[Biojava-dev] Chromatogram packages nearly ready to go

[Rhett Sutphin]

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