[Biojava-dev] Chromatogram packages nearly ready to go
Matthew Pocock
matthew_pocock at yahoo.co.uk
Mon Mar 17 17:29:24 EST 2003
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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