Forwarding this to the users mailing list also, as there might be some interest in the documentation.
---------- Forwarded message ---------- From: Tiago Antão <[email protected]> Date: 2009/11/17 Subject: Re: [Biojava-l] Newick parser To: Richard Holland <[email protected]> Cc: Andreas Prlic <[email protected]>, biojava-dev <[email protected]> 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 <[email protected]>: > 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 <[email protected]>: >>> Patch applied to the trunk of biojava-live. Thanks for fixing it! >>> >>> cheers, >>> Richard >>> >>> On 15 Nov 2009, at 23:19, Tiago Antão 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 - [email protected] >>>> 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: [email protected] >>> http://www.eaglegenomics.com/ >>> >>> >>> _______________________________________________ >>> Biojava-l mailing list - [email protected] >>> 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: [email protected] > http://www.eaglegenomics.com/ > > -- “Pessimism of the Intellect; Optimism of the Will” -Antonio Gramsci -- “Pessimism of the Intellect; Optimism of the Will” -Antonio Gramsci _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
