[Biojava-l] Attempt at Cookbook

[Andreas Prlic]

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 <leapingfrog at yahoo.com> 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
>
>
>
>
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