[Biojava-dev] CrossProductAlphabet index breaking Serialization

[Schreiber, Mark]

Hi -

I am getting a different error now, very strange one too. Details are below. JDK 1.3.1 on True64, Maybe I need to switch to 1.4??

Testsuite: org.biojava.bio.symbol.AlphabetSerializationTest
Tests run: 6, Failures: 0, Errors: 1, Time elapsed: 1.86 sec
------------- Standard Output ---------------
[org.biojava.bio.symbol.LinearAlphabetIndex at 8090cc5, org.biojava.bio.symbol.LinearAlphabetIndex at 80a0900]
------------- ---------------- ---------------

Testcase: testIntegerSerialization took 1.598 sec
Testcase: testDoubleSerialization took 0.009 sec
Testcase: testSubInt took 0.02 sec
Testcase: testDNASerialization took 0.021 sec
Testcase: testPhredSerialization took 0.177 sec
        Caused an ERROR
null
org.biojava.bio.symbol.IllegalSymbolException: Can't find symbol for [org.biojava.bio.symbol.IntegerAlphabet$IntegerSymbol at 275, org.biojava.bio.s
ymbol.AlphabetManager$WellKnownAtomicSymbol at 8076f38] in alphabet (DNA x SubIntegerAlphabet[0..99])
        at org.biojava.bio.symbol.SimpleCrossProductAlphabet.getSymbolImpl (SimpleCrossProductAlphabet.java:176) (pc 51)
        at org.biojava.bio.symbol.AbstractAlphabet.getSymbol (AbstractAlphabet.java:188) (pc 174)
        at org.biojava.bio.symbol.CrossProductAlphabetIndex.symbolForIndex (CrossProductAlphabetIndex.java:139) (pc 87)
rethrown as org.biojava.bio.BioError
        at org.biojava.bio.symbol.CrossProductAlphabetIndex.symbolForIndex (CrossProductAlphabetIndex.java:142) (pc 99)
        at org.biojava.bio.symbol.AlphabetSerializationTest.equalSymbols (pc 28)
        at org.biojava.bio.symbol.AlphabetSerializationTest.testPhredSerialization (pc 60)
        at java.lang.reflect.Method.invoke (Method.java)

Testcase: testPhredSerializationTestcase: testCustom took 0.003 sec

> -----Original Message-----
> From: Matthew Pocock [mailto:matthew_pocock at yahoo.co.uk] 
> Sent: Tuesday, 28 January 2003 11:38 p.m.
> To: Kalle Näslund
> Cc: Schreiber, Mark; biojava-dev at biojava.org
> Subject: Re: [Biojava-dev] CrossProductAlphabet index 
> breaking Serialization
> 
> 
> Test passes for me now. In CVS. Could you check it works for you?
> 
> Kalle Näslund wrote:
> > Schreiber, Mark wrote:
> > 
> >> Hi -
> >>
> >> The recent changes to Alphabet indexing are breaking the 
> >> serialization of crossproduct alphabets like the phred alphabet. 
> >> Specifically, in line 131 of the AlphabetSerializationTest.
> >>
> >> It used to work really well! Can someone fix this or roll back the 
> >> changes please?
> >>
> >>  
> >>
> > Hi!
> > 
> > I might be the culprit responsible for this :/ I recently commited a
> > class called
> > CrossProductAlphabetIndex, but, i havent touched any other 
> code at all. 
> > So i am
> > a bit baffled on how this resulted in serialization 
> breaking for other 
> > classes. You got
> > any clues on how me adding a single class, with no changes 
> whatsoever to 
> > other code
> > might result in this ?
> > 
> > I wil try to figure this out tommorow though.
> > 
> > hope i didnt cause to much trouble
> > 
> > mvh Kalle
> > 
> > 
> > 
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at biojava.org 
> > http://biojava.org/mailman/listinfo/biojava-dev
> > 
> 
> 
> -- 
> BioJava Consulting LTD - Support and training for BioJava 
> http://www.biojava.co.uk
> 
> 
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