[Biojava-l] DNA sequence alignment - class AlignmentPair

[Andreas Dräger]

Hi Katerina,

>  First, I want to ask if there is any problem with my code because I get the
> this error when I build it:
> 
>   cannot access org.biojava.bio.alignment.SimpleAlignment
>   class file for org.biojava.bio.alignment.SimpleAlignment not found
>   System.out.println("Align Results: "+aligner.getPercentIdentitySubject());
> 
> It seems to me that the problem is in the class AlignmentPair. I have also
> downloaded all the source files from SVN and noticed that the class
> AlignmentPair is supposed to extend the class SimpleAlignment which doesn't
> exist in the alignment module from SVN. Is this actually where the problem
> lies or am I doing something wrong?

Your code example looks perfect to me! Actually, I don't think that your 
version of the class AlignmentPair is broken. It seems to me that you 
require additional parts of BioJava. The class SimpleAlignment is 
missing. Did you check the content of the jar file you downloaded? I bet 
this class is not in there.

Cheers
Andreas

-- 
Dipl.-Bioinform. Andreas Dräger
Eberhard Karls University Tübingen
Center for Bioinformatics (ZBIT)
Sand 1
72076 Tübingen
Germany

Phone: +49-7071-29-70436
Fax:   +49-7071-29-5091