[Biojava-dev] [Biojava-l] Newick parser

[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 <holland at eaglegenomics.com>:
>> 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  -  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/