Hi David, Some of the access methods in Alignments.java were not public... now fixed in SVN.
Andreas On Sat, Jan 29, 2011 at 11:04 PM, David Scott <[email protected]> wrote: > 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 > > > > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
