[Biojava-dev] Contributing chromatogram support to BioJava

[Matthew Pocock]

Hi Rhett,

Sounds great! I for one could realy use this stuff.
Could you dump the javadoc somewhere so that we can
just double-check the API, and then we can sort you
out. Are you intending to dump the code into biojava
and forget about it or do you want to help maintain
it? If the latter, we can get you a read/write account
rather than maintaining the code via one of us.

Matthew

 --- Rhett Sutphin <rhett-sutphin at uiowa.edu> wrote: >
Hi,
> 
> I've developed an interface and a set of parsers and
> related objects 
> for reading chromatogram files in Java.  I've gotten
> permission to 
> contribute them to BioJava if the community finds
> them worthwhile.
> 
> Specifically, I'd be contributing:
>    * A Chromatogram interface
>    * A SimpleChromatogram implementation of this
> interface
>    * An implementation of this interface that loads
> the chromatogram 
> (and all other fields) from an SCF file
>    * An implementation of this interface that loads
> the chromatogram 
> from an ABI trace file
>    * A ChromatogramFactory that examines the "magic
> number" of an input 
> file to create a Chromatogram of the appropriate
> type
>    * An object which encapsulates the procedure of
> drawing a 
> chromatogram onto a Graphics2D object
>    * Various support objects (e.g., exceptions)
>    * A couple of command-line demo programs
> (Chromat2Fasta & DumpChromat)
> 
> I noticed recently that there is an ABITrace class
> in the programs.abi 
> package that hasn't been released yet.  I think the
> code I'd be 
> contributing is better for the standard software
> engineering reasons:  
> abstraction and extensibility.  The Chromatogram
> abstraction allows SCF 
> and ABI traces to be treated the same by, e.g., the
> the drawing object. 
>   The Chromatogram abstraction also allows future
> format implementations 
> to transparently use code that requires a
> Chromatogram.  But I don't 
> need to explain that to you folks -- BioJava on the
> whole is an 
> object-oriented delight.
> 
> The code needs to be refactored slightly to fit in
> with BioJava norms 
> (for instance, I used my own flyweight nucleotide
> class), but I'll take 
> care of that if there is interest.  Is there?
> 
> Rhett
> 
> --
> Rhett Sutphin
> Research Assistant (Software)
> Coordinated Laboratory for Computational Genomics
>    and the Center for Macular Degeneration
> University of Iowa - Iowa City, IA 52242 - USA
> 4111 MEBRF - email: rhett-sutphin at uiowa.edu
> 
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> biojava-dev mailing list
> biojava-dev at biojava.org
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