Hi Heather,
If you look at the API docs under the Chromatogram and trace file support
http://www.biojava.org/docs/api14/index.html there are the classes that
biojava has to support traces.
The best package to use is org.biojava.bio.chromatogram.
One possible way would be to do something like this...
Chromatogram c1 = ChromatogramFactory.create(file1);
Chromatogram c2 = ChromatogramFactory.create(file2);
SimpleChromatogram mergeChrom = new SimpleChromatogram();
//repeat all steps below for each DNA base, eg replace DNATools.a() with
DNATools.g() etc
int[] a1 = c1.getTrace(DNATools.a());
int[] a2 = c2.getTrace(DNATools.a());
int[] merged = new int[a1.length + a2.lenght]
//use a loop here to copy a1 and a2 into merged
//now set the DNATools.a() trace for mergeChrom
mergeChrom.setTraceValues(DNATools.a(), merged, merged.length);
Hope this works!
- Mark
Heather Kent <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
02/02/2006 02:41 PM
To: biojava-l@biojava.org
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject: [Biojava-l] concatenating chromatograms
I would like to write a small application that would concatenate abi or
scf
chromatograms and write out a new chromatogram file..
has anyone done something similar to this or seen any code that would be
helpful for me, i am new at programming
and have been looking through the Biojava API
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