[Biojava-l] CookbookMSAProfiler.java

[David Scott]

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