[Biojava-l] CookbookMSAProfiler.java

[Andreas Prlic]

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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