info.bioinfweb.jphyloio.formats.phylip

Class SequentialPhylipFactory

java.lang.Object

info.bioinfweb.jphyloio.factory.AbstractSingleReaderWriterFactory

info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipFactory

info.bioinfweb.jphyloio.formats.phylip.SequentialPhylipFactory

All Implemented Interfaces:

SingleReaderWriterFactory, JPhyloIOFormatIDs, PhylipConstants

public class SequentialPhylipFactory
extends AbstractPhylipFactory

Reader and writer factory for the sequential Phylip format. Note that the checkFormat() methods of this factory cannot determine the difference between sequential and non-sequential Phylip.

Since:

0.0.0

Author:

Ben Stöver

See Also:

PhylipFactory

Field Summary

Fields inherited from class info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipFactory

MAXIMUM_EXPECTED_DIGITS_OR_WHITESPACE

Fields inherited from interface info.bioinfweb.jphyloio.formats.phylip.PhylipConstants

DEFAULT_NAME_LENGTH, PHYLIP_FORMAT_NAME, PREMATURE_NAME_END_CHARACTER, RELAXED_PHYLIP_NAME_PATTERN, SEQUENTIAL_PHYLIP_FORMAT_NAME

Fields inherited from interface info.bioinfweb.jphyloio.formats.JPhyloIOFormatIDs

FASTA_FORMAT_ID, FORMAT_ID_PREFIX, MEGA_FORMAT_ID, NEWICK_FORMAT_ID, NEXML_FORMAT_ID, NEXUS_FORMAT_ID, PDE_FORMAT_ID, PHYLIP_FORMAT_ID, PHYLOXML_FORMAT_ID, SEQUENTIAL_PHYLIP_FORMAT_ID, XTG_FORMAT_ID

Constructor Summary

Constructors

Constructor and Description
SequentialPhylipFactory()

Method Summary

Modifier and Type	Method and Description
protected JPhyloIOFormatInfo	createFormatInfo()
JPhyloIOEventReader	getReader(java.io.InputStream stream, ReadWriteParameterMap parameters) Creates a new reader instance for the target format of this factory.
JPhyloIOEventReader	getReader(java.io.Reader reader, ReadWriteParameterMap parameters) Creates a new reader instance for the target format of this factory.

Methods inherited from class info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipFactory

checkFormat, createFormatInfo, getWriter, hasReader, hasWriter

Methods inherited from class info.bioinfweb.jphyloio.factory.AbstractSingleReaderWriterFactory

checkFormat, getFormatInfo

Methods inherited from class java.lang.Object

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

Methods inherited from interface info.bioinfweb.jphyloio.factory.SingleReaderWriterFactory

checkFormat, getFormatInfo

Constructor Detail

SequentialPhylipFactory

public SequentialPhylipFactory()

Method Detail

getReader

public JPhyloIOEventReader getReader(java.io.InputStream stream,
                                     ReadWriteParameterMap parameters)
                              throws java.io.IOException

Description copied from interface: SingleReaderWriterFactory

Creates a new reader instance for the target format of this factory.

Parameters:

stream - the stream to provide the content for the reader

parameters - the parameter map for the new reader instance

Returns:

the new reader instance

Throws:

java.io.IOException

getReader

public JPhyloIOEventReader getReader(java.io.Reader reader,
                                     ReadWriteParameterMap parameters)
                              throws java.io.IOException

Description copied from interface: SingleReaderWriterFactory

Creates a new reader instance for the target format of this factory.

parameters - the parameter map for the new reader instance

Returns:

the new reader instance or null if this factory is not able to create readers

Throws:

java.io.IOException

See Also:

SingleReaderWriterFactory.hasReader()

createFormatInfo

protected JPhyloIOFormatInfo createFormatInfo()

Specified by:

createFormatInfo in class AbstractSingleReaderWriterFactory