[Biojava-l] Issues with biojava-20010702 and Windows

[Dan Siroker]

I spent the last couple of days trying to get BioJava running on my
Windows 2000 system by any means necessary (downloading the source and
compiling, CVSing and compiling, and using the binaries, and desperate
hacks when necessary).

Compiling the source went generally okay, yet when I tried running the
eventbasedparsing demo with java (JDK 1.3.1) under the Windows command
line (with attempts through Microsoft J++ as well) it failed with the
following exceptions. I followed the tutorial off of the biojava.org
site for instructions.

>java eventbasedparsing/TutorialEx1 files/ncbiblast/shortBlastn.out

Exception in thread "main" java.lang.NoSuchMethodError
        at
org.biojava.bio.program.sax.BlastLikeAlignmentSAXParser.parseLine(BlastL
ikeAlignmentSAXPa
rser.java:306)
        at
org.biojava.bio.program.sax.BlastLikeAlignmentSAXParser.parse(BlastLikeA
lignmentSAXParser
.java:119)
        at
org.biojava.bio.program.sax.HitSectionSAXParser.outputHSPInfo(HitSection
SAXParser.java:51
2)
        at
org.biojava.bio.program.sax.HitSectionSAXParser.interpretHSP(HitSectionS
AXParser.java:357
)
        at
org.biojava.bio.program.sax.HitSectionSAXParser.firstHSPEvent(HitSection
SAXParser.java:27
8)
        at
org.biojava.bio.program.sax.HitSectionSAXParser.interpret(HitSectionSAXP
arser.java:249)
        at
org.biojava.bio.program.sax.HitSectionSAXParser.parse(HitSectionSAXParse
r.java:116)
        at
org.biojava.bio.program.sax.BlastSAXParser.hitsSectionReached(BlastSAXPa
rser.java:519)
        at
org.biojava.bio.program.sax.BlastSAXParser.interpret(BlastSAXParser.java
:279)
        at
org.biojava.bio.program.sax.BlastSAXParser.parse(BlastSAXParser.java:162
)
        at
org.biojava.bio.program.sax.BlastLikeSAXParser.onNewDataSet(BlastLikeSAX
Parser.java:306)
        at
org.biojava.bio.program.sax.BlastLikeSAXParser.interpret(BlastLikeSAXPar
ser.java:267)
        at
org.biojava.bio.program.sax.BlastLikeSAXParser.parse(BlastLikeSAXParser.
java:160)
        at eventbasedparsing.TutorialEx1.main(TutorialEx1.java:91)


This essentially means that there is a linking error.
Biojava-20010702.jar DOES contain the above methods, yet something
doesn't connect properly. A simple solution was replacing
biojava-20010702 (released 02-Jul-2001 05:29) with biojava-20010126.jar
(released 26-Jan-2001 11:11). After that everything clicked with no
other changes. I assume this problem might only local to Windows 2000
otherwise this release of biojava.jar wouldn't have been made available
in it's current state. I just thought I'd put anyone else struggling
with the same issue out of their misery. Any insight would be welcome.

Thanks,
Dan