edu.mssm.crover.imports
Class SequenceReaderFactoryImpl

java.lang.Object
  |
  +--edu.mssm.crover.imports.SequenceReaderFactoryImpl

All Implemented Interfaces:

SequenceReaderFactory

public class SequenceReaderFactoryImpl

extends java.lang.Object

implements SequenceReaderFactory

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.

Constructor Summary

SequenceReaderFactoryImpl()

Method Summary

void	addReader(SequenceReader r) This SequenceReaderFactory supports the addition of new SequenceReaders at runtime.
protected ReaderType	findReaderTypeFromExtension(java.lang.String ext)
ReaderType[]	getSupportedTypes() Returns the ReaderTypes supported by this factory implementation.
ReaderType	guessReaderType(java.lang.String filename) Attempt to determine a ReaderType suitable to parse the sequence encoding from a filename extension.
static void	main(java.lang.String[] args) Test of the factory implementation.
AnnotatedBioSequence[]	readSequences(java.io.InputStream seqstream, ReaderType type)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SequenceReaderFactoryImpl

public SequenceReaderFactoryImpl()

Method Detail

addReader

public void addReader(SequenceReader r)

This SequenceReaderFactory supports the addition of new SequenceReaders at runtime. Call this method with the new reader and the factory will be able to read files of the format your reader recognizes.

getSupportedTypes

public ReaderType[] getSupportedTypes()

Description copied from interface: SequenceReaderFactory

Returns the ReaderTypes supported by this factory implementation. The calls to readSequences should use one of the type returned by this method or the UnregisteredReaderTypeException is likely to be raised.

Specified by:

getSupportedTypes in interface SequenceReaderFactory

readSequences

public AnnotatedBioSequence[] readSequences(java.io.InputStream seqstream,
                                            ReaderType type)
                                     throws edu.mssm.crover.imports.UnregisteredReaderTypeException,
                                            UnsupportedFileFormatException,
                                            SyntaxErrorException

Specified by:

readSequences in interface SequenceReaderFactory

edu.mssm.crover.imports.UnregisteredReaderTypeException

UnsupportedFileFormatException

SyntaxErrorException

guessReaderType

public ReaderType guessReaderType(java.lang.String filename)

Attempt to determine a ReaderType suitable to parse the sequence encoding from a filename extension. Pass "a.sw" to get the swissprot parser for instance. The default readerType returned (when no sensible match can be determined) is FASTA/Pearson).

Specified by:

guessReaderType in interface SequenceReaderFactory

findReaderTypeFromExtension

protected ReaderType findReaderTypeFromExtension(java.lang.String ext)

main

public static void main(java.lang.String[] args)

Test of the factory implementation.