I started looking for a fireXXX method immediately and automatically started thinking about the EventDispatchingThread and synchronization. As far as I see, this is a direct handler delegate, the parser delegates some method calls to a given handler callback method, no events are fired (there is not even an Event class that could be fired) and no event dispatching is involved. Also, the io seem to focus on the output of alignment. What about trees and distance/character matrices ? And a really important point is the name handling. The method private static String formatSequenceLabel(String label) in PHYLIPFileFormat simply cuts names that are longer than 10 characters. I know that phylip has this stupid limitation. But cutting will not work in a lot of cases. If just two sequence names are identical over the first ten characters, the resulting phylip file is corrupted and can not be used by most of the phylip executables. Maybe the handler can do a renaming and keep track of the map. Then one can use the parser to write some phylip file, start a phylip method on that file, read in the results and do an automatic remapping of the names ? I also wanted to take a look on the tree model. Is this already in the CVS ? I found biojava-live/src/org/biojavax/bio/phylo/tree, but it was empty ? regards, thasso On 01.08.2007, at 20:03, Richard Holland wrote: > Hi Thasso. > > Thanks for your interest! We always welcome all contributions of > code and > documentation to the BioJava project. > > Our GSOC project is well under way and has a plan as you have already > noticed. The items on that plan are what was agreed with our > student, Boh > Yun Lee, and will be implemented by the time that GSOC is over (early > September) - or at least, most of them will, and any that aren't > will be > flagged as such. > > If you have suggestions to make about code already committed, we would > welcome them. Such feedback is a necessary part of the development > cycle. > Likewise we would welcome contributions of code not already > mentioned as > being planned on the GSOC pages. > > However, if your existing code implements something that is on the > to-do > list on the GSOC page, then the best thing would be to hang on till > the > end of the GSOC project then contribute any items that did not get > implemented. > > cheers, > Richard > > On Wed, August 1, 2007 6:19 pm, Thasso Griebel wrote: >> hi, >> >> i recently explored the phylogeny code base in biojava. I am >> currently working on a phylogeny framework similar to mesquite >> (http://www.bio.informatik.uni-jena.de/epos) and i would like to add >> some functionality using biojava (the sequence stuff and the nexus >> parser). >> >> I saw the PhyloSOC07 page ( http://biojava.org/wiki/ >> BioJava:PhyloSOC07 ) and i might be able to help out with some of the >> methods, so is there a way to contribute ? Or is this closed to >> participants of the google summer of code ? >> >> I have code for n-consensus and adams consensus methods and some >> possible extensions for UPGMA (provide other distance computations, >> i.e wpgma, sigle linkage and complete linkage) and NJ ( outgroup and >> rooting support ). As our research groups has a focus on supertree >> construction, we have java implementations for several graph based >> supertree methods (aho's build, mincut, modified mincut, ranked tree, >> ancestral build). >> >> >> Regards, >> >> Thasso >> >> -- >> Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer >> Bioinformatik >> Office 3426--http://bio.informatik.uni-jena.de--Institut fuer >> Informatik >> Phone +49 (0)3641 9-46454-----------Friedrich-Schiller- >> Universitaet Jena >> Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, >> Germany >> >> >> >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> > > > -- > Richard Holland > BioMart (http://www.biomart.org/) > EMBL-EBI > Hinxton, Cambridgeshire CB10 1SD, UK -- Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer Bioinformatik Office 3426--http://bio.informatik.uni-jena.de--Institut fuer Informatik Phone +49 (0)3641 9-46454-----------Friedrich-Schiller-Universitaet Jena Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, Germany ------------------------------ Message: 4 Date: Tue, 07 Aug 2007 08:48:05 +0100 From: Richard Holland Subject: Re: [Biojava-dev] phylo code To: Thasso Griebel Cc: biojava-dev at biojava.org Message-ID: <46B823B5.1010401 at ebi.ac.uk> Content-Type: text/plain; charset=ISO-8859-1 -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Thanks for your feedback Thasso. The fire/events thing is certainly a misnomer - guilty as charged (I wrote the code...) - but I suppose I wasn't expecting the naming to matter much. I'll bear that in mind for future code. We can't really change the existing interfaces now as they've been released and it is not nice to users for us to change public interfaces that might already be in use. The PHYLIP format handler was written by Jim Balhoff. Jim - do you have any responses to Thasso's comments about the output options? I like the sound of your PHYLIP short-name map. You could definitely go ahead and contribute an update which implemented that. (Don't forget to make your code clear the map between one file and the next!) The tree model never materialised in the end. We chose instead to use the external JGraphT package to represent our trees. The exact way in which this is done will be documented by Boh-Yun as part of the GSOC project. cheers, Richard Thasso Griebel wrote: > Hi, > > thanks for the fast answer. > > So, I would really like to contribute to the BioJava Phylogeny > Package, but I will wait until the GSOC project is finished and I am > back from my vacation ;) For now, I just took a look on the io > package, especially the three classes concerning phylip io. > Some personal feeling about the naming. > I wouldn't mention "fire" and "events" in the documentation and > rename PHYLIPFileListener to something else, i.e. PHYLIPFileHandler. > For me, this was irritating. I started looking for a fireXXX method > immediately and automatically started thinking about the > EventDispatchingThread and synchronization. As far as I see, this is > a direct handler delegate, the parser delegates some method calls to > a given handler callback method, no events are fired (there is not > even an Event class that could be fired) and no event dispatching is > involved. > Also, the io seem to focus on the output of alignment. What about > trees and distance/character matrices ? > And a really important point is the name handling. The method > > private static String formatSequenceLabel(String label) > > in PHYLIPFileFormat simply cuts names that are longer than 10 > characters. I know that phylip has this stupid limitation. But > cutting will not work in a lot of cases. If just two sequence names > are identical over the first ten characters, the resulting phylip > file is corrupted and can not be used by most of the phylip > executables. Maybe the handler can do a renaming and keep track of > the map. Then one can use the parser to write some phylip file, start > a phylip method on that file, read in the results and do an automatic > remapping of the names ? > > I also wanted to take a look on the tree model. Is this already in > the CVS ? I found biojava-live/src/org/biojavax/bio/phylo/tree, but > it was empty ? > > regards, > > thasso > > > > On 01.08.2007, at 20:03, Richard Holland wrote: > >> Hi Thasso. >> >> Thanks for your interest! We always welcome all contributions of >> code and >> documentation to the BioJava project. >> >> Our GSOC project is well under way and has a plan as you have already >> noticed. The items on that plan are what was agreed with our >> student, Boh >> Yun Lee, and will be implemented by the time that GSOC is over (early >> September) - or at least, most of them will, and any that aren't >> will be >> flagged as such. >> >> If you have suggestions to make about code already committed, we would >> welcome them. Such feedback is a necessary part of the development >> cycle. >> Likewise we would welcome contributions of code not already >> mentioned as >> being planned on the GSOC pages. >> >> However, if your existing code implements something that is on the >> to-do >> list on the GSOC page, then the best thing would be to hang on till >> the >> end of the GSOC project then contribute any items that did not get >> implemented. >> >> cheers, >> Richard >> >> On Wed, August 1, 2007 6:19 pm, Thasso Griebel wrote: >>> hi, >>> >>> i recently explored the phylogeny code base in biojava. I am >>> currently working on a phylogeny framework similar to mesquite >>> (http://www.bio.informatik.uni-jena.de/epos) and i would like to add >>> some functionality using biojava (the sequence stuff and the nexus >>> parser). >>> >>> I saw the PhyloSOC07 page ( http://biojava.org/wiki/ >>> BioJava:PhyloSOC07 ) and i might be able to help out with some of the >>> methods, so is there a way to contribute ? Or is this closed to >>> participants of the google summer of code ? >>> >>> I have code for n-consensus and adams consensus methods and some >>> possible extensions for UPGMA (provide other distance computations, >>> i.e wpgma, sigle linkage and complete linkage) and NJ ( outgroup and >>> rooting support ). As our research groups has a focus on supertree >>> construction, we have java implementations for several graph based >>> supertree methods (aho's build, mincut, modified mincut, ranked tree, >>> ancestral build). >>> >>> >>> Regards, >>> >>> Thasso >>> >>> -- >>> Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer >>> Bioinformatik >>> Office 3426--http://bio.informatik.uni-jena.de--Institut fuer >>> Informatik >>> Phone +49 (0)3641 9-46454-----------Friedrich-Schiller- >>> Universitaet Jena >>> Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, >>> Germany >>> >>> >>> >>> _______________________________________________ >>> biojava-dev mailing list >>> biojava-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >>> >> >> -- >> Richard Holland >> BioMart (http://www.biomart.org/) >> EMBL-EBI >> Hinxton, Cambridgeshire CB10 1SD, UK > > -- > Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer Bioinformatik > Office 3426--http://bio.informatik.uni-jena.de--Institut fuer Informatik > Phone +49 (0)3641 9-46454-----------Friedrich-Schiller-Universitaet Jena > Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, Germany > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGuCO04C5LeMEKA/QRAritAJ0eFpRIQ7YP/NROSfoToo/+4aTfEwCfbFUU Hbne6alMOuzmr8CxX/hqsfs= =U4gJ -----END PGP SIGNATURE----- ------------------------------ Message: 5 Date: Tue, 7 Aug 2007 10:29:08 +0200 From: Thasso Griebel Subject: Re: [Biojava-dev] phylo code To: Richard Holland Cc: biojava-dev at biojava.org Message-ID: Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Hi, On the fire/event thing. You are right, it is not a good idea to change this if the code is already released. But maybe a little helper class with some static methods ( like IOTools ) would help. Something like PhylipIO.readTree(File) or PhylipIO.readAlignment (File) might do the job, the interfaces do not have to change and when it avoids direct contact with the parser implementation as long as standard phylip dataypes are concerned. And, as far as I see, this would follow the main path IO is done in BioJava. I can ( and will ) definitely work on the short-name map, but this has to wait at least 5 week as I am going on vacation ( yeah, 5 weeks without a computer nearby !!!). But currently I am really interested in a good phylip parser, so I will work on that. One thing about JGraphT. I used and use that a lot when doing phylogenetics, and its a great library. But you might consider adding a little interface structure on top at some point to decouple the the usage from the library. This would allow BioJava compatible tree implementations without the need of JGraphT. JGraphT is great for all the simple, and even the complex jobs, but for me there is one little drawback. You can fill in every Object as a graph vertex, which is great, but this makes the underlying implementation rather complex. I do not remember exactly, but I think they use a large set of HashMap structures and some complex mapping mechanism to build up a graph. There are situations where this makes it hard to extend. For example, for one of our supertree algorithm implementations we needed a MultiGraph, a graph with different edge types, and it was a real pain to add that to the library without reimplementing JGraphT's Graph interface completely. I think a Tree interface structure on top would be simple and easy and might be really helpful at some point. regards, thasso On 07.08.2007, at 09:48, Richard Holland wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Thanks for your feedback Thasso. > > The fire/events thing is certainly a misnomer - guilty as charged (I > wrote the code...) - but I suppose I wasn't expecting the naming to > matter much. I'll bear that in mind for future code. We can't really > change the existing interfaces now as they've been released and it is > not nice to users for us to change public interfaces that might > already > be in use. > > The PHYLIP format handler was written by Jim Balhoff. Jim - do you > have > any responses to Thasso's comments about the output options? > > I like the sound of your PHYLIP short-name map. You could > definitely go > ahead and contribute an update which implemented that. (Don't > forget to > make your code clear the map between one file and the next!) > > The tree model never materialised in the end. We chose instead to use > the external JGraphT package to represent our trees. The exact way in > which this is done will be documented by Boh-Yun as part of the GSOC > project. > > cheers, > Richard > > > Thasso Griebel wrote: >> Hi, >> >> thanks for the fast answer. >> >> So, I would really like to contribute to the BioJava Phylogeny >> Package, but I will wait until the GSOC project is finished and I am >> back from my vacation ;) For now, I just took a look on the io >> package, especially the three classes concerning phylip io. >> Some personal feeling about the naming. >> I wouldn't mention "fire" and "events" in the documentation and >> rename PHYLIPFileListener to something else, i.e. PHYLIPFileHandler. >> For me, this was irritating. I started looking for a fireXXX method >> immediately and automatically started thinking about the >> EventDispatchingThread and synchronization. As far as I see, this is >> a direct handler delegate, the parser delegates some method calls to >> a given handler callback method, no events are fired (there is not >> even an Event class that could be fired) and no event dispatching is >> involved. >> Also, the io seem to focus on the output of alignment. What about >> trees and distance/character matrices ? >> And a really important point is the name handling. The method >> >> private static String formatSequenceLabel(String label) >> >> in PHYLIPFileFormat simply cuts names that are longer than 10 >> characters. I know that phylip has this stupid limitation. But >> cutting will not work in a lot of cases. If just two sequence names >> are identical over the first ten characters, the resulting phylip >> file is corrupted and can not be used by most of the phylip >> executables. Maybe the handler can do a renaming and keep track of >> the map. Then one can use the parser to write some phylip file, start >> a phylip method on that file, read in the results and do an automatic >> remapping of the names ? >> >> I also wanted to take a look on the tree model. Is this already in >> the CVS ? I found biojava-live/src/org/biojavax/bio/phylo/tree, but >> it was empty ? >> >> regards, >> >> thasso >> >> >> >> On 01.08.2007, at 20:03, Richard Holland wrote: >> >>> Hi Thasso. >>> >>> Thanks for your interest! We always welcome all contributions of >>> code and >>> documentation to the BioJava project. >>> >>> Our GSOC project is well under way and has a plan as you have >>> already >>> noticed. The items on that plan are what was agreed with our >>> student, Boh >>> Yun Lee, and will be implemented by the time that GSOC is over >>> (early >>> September) - or at least, most of them will, and any that aren't >>> will be >>> flagged as such. >>> >>> If you have suggestions to make about code already committed, we >>> would >>> welcome them. Such feedback is a necessary part of the development >>> cycle. >>> Likewise we would welcome contributions of code not already >>> mentioned as >>> being planned on the GSOC pages. >>> >>> However, if your existing code implements something that is on the >>> to-do >>> list on the GSOC page, then the best thing would be to hang on till >>> the >>> end of the GSOC project then contribute any items that did not get >>> implemented. >>> >>> cheers, >>> Richard >>> >>> On Wed, August 1, 2007 6:19 pm, Thasso Griebel wrote: >>>> hi, >>>> >>>> i recently explored the phylogeny code base in biojava. I am >>>> currently working on a phylogeny framework similar to mesquite >>>> (http://www.bio.informatik.uni-jena.de/epos) and i would like to >>>> add >>>> some functionality using biojava (the sequence stuff and the nexus >>>> parser). >>>> >>>> I saw the PhyloSOC07 page ( http://biojava.org/wiki/ >>>> BioJava:PhyloSOC07 ) and i might be able to help out with some >>>> of the >>>> methods, so is there a way to contribute ? Or is this closed to >>>> participants of the google summer of code ? >>>> >>>> I have code for n-consensus and adams consensus methods and some >>>> possible extensions for UPGMA (provide other distance computations, >>>> i.e wpgma, sigle linkage and complete linkage) and NJ ( outgroup >>>> and >>>> rooting support ). As our research groups has a focus on supertree >>>> construction, we have java implementations for several graph based >>>> supertree methods (aho's build, mincut, modified mincut, ranked >>>> tree, >>>> ancestral build). >>>> >>>> >>>> Regards, >>>> >>>> Thasso >>>> >>>> -- >>>> Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer >>>> Bioinformatik >>>> Office 3426--http://bio.informatik.uni-jena.de--Institut fuer >>>> Informatik >>>> Phone +49 (0)3641 9-46454-----------Friedrich-Schiller- >>>> Universitaet Jena >>>> Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, >>>> Germany >>>> >>>> >>>> >>>> _______________________________________________ >>>> biojava-dev mailing list >>>> biojava-dev at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev >>>> >>> >>> -- >>> Richard Holland >>> BioMart (http://www.biomart.org/) >>> EMBL-EBI >>> Hinxton, Cambridgeshire CB10 1SD, UK >> >> -- >> Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer >> Bioinformatik >> Office 3426--http://bio.informatik.uni-jena.de--Institut fuer >> Informatik >> Phone +49 (0)3641 9-46454-----------Friedrich-Schiller- >> Universitaet Jena >> Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, >> Germany >> >> >> >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev >> > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.2.2 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iD8DBQFGuCO04C5LeMEKA/QRAritAJ0eFpRIQ7YP/NROSfoToo/+4aTfEwCfbFUU > Hbne6alMOuzmr8CxX/hqsfs= > =U4gJ > -----END PGP SIGNATURE----- -- Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer Bioinformatik Office 3426--http://bio.informatik.uni-jena.de--Institut fuer Informatik Phone +49 (0)3641 9-46454-----------Friedrich-Schiller-Universitaet Jena Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, Germany ------------------------------ _______________________________________________ biojava-dev mailing list biojava-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-dev End of biojava-dev Digest, Vol 54, Issue 1 ****************************************** From simpleyrx at 163.com Wed Aug 8 01:38:03 2007 From: simpleyrx at 163.com (simpleyrx) Date: Wed, 8 Aug 2007 09:38:03 +0800 (CST) Subject: [Biojava-dev] could I join in developing biojava ? Message-ID: <1941424432.747191186537083813.JavaMail.coremail@bj163app105.163.com> Dear sir, Thank you for your message for biojava. I am very interested in it. I am a graduate student of China Agriculture University and my major is bioinformatics and I love java programming. I would like to know that if I can join in developing biojava ? student simple From holland at ebi.ac.uk Wed Aug 8 07:40:38 2007 From: holland at ebi.ac.uk (Richard Holland) Date: Wed, 08 Aug 2007 08:40:38 +0100 Subject: [Biojava-dev] could I join in developing biojava ? In-Reply-To: <1941424432.747191186537083813.JavaMail.coremail@bj163app105.163.com> References: <1941424432.747191186537083813.JavaMail.coremail@bj163app105.163.com> Message-ID: <46B97376.5040902@ebi.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi there. We welcome all contributions. You can read about existing capabilities on the BioJava website, then if you identify any areas which need improving you can contact this mailing list with your ideas and/or code. Someone will then check that the idea and/or code works, and make the appropriate changes. I look forward to seeing your suggestions on this list! The website is: http://www.biojava.org/ cheers, Richard simpleyrx wrote: > Dear sir, > > Thank you for your message for biojava. I am very interested in it. > I am a graduate student of China Agriculture University and my major is bioinformatics and I love java programming. I would like to know that if I can join in developing biojava ? > > > > student simple > > > ------------------------------------------------------------------------ > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGuXN14C5LeMEKA/QRAuUBAJ9UTaq0nmn4RU37juqQEduyP0pZawCfQb2I OpQScyV3G3Y0NHRY/NZm75U= =Xv6y -----END PGP SIGNATURE----- From Robin.Emig at pioneer.com Fri Aug 10 22:43:38 2007 From: Robin.Emig at pioneer.com (Emig, Robin) Date: Fri, 10 Aug 2007 15:43:38 -0700 Subject: [Biojava-dev] RichSequence output without namespace In-Reply-To: <4694896A.9050707@ebi.ac.uk> References: <4694896A.9050707@ebi.ac.uk> Message-ID: Is there anyway to use RichSequence.IOTools.writeFasta to output just the sequence name as the name and nothing else? Ie >SeqName Aatg Vs >Namespace|Seqname|SeqName Or >|Seqname|Seqname Thanks -Robin This communication is for use by the intended recipient and contains information that may be Privileged, confidential or copyrighted under applicable law. If you are not the intended recipient, you are hereby formally notified that any use, copying or distribution of this e-mail, in whole or in part, is strictly prohibited. Please notify the sender by return e-mail and delete this e-mail from your system. Unless explicitly and conspicuously designated as "E-Contract Intended", this e-mail does not constitute a contract offer, a contract amendment, or an acceptance of a contract offer. This e-mail does not constitute a consent to the use of sender's contact information for direct marketing purposes or for transfers of data to third parties. Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean http://www.DuPont.com/corp/email_disclaimer.html From markjschreiber at gmail.com Sat Aug 11 03:51:18 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Sat, 11 Aug 2007 11:51:18 +0800 Subject: [Biojava-dev] RichSequence output without namespace In-Reply-To: References: <4694896A.9050707@ebi.ac.uk> Message-ID: <93b45ca50708102051r24bbe45ct57284447cdedd2b1@mail.gmail.com> Hi Robin - RichSequenceIOTools.writeFasta uses the FastaFormat object to construct the sequence name. It might be worth extending FastaFormat to add methods that let you modify what is output in the name line. If you do it would probably be worth checking in to the CVS. You could then look at providing an overloaded writeFasta method that allows you to configure the output. - Mark On 8/11/07, Emig, Robin wrote: > Is there anyway to use RichSequence.IOTools.writeFasta to output just > the sequence name as the name and nothing else? > Ie > >SeqName > Aatg > > Vs > > >Namespace|Seqname|SeqName > Or > >|Seqname|Seqname > > > Thanks > -Robin > > This communication is for use by the intended recipient and contains > information that may be Privileged, confidential or copyrighted under > applicable law. If you are not the intended recipient, you are hereby > formally notified that any use, copying or distribution of this e-mail, > in whole or in part, is strictly prohibited. Please notify the sender by > return e-mail and delete this e-mail from your system. Unless explicitly > and conspicuously designated as "E-Contract Intended", this e-mail does > not constitute a contract offer, a contract amendment, or an acceptance > of a contract offer. This e-mail does not constitute a consent to the > use of sender's contact information for direct marketing purposes or for > transfers of data to third parties. > > Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean > > http://www.DuPont.com/corp/email_disclaimer.html > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From yp_riverol at yahoo.com Thu Aug 23 01:23:16 2007 From: yp_riverol at yahoo.com (yasset perez riverol) Date: Wed, 22 Aug 2007 20:23:16 -0500 (CDT) Subject: [Biojava-dev] Problem With Isoelectric point Message-ID: <799294.30713.qm@web37909.mail.mud.yahoo.com> Hi, I have a problem when I execute the Isoelectrc Point calculation for this peptides: ALLIDLPV FDIYAGTPV SVLLMSAEI PTGDTTGYLANPEEV I all the case I receive this error : Error, the peptide probably contains only positive or negative charges. Well I try to calculate the isoelectric Point for all the peptides with de Expasy Calculator and I obtained: ALLIDLPV: Theoretical pI: 3.80 Molecular weight (average): 853.07 FDIYAGTPV: Theoretical pI: 3.80 Molecular weight (average): 982.10 SVLLMSAEI: Theoretical pI: 4.00 Molecular weight (average): 962.17 PTGDTTGYLANPEEV: Theoretical pI: 3.57 Molecular weight (average): 1563.64 My code is this: OBioSeq = ProteinTools.createProtein(Sequence); IsoelectricPointCalc OBioIsoc = new IsoelectricPointCalc(); double dIsoelec = 0.0; dIsoelec = OBioIsoc.getPI(OBioSeq,true,true); Thanks in advance Centen of Molecular Biology. Havana University Cuba. __________________________________________________ Correo Yahoo! Espacio para todos tus mensajes, antivirus y antispam ?gratis! Reg?strate ya - http://correo.espanol.yahoo.com/ From yp_riverol at yahoo.com Mon Aug 27 13:45:16 2007 From: yp_riverol at yahoo.com (yasset perez riverol) Date: Mon, 27 Aug 2007 08:45:16 -0500 (CDT) Subject: [Biojava-dev] Retention Time Calculations In-Reply-To: <50890.74.232.148.95.1188111871.squirrel@webmail.cc.gatech.edu> Message-ID: <644850.61203.qm@web37909.mail.mud.yahoo.com> Hi all, I will try to compute the retention time for a peptide, but in biojava do not exist this kind of function, but in other bio-packages as InsilicoSpectro (Perl), these functions are implemented. Any help with this topic? Thank in advance Yasset. __________________________________________________ Correo Yahoo! Espacio para todos tus mensajes, antivirus y antispam ?gratis! Reg?strate ya - http://correo.espanol.yahoo.com/ From ap3 at sanger.ac.uk Tue Aug 28 15:42:55 2007 From: ap3 at sanger.ac.uk (Andreas Prlic) Date: Tue, 28 Aug 2007 16:42:55 +0100 Subject: [Biojava-dev] cruisecontrol Message-ID: Hi biojava - devs, would you be interested in getting CruiseControl running for BioJava? It would allow us to * provide nightly builds of biojava, * run unit test in regular intervals, * get a notification email sent to biojava-dev if the CVS does not build http://cruisecontrol.sourceforge.net/ If there is interest for this I will set it up, Andreas ----------------------------------------------------------------------- Andreas Prlic Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA, UK +44 (0) 1223 49 6891 ----------------------------------------------------------------------- -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From markjschreiber at gmail.com Wed Aug 29 00:16:06 2007 From: markjschreiber at gmail.com (Mark Schreiber) Date: Wed, 29 Aug 2007 08:16:06 +0800 Subject: [Biojava-dev] cruisecontrol In-Reply-To: References: Message-ID: <93b45ca50708281716x3c2cadc9me9cb0b00b52647a2@mail.gmail.com> Sounds good. Thomas had a script running off his home machine a while ago for nightly builds which I have missed since he stopped running it. Notifications of failed tests would be good too. - Mark On 8/28/07, Andreas Prlic wrote: > Hi biojava - devs, > > would you be interested in getting CruiseControl running for BioJava? > > It would allow us to > > * provide nightly builds of biojava, > * run unit test in regular intervals, > * get a notification email sent to biojava-dev if the CVS does not build > > http://cruisecontrol.sourceforge.net/ > > If there is interest for this I will set it up, > > Andreas > > ----------------------------------------------------------------------- > > Andreas Prlic Wellcome Trust Sanger Institute > Hinxton, Cambridge CB10 1SA, UK > +44 (0) 1223 49 6891 > > ----------------------------------------------------------------------- > > > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a > company registered in England with number 2742969, whose registered > office is 215 Euston Road, London, NW1 2BE. > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev >