edu.mssm.crover.imports
Interface SequenceReader

All Known Implementing Classes:
FastaReader, PDBReader, PIRReader, SwissProtReader

public interface SequenceReader

SequenceReader are used by a SequenceReaderFactory. The factory is responsible for selecting the appropriate SequenceReader according to the format indicated by the user or the file extension. This allows to keep the Reader simple. A Reader should come with associated ReaderType objects that describe what the reader is supposed to be able to parse to create a BiologicalSequence. The ReaderType objects can be presented to the user to help his choice of a ReaderType suitable to read his/her file.


Method Summary
 ReaderType getSupportedType()
           
 AnnotatedBioSequence[] readFile(java.io.InputStream seqstream)
           
 

Method Detail

readFile

AnnotatedBioSequence[] readFile(java.io.InputStream seqstream)
                                throws UnsupportedFileFormatException,
                                       SyntaxErrorException
Throws:
UnsupportedFileFormatException
SyntaxErrorException

getSupportedType

ReaderType getSupportedType()


Copyright © 2003-2013 Institute for Computational Biomedicine, All Rights Reserved.