[Biojava-dev] Chromatogram packages nearly ready to go

[Matthew Pocock]

The packages look prety good to me. Personaly, I'd be temted to make the 
two format packages children of teh chromatogram one, but I don't think 
we have any policies for this sort of thing, so either way is fine with me.

I look forward to playing with this.

Matthew

Rhett Sutphin wrote:
> Hi,
> 
> The chromatogram support code is nearly ready to go.  The 
> virtually-final javadoc is at 
> http://www.detailedbalance.net/~rhett/dev/biojava/chromat-contrib/doc/ .
> 
> All I need before I can contribute it is an okay on the final package 
> structure (which is not reflected in the above-referenced javadoc).  
> Here's what I'm planning to do:
> 
> org.biojava.bio.chromatogram:
>   Chromatogram
>     (the interface)
>   AbstractChromatogram
>     (a detailed abstract base for implementations)
>   SimpleChromatogram
>     (a very simple implementation)
>   ChromatogramTools
>     (Utility/shortcut methods for dealing with Chromatogram instances)
>   ChromatogramFactory
>     (A factory that creates an appropriate instance of a known 
> chromatogram format from a file or stream)
>   UnsupportedChromatogramFormatException
>     (The basic exception)
> 
> org.biojava.bio.programs.abi:
>   ABIFParser
>     (A general parser for files/streams in the ABIF format)
>   ABIFChromatogram
>     (An implementation of a Chromatogram that is read from an ABIF 
> file/stream)
> 
> org.biojava.bio.programs.scf:
>   SCF
>     (An implementation of a Chromatogram that is read from an SCF 
> file/stream)
> 
> org.biojava.utils.io:
>   Seekable
>     (An interface for an I/O class that indicates you can seek in it)
>   CachingInputStream
>     (A wrapper for an InputStream that provides a memory cache to 
> support seeking)
> 
> [The two io classes are in support of the ABI format, which requires 
> random access, but which one might reasonably want to read in a 
> situation where a RandomAccessFile is not available.]
> 
> And then there are also two command-line demo programs (Chromat2Fasta & 
> DumpChromat), which I imagine would just go in /demos/chromatogram in 
> the CVS tree.
> 
> If there's no objection to this packaging, I'll have the code ready to 
> go tomorrow.
> 
> Thanks for your input.
> 
> 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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