info.bioinfweb.jphyloio.formats.phylip

Class PhylipFactory

java.lang.Object

info.bioinfweb.jphyloio.factory.AbstractSingleReaderWriterFactory

info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipFactory

info.bioinfweb.jphyloio.formats.phylip.PhylipFactory

All Implemented Interfaces:

SingleReaderWriterFactory, JPhyloIOFormatIDs, PhylipConstants

public class PhylipFactory
extends AbstractPhylipFactory

Reader and writer factory for the (non-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:

SequentialPhylipFactory

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
PhylipFactory()

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

PhylipFactory

public PhylipFactory()

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