[Biojava-l] BioJava 1.5 in Matlab and DNATools Class

[Andrew Craig]

Dear List,

I am trying to use BioJava-1.5 from Matlab (7.2), in order to retrieve the
raw chromatogram data from some .AB1 files.
 
I have added biojava-1.5.jar to the Matlab java class path. I then import
the following classes.
import java.io.*;
import java.util.*;
import org.biojava.bio.*;
import org.biojava.bio.chromatogram.*;
import org.biojava.bio.program.abi.*;
import org.biojava.bio.seq.*; 
import org.biojava.bio.seq.impl.*;
import org.biojava.bio.seq.io.*;
import org.biojava.bio.symbol.*;

Next I read the raw chromatogram file with

myTrace     = ChromatogramFactory.create(myFile);

Then I try to retrieve the raw data for the a base using

raw_a       = myTrace.getTrace(DNATools.a());

This works fine for a, t and g bases. My problem is when I call DNATools.c()
it returns the following error 

??? No method 'c' with matching signature found for class
'org.biojava.bio.seq.DNATools'

Can anyone diagnose what is wrong and why only the .c method is giving an
error? I can get around this by using DNATools.complement(G) but I would
prefer to understand what is going on and get things working properly.

Best regards,

Andrew Craig

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Andrew Craig                andrew.craig at cambridgebluegnome.com
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