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

[Andreas Prlic]

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
>>
>> _______________________________________________
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>
> --
> 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/
>
>
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