[Biojava-l] CookbookMSAProfiler.java

[Spencer Bliven]

Perhaps maven has an older version installed that is being used?


On Mon, Jul 15, 2013 at 5:04 PM, Andreas Prlic <andreas at sdsc.edu> wrote:

> Hi David,
>
> I would recommend against moving 3rd party jars into jre/lib/ext in
> general. This can easily lead to classpath problems and it sounds a bit
> like you are having that... I'd delete the alignment.jar from there and
> make sure there is no other reference to that jar in you classpath.
>
> Andreas
>
>
>
>
> On Sun, Jul 14, 2013 at 6:21 PM, David Scott <leapingfrog at yahoo.com>
> wrote:
>
> > Unable to run this without an Illegal Access Error even when I changed
> all
> > the routines
> > to be public in Alignment.java
> >
> > I unjarred biojava3-alignment, changed access to public, and executed the
> > CookbookMSA
> > Profiller in the same package space.  Still refers to the same access
> > error:
> >
> >
> > C:\Program
> > Files\Java\jdk1.7.0_25\jre\lib\ext\biojava3-alignment-3.0.5-sources>java
> > org.biojava3.alignment.CookbookMSAProfiler bones.fasta
> > Loading sequences from bones.fasta... 2 sequences in 48 ms using 15872 kB
> >
> > Stage 1: pairwise similarity calculation... Exception in thread "main"
> > java.lang.IllegalAccessError: tried to access method
> >
> org.biojava3.alignment.Alignments.getAllPairsScorers(Ljava/util/List;Lorg/biojava3/alignment/Alignments$PairwiseSequenceScorerType;Lorg/biojava3/alignment/template/GapPenalty;Lorg/biojava3/alignment/template/SubstitutionMatrix;)Ljava/util/List;
> > from class org.biojava3.alignment.CookbookMSAProfiler at
> >
> org.biojava3.alignment.CookbookMSAProfiler.main(CookbookMSAProfiler.java:84)
> >
> > C:\Program
> > Files\Java\jdk1.7.0_25\jre\lib\ext\biojava3-alignment-3.0.5-sources>
> >
> > Any ideas on what I'm doing wrong?
> >
> > I have all the BioJava jar files in the ext area.  Should I be removing
> > the alignment jar from the
> > jre/lib/ext area so that Java uses only the recompiled Alignment.java?
>  Or
> > is the problem somewhere
> > else?
> >
> > Any ideas?
> >
> >
> > Thanks,
> >
> > David Scott
> >
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> >
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