Package edu.mssm.crover.imports

Provides for the import of sequences from files.


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).
FortranOutputParser Parses lines of fortran formated output.
PDBReader The PDB Header Reader.
PDBReaderType Describes the PDB reader for the sake of a GUI.
PIRReader Reads BNRF/PIR files as Clustal outputs them.
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.
SeqUtils Provides methods of common interest to this package, related to sequence operations.
SwissProtReader The SwissProt Reader.
SwissProtReaderType Information about the SwissProtReader.

Exception Summary
InvalidFieldLimits Thrown when the field limits were incorrectly specified.

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 addtional 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).

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