Attempt at Cookbook
David Scott <[email protected]>
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <[email protected]> |
Copied code from Alignment section of biojava3 Cookbook on
"how can I profile the time and memory requirements of a Multiple Sequence
Alignment?"
Created a series of FASTA proteins (sod) from NIH.
It compiles fine on a Windows machine and I print out the sequences to make sure
they look like they are read okay.
I added a snippet of code to see it read okay:
Iterator it = list.iterator();
System.out.println();
while ( it.hasNext() ) {
System.out.println( it.next() );
}
System.out.println();
The follow error occurs when I run it:
C:\biojava1\w11>java org/biojava3/alignment/CookbookMSAProfiler sod.fasta
Loading sequences from sod.fasta... 3
HINHSIFWTNLCKDGGEPSGKLLQAINRDFGSLQGLQARLNAIAIAVQGSGWGWLGYNKIDKRLEVACCPNQDPLEPTTG
LVPLFGIDVWEHAYYLQYK
HINHSIFWTNLCKDGGEPSGKLLQAINRDFGSLQVLQARLNAIAIAVQGSGWGWLGYNKIDKRLEVACCPNQDPLEPTTG
LVPLFGIDVWEHAYYLQYK
KHSLPDLPYDYGALEPHINAQIMQLHHSKHHAANVNNLNVTEEKYQEALAKGDVTAQIALQPALKFNGGGHINHSIFWTN
LSPNGGGEPKGELLEAIKRDFGSFDKFKEKLTAASVGVQGSGWGWLGFNKERGHLQIAACPNQDPLQGTTGLIPLLGIDV
WEHAYYLQYKNVRPDYLKAIWNVINWENVTERYMACKK
sequences in 39 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:86)
Sincerely,
David Scott
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