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

[Andrew Craig]

Dear Mark,

Thanks for your suggestion.

I have checked my Matlab install directories and there are no biojava jar
files. I am using Matlab without any additional Mathworks toolboxes but
perhaps what you say applies to the Mathworks Bioinformatics toolbox?

In any case I don't think that is causing my problem here. 

Does anyone else have another suggestion?

Best wishes,

Andrew Craig

-----Original Message-----
From: Mark Schreiber [mailto:markjschreiber at gmail.com] 
Sent: 01 September 2007 02:47
To: Andrew Craig
Cc: biojava-l at lists.open-bio.org
Subject: Re: [Biojava-l] BioJava 1.5 in Matlab and DNATools Class

Hi -

I know that some parts of matlab use biojava. Probably version 1.4 or
1.3. It may be that it is using this jar file instead of the one you
want it not. I'm not a matlab expert so I don't know how you can
resolve this.

- Mark

On 9/1/07, Andrew Craig <andrew.craig at cambridgebluegnome.com> wrote:
> 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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