info.bioinfweb.jphyloio.formats.phylip

Class AbstractPhylipFactory

java.lang.Object

info.bioinfweb.jphyloio.factory.AbstractSingleReaderWriterFactory

info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipFactory

All Implemented Interfaces:

SingleReaderWriterFactory, JPhyloIOFormatIDs, PhylipConstants

Direct Known Subclasses:

PhylipFactory, SequentialPhylipFactory

public abstract class AbstractPhylipFactory
extends AbstractSingleReaderWriterFactory
implements SingleReaderWriterFactory, PhylipConstants, JPhyloIOFormatIDs

Implements shared functionality for Phylip factories.

Since:

0.0.0

Author:

Ben Stöver

Field Summary

Fields

Modifier and Type	Field and Description
static int	MAXIMUM_EXPECTED_DIGITS_OR_WHITESPACE Defines the maximum number of digits in a column or line count definition of a Phylip file.

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
AbstractPhylipFactory()

Method Summary

Modifier and Type	Method and Description
boolean	checkFormat(java.io.Reader reader, ReadWriteParameterMap parameters) Implementations should read the start of the characters returned by the reader here and determine whether the content could be valid according to the target format.
protected JPhyloIOFormatInfo	createFormatInfo(java.lang.String formatID, java.lang.String formatName, java.util.Set<java.lang.String> supportedReaderParameters, java.util.Set<java.lang.String> supportedWriterParameters, java.lang.String adapterDescription)
JPhyloIOEventWriter	getWriter() Creates a new writer instance for the target format of this factory.
boolean	hasReader() Determines whether this factory is able to create reader instances for its target format.
boolean	hasWriter() Determines whether this factory is able to create writer instances for its target format.

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

checkFormat, createFormatInfo, 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, getReader, getReader

Field Detail

MAXIMUM_EXPECTED_DIGITS_OR_WHITESPACE

public static final int MAXIMUM_EXPECTED_DIGITS_OR_WHITESPACE

Defines the maximum number of digits in a column or line count definition of a Phylip file. Using this constant avoids parsing files completely that are not Phylip and just contain many digits in checkFormat().

See Also:

Constant Field Values

Constructor Detail

AbstractPhylipFactory

public AbstractPhylipFactory()

Method Detail

checkFormat

public boolean checkFormat(java.io.Reader reader,
                           ReadWriteParameterMap parameters)
                    throws java.io.IOException

Description copied from interface: SingleReaderWriterFactory

Implementations should read the start of the characters returned by the reader here and determine whether the content could be valid according to the target format.

Specified by:

checkFormat in interface SingleReaderWriterFactory

Parameters:

reader - the reader to read the first bytes from

parameters - the parameters map that would also be used to create a reader

Returns:

true if the tested reader may return content in target format or false if the content is not in valid target format

Throws:

java.io.IOException

getWriter

public JPhyloIOEventWriter getWriter()

Description copied from interface: SingleReaderWriterFactory

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

Specified by:

getWriter in interface SingleReaderWriterFactory

Returns:

the new writer instance or null if this factory is not able to create writers

See Also:

SingleReaderWriterFactory.hasWriter()

hasReader

public boolean hasReader()

Description copied from interface: SingleReaderWriterFactory

Determines whether this factory is able to create reader instances for its target format.

Specified by:

hasReader in interface SingleReaderWriterFactory

Returns:

true if creating readers is supported or false otherwise

hasWriter

public boolean hasWriter()

Description copied from interface: SingleReaderWriterFactory

Determines whether this factory is able to create writer instances for its target format.

Specified by:

hasWriter in interface SingleReaderWriterFactory

Returns:

true if creating writers is supported or false otherwise

createFormatInfo

protected JPhyloIOFormatInfo createFormatInfo(java.lang.String formatID,
                                              java.lang.String formatName,
                                              java.util.Set<java.lang.String> supportedReaderParameters,
                                              java.util.Set<java.lang.String> supportedWriterParameters,
                                              java.lang.String adapterDescription)