[Biojava-l] Attempt at Cookbook

[David Scott]

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