info.bioinfweb.jphyloio.formats.phylip

Class PhylipEventWriter

java.lang.Object

info.bioinfweb.jphyloio.AbstractEventWriter<P>

info.bioinfweb.jphyloio.formats.text.AbstractTextEventWriter<P>

info.bioinfweb.jphyloio.AbstractSingleMatrixEventWriter<TextWriterStreamDataProvider<PhylipEventWriter>>

info.bioinfweb.jphyloio.formats.phylip.PhylipEventWriter

All Implemented Interfaces:

PhylipConstants, JPhyloIOEventWriter, JPhyloIOFormatSpecificObject

public class PhylipEventWriter
extends AbstractSingleMatrixEventWriter<TextWriterStreamDataProvider<PhylipEventWriter>>
implements PhylipConstants

Event based writer for the Phylip format.

This write is able to write sequence data to Phylip formatted streams. It will ignore any data for phylogenetic trees and networks that are provided by DocumentDataAdapter#getTreeNetworkIterator(ReadWriteParameterMap), because the Phylip format does not support such data.

Note that sequence names may have to be edited according to the (length) constrains the Phylip format imposes. According edits can be obtained using the LabelEditingReporter which is returned via the parameters map (using ReadWriteParameterNames.KEY_LABEL_EDITING_REPORTER).

Since Phylip does not support OTU or taxon lists as well, such a list (if provided by DocumentDataAdapter.getOTUListIterator(ReadWriteParameterMap)) will also not be written. OTU definitions (if present) will though be used, if a sequence with a linked OTU ID but without a label is specified. In such cases OTUListDataAdapter#getOTUStartEvent(String) will be used to determine the according OTU label. If that OTU label is also null, the sequence ID will be used as the sequence name in Phylip.

Comments and metadata nested in any of the supported elements will be ignored.

Recognized parameters:

• ReadWriteParameterNames.KEY_SEQUENCE_EXTENSION_TOKEN
• ReadWriteParameterNames.KEY_MAXIMUM_NAME_LENGTH
• ReadWriteParameterNames.KEY_LABEL_EDITING_REPORTER
• ReadWriteParameterNames.KEY_LOGGER
• ReadWriteParameterNames.KEY_LINE_SEPARATOR
• ReadWriteParameterNames.KEY_MAXIMUM_NAME_LENGTH (If this parameter is omitted, PhylipConstants.DEFAULT_NAME_LENGTH will be used.)
• ReadWriteParameterNames.KEY_LABEL_EDITING_REPORTER

Since:

0.0.0

Author:

Ben Stöver

Nested Class Summary

Nested classes/interfaces inherited from class info.bioinfweb.jphyloio.AbstractEventWriter

AbstractEventWriter.NoEditUniqueLabelHandler, AbstractEventWriter.UniqueLabelHandler

Field Summary

Fields inherited from class info.bioinfweb.jphyloio.AbstractEventWriter

EDITED_LABEL_SEPARATOR

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

Constructor Summary

Constructors

Constructor and Description
PhylipEventWriter() Creates a new instance of this class.

Method Summary

Modifier and Type	Method and Description
protected TextWriterStreamDataProvider<PhylipEventWriter>	createStreamDataProvider() This method is called in the constructor of AbstractEventWriter to initialize the stream data provider that will be returned by AbstractEventWriter.getStreamDataProvider().
java.lang.String	getFormatID() Returns a string ID uniquely identifying the target format of this instance.
protected java.lang.String	maskReservedLabelCharacters(java.lang.String label)
static java.lang.String	maskReservedPhylipLabelCharacters(java.lang.String label) Replaces characters that may not occur in Phylip labels according to this definition.
protected void	writeSingleMatrix(DocumentDataAdapter document, MatrixDataAdapter matrix, java.util.Iterator<java.lang.String> sequenceIDIterator, ReadWriteParameterMap parameters) Implementations of this method should write a single matrix to their target format.

Methods inherited from class info.bioinfweb.jphyloio.AbstractSingleMatrixEventWriter

doWriteDocument, editSequenceOrNodeLabel

Methods inherited from class info.bioinfweb.jphyloio.formats.text.AbstractTextEventWriter

getWriter

Methods inherited from class info.bioinfweb.jphyloio.AbstractEventWriter

createUniqueLabel, createUniqueLabel, createUniqueLabel, createUniqueLinkedOTULabel, decreaseIndention, determineMaxSequenceLength, extendSequence, getFileStartInfo, getIndention, getLabeledIDName, getLinkedOTUNameOTUFirst, getLinkedOTUNameOwnFirst, getReferencedOTUList, getStreamDataProvider, increaseIndention, logIngnoredOTULists, writeDocument, writeDocument, writeDocument, writeLineBreak, writeLineStart

Methods inherited from class java.lang.Object

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

Constructor Detail

PhylipEventWriter

public PhylipEventWriter()

Creates a new instance of this class. (Instances may be reused for different documents in subsequent calls of the different #writeDocument() methods.)

Method Detail

getFormatID

public java.lang.String getFormatID()

Description copied from interface: JPhyloIOFormatSpecificObject

Returns a string ID uniquely identifying the target format of this instance. Additional information on the format can be retrieved by passing the returned ID to JPhyloIOReaderWriterFactory.getFormatInfo(String).

Third party developers that create readers or writers for additional formats must make sure to use a globally unique format ID. It is strongly recommended to use owned reverse domain names for this (e.g. org.example.additionalformat).

Specified by:

getFormatID in interface JPhyloIOFormatSpecificObject

Returns:

the ID of the target format of this instance

See Also:

JPhyloIOReaderWriterFactory.getFormatInfo(String)

createStreamDataProvider

protected TextWriterStreamDataProvider<PhylipEventWriter> createStreamDataProvider()

Description copied from class: AbstractEventWriter

This method is called in the constructor of AbstractEventWriter to initialize the stream data provider that will be returned by AbstractEventWriter.getStreamDataProvider(). Inheriting classes that use their own stream data provider implementation should overwrite this method.

This default implementation creates a new instance of WriterStreamDataProvider.

Overrides:

createStreamDataProvider in class AbstractEventWriter<TextWriterStreamDataProvider<PhylipEventWriter>>

Returns:

the stream data provider to be used with this instance

maskReservedPhylipLabelCharacters

public static java.lang.String maskReservedPhylipLabelCharacters(java.lang.String label)

Replaces characters that may not occur in Phylip labels according to this definition.

The following replacements are performed:

• '(' → '<'
• ')' → '>'
• '[' → '<'
• ']' → '>'
• ':' → '|'
• ';' → '|'
• ',' → '|'

Parameters:

label - the label to be edited

Returns:

the edited label (not containing any reserved characters anymore)

maskReservedLabelCharacters

protected java.lang.String maskReservedLabelCharacters(java.lang.String label)

Specified by:

maskReservedLabelCharacters in class AbstractSingleMatrixEventWriter<TextWriterStreamDataProvider<PhylipEventWriter>>

writeSingleMatrix

protected void writeSingleMatrix(DocumentDataAdapter document,
                                 MatrixDataAdapter matrix,
                                 java.util.Iterator<java.lang.String> sequenceIDIterator,
                                 ReadWriteParameterMap parameters)
                          throws java.io.IOException

Description copied from class: AbstractSingleMatrixEventWriter

Implementations of this method should write a single matrix to their target format.

Specified by:

writeSingleMatrix in class AbstractSingleMatrixEventWriter<TextWriterStreamDataProvider<PhylipEventWriter>>

Parameters:

document - the document containing the matrix

matrix - the (non-empty) matrix to be written

sequenceIDIterator - an iterator oder all sequences in matrix positioned before the first sequence

parameters - the parameter map for the writer implementation

Throws:

java.io.IOException