Package edu.mssm.crover.imports

Provides for the import of sequences from files.

See:
Description

Interface Summary

ReaderType	ReaderType encapsulates the information about a sequence "file format".
SequenceReader	SequenceReader are used by a SequenceReaderFactory.
SequenceReaderFactory	Gives access to specialized Sequence readers.

Class Summary

FastaReader	The fasta reader is very simple and cannot do a lot of error checking (because the FASTA format does not provide enough information to cross check).
FastaReaderType
SequenceReaderFactoryImpl	This default implementation of SequenceReaderFactory allows to read sequence files in the following formats: FASTA/Pearson PIR SwissProt with some annotations PDB headers with SEQRES and with secondary structure annotations.

Exception Summary

InvalidFieldLimits	Thrown when the field limits were incorrectly specified.
SyntaxErrorException
UnsupportedFileFormatException
UnsupportedResidueType

Package edu.mssm.crover.imports Description

Provides for the import of sequences from files. The package relies on edu.mssm.crover.representation for the representation of the sequences extracted from the file. Annotations defined in the representation package are parsed (when the file format provides this kind of annotation) and inserted in the representation data structure. The package makes use heavily of the factory pattern (see [GangOf4]). An interface (SequenceReader is specified that model the interaction between a client an a Reader implementation (specialized for a given file format, Fasta, SwissProt, etc.). The factory (SequenceReaderFactory) has additional methods to handle the selection of the given reader implementation from a file name extension, or a user selection (from a list of supported format).

    @BOOK{GangOf4,
    AUTHOR = {Gamma, Erich and Helm, Richard and Johnson, Ralph
    and Vlissides, John},

    TITLE = {{Design Patterns --- Catalogue de mod�les de
    conception r�utilisables}},
    PUBLISHER = {International Thompson Publishing France},
    YEAR = {1996},
    NOTE = {ISBN: 2-84180-054-7}
    }