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 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
