From bugzilla-daemon at portal.open-bio.org Mon Nov 2 12:52:52 2009 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 2 Nov 2009 12:52:52 -0500 Subject: [Biojava-dev] [Bug 2941] NEXUS parser fails with tree nodes called p[0-9]+ In-Reply-To: Message-ID: <200911021752.nA2HqqpR018934@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2941 ------- Comment #1 from holland at ebi.ac.uk 2009-11-02 12:52 EST ------- The reason this is happening is because JGraphT expects all nodes to have a name, but the tree strings in Nexus files don't have names for all nodes (in your case, the tree string you provide does not have a name for the sub-tree mapped to :0.15). ((1:0.1,2:0.2):0.15,p1:0.3) The 'p' notation is used internally to assign names to grouped nodes that don't have names explicitly set in the tree string. It would be good to have this as a modifiable setting, but it would still have to be set to something by default, and users would still have to check that the setting they use does not clash with any of their existing names. Volunteers to modify please? -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Sun Nov 15 18:14:40 2009 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Sun, 15 Nov 2009 18:14:40 -0500 Subject: [Biojava-dev] [Bug 2941] NEXUS parser fails with tree nodes called p[0-9]+ In-Reply-To: Message-ID: <200911152314.nAFNEeoT015030@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2941 ------- Comment #2 from tiagoantao at gmail.com 2009-11-15 18:14 EST ------- Created an attachment (id=1397) --> (http://bugzilla.open-bio.org/attachment.cgi?id=1397&action=view) Patch -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Sun Nov 15 18:17:00 2009 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Sun, 15 Nov 2009 18:17:00 -0500 Subject: [Biojava-dev] [Bug 2941] NEXUS parser fails with tree nodes called p[0-9]+ In-Reply-To: Message-ID: <200911152317.nAFNH0m1015213@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2941 ------- Comment #3 from tiagoantao at gmail.com 2009-11-15 18:16 EST ------- I've attached a patch for: 1. p* 2. Support for more than binary trees 3. Getting the top node of a tree (root in rooted trees) -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Nov 16 03:39:36 2009 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 16 Nov 2009 03:39:36 -0500 Subject: [Biojava-dev] [Bug 2941] NEXUS parser fails with tree nodes called p[0-9]+ In-Reply-To: Message-ID: <200911160839.nAG8dasi029568@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2941 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #4 from holland at ebi.ac.uk 2009-11-16 03:39 EST ------- I have applied the patch on the trunk of biojava-live (now under the phylo module). -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From matias.piipari at gmail.com Mon Nov 16 09:53:22 2009 From: matias.piipari at gmail.com (Matias Piipari) Date: Mon, 16 Nov 2009 14:53:22 +0000 Subject: [Biojava-dev] HashMap ==> LinkedHashMap in HashSequenceDB Message-ID: <15cdf3360911160653q4602960fwe02924c01b976405@mail.gmail.com> Hello I'd like to propose a change to org.biojava.bio.seq.db.HashSequenceDB: swap the map implementation used to store the sequence-by-id map from HashMap to LinkedHashMap. This would allow iterating the sequences in a defined order (the order in which they were added to the map). Best wishes Matias An example patch relative to rev 7059: --- src/org/biojava/bio/seq/db/HashSequenceDB.java (revision 7059) +++ src/org/biojava/bio/seq/db/HashSequenceDB.java (working copy) @@ -22,8 +22,8 @@ package org.biojava.bio.seq.db; import java.io.Serializable; -import java.util.HashMap; import java.util.Iterator; +import java.util.LinkedHashMap; import java.util.Map; import java.util.Set; @@ -203,6 +203,6 @@ public HashSequenceDB(org.biojava.bio.seq.db.IDMaker idMaker, String name) { this.idMaker = idMaker; this.name = name; - this.sequenceByID = new HashMap(); + this.sequenceByID = new LinkedHashMap(); } } From holland at eaglegenomics.com Mon Nov 16 09:59:19 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Mon, 16 Nov 2009 14:59:19 +0000 Subject: [Biojava-dev] HashMap ==> LinkedHashMap in HashSequenceDB In-Reply-To: <15cdf3360911160653q4602960fwe02924c01b976405@mail.gmail.com> References: <15cdf3360911160653q4602960fwe02924c01b976405@mail.gmail.com> Message-ID: <32ED0451-526B-4848-8FD2-A85545851922@eaglegenomics.com> Sounds like a plan - are there any performance implications? On 16 Nov 2009, at 14:53, Matias Piipari wrote: > Hello > > I'd like to propose a change to org.biojava.bio.seq.db.HashSequenceDB: swap > the map implementation used to store the sequence-by-id map from HashMap to > LinkedHashMap. This would allow iterating the sequences in a defined order > (the order in which they were added to the map). > > Best wishes > Matias > > > An example patch relative to rev 7059: > > --- src/org/biojava/bio/seq/db/HashSequenceDB.java (revision 7059) > +++ src/org/biojava/bio/seq/db/HashSequenceDB.java (working copy) > @@ -22,8 +22,8 @@ > package org.biojava.bio.seq.db; > > import java.io.Serializable; > -import java.util.HashMap; > import java.util.Iterator; > +import java.util.LinkedHashMap; > import java.util.Map; > import java.util.Set; > > @@ -203,6 +203,6 @@ > public HashSequenceDB(org.biojava.bio.seq.db.IDMaker idMaker, String > name) { > this.idMaker = idMaker; > this.name = name; > - this.sequenceByID = new HashMap(); > + this.sequenceByID = new LinkedHashMap(); > } > } > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From andreas at sdsc.edu Mon Nov 16 12:40:15 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Mon, 16 Nov 2009 09:40:15 -0800 Subject: [Biojava-dev] HashMap ==> LinkedHashMap in HashSequenceDB In-Reply-To: <32ED0451-526B-4848-8FD2-A85545851922@eaglegenomics.com> References: <15cdf3360911160653q4602960fwe02924c01b976405@mail.gmail.com> <32ED0451-526B-4848-8FD2-A85545851922@eaglegenomics.com> Message-ID: <59a41c430911160940m42ed1a94naceb3ec514f63e20@mail.gmail.com> Talking about Map implementations... I recently added org.biojava.utils.io.SoftHashMap It can be used to create temporary in-memory caches. It allows the Garbage Collector to clean up objects, and one does not have to take care of removing the objects from the cache. I use it to cache small files that are more efficiently read from the memory, rather than going to the hard disk (or NFS...) The code is based on http://java-interview-faqs.blogspot.com/2008/09/building-faster-and-efficient-cache.html Andreas On Mon, Nov 16, 2009 at 6:59 AM, Richard Holland wrote: > Sounds like a plan - are there any performance implications? > > On 16 Nov 2009, at 14:53, Matias Piipari wrote: > >> Hello >> >> I'd like to propose a change to org.biojava.bio.seq.db.HashSequenceDB: swap >> the map implementation used to store the sequence-by-id map from HashMap to >> LinkedHashMap. This would allow iterating the sequences in a defined order >> (the order in which they were added to the map). >> >> Best wishes >> Matias >> >> >> An example patch relative to rev 7059: >> >> --- src/org/biojava/bio/seq/db/HashSequenceDB.java ? ? ?(revision 7059) >> +++ src/org/biojava/bio/seq/db/HashSequenceDB.java ? ? ?(working copy) >> @@ -22,8 +22,8 @@ >> package org.biojava.bio.seq.db; >> >> import java.io.Serializable; >> -import java.util.HashMap; >> import java.util.Iterator; >> +import java.util.LinkedHashMap; >> import java.util.Map; >> import java.util.Set; >> >> @@ -203,6 +203,6 @@ >> ? public HashSequenceDB(org.biojava.bio.seq.db.IDMaker idMaker, String >> name) { >> ? ? this.idMaker = idMaker; >> ? ? this.name = name; >> - ? ?this.sequenceByID = new HashMap(); >> + ? ?this.sequenceByID = new LinkedHashMap(); >> ? } >> } >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev > > -- > Richard Holland, BSc MBCS > Operations and Delivery Director, Eagle Genomics Ltd > T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com > http://www.eaglegenomics.com/ > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From bugzilla-daemon at portal.open-bio.org Mon Nov 16 12:52:28 2009 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 16 Nov 2009 12:52:28 -0500 Subject: [Biojava-dev] [Bug 2679] NEXUS parse fails on extraneous comma (TREES/TRANSLATE) In-Reply-To: Message-ID: <200911161752.nAGHqSbm014843@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2679 ------- Comment #4 from tiagoantao at gmail.com 2009-11-16 12:52 EST ------- Created an attachment (id=1399) --> (http://bugzilla.open-bio.org/attachment.cgi?id=1399&action=view) Patch This solves the bug, hopefully. In theory it creates a new one, in case the initial node name (before translation) is called "tree". But that is much less likely. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Nov 16 13:11:18 2009 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 16 Nov 2009 13:11:18 -0500 Subject: [Biojava-dev] [Bug 2679] NEXUS parse fails on extraneous comma (TREES/TRANSLATE) In-Reply-To: Message-ID: <200911161811.nAGIBIIb015514@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2679 holland at eaglegenomics.com changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #5 from holland at eaglegenomics.com 2009-11-16 13:11 EST ------- Applied to trunk of biojava-live/phylo module. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From holland at eaglegenomics.com Mon Nov 16 13:13:24 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Mon, 16 Nov 2009 18:13:24 +0000 Subject: [Biojava-dev] HashMap ==> LinkedHashMap in HashSequenceDB In-Reply-To: <15cdf3360911160653q4602960fwe02924c01b976405@mail.gmail.com> References: <15cdf3360911160653q4602960fwe02924c01b976405@mail.gmail.com> Message-ID: <8731EAB9-E8A9-43C8-95E7-C4AABD9A4FBB@eaglegenomics.com> I've applied the patch to the trunk of biojava-live/core. On 16 Nov 2009, at 14:53, Matias Piipari wrote: > Hello > > I'd like to propose a change to org.biojava.bio.seq.db.HashSequenceDB: swap > the map implementation used to store the sequence-by-id map from HashMap to > LinkedHashMap. This would allow iterating the sequences in a defined order > (the order in which they were added to the map). > > Best wishes > Matias > > > An example patch relative to rev 7059: > > --- src/org/biojava/bio/seq/db/HashSequenceDB.java (revision 7059) > +++ src/org/biojava/bio/seq/db/HashSequenceDB.java (working copy) > @@ -22,8 +22,8 @@ > package org.biojava.bio.seq.db; > > import java.io.Serializable; > -import java.util.HashMap; > import java.util.Iterator; > +import java.util.LinkedHashMap; > import java.util.Map; > import java.util.Set; > > @@ -203,6 +203,6 @@ > public HashSequenceDB(org.biojava.bio.seq.db.IDMaker idMaker, String > name) { > this.idMaker = idMaker; > this.name = name; > - this.sequenceByID = new HashMap(); > + this.sequenceByID = new LinkedHashMap(); > } > } > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From andreas at sdsc.edu Tue Nov 17 14:23:44 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Tue, 17 Nov 2009 11:23:44 -0800 Subject: [Biojava-dev] [Biojava-l] Newick parser In-Reply-To: References: <6d941f120911151519s732144fu1150d672107fca1e@mail.gmail.com> Message-ID: <59a41c430911171123j43806c25vda67e406aa2d3caa@mail.gmail.com> Hi Richard, I just did an update of my checkout and it seems the -phylo unit tests don't compile any more. Can you take a look? Thanks, Andreas Test set: org.biojavax.bio.phylo.io.nexus.TreesBlockTest ------------------------------------------------------------------------------- Tests run: 9, Failures: 0, Errors: 9, Skipped: 0, Time elapsed: 0.063 sec <<< FAILURE! testSimple(org.biojavax.bio.phylo.io.nexus.TreesBlockTest) Time elapsed: 0.021 sec <<< ERROR! java.lang.NullPointerException at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTreeNode(TreesBlockTest.java:160) at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTree(TreesBlockTest.java:175) at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.doVertexCount(TreesBlockTest.java:139) at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.testSimple(TreesBlockTest.java:63) testThreeOffspring(org.biojavax.bio.phylo.io.nexus.TreesBlockTest) Time elapsed: 0.002 sec <<< ERROR! java.lang.NullPointerException at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTreeNode(TreesBlockTest.java:160) at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTree(TreesBlockTest.java:175) at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.doVertexCount(TreesBlockTest.java:139) at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.testThreeOffspring(TreesBlockTest.java:70 2009/11/16 Richard Holland : > Patch applied to the trunk of biojava-live. Thanks for fixing it! > > cheers, > Richard > > On 15 Nov 2009, at 23:19, Tiago Ant?o wrote: > >> Hi, >> >> I have made the changes as discussed, the code is attached to the >> bugzilla bug concerning part of the issues that were found. >> A few notes: >> >> 1. There is a ParserException raised on TreeBlock. Tough there is a >> TreeBlockParser, most of the important parsing was (and still is!) >> being made on TreeBlock. I would imagine that this is not the best >> design, but I did not change it. >> 2. I made some test cases. Also included. >> 3. I don't mind producing some documentation, in case you accept the code. >> 4. I noticed a few minor bugs more (like eating spaces in the names of >> nodes). But they are really minor. >> 5. The API was changed, but I suppose not many people were parsing >> trees. If there were people parsing trees most probably the bug on not >> being able to process trees that are not binary would have been >> detected as it is pretty major. >> >> Tiago >> >> -- >> ?Pessimism of the Intellect; Optimism of the Will? -Antonio Gramsci >> >> _______________________________________________ >> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l > > -- > Richard Holland, BSc MBCS > Operations and Delivery Director, Eagle Genomics Ltd > T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com > http://www.eaglegenomics.com/ > > > _______________________________________________ > Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From andreas at sdsc.edu Tue Nov 17 14:50:40 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Tue, 17 Nov 2009 11:50:40 -0800 Subject: [Biojava-dev] [Biojava-l] Newick parser In-Reply-To: References: <6d941f120911151519s732144fu1150d672107fca1e@mail.gmail.com> <59a41c430911171123j43806c25vda67e406aa2d3caa@mail.gmail.com> Message-ID: <59a41c430911171150p22badd1cx223b651cc5a54959@mail.gmail.com> thanks for the quick fix, compiles fine now. A 2009/11/17 Richard Holland : > Sorry - forgot to change the filenames in the test (under the new modular system they're in a different place than in the non-modular codebase that Tiago was working from). Fixed and committed. > > On 17 Nov 2009, at 19:23, Andreas Prlic wrote: > >> Hi Richard, >> >> I just did an update of my checkout and it seems the -phylo unit tests >> don't compile any more. Can you take a look? >> >> Thanks, >> Andreas >> >> Test set: org.biojavax.bio.phylo.io.nexus.TreesBlockTest >> ------------------------------------------------------------------------------- >> Tests run: 9, Failures: 0, Errors: 9, Skipped: 0, Time elapsed: 0.063 >> sec <<< FAILURE! >> testSimple(org.biojavax.bio.phylo.io.nexus.TreesBlockTest) ?Time >> elapsed: 0.021 sec ?<<< ERROR! >> java.lang.NullPointerException >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTreeNode(TreesBlockTest.java:160) >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTree(TreesBlockTest.java:175) >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.doVertexCount(TreesBlockTest.java:139) >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.testSimple(TreesBlockTest.java:63) >> >> testThreeOffspring(org.biojavax.bio.phylo.io.nexus.TreesBlockTest) >> Time elapsed: 0.002 sec ?<<< ERROR! >> java.lang.NullPointerException >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTreeNode(TreesBlockTest.java:160) >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTree(TreesBlockTest.java:175) >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.doVertexCount(TreesBlockTest.java:139) >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.testThreeOffspring(TreesBlockTest.java:70 >> >> 2009/11/16 Richard Holland : >>> Patch applied to the trunk of biojava-live. Thanks for fixing it! >>> >>> cheers, >>> Richard >>> >>> On 15 Nov 2009, at 23:19, Tiago Ant?o wrote: >>> >>>> Hi, >>>> >>>> I have made the changes as discussed, the code is attached to the >>>> bugzilla bug concerning part of the issues that were found. >>>> A few notes: >>>> >>>> 1. There is a ParserException raised on TreeBlock. Tough there is a >>>> TreeBlockParser, most of the important parsing was (and still is!) >>>> being made on TreeBlock. I would imagine that this is not the best >>>> design, but I did not change it. >>>> 2. I made some test cases. Also included. >>>> 3. I don't mind producing some documentation, in case you accept the code. >>>> 4. I noticed a few minor bugs more (like eating spaces in the names of >>>> nodes). But they are really minor. >>>> 5. The API was changed, but I suppose not many people were parsing >>>> trees. If there were people parsing trees most probably the bug on not >>>> being able to process trees that are not binary would have been >>>> detected as it is pretty major. >>>> >>>> Tiago >>>> >>>> -- >>>> ?Pessimism of the Intellect; Optimism of the Will? -Antonio Gramsci >>>> >>>> _______________________________________________ >>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>> >>> -- >>> Richard Holland, BSc MBCS >>> Operations and Delivery Director, Eagle Genomics Ltd >>> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com >>> http://www.eaglegenomics.com/ >>> >>> >>> _______________________________________________ >>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>> > > -- > Richard Holland, BSc MBCS > Operations and Delivery Director, Eagle Genomics Ltd > T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com > http://www.eaglegenomics.com/ > > From holland at eaglegenomics.com Tue Nov 17 14:47:44 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Tue, 17 Nov 2009 19:47:44 +0000 Subject: [Biojava-dev] [Biojava-l] Newick parser In-Reply-To: <59a41c430911171123j43806c25vda67e406aa2d3caa@mail.gmail.com> References: <6d941f120911151519s732144fu1150d672107fca1e@mail.gmail.com> <59a41c430911171123j43806c25vda67e406aa2d3caa@mail.gmail.com> Message-ID: Sorry - forgot to change the filenames in the test (under the new modular system they're in a different place than in the non-modular codebase that Tiago was working from). Fixed and committed. On 17 Nov 2009, at 19:23, Andreas Prlic wrote: > Hi Richard, > > I just did an update of my checkout and it seems the -phylo unit tests > don't compile any more. Can you take a look? > > Thanks, > Andreas > > Test set: org.biojavax.bio.phylo.io.nexus.TreesBlockTest > ------------------------------------------------------------------------------- > Tests run: 9, Failures: 0, Errors: 9, Skipped: 0, Time elapsed: 0.063 > sec <<< FAILURE! > testSimple(org.biojavax.bio.phylo.io.nexus.TreesBlockTest) Time > elapsed: 0.021 sec <<< ERROR! > java.lang.NullPointerException > at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTreeNode(TreesBlockTest.java:160) > at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTree(TreesBlockTest.java:175) > at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.doVertexCount(TreesBlockTest.java:139) > at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.testSimple(TreesBlockTest.java:63) > > testThreeOffspring(org.biojavax.bio.phylo.io.nexus.TreesBlockTest) > Time elapsed: 0.002 sec <<< ERROR! > java.lang.NullPointerException > at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTreeNode(TreesBlockTest.java:160) > at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTree(TreesBlockTest.java:175) > at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.doVertexCount(TreesBlockTest.java:139) > at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.testThreeOffspring(TreesBlockTest.java:70 > > 2009/11/16 Richard Holland : >> Patch applied to the trunk of biojava-live. Thanks for fixing it! >> >> cheers, >> Richard >> >> On 15 Nov 2009, at 23:19, Tiago Ant?o wrote: >> >>> Hi, >>> >>> I have made the changes as discussed, the code is attached to the >>> bugzilla bug concerning part of the issues that were found. >>> A few notes: >>> >>> 1. There is a ParserException raised on TreeBlock. Tough there is a >>> TreeBlockParser, most of the important parsing was (and still is!) >>> being made on TreeBlock. I would imagine that this is not the best >>> design, but I did not change it. >>> 2. I made some test cases. Also included. >>> 3. I don't mind producing some documentation, in case you accept the code. >>> 4. I noticed a few minor bugs more (like eating spaces in the names of >>> nodes). But they are really minor. >>> 5. The API was changed, but I suppose not many people were parsing >>> trees. If there were people parsing trees most probably the bug on not >>> being able to process trees that are not binary would have been >>> detected as it is pretty major. >>> >>> Tiago >>> >>> -- >>> ?Pessimism of the Intellect; Optimism of the Will? -Antonio Gramsci >>> >>> _______________________________________________ >>> Biojava-l mailing list - Biojava-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biojava-l >> >> -- >> Richard Holland, BSc MBCS >> Operations and Delivery Director, Eagle Genomics Ltd >> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com >> http://www.eaglegenomics.com/ >> >> >> _______________________________________________ >> Biojava-l mailing list - Biojava-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From matias.piipari at gmail.com Wed Nov 18 07:07:40 2009 From: matias.piipari at gmail.com (Matias Piipari) Date: Wed, 18 Nov 2009 12:07:40 +0000 Subject: [Biojava-dev] HashMap ==> LinkedHashMap in HashSequenceDB In-Reply-To: <32ED0451-526B-4848-8FD2-A85545851922@eaglegenomics.com> References: <15cdf3360911160653q4602960fwe02924c01b976405@mail.gmail.com> <32ED0451-526B-4848-8FD2-A85545851922@eaglegenomics.com> Message-ID: <15cdf3360911180407v300a2c2fkb2fde6cb6dadf8fe@mail.gmail.com> According to this performance benchmark: http://www.artima.com/weblogs/viewpost.jsp?thread=122295 "*LinkedHashMap* tends to be slower than *HashMap* for insertions because it maintains the linked list (to preserve insertion order) in addition to the hashed data structure. Because of this list, iteration is faster." Relative to HashMap, LinkedHashMap takes approx 2.x time with put, approx 1.3x with get, 0.6x with iterate. I wouldn't expect real life performance changes from this (key-value insertion to a sequence database object probably not a common performance bottleneck in apps using biojava - am I correct?) On Mon, Nov 16, 2009 at 2:59 PM, Richard Holland wrote: > Sounds like a plan - are there any performance implications? > > On 16 Nov 2009, at 14:53, Matias Piipari wrote: > > > Hello > > > > I'd like to propose a change to org.biojava.bio.seq.db.HashSequenceDB: > swap > > the map implementation used to store the sequence-by-id map from HashMap > to > > LinkedHashMap. This would allow iterating the sequences in a defined > order > > (the order in which they were added to the map). > > > > Best wishes > > Matias > > > > > > An example patch relative to rev 7059: > > > > --- src/org/biojava/bio/seq/db/HashSequenceDB.java (revision 7059) > > +++ src/org/biojava/bio/seq/db/HashSequenceDB.java (working copy) > > @@ -22,8 +22,8 @@ > > package org.biojava.bio.seq.db; > > > > import java.io.Serializable; > > -import java.util.HashMap; > > import java.util.Iterator; > > +import java.util.LinkedHashMap; > > import java.util.Map; > > import java.util.Set; > > > > @@ -203,6 +203,6 @@ > > public HashSequenceDB(org.biojava.bio.seq.db.IDMaker idMaker, String > > name) { > > this.idMaker = idMaker; > > this.name = name; > > - this.sequenceByID = new HashMap(); > > + this.sequenceByID = new LinkedHashMap(); > > } > > } > > _______________________________________________ > > biojava-dev mailing list > > biojava-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-dev > > -- > Richard Holland, BSc MBCS > Operations and Delivery Director, Eagle Genomics Ltd > T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com > http://www.eaglegenomics.com/ > > From thomas.a.down at googlemail.com Wed Nov 18 07:14:39 2009 From: thomas.a.down at googlemail.com (Thomas Down) Date: Wed, 18 Nov 2009 12:14:39 +0000 Subject: [Biojava-dev] HashMap ==> LinkedHashMap in HashSequenceDB In-Reply-To: <15cdf3360911180407v300a2c2fkb2fde6cb6dadf8fe@mail.gmail.com> References: <15cdf3360911160653q4602960fwe02924c01b976405@mail.gmail.com> <32ED0451-526B-4848-8FD2-A85545851922@eaglegenomics.com> <15cdf3360911180407v300a2c2fkb2fde6cb6dadf8fe@mail.gmail.com> Message-ID: <6a132cea0911180414l7021f3c5xb3a2a3de677fe627@mail.gmail.com> I'd be utterly shocked if this turned out to be a noticeable difference. Thomas. On Wed, Nov 18, 2009 at 12:07 PM, Matias Piipari wrote: > According to this performance benchmark: > http://www.artima.com/weblogs/viewpost.jsp?thread=122295 > > "*LinkedHashMap* tends to be slower than *HashMap* for insertions because > it > maintains the linked list (to preserve insertion order) in addition to the > hashed data structure. Because of this list, iteration is faster." > > Relative to HashMap, LinkedHashMap takes approx 2.x time with put, approx > 1.3x with get, 0.6x with iterate. > I wouldn't expect real life performance changes from this (key-value > insertion to a sequence database object probably not a common performance > bottleneck in apps using biojava - am I correct?) > > On Mon, Nov 16, 2009 at 2:59 PM, Richard Holland > wrote: > > > Sounds like a plan - are there any performance implications? > > > > On 16 Nov 2009, at 14:53, Matias Piipari wrote: > > > > > Hello > > > > > > I'd like to propose a change to org.biojava.bio.seq.db.HashSequenceDB: > > swap > > > the map implementation used to store the sequence-by-id map from > HashMap > > to > > > LinkedHashMap. This would allow iterating the sequences in a defined > > order > > > (the order in which they were added to the map). > > > > > > Best wishes > > > Matias > > > > > > > > > An example patch relative to rev 7059: > > > > > > --- src/org/biojava/bio/seq/db/HashSequenceDB.java (revision 7059) > > > +++ src/org/biojava/bio/seq/db/HashSequenceDB.java (working copy) > > > @@ -22,8 +22,8 @@ > > > package org.biojava.bio.seq.db; > > > > > > import java.io.Serializable; > > > -import java.util.HashMap; > > > import java.util.Iterator; > > > +import java.util.LinkedHashMap; > > > import java.util.Map; > > > import java.util.Set; > > > > > > @@ -203,6 +203,6 @@ > > > public HashSequenceDB(org.biojava.bio.seq.db.IDMaker idMaker, String > > > name) { > > > this.idMaker = idMaker; > > > this.name = name; > > > - this.sequenceByID = new HashMap(); > > > + this.sequenceByID = new LinkedHashMap(); > > > } > > > } > > > _______________________________________________ > > > biojava-dev mailing list > > > biojava-dev at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/biojava-dev > > > > -- > > Richard Holland, BSc MBCS > > Operations and Delivery Director, Eagle Genomics Ltd > > T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com > > http://www.eaglegenomics.com/ > > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From tiagoantao at gmail.com Tue Nov 17 14:54:21 2009 From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=) Date: Tue, 17 Nov 2009 19:54:21 +0000 Subject: [Biojava-dev] [Biojava-l] Newick parser In-Reply-To: References: <6d941f120911151519s732144fu1150d672107fca1e@mail.gmail.com> <59a41c430911171123j43806c25vda67e406aa2d3caa@mail.gmail.com> Message-ID: <6d941f120911171154q31df1c32taff20f5b282867bc@mail.gmail.com> As this was all fresh in my head, I wrote a small tutorial: http://tiago.org/cc/2009/11/17/reading-newicknexus-phylogenetic-trees-with-biojava/ As I don't follow the biojava mailing list regularly (or bug reports), if some bug arises on this code, feel free to send me an email to my personal account: If I have some time to spare, I will have a look at it. Tiago 2009/11/17 Richard Holland : > Sorry - forgot to change the filenames in the test (under the new modular system they're in a different place than in the non-modular codebase that Tiago was working from). Fixed and committed. > > On 17 Nov 2009, at 19:23, Andreas Prlic wrote: > >> Hi Richard, >> >> I just did an update of my checkout and it seems the -phylo unit tests >> don't compile any more. Can you take a look? >> >> Thanks, >> Andreas >> >> Test set: org.biojavax.bio.phylo.io.nexus.TreesBlockTest >> ------------------------------------------------------------------------------- >> Tests run: 9, Failures: 0, Errors: 9, Skipped: 0, Time elapsed: 0.063 >> sec <<< FAILURE! >> testSimple(org.biojavax.bio.phylo.io.nexus.TreesBlockTest) ?Time >> elapsed: 0.021 sec ?<<< ERROR! >> java.lang.NullPointerException >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTreeNode(TreesBlockTest.java:160) >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTree(TreesBlockTest.java:175) >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.doVertexCount(TreesBlockTest.java:139) >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.testSimple(TreesBlockTest.java:63) >> >> testThreeOffspring(org.biojavax.bio.phylo.io.nexus.TreesBlockTest) >> Time elapsed: 0.002 sec ?<<< ERROR! >> java.lang.NullPointerException >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTreeNode(TreesBlockTest.java:160) >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTree(TreesBlockTest.java:175) >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.doVertexCount(TreesBlockTest.java:139) >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.testThreeOffspring(TreesBlockTest.java:70 >> >> 2009/11/16 Richard Holland : >>> Patch applied to the trunk of biojava-live. Thanks for fixing it! >>> >>> cheers, >>> Richard >>> >>> On 15 Nov 2009, at 23:19, Tiago Ant?o wrote: >>> >>>> Hi, >>>> >>>> I have made the changes as discussed, the code is attached to the >>>> bugzilla bug concerning part of the issues that were found. >>>> A few notes: >>>> >>>> 1. There is a ParserException raised on TreeBlock. Tough there is a >>>> TreeBlockParser, most of the important parsing was (and still is!) >>>> being made on TreeBlock. I would imagine that this is not the best >>>> design, but I did not change it. >>>> 2. I made some test cases. Also included. >>>> 3. I don't mind producing some documentation, in case you accept the code. >>>> 4. I noticed a few minor bugs more (like eating spaces in the names of >>>> nodes). But they are really minor. >>>> 5. The API was changed, but I suppose not many people were parsing >>>> trees. If there were people parsing trees most probably the bug on not >>>> being able to process trees that are not binary would have been >>>> detected as it is pretty major. >>>> >>>> Tiago >>>> >>>> -- >>>> ?Pessimism of the Intellect; Optimism of the Will? -Antonio Gramsci >>>> >>>> _______________________________________________ >>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>> >>> -- >>> Richard Holland, BSc MBCS >>> Operations and Delivery Director, Eagle Genomics Ltd >>> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com >>> http://www.eaglegenomics.com/ >>> >>> >>> _______________________________________________ >>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>> > > -- > Richard Holland, BSc MBCS > Operations and Delivery Director, Eagle Genomics Ltd > T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com > http://www.eaglegenomics.com/ > > -- ?Pessimism of the Intellect; Optimism of the Will? -Antonio Gramsci From invite+maeygmgn at facebookmail.com Mon Nov 23 00:52:13 2009 From: invite+maeygmgn at facebookmail.com (Biswaroop Ghosh) Date: Sun, 22 Nov 2009 21:52:13 -0800 Subject: [Biojava-dev] Check out my photos on Facebook Message-ID: Hi Biojava-dev, I set up a Facebook profile where I can post my pictures, videos and events and I want to add you as a friend so you can see it. First, you need to join Facebook! Once you join, you can also create your own profile. Thanks, Biswaroop To sign up for Facebook, follow the link below: http://www.facebook.com/p.php?i=695556070&k=4V1Y3XW3UTXN3CD1RKWVPVT2ZPFF4X&r Already have an account? Add this email address to your account http://www.facebook.com/n/?merge_accounts.php&e=biojava-dev at biojava.org&c=a29fd3b2297228c482384df0f8e6b128.biojava-dev at biojava.org was invited to join Facebook by Biswaroop Ghosh. If you do not wish to receive this type of email from Facebook in the future, please click on the link below to unsubscribe. http://www.facebook.com/o.php?k=e57693&u=693100398&mid=174203bG294fdf6eG0G8 Facebook's offices are located at 1601 S. California Ave., Palo Alto, CA 94304. From holland at eaglegenomics.com Tue Nov 24 10:27:20 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Tue, 24 Nov 2009 15:27:20 +0000 Subject: [Biojava-dev] Hackathon in January Message-ID: <1235107C-E1D2-4EEB-8A5F-2335751120EE@eaglegenomics.com> Hi all. To anyone planning on attending the BioJava hackathon in Cambridge (UK) in January, now would be a good time to sort out travel arrangements. If you're intending to come but haven't yet said so, please do let me know so that I can ensure we get a big enough room to work in! cheers, Richard -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From andreas at sdsc.edu Tue Nov 24 12:54:38 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Tue, 24 Nov 2009 09:54:38 -0800 Subject: [Biojava-dev] [Biojava-l] Hackathon in January In-Reply-To: <1235107C-E1D2-4EEB-8A5F-2335751120EE@eaglegenomics.com> References: <1235107C-E1D2-4EEB-8A5F-2335751120EE@eaglegenomics.com> Message-ID: <59a41c430911240954g589496dbg60a829d711131fab@mail.gmail.com> * Is anybody interested in following the ongoings at the hackaton via an online-stream? - I received a request about this and am wondering if more people would be interested in this. * Just to repeat the current status regarding the program: So far the plan is to continue working on the new modules. Ideally we will have a brand new biojava 3 ready soon after the hackaton. A more detailed program for the week will be sent out in January. If anybody wants to propose feature requests, you can have a look at the current todo list for the modules: http://biojava.org/wiki/BioJava:Modules Andreas On Tue, Nov 24, 2009 at 7:27 AM, Richard Holland wrote: > Hi all. > > To anyone planning on attending the BioJava hackathon in Cambridge (UK) in January, now would be a good time to sort out travel arrangements. If you're intending to come but haven't yet said so, please do let me know so that I can ensure we get a big enough room to work in! > > cheers, > Richard > > -- > Richard Holland, BSc MBCS > Operations and Delivery Director, Eagle Genomics Ltd > T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com > http://www.eaglegenomics.com/ > > > _______________________________________________ > Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From ayates at ebi.ac.uk Wed Nov 25 07:51:23 2009 From: ayates at ebi.ac.uk (Andy Yates) Date: Wed, 25 Nov 2009 12:51:23 +0000 Subject: [Biojava-dev] [Biojava-l] Hackathon in January In-Reply-To: <59a41c430911240954g589496dbg60a829d711131fab@mail.gmail.com> References: <1235107C-E1D2-4EEB-8A5F-2335751120EE@eaglegenomics.com> <59a41c430911240954g589496dbg60a829d711131fab@mail.gmail.com> Message-ID: <4DA69755-069B-4E70-BBE2-AEB408AE7E02@ebi.ac.uk> By online stream do you mean Wave or Twitter or something else trendy? :) Andy On 24 Nov 2009, at 17:54, Andreas Prlic wrote: > * Is anybody interested in following the ongoings at the hackaton via > an online-stream? - I received a request about this and am wondering > if more people would be interested in this. > > * Just to repeat the current status regarding the program: So far the > plan is to continue working on the new modules. Ideally we will have a > brand new biojava 3 ready soon after the hackaton. A more detailed > program for the week will be sent out in January. > > If anybody wants to propose feature requests, you can have a look at > the current todo list for the modules: > http://biojava.org/wiki/BioJava:Modules > > Andreas > > > > On Tue, Nov 24, 2009 at 7:27 AM, Richard Holland > wrote: >> Hi all. >> >> To anyone planning on attending the BioJava hackathon in Cambridge >> (UK) in January, now would be a good time to sort out travel >> arrangements. If you're intending to come but haven't yet said so, >> please do let me know so that I can ensure we get a big enough room >> to work in! >> >> cheers, >> Richard >> >> -- >> Richard Holland, BSc MBCS >> Operations and Delivery Director, Eagle Genomics Ltd >> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com >> http://www.eaglegenomics.com/ >> >> >> _______________________________________________ >> Biojava-l mailing list - Biojava-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev From heuermh at acm.org Wed Nov 25 14:05:22 2009 From: heuermh at acm.org (Michael Heuer) Date: Wed, 25 Nov 2009 14:05:22 -0500 (EST) Subject: [Biojava-dev] [Biojava-l] Hackathon in January In-Reply-To: <4DA69755-069B-4E70-BBE2-AEB408AE7E02@ebi.ac.uk> Message-ID: I would be fine with irc and the biojava wiki. We might set up a channel on freenode for biojava, or perhaps one for all of open-bio http://freenode.net/group_registration.shtml michael Andy Yates wrote: > By online stream do you mean Wave or Twitter or something else > trendy? :) > > Andy > > On 24 Nov 2009, at 17:54, Andreas Prlic wrote: > > > * Is anybody interested in following the ongoings at the hackaton via > > an online-stream? - I received a request about this and am wondering > > if more people would be interested in this. > > > > * Just to repeat the current status regarding the program: So far the > > plan is to continue working on the new modules. Ideally we will have a > > brand new biojava 3 ready soon after the hackaton. A more detailed > > program for the week will be sent out in January. > > > > If anybody wants to propose feature requests, you can have a look at > > the current todo list for the modules: > > http://biojava.org/wiki/BioJava:Modules > > > > Andreas > > > > > > > > On Tue, Nov 24, 2009 at 7:27 AM, Richard Holland > > wrote: > >> Hi all. > >> > >> To anyone planning on attending the BioJava hackathon in Cambridge > >> (UK) in January, now would be a good time to sort out travel > >> arrangements. If you're intending to come but haven't yet said so, > >> please do let me know so that I can ensure we get a big enough room > >> to work in! > >> > >> cheers, > >> Richard > >> > >> -- > >> Richard Holland, BSc MBCS > >> Operations and Delivery Director, Eagle Genomics Ltd > >> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com > >> http://www.eaglegenomics.com/ > >> > >> > >> _______________________________________________ > >> Biojava-l mailing list - Biojava-l at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/biojava-l > >> > > > > _______________________________________________ > > biojava-dev mailing list > > biojava-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-dev > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From andreas at sdsc.edu Wed Nov 25 15:08:33 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Wed, 25 Nov 2009 12:08:33 -0800 Subject: [Biojava-dev] [Biojava-l] Hackathon in January In-Reply-To: <4DA69755-069B-4E70-BBE2-AEB408AE7E02@ebi.ac.uk> References: <1235107C-E1D2-4EEB-8A5F-2335751120EE@eaglegenomics.com> <59a41c430911240954g589496dbg60a829d711131fab@mail.gmail.com> <4DA69755-069B-4E70-BBE2-AEB408AE7E02@ebi.ac.uk> Message-ID: <59a41c430911251208u44bb1218l7cb0065657ed7227@mail.gmail.com> I was thinking about video... I would expect that some of the participants will do some sort of tweeting, blogging, etc. Andreas On Wed, Nov 25, 2009 at 4:51 AM, Andy Yates wrote: > By online stream do you mean Wave or Twitter or something else trendy? :) > > Andy > > On 24 Nov 2009, at 17:54, Andreas Prlic wrote: > >> * Is anybody interested in following the ongoings at the hackaton via >> an online-stream? - I received a request about this and am wondering >> if more people would be interested in this. >> >> * Just to repeat the current status regarding the program: So far the >> plan is to continue working on the new modules. Ideally we will have a >> brand new biojava 3 ready soon after the hackaton. A more detailed >> program for the week will be sent out in January. >> >> If anybody wants to propose feature requests, you can have a look at >> the current todo list for the modules: >> http://biojava.org/wiki/BioJava:Modules >> >> Andreas >> >> >> >> On Tue, Nov 24, 2009 at 7:27 AM, Richard Holland >> wrote: >>> >>> Hi all. >>> >>> To anyone planning on attending the BioJava hackathon in Cambridge (UK) >>> in January, now would be a good time to sort out travel arrangements. If >>> you're intending to come but haven't yet said so, please do let me know so >>> that I can ensure we get a big enough room to work in! >>> >>> cheers, >>> Richard >>> >>> -- >>> Richard Holland, BSc MBCS >>> Operations and Delivery Director, Eagle Genomics Ltd >>> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com >>> http://www.eaglegenomics.com/ >>> >>> >>> _______________________________________________ >>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>> >> >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev > > From jw12 at sanger.ac.uk Thu Nov 26 09:57:35 2009 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Thu, 26 Nov 2009 14:57:35 +0000 Subject: [Biojava-dev] DAS workshop 7th-9th April 2010 Message-ID: We are considering running a Distributed Annotation System workshop here at the Sanger/EBI in the UK subject to decent demand. The workshop will be held from Wednesday 7th-Friday 9th April 2010. If you would be interested in attending either to present or just take part then please email me jw12 at sanger.ac.uk The format of the workshop is likely to be similar to last years (1st day for beginners, 2nd for both beginners and advanced users, 3rd day for advanced), information for which can be found here: http://www.dasregistry.org/course.jsp If you would like to present then please send a short summary of what you would like to talk about. Thanks Jonathan. Jonathan Warren Senior Developer and DAS coordinator jw12 at sanger.ac.uk -- 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 suzi at berkeleybop.org Sun Nov 29 23:03:09 2009 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Sun, 29 Nov 2009 20:03:09 -0800 Subject: [Biojava-dev] [DAS] DAS workshop 7th-9th April 2010 In-Reply-To: References: Message-ID: <3AD3C819-4BAA-4D90-B141-9611F48C5CAD@ berkeleybop.org> I/we (Gregg) would be interested in attending. We'd present an update on the collaborative, web-based version of Apollo. We will be working with Ian Holmes and Mitch Skinner using JBrowse for basic display. -S On Nov 26, 2009, at 6:57 AM, Jonathan Warren wrote: > We are considering running a Distributed Annotation System workshop here at the Sanger/EBI in the UK subject to decent demand. > The workshop will be held from Wednesday 7th-Friday 9th April 2010. If you would be interested in attending either to present or just take part > then please email me jw12 at sanger.ac.uk > > The format of the workshop is likely to be similar to last years (1st day for beginners, 2nd for both beginners and advanced users, 3rd day for advanced), information for which can be found here: > http://www.dasregistry.org/course.jsp > > If you would like to present then please send a short summary of what you would like to talk about. > > Thanks > > Jonathan. > > Jonathan Warren > Senior Developer and DAS coordinator > jw12 at sanger.ac.uk > > > > > > > > > > -- > The Wellcome Trust Sanger Institute is operated by Genome ResearchLimited, a charity registered in England with number 1021457 and acompany registered in England with number 2742969, whose registeredoffice is 215 Euston Road, London, NW1 2BE._______________________________________________ > DAS mailing list > DAS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das > From mauricio at open-bio.org Thu Nov 26 16:45:43 2009 From: mauricio at open-bio.org (Mauricio Herrera Cuadra) Date: Thu, 26 Nov 2009 15:45:43 -0600 Subject: [Biojava-dev] [DAS] DAS workshop 7th-9th April 2010 In-Reply-To: References: Message-ID: <4B0EF707.6080202@open-bio.org> Hi Jonathan, Any chance it can be webcasted? I'm sure it would attract a lot of remote attendees ;) Regards, Mauricio. Jonathan Warren wrote: > We are considering running a Distributed Annotation System workshop here > at the Sanger/EBI in the UK subject to decent demand. > The workshop will be held from Wednesday 7th-Friday 9th April 2010. If > you would be interested in attending either to present or just take part > then please email me jw12 at sanger.ac.uk > > The format of the workshop is likely to be similar to last years (1st > day for beginners, 2nd for both beginners and advanced users, 3rd day > for advanced), information for which can be found here: > http://www.dasregistry.org/course.jsp > > If you would like to present then please send a short summary of what > you would like to talk about. > > Thanks > > Jonathan. > > Jonathan Warren > Senior Developer and DAS coordinator > jw12 at sanger.ac.uk > > > > > > > > > From bugzilla-daemon at portal.open-bio.org Mon Nov 2 17:52:52 2009 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 2 Nov 2009 12:52:52 -0500 Subject: [Biojava-dev] [Bug 2941] NEXUS parser fails with tree nodes called p[0-9]+ In-Reply-To: Message-ID: <200911021752.nA2HqqpR018934@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2941 ------- Comment #1 from holland at ebi.ac.uk 2009-11-02 12:52 EST ------- The reason this is happening is because JGraphT expects all nodes to have a name, but the tree strings in Nexus files don't have names for all nodes (in your case, the tree string you provide does not have a name for the sub-tree mapped to :0.15). ((1:0.1,2:0.2):0.15,p1:0.3) The 'p' notation is used internally to assign names to grouped nodes that don't have names explicitly set in the tree string. It would be good to have this as a modifiable setting, but it would still have to be set to something by default, and users would still have to check that the setting they use does not clash with any of their existing names. Volunteers to modify please? -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Sun Nov 15 23:14:40 2009 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Sun, 15 Nov 2009 18:14:40 -0500 Subject: [Biojava-dev] [Bug 2941] NEXUS parser fails with tree nodes called p[0-9]+ In-Reply-To: Message-ID: <200911152314.nAFNEeoT015030@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2941 ------- Comment #2 from tiagoantao at gmail.com 2009-11-15 18:14 EST ------- Created an attachment (id=1397) --> (http://bugzilla.open-bio.org/attachment.cgi?id=1397&action=view) Patch -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Sun Nov 15 23:17:00 2009 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Sun, 15 Nov 2009 18:17:00 -0500 Subject: [Biojava-dev] [Bug 2941] NEXUS parser fails with tree nodes called p[0-9]+ In-Reply-To: Message-ID: <200911152317.nAFNH0m1015213@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2941 ------- Comment #3 from tiagoantao at gmail.com 2009-11-15 18:16 EST ------- I've attached a patch for: 1. p* 2. Support for more than binary trees 3. Getting the top node of a tree (root in rooted trees) -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Nov 16 08:39:36 2009 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 16 Nov 2009 03:39:36 -0500 Subject: [Biojava-dev] [Bug 2941] NEXUS parser fails with tree nodes called p[0-9]+ In-Reply-To: Message-ID: <200911160839.nAG8dasi029568@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2941 holland at ebi.ac.uk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #4 from holland at ebi.ac.uk 2009-11-16 03:39 EST ------- I have applied the patch on the trunk of biojava-live (now under the phylo module). -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From matias.piipari at gmail.com Mon Nov 16 14:53:22 2009 From: matias.piipari at gmail.com (Matias Piipari) Date: Mon, 16 Nov 2009 14:53:22 +0000 Subject: [Biojava-dev] HashMap ==> LinkedHashMap in HashSequenceDB Message-ID: <15cdf3360911160653q4602960fwe02924c01b976405@mail.gmail.com> Hello I'd like to propose a change to org.biojava.bio.seq.db.HashSequenceDB: swap the map implementation used to store the sequence-by-id map from HashMap to LinkedHashMap. This would allow iterating the sequences in a defined order (the order in which they were added to the map). Best wishes Matias An example patch relative to rev 7059: --- src/org/biojava/bio/seq/db/HashSequenceDB.java (revision 7059) +++ src/org/biojava/bio/seq/db/HashSequenceDB.java (working copy) @@ -22,8 +22,8 @@ package org.biojava.bio.seq.db; import java.io.Serializable; -import java.util.HashMap; import java.util.Iterator; +import java.util.LinkedHashMap; import java.util.Map; import java.util.Set; @@ -203,6 +203,6 @@ public HashSequenceDB(org.biojava.bio.seq.db.IDMaker idMaker, String name) { this.idMaker = idMaker; this.name = name; - this.sequenceByID = new HashMap(); + this.sequenceByID = new LinkedHashMap(); } } From holland at eaglegenomics.com Mon Nov 16 14:59:19 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Mon, 16 Nov 2009 14:59:19 +0000 Subject: [Biojava-dev] HashMap ==> LinkedHashMap in HashSequenceDB In-Reply-To: <15cdf3360911160653q4602960fwe02924c01b976405@mail.gmail.com> References: <15cdf3360911160653q4602960fwe02924c01b976405@mail.gmail.com> Message-ID: <32ED0451-526B-4848-8FD2-A85545851922@eaglegenomics.com> Sounds like a plan - are there any performance implications? On 16 Nov 2009, at 14:53, Matias Piipari wrote: > Hello > > I'd like to propose a change to org.biojava.bio.seq.db.HashSequenceDB: swap > the map implementation used to store the sequence-by-id map from HashMap to > LinkedHashMap. This would allow iterating the sequences in a defined order > (the order in which they were added to the map). > > Best wishes > Matias > > > An example patch relative to rev 7059: > > --- src/org/biojava/bio/seq/db/HashSequenceDB.java (revision 7059) > +++ src/org/biojava/bio/seq/db/HashSequenceDB.java (working copy) > @@ -22,8 +22,8 @@ > package org.biojava.bio.seq.db; > > import java.io.Serializable; > -import java.util.HashMap; > import java.util.Iterator; > +import java.util.LinkedHashMap; > import java.util.Map; > import java.util.Set; > > @@ -203,6 +203,6 @@ > public HashSequenceDB(org.biojava.bio.seq.db.IDMaker idMaker, String > name) { > this.idMaker = idMaker; > this.name = name; > - this.sequenceByID = new HashMap(); > + this.sequenceByID = new LinkedHashMap(); > } > } > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From andreas at sdsc.edu Mon Nov 16 17:40:15 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Mon, 16 Nov 2009 09:40:15 -0800 Subject: [Biojava-dev] HashMap ==> LinkedHashMap in HashSequenceDB In-Reply-To: <32ED0451-526B-4848-8FD2-A85545851922@eaglegenomics.com> References: <15cdf3360911160653q4602960fwe02924c01b976405@mail.gmail.com> <32ED0451-526B-4848-8FD2-A85545851922@eaglegenomics.com> Message-ID: <59a41c430911160940m42ed1a94naceb3ec514f63e20@mail.gmail.com> Talking about Map implementations... I recently added org.biojava.utils.io.SoftHashMap It can be used to create temporary in-memory caches. It allows the Garbage Collector to clean up objects, and one does not have to take care of removing the objects from the cache. I use it to cache small files that are more efficiently read from the memory, rather than going to the hard disk (or NFS...) The code is based on http://java-interview-faqs.blogspot.com/2008/09/building-faster-and-efficient-cache.html Andreas On Mon, Nov 16, 2009 at 6:59 AM, Richard Holland wrote: > Sounds like a plan - are there any performance implications? > > On 16 Nov 2009, at 14:53, Matias Piipari wrote: > >> Hello >> >> I'd like to propose a change to org.biojava.bio.seq.db.HashSequenceDB: swap >> the map implementation used to store the sequence-by-id map from HashMap to >> LinkedHashMap. This would allow iterating the sequences in a defined order >> (the order in which they were added to the map). >> >> Best wishes >> Matias >> >> >> An example patch relative to rev 7059: >> >> --- src/org/biojava/bio/seq/db/HashSequenceDB.java ? ? ?(revision 7059) >> +++ src/org/biojava/bio/seq/db/HashSequenceDB.java ? ? ?(working copy) >> @@ -22,8 +22,8 @@ >> package org.biojava.bio.seq.db; >> >> import java.io.Serializable; >> -import java.util.HashMap; >> import java.util.Iterator; >> +import java.util.LinkedHashMap; >> import java.util.Map; >> import java.util.Set; >> >> @@ -203,6 +203,6 @@ >> ? public HashSequenceDB(org.biojava.bio.seq.db.IDMaker idMaker, String >> name) { >> ? ? this.idMaker = idMaker; >> ? ? this.name = name; >> - ? ?this.sequenceByID = new HashMap(); >> + ? ?this.sequenceByID = new LinkedHashMap(); >> ? } >> } >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev > > -- > Richard Holland, BSc MBCS > Operations and Delivery Director, Eagle Genomics Ltd > T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com > http://www.eaglegenomics.com/ > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From bugzilla-daemon at portal.open-bio.org Mon Nov 16 17:52:28 2009 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 16 Nov 2009 12:52:28 -0500 Subject: [Biojava-dev] [Bug 2679] NEXUS parse fails on extraneous comma (TREES/TRANSLATE) In-Reply-To: Message-ID: <200911161752.nAGHqSbm014843@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2679 ------- Comment #4 from tiagoantao at gmail.com 2009-11-16 12:52 EST ------- Created an attachment (id=1399) --> (http://bugzilla.open-bio.org/attachment.cgi?id=1399&action=view) Patch This solves the bug, hopefully. In theory it creates a new one, in case the initial node name (before translation) is called "tree". But that is much less likely. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Nov 16 18:11:18 2009 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org) Date: Mon, 16 Nov 2009 13:11:18 -0500 Subject: [Biojava-dev] [Bug 2679] NEXUS parse fails on extraneous comma (TREES/TRANSLATE) In-Reply-To: Message-ID: <200911161811.nAGIBIIb015514@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=2679 holland at eaglegenomics.com changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Comment #5 from holland at eaglegenomics.com 2009-11-16 13:11 EST ------- Applied to trunk of biojava-live/phylo module. -- Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From holland at eaglegenomics.com Mon Nov 16 18:13:24 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Mon, 16 Nov 2009 18:13:24 +0000 Subject: [Biojava-dev] HashMap ==> LinkedHashMap in HashSequenceDB In-Reply-To: <15cdf3360911160653q4602960fwe02924c01b976405@mail.gmail.com> References: <15cdf3360911160653q4602960fwe02924c01b976405@mail.gmail.com> Message-ID: <8731EAB9-E8A9-43C8-95E7-C4AABD9A4FBB@eaglegenomics.com> I've applied the patch to the trunk of biojava-live/core. On 16 Nov 2009, at 14:53, Matias Piipari wrote: > Hello > > I'd like to propose a change to org.biojava.bio.seq.db.HashSequenceDB: swap > the map implementation used to store the sequence-by-id map from HashMap to > LinkedHashMap. This would allow iterating the sequences in a defined order > (the order in which they were added to the map). > > Best wishes > Matias > > > An example patch relative to rev 7059: > > --- src/org/biojava/bio/seq/db/HashSequenceDB.java (revision 7059) > +++ src/org/biojava/bio/seq/db/HashSequenceDB.java (working copy) > @@ -22,8 +22,8 @@ > package org.biojava.bio.seq.db; > > import java.io.Serializable; > -import java.util.HashMap; > import java.util.Iterator; > +import java.util.LinkedHashMap; > import java.util.Map; > import java.util.Set; > > @@ -203,6 +203,6 @@ > public HashSequenceDB(org.biojava.bio.seq.db.IDMaker idMaker, String > name) { > this.idMaker = idMaker; > this.name = name; > - this.sequenceByID = new HashMap(); > + this.sequenceByID = new LinkedHashMap(); > } > } > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From andreas at sdsc.edu Tue Nov 17 19:23:44 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Tue, 17 Nov 2009 11:23:44 -0800 Subject: [Biojava-dev] [Biojava-l] Newick parser In-Reply-To: References: <6d941f120911151519s732144fu1150d672107fca1e@mail.gmail.com> Message-ID: <59a41c430911171123j43806c25vda67e406aa2d3caa@mail.gmail.com> Hi Richard, I just did an update of my checkout and it seems the -phylo unit tests don't compile any more. Can you take a look? Thanks, Andreas Test set: org.biojavax.bio.phylo.io.nexus.TreesBlockTest ------------------------------------------------------------------------------- Tests run: 9, Failures: 0, Errors: 9, Skipped: 0, Time elapsed: 0.063 sec <<< FAILURE! testSimple(org.biojavax.bio.phylo.io.nexus.TreesBlockTest) Time elapsed: 0.021 sec <<< ERROR! java.lang.NullPointerException at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTreeNode(TreesBlockTest.java:160) at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTree(TreesBlockTest.java:175) at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.doVertexCount(TreesBlockTest.java:139) at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.testSimple(TreesBlockTest.java:63) testThreeOffspring(org.biojavax.bio.phylo.io.nexus.TreesBlockTest) Time elapsed: 0.002 sec <<< ERROR! java.lang.NullPointerException at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTreeNode(TreesBlockTest.java:160) at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTree(TreesBlockTest.java:175) at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.doVertexCount(TreesBlockTest.java:139) at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.testThreeOffspring(TreesBlockTest.java:70 2009/11/16 Richard Holland : > Patch applied to the trunk of biojava-live. Thanks for fixing it! > > cheers, > Richard > > On 15 Nov 2009, at 23:19, Tiago Ant?o wrote: > >> Hi, >> >> I have made the changes as discussed, the code is attached to the >> bugzilla bug concerning part of the issues that were found. >> A few notes: >> >> 1. There is a ParserException raised on TreeBlock. Tough there is a >> TreeBlockParser, most of the important parsing was (and still is!) >> being made on TreeBlock. I would imagine that this is not the best >> design, but I did not change it. >> 2. I made some test cases. Also included. >> 3. I don't mind producing some documentation, in case you accept the code. >> 4. I noticed a few minor bugs more (like eating spaces in the names of >> nodes). But they are really minor. >> 5. The API was changed, but I suppose not many people were parsing >> trees. If there were people parsing trees most probably the bug on not >> being able to process trees that are not binary would have been >> detected as it is pretty major. >> >> Tiago >> >> -- >> ?Pessimism of the Intellect; Optimism of the Will? -Antonio Gramsci >> >> _______________________________________________ >> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l > > -- > Richard Holland, BSc MBCS > Operations and Delivery Director, Eagle Genomics Ltd > T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com > http://www.eaglegenomics.com/ > > > _______________________________________________ > Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From andreas at sdsc.edu Tue Nov 17 19:50:40 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Tue, 17 Nov 2009 11:50:40 -0800 Subject: [Biojava-dev] [Biojava-l] Newick parser In-Reply-To: References: <6d941f120911151519s732144fu1150d672107fca1e@mail.gmail.com> <59a41c430911171123j43806c25vda67e406aa2d3caa@mail.gmail.com> Message-ID: <59a41c430911171150p22badd1cx223b651cc5a54959@mail.gmail.com> thanks for the quick fix, compiles fine now. A 2009/11/17 Richard Holland : > Sorry - forgot to change the filenames in the test (under the new modular system they're in a different place than in the non-modular codebase that Tiago was working from). Fixed and committed. > > On 17 Nov 2009, at 19:23, Andreas Prlic wrote: > >> Hi Richard, >> >> I just did an update of my checkout and it seems the -phylo unit tests >> don't compile any more. Can you take a look? >> >> Thanks, >> Andreas >> >> Test set: org.biojavax.bio.phylo.io.nexus.TreesBlockTest >> ------------------------------------------------------------------------------- >> Tests run: 9, Failures: 0, Errors: 9, Skipped: 0, Time elapsed: 0.063 >> sec <<< FAILURE! >> testSimple(org.biojavax.bio.phylo.io.nexus.TreesBlockTest) ?Time >> elapsed: 0.021 sec ?<<< ERROR! >> java.lang.NullPointerException >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTreeNode(TreesBlockTest.java:160) >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTree(TreesBlockTest.java:175) >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.doVertexCount(TreesBlockTest.java:139) >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.testSimple(TreesBlockTest.java:63) >> >> testThreeOffspring(org.biojavax.bio.phylo.io.nexus.TreesBlockTest) >> Time elapsed: 0.002 sec ?<<< ERROR! >> java.lang.NullPointerException >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTreeNode(TreesBlockTest.java:160) >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTree(TreesBlockTest.java:175) >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.doVertexCount(TreesBlockTest.java:139) >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.testThreeOffspring(TreesBlockTest.java:70 >> >> 2009/11/16 Richard Holland : >>> Patch applied to the trunk of biojava-live. Thanks for fixing it! >>> >>> cheers, >>> Richard >>> >>> On 15 Nov 2009, at 23:19, Tiago Ant?o wrote: >>> >>>> Hi, >>>> >>>> I have made the changes as discussed, the code is attached to the >>>> bugzilla bug concerning part of the issues that were found. >>>> A few notes: >>>> >>>> 1. There is a ParserException raised on TreeBlock. Tough there is a >>>> TreeBlockParser, most of the important parsing was (and still is!) >>>> being made on TreeBlock. I would imagine that this is not the best >>>> design, but I did not change it. >>>> 2. I made some test cases. Also included. >>>> 3. I don't mind producing some documentation, in case you accept the code. >>>> 4. I noticed a few minor bugs more (like eating spaces in the names of >>>> nodes). But they are really minor. >>>> 5. The API was changed, but I suppose not many people were parsing >>>> trees. If there were people parsing trees most probably the bug on not >>>> being able to process trees that are not binary would have been >>>> detected as it is pretty major. >>>> >>>> Tiago >>>> >>>> -- >>>> ?Pessimism of the Intellect; Optimism of the Will? -Antonio Gramsci >>>> >>>> _______________________________________________ >>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>> >>> -- >>> Richard Holland, BSc MBCS >>> Operations and Delivery Director, Eagle Genomics Ltd >>> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com >>> http://www.eaglegenomics.com/ >>> >>> >>> _______________________________________________ >>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>> > > -- > Richard Holland, BSc MBCS > Operations and Delivery Director, Eagle Genomics Ltd > T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com > http://www.eaglegenomics.com/ > > From holland at eaglegenomics.com Tue Nov 17 19:47:44 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Tue, 17 Nov 2009 19:47:44 +0000 Subject: [Biojava-dev] [Biojava-l] Newick parser In-Reply-To: <59a41c430911171123j43806c25vda67e406aa2d3caa@mail.gmail.com> References: <6d941f120911151519s732144fu1150d672107fca1e@mail.gmail.com> <59a41c430911171123j43806c25vda67e406aa2d3caa@mail.gmail.com> Message-ID: Sorry - forgot to change the filenames in the test (under the new modular system they're in a different place than in the non-modular codebase that Tiago was working from). Fixed and committed. On 17 Nov 2009, at 19:23, Andreas Prlic wrote: > Hi Richard, > > I just did an update of my checkout and it seems the -phylo unit tests > don't compile any more. Can you take a look? > > Thanks, > Andreas > > Test set: org.biojavax.bio.phylo.io.nexus.TreesBlockTest > ------------------------------------------------------------------------------- > Tests run: 9, Failures: 0, Errors: 9, Skipped: 0, Time elapsed: 0.063 > sec <<< FAILURE! > testSimple(org.biojavax.bio.phylo.io.nexus.TreesBlockTest) Time > elapsed: 0.021 sec <<< ERROR! > java.lang.NullPointerException > at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTreeNode(TreesBlockTest.java:160) > at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTree(TreesBlockTest.java:175) > at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.doVertexCount(TreesBlockTest.java:139) > at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.testSimple(TreesBlockTest.java:63) > > testThreeOffspring(org.biojavax.bio.phylo.io.nexus.TreesBlockTest) > Time elapsed: 0.002 sec <<< ERROR! > java.lang.NullPointerException > at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTreeNode(TreesBlockTest.java:160) > at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTree(TreesBlockTest.java:175) > at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.doVertexCount(TreesBlockTest.java:139) > at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.testThreeOffspring(TreesBlockTest.java:70 > > 2009/11/16 Richard Holland : >> Patch applied to the trunk of biojava-live. Thanks for fixing it! >> >> cheers, >> Richard >> >> On 15 Nov 2009, at 23:19, Tiago Ant?o wrote: >> >>> Hi, >>> >>> I have made the changes as discussed, the code is attached to the >>> bugzilla bug concerning part of the issues that were found. >>> A few notes: >>> >>> 1. There is a ParserException raised on TreeBlock. Tough there is a >>> TreeBlockParser, most of the important parsing was (and still is!) >>> being made on TreeBlock. I would imagine that this is not the best >>> design, but I did not change it. >>> 2. I made some test cases. Also included. >>> 3. I don't mind producing some documentation, in case you accept the code. >>> 4. I noticed a few minor bugs more (like eating spaces in the names of >>> nodes). But they are really minor. >>> 5. The API was changed, but I suppose not many people were parsing >>> trees. If there were people parsing trees most probably the bug on not >>> being able to process trees that are not binary would have been >>> detected as it is pretty major. >>> >>> Tiago >>> >>> -- >>> ?Pessimism of the Intellect; Optimism of the Will? -Antonio Gramsci >>> >>> _______________________________________________ >>> Biojava-l mailing list - Biojava-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biojava-l >> >> -- >> Richard Holland, BSc MBCS >> Operations and Delivery Director, Eagle Genomics Ltd >> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com >> http://www.eaglegenomics.com/ >> >> >> _______________________________________________ >> Biojava-l mailing list - Biojava-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From matias.piipari at gmail.com Wed Nov 18 12:07:40 2009 From: matias.piipari at gmail.com (Matias Piipari) Date: Wed, 18 Nov 2009 12:07:40 +0000 Subject: [Biojava-dev] HashMap ==> LinkedHashMap in HashSequenceDB In-Reply-To: <32ED0451-526B-4848-8FD2-A85545851922@eaglegenomics.com> References: <15cdf3360911160653q4602960fwe02924c01b976405@mail.gmail.com> <32ED0451-526B-4848-8FD2-A85545851922@eaglegenomics.com> Message-ID: <15cdf3360911180407v300a2c2fkb2fde6cb6dadf8fe@mail.gmail.com> According to this performance benchmark: http://www.artima.com/weblogs/viewpost.jsp?thread=122295 "*LinkedHashMap* tends to be slower than *HashMap* for insertions because it maintains the linked list (to preserve insertion order) in addition to the hashed data structure. Because of this list, iteration is faster." Relative to HashMap, LinkedHashMap takes approx 2.x time with put, approx 1.3x with get, 0.6x with iterate. I wouldn't expect real life performance changes from this (key-value insertion to a sequence database object probably not a common performance bottleneck in apps using biojava - am I correct?) On Mon, Nov 16, 2009 at 2:59 PM, Richard Holland wrote: > Sounds like a plan - are there any performance implications? > > On 16 Nov 2009, at 14:53, Matias Piipari wrote: > > > Hello > > > > I'd like to propose a change to org.biojava.bio.seq.db.HashSequenceDB: > swap > > the map implementation used to store the sequence-by-id map from HashMap > to > > LinkedHashMap. This would allow iterating the sequences in a defined > order > > (the order in which they were added to the map). > > > > Best wishes > > Matias > > > > > > An example patch relative to rev 7059: > > > > --- src/org/biojava/bio/seq/db/HashSequenceDB.java (revision 7059) > > +++ src/org/biojava/bio/seq/db/HashSequenceDB.java (working copy) > > @@ -22,8 +22,8 @@ > > package org.biojava.bio.seq.db; > > > > import java.io.Serializable; > > -import java.util.HashMap; > > import java.util.Iterator; > > +import java.util.LinkedHashMap; > > import java.util.Map; > > import java.util.Set; > > > > @@ -203,6 +203,6 @@ > > public HashSequenceDB(org.biojava.bio.seq.db.IDMaker idMaker, String > > name) { > > this.idMaker = idMaker; > > this.name = name; > > - this.sequenceByID = new HashMap(); > > + this.sequenceByID = new LinkedHashMap(); > > } > > } > > _______________________________________________ > > biojava-dev mailing list > > biojava-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-dev > > -- > Richard Holland, BSc MBCS > Operations and Delivery Director, Eagle Genomics Ltd > T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com > http://www.eaglegenomics.com/ > > From thomas.a.down at googlemail.com Wed Nov 18 12:14:39 2009 From: thomas.a.down at googlemail.com (Thomas Down) Date: Wed, 18 Nov 2009 12:14:39 +0000 Subject: [Biojava-dev] HashMap ==> LinkedHashMap in HashSequenceDB In-Reply-To: <15cdf3360911180407v300a2c2fkb2fde6cb6dadf8fe@mail.gmail.com> References: <15cdf3360911160653q4602960fwe02924c01b976405@mail.gmail.com> <32ED0451-526B-4848-8FD2-A85545851922@eaglegenomics.com> <15cdf3360911180407v300a2c2fkb2fde6cb6dadf8fe@mail.gmail.com> Message-ID: <6a132cea0911180414l7021f3c5xb3a2a3de677fe627@mail.gmail.com> I'd be utterly shocked if this turned out to be a noticeable difference. Thomas. On Wed, Nov 18, 2009 at 12:07 PM, Matias Piipari wrote: > According to this performance benchmark: > http://www.artima.com/weblogs/viewpost.jsp?thread=122295 > > "*LinkedHashMap* tends to be slower than *HashMap* for insertions because > it > maintains the linked list (to preserve insertion order) in addition to the > hashed data structure. Because of this list, iteration is faster." > > Relative to HashMap, LinkedHashMap takes approx 2.x time with put, approx > 1.3x with get, 0.6x with iterate. > I wouldn't expect real life performance changes from this (key-value > insertion to a sequence database object probably not a common performance > bottleneck in apps using biojava - am I correct?) > > On Mon, Nov 16, 2009 at 2:59 PM, Richard Holland > wrote: > > > Sounds like a plan - are there any performance implications? > > > > On 16 Nov 2009, at 14:53, Matias Piipari wrote: > > > > > Hello > > > > > > I'd like to propose a change to org.biojava.bio.seq.db.HashSequenceDB: > > swap > > > the map implementation used to store the sequence-by-id map from > HashMap > > to > > > LinkedHashMap. This would allow iterating the sequences in a defined > > order > > > (the order in which they were added to the map). > > > > > > Best wishes > > > Matias > > > > > > > > > An example patch relative to rev 7059: > > > > > > --- src/org/biojava/bio/seq/db/HashSequenceDB.java (revision 7059) > > > +++ src/org/biojava/bio/seq/db/HashSequenceDB.java (working copy) > > > @@ -22,8 +22,8 @@ > > > package org.biojava.bio.seq.db; > > > > > > import java.io.Serializable; > > > -import java.util.HashMap; > > > import java.util.Iterator; > > > +import java.util.LinkedHashMap; > > > import java.util.Map; > > > import java.util.Set; > > > > > > @@ -203,6 +203,6 @@ > > > public HashSequenceDB(org.biojava.bio.seq.db.IDMaker idMaker, String > > > name) { > > > this.idMaker = idMaker; > > > this.name = name; > > > - this.sequenceByID = new HashMap(); > > > + this.sequenceByID = new LinkedHashMap(); > > > } > > > } > > > _______________________________________________ > > > biojava-dev mailing list > > > biojava-dev at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/biojava-dev > > > > -- > > Richard Holland, BSc MBCS > > Operations and Delivery Director, Eagle Genomics Ltd > > T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com > > http://www.eaglegenomics.com/ > > > > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev > From tiagoantao at gmail.com Tue Nov 17 19:54:21 2009 From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=) Date: Tue, 17 Nov 2009 19:54:21 +0000 Subject: [Biojava-dev] [Biojava-l] Newick parser In-Reply-To: References: <6d941f120911151519s732144fu1150d672107fca1e@mail.gmail.com> <59a41c430911171123j43806c25vda67e406aa2d3caa@mail.gmail.com> Message-ID: <6d941f120911171154q31df1c32taff20f5b282867bc@mail.gmail.com> As this was all fresh in my head, I wrote a small tutorial: http://tiago.org/cc/2009/11/17/reading-newicknexus-phylogenetic-trees-with-biojava/ As I don't follow the biojava mailing list regularly (or bug reports), if some bug arises on this code, feel free to send me an email to my personal account: If I have some time to spare, I will have a look at it. Tiago 2009/11/17 Richard Holland : > Sorry - forgot to change the filenames in the test (under the new modular system they're in a different place than in the non-modular codebase that Tiago was working from). Fixed and committed. > > On 17 Nov 2009, at 19:23, Andreas Prlic wrote: > >> Hi Richard, >> >> I just did an update of my checkout and it seems the -phylo unit tests >> don't compile any more. Can you take a look? >> >> Thanks, >> Andreas >> >> Test set: org.biojavax.bio.phylo.io.nexus.TreesBlockTest >> ------------------------------------------------------------------------------- >> Tests run: 9, Failures: 0, Errors: 9, Skipped: 0, Time elapsed: 0.063 >> sec <<< FAILURE! >> testSimple(org.biojavax.bio.phylo.io.nexus.TreesBlockTest) ?Time >> elapsed: 0.021 sec ?<<< ERROR! >> java.lang.NullPointerException >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTreeNode(TreesBlockTest.java:160) >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTree(TreesBlockTest.java:175) >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.doVertexCount(TreesBlockTest.java:139) >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.testSimple(TreesBlockTest.java:63) >> >> testThreeOffspring(org.biojavax.bio.phylo.io.nexus.TreesBlockTest) >> Time elapsed: 0.002 sec ?<<< ERROR! >> java.lang.NullPointerException >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTreeNode(TreesBlockTest.java:160) >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.getTree(TreesBlockTest.java:175) >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.doVertexCount(TreesBlockTest.java:139) >> ? ? ? at org.biojavax.bio.phylo.io.nexus.TreesBlockTest.testThreeOffspring(TreesBlockTest.java:70 >> >> 2009/11/16 Richard Holland : >>> Patch applied to the trunk of biojava-live. Thanks for fixing it! >>> >>> cheers, >>> Richard >>> >>> On 15 Nov 2009, at 23:19, Tiago Ant?o wrote: >>> >>>> Hi, >>>> >>>> I have made the changes as discussed, the code is attached to the >>>> bugzilla bug concerning part of the issues that were found. >>>> A few notes: >>>> >>>> 1. There is a ParserException raised on TreeBlock. Tough there is a >>>> TreeBlockParser, most of the important parsing was (and still is!) >>>> being made on TreeBlock. I would imagine that this is not the best >>>> design, but I did not change it. >>>> 2. I made some test cases. Also included. >>>> 3. I don't mind producing some documentation, in case you accept the code. >>>> 4. I noticed a few minor bugs more (like eating spaces in the names of >>>> nodes). But they are really minor. >>>> 5. The API was changed, but I suppose not many people were parsing >>>> trees. If there were people parsing trees most probably the bug on not >>>> being able to process trees that are not binary would have been >>>> detected as it is pretty major. >>>> >>>> Tiago >>>> >>>> -- >>>> ?Pessimism of the Intellect; Optimism of the Will? -Antonio Gramsci >>>> >>>> _______________________________________________ >>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>> >>> -- >>> Richard Holland, BSc MBCS >>> Operations and Delivery Director, Eagle Genomics Ltd >>> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com >>> http://www.eaglegenomics.com/ >>> >>> >>> _______________________________________________ >>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>> > > -- > Richard Holland, BSc MBCS > Operations and Delivery Director, Eagle Genomics Ltd > T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com > http://www.eaglegenomics.com/ > > -- ?Pessimism of the Intellect; Optimism of the Will? -Antonio Gramsci From invite+maeygmgn at facebookmail.com Mon Nov 23 05:52:13 2009 From: invite+maeygmgn at facebookmail.com (Biswaroop Ghosh) Date: Sun, 22 Nov 2009 21:52:13 -0800 Subject: [Biojava-dev] Check out my photos on Facebook Message-ID: Hi Biojava-dev, I set up a Facebook profile where I can post my pictures, videos and events and I want to add you as a friend so you can see it. First, you need to join Facebook! Once you join, you can also create your own profile. Thanks, Biswaroop To sign up for Facebook, follow the link below: http://www.facebook.com/p.php?i=695556070&k=4V1Y3XW3UTXN3CD1RKWVPVT2ZPFF4X&r Already have an account? Add this email address to your account http://www.facebook.com/n/?merge_accounts.php&e=biojava-dev at biojava.org&c=a29fd3b2297228c482384df0f8e6b128.biojava-dev at biojava.org was invited to join Facebook by Biswaroop Ghosh. If you do not wish to receive this type of email from Facebook in the future, please click on the link below to unsubscribe. http://www.facebook.com/o.php?k=e57693&u=693100398&mid=174203bG294fdf6eG0G8 Facebook's offices are located at 1601 S. California Ave., Palo Alto, CA 94304. From holland at eaglegenomics.com Tue Nov 24 15:27:20 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Tue, 24 Nov 2009 15:27:20 +0000 Subject: [Biojava-dev] Hackathon in January Message-ID: <1235107C-E1D2-4EEB-8A5F-2335751120EE@eaglegenomics.com> Hi all. To anyone planning on attending the BioJava hackathon in Cambridge (UK) in January, now would be a good time to sort out travel arrangements. If you're intending to come but haven't yet said so, please do let me know so that I can ensure we get a big enough room to work in! cheers, Richard -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From andreas at sdsc.edu Tue Nov 24 17:54:38 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Tue, 24 Nov 2009 09:54:38 -0800 Subject: [Biojava-dev] [Biojava-l] Hackathon in January In-Reply-To: <1235107C-E1D2-4EEB-8A5F-2335751120EE@eaglegenomics.com> References: <1235107C-E1D2-4EEB-8A5F-2335751120EE@eaglegenomics.com> Message-ID: <59a41c430911240954g589496dbg60a829d711131fab@mail.gmail.com> * Is anybody interested in following the ongoings at the hackaton via an online-stream? - I received a request about this and am wondering if more people would be interested in this. * Just to repeat the current status regarding the program: So far the plan is to continue working on the new modules. Ideally we will have a brand new biojava 3 ready soon after the hackaton. A more detailed program for the week will be sent out in January. If anybody wants to propose feature requests, you can have a look at the current todo list for the modules: http://biojava.org/wiki/BioJava:Modules Andreas On Tue, Nov 24, 2009 at 7:27 AM, Richard Holland wrote: > Hi all. > > To anyone planning on attending the BioJava hackathon in Cambridge (UK) in January, now would be a good time to sort out travel arrangements. If you're intending to come but haven't yet said so, please do let me know so that I can ensure we get a big enough room to work in! > > cheers, > Richard > > -- > Richard Holland, BSc MBCS > Operations and Delivery Director, Eagle Genomics Ltd > T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com > http://www.eaglegenomics.com/ > > > _______________________________________________ > Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From ayates at ebi.ac.uk Wed Nov 25 12:51:23 2009 From: ayates at ebi.ac.uk (Andy Yates) Date: Wed, 25 Nov 2009 12:51:23 +0000 Subject: [Biojava-dev] [Biojava-l] Hackathon in January In-Reply-To: <59a41c430911240954g589496dbg60a829d711131fab@mail.gmail.com> References: <1235107C-E1D2-4EEB-8A5F-2335751120EE@eaglegenomics.com> <59a41c430911240954g589496dbg60a829d711131fab@mail.gmail.com> Message-ID: <4DA69755-069B-4E70-BBE2-AEB408AE7E02@ebi.ac.uk> By online stream do you mean Wave or Twitter or something else trendy? :) Andy On 24 Nov 2009, at 17:54, Andreas Prlic wrote: > * Is anybody interested in following the ongoings at the hackaton via > an online-stream? - I received a request about this and am wondering > if more people would be interested in this. > > * Just to repeat the current status regarding the program: So far the > plan is to continue working on the new modules. Ideally we will have a > brand new biojava 3 ready soon after the hackaton. A more detailed > program for the week will be sent out in January. > > If anybody wants to propose feature requests, you can have a look at > the current todo list for the modules: > http://biojava.org/wiki/BioJava:Modules > > Andreas > > > > On Tue, Nov 24, 2009 at 7:27 AM, Richard Holland > wrote: >> Hi all. >> >> To anyone planning on attending the BioJava hackathon in Cambridge >> (UK) in January, now would be a good time to sort out travel >> arrangements. If you're intending to come but haven't yet said so, >> please do let me know so that I can ensure we get a big enough room >> to work in! >> >> cheers, >> Richard >> >> -- >> Richard Holland, BSc MBCS >> Operations and Delivery Director, Eagle Genomics Ltd >> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com >> http://www.eaglegenomics.com/ >> >> >> _______________________________________________ >> Biojava-l mailing list - Biojava-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev From heuermh at acm.org Wed Nov 25 19:05:22 2009 From: heuermh at acm.org (Michael Heuer) Date: Wed, 25 Nov 2009 14:05:22 -0500 (EST) Subject: [Biojava-dev] [Biojava-l] Hackathon in January In-Reply-To: <4DA69755-069B-4E70-BBE2-AEB408AE7E02@ebi.ac.uk> Message-ID: I would be fine with irc and the biojava wiki. We might set up a channel on freenode for biojava, or perhaps one for all of open-bio http://freenode.net/group_registration.shtml michael Andy Yates wrote: > By online stream do you mean Wave or Twitter or something else > trendy? :) > > Andy > > On 24 Nov 2009, at 17:54, Andreas Prlic wrote: > > > * Is anybody interested in following the ongoings at the hackaton via > > an online-stream? - I received a request about this and am wondering > > if more people would be interested in this. > > > > * Just to repeat the current status regarding the program: So far the > > plan is to continue working on the new modules. Ideally we will have a > > brand new biojava 3 ready soon after the hackaton. A more detailed > > program for the week will be sent out in January. > > > > If anybody wants to propose feature requests, you can have a look at > > the current todo list for the modules: > > http://biojava.org/wiki/BioJava:Modules > > > > Andreas > > > > > > > > On Tue, Nov 24, 2009 at 7:27 AM, Richard Holland > > wrote: > >> Hi all. > >> > >> To anyone planning on attending the BioJava hackathon in Cambridge > >> (UK) in January, now would be a good time to sort out travel > >> arrangements. If you're intending to come but haven't yet said so, > >> please do let me know so that I can ensure we get a big enough room > >> to work in! > >> > >> cheers, > >> Richard > >> > >> -- > >> Richard Holland, BSc MBCS > >> Operations and Delivery Director, Eagle Genomics Ltd > >> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com > >> http://www.eaglegenomics.com/ > >> > >> > >> _______________________________________________ > >> Biojava-l mailing list - Biojava-l at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/biojava-l > >> > > > > _______________________________________________ > > biojava-dev mailing list > > biojava-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/biojava-dev > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From andreas at sdsc.edu Wed Nov 25 20:08:33 2009 From: andreas at sdsc.edu (Andreas Prlic) Date: Wed, 25 Nov 2009 12:08:33 -0800 Subject: [Biojava-dev] [Biojava-l] Hackathon in January In-Reply-To: <4DA69755-069B-4E70-BBE2-AEB408AE7E02@ebi.ac.uk> References: <1235107C-E1D2-4EEB-8A5F-2335751120EE@eaglegenomics.com> <59a41c430911240954g589496dbg60a829d711131fab@mail.gmail.com> <4DA69755-069B-4E70-BBE2-AEB408AE7E02@ebi.ac.uk> Message-ID: <59a41c430911251208u44bb1218l7cb0065657ed7227@mail.gmail.com> I was thinking about video... I would expect that some of the participants will do some sort of tweeting, blogging, etc. Andreas On Wed, Nov 25, 2009 at 4:51 AM, Andy Yates wrote: > By online stream do you mean Wave or Twitter or something else trendy? :) > > Andy > > On 24 Nov 2009, at 17:54, Andreas Prlic wrote: > >> * Is anybody interested in following the ongoings at the hackaton via >> an online-stream? - I received a request about this and am wondering >> if more people would be interested in this. >> >> * Just to repeat the current status regarding the program: So far the >> plan is to continue working on the new modules. Ideally we will have a >> brand new biojava 3 ready soon after the hackaton. A more detailed >> program for the week will be sent out in January. >> >> If anybody wants to propose feature requests, you can have a look at >> the current todo list for the modules: >> http://biojava.org/wiki/BioJava:Modules >> >> Andreas >> >> >> >> On Tue, Nov 24, 2009 at 7:27 AM, Richard Holland >> wrote: >>> >>> Hi all. >>> >>> To anyone planning on attending the BioJava hackathon in Cambridge (UK) >>> in January, now would be a good time to sort out travel arrangements. If >>> you're intending to come but haven't yet said so, please do let me know so >>> that I can ensure we get a big enough room to work in! >>> >>> cheers, >>> Richard >>> >>> -- >>> Richard Holland, BSc MBCS >>> Operations and Delivery Director, Eagle Genomics Ltd >>> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com >>> http://www.eaglegenomics.com/ >>> >>> >>> _______________________________________________ >>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>> >> >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-dev > > From jw12 at sanger.ac.uk Thu Nov 26 14:57:35 2009 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Thu, 26 Nov 2009 14:57:35 +0000 Subject: [Biojava-dev] DAS workshop 7th-9th April 2010 Message-ID: We are considering running a Distributed Annotation System workshop here at the Sanger/EBI in the UK subject to decent demand. The workshop will be held from Wednesday 7th-Friday 9th April 2010. If you would be interested in attending either to present or just take part then please email me jw12 at sanger.ac.uk The format of the workshop is likely to be similar to last years (1st day for beginners, 2nd for both beginners and advanced users, 3rd day for advanced), information for which can be found here: http://www.dasregistry.org/course.jsp If you would like to present then please send a short summary of what you would like to talk about. Thanks Jonathan. Jonathan Warren Senior Developer and DAS coordinator jw12 at sanger.ac.uk -- 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 suzi at berkeleybop.org Mon Nov 30 04:03:09 2009 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Sun, 29 Nov 2009 20:03:09 -0800 Subject: [Biojava-dev] [DAS] DAS workshop 7th-9th April 2010 In-Reply-To: References: Message-ID: <3AD3C819-4BAA-4D90-B141-9611F48C5CAD@ berkeleybop.org> I/we (Gregg) would be interested in attending. We'd present an update on the collaborative, web-based version of Apollo. We will be working with Ian Holmes and Mitch Skinner using JBrowse for basic display. -S On Nov 26, 2009, at 6:57 AM, Jonathan Warren wrote: > We are considering running a Distributed Annotation System workshop here at the Sanger/EBI in the UK subject to decent demand. > The workshop will be held from Wednesday 7th-Friday 9th April 2010. If you would be interested in attending either to present or just take part > then please email me jw12 at sanger.ac.uk > > The format of the workshop is likely to be similar to last years (1st day for beginners, 2nd for both beginners and advanced users, 3rd day for advanced), information for which can be found here: > http://www.dasregistry.org/course.jsp > > If you would like to present then please send a short summary of what you would like to talk about. > > Thanks > > Jonathan. > > Jonathan Warren > Senior Developer and DAS coordinator > jw12 at sanger.ac.uk > > > > > > > > > > -- > The Wellcome Trust Sanger Institute is operated by Genome ResearchLimited, a charity registered in England with number 1021457 and acompany registered in England with number 2742969, whose registeredoffice is 215 Euston Road, London, NW1 2BE._______________________________________________ > DAS mailing list > DAS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das > From mauricio at open-bio.org Thu Nov 26 21:45:43 2009 From: mauricio at open-bio.org (Mauricio Herrera Cuadra) Date: Thu, 26 Nov 2009 15:45:43 -0600 Subject: [Biojava-dev] [DAS] DAS workshop 7th-9th April 2010 In-Reply-To: References: Message-ID: <4B0EF707.6080202@open-bio.org> Hi Jonathan, Any chance it can be webcasted? I'm sure it would attract a lot of remote attendees ;) Regards, Mauricio. Jonathan Warren wrote: > We are considering running a Distributed Annotation System workshop here > at the Sanger/EBI in the UK subject to decent demand. > The workshop will be held from Wednesday 7th-Friday 9th April 2010. If > you would be interested in attending either to present or just take part > then please email me jw12 at sanger.ac.uk > > The format of the workshop is likely to be similar to last years (1st > day for beginners, 2nd for both beginners and advanced users, 3rd day > for advanced), information for which can be found here: > http://www.dasregistry.org/course.jsp > > If you would like to present then please send a short summary of what > you would like to talk about. > > Thanks > > Jonathan. > > Jonathan Warren > Senior Developer and DAS coordinator > jw12 at sanger.ac.uk > > > > > > > > >