info.bioinfweb.jphyloio

Class AbstractSingleMatrixEventWriter<P extends TextWriterStreamDataProvider<? extends AbstractTextEventWriter<P>>>

java.lang.Object

info.bioinfweb.jphyloio.AbstractEventWriter<P>

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

info.bioinfweb.jphyloio.AbstractSingleMatrixEventWriter<P>

All Implemented Interfaces:

JPhyloIOEventWriter, JPhyloIOFormatSpecificObject

Direct Known Subclasses:

FASTAEventWriter, PhylipEventWriter

public abstract class AbstractSingleMatrixEventWriter<P extends TextWriterStreamDataProvider<? extends AbstractTextEventWriter<P>>>
extends AbstractTextEventWriter<P>

Default implementation for writers that can only write a single matrix (multiple sequence alignment) to their target format, because that format does not support additional data.

This abstract implementation will log according warnings for the other data that has not been written and than calls #writeSingleMatrix(DocumentDataAdapter, MatrixDataAdapter, Iterator, Writer, ReadWriteParameterMap) which must be implemented by inherited classes accordingly.

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

Constructor Summary

Constructors

Constructor and Description
AbstractSingleMatrixEventWriter(java.lang.String formatName) Creates a new instance of this class.

Method Summary

Modifier and Type	Method and Description
protected void	doWriteDocument(DocumentDataAdapter document, java.io.Writer writer, ReadWriteParameterMap parameters)
protected java.lang.String	editSequenceOrNodeLabel(LinkedLabeledIDEvent event, ReadWriteParameterMap parameters, OTUListDataAdapter otuList)
protected abstract java.lang.String	maskReservedLabelCharacters(java.lang.String label)
protected abstract 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.formats.text.AbstractTextEventWriter

getWriter

Methods inherited from class info.bioinfweb.jphyloio.AbstractEventWriter

createStreamDataProvider, 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

Methods inherited from interface info.bioinfweb.jphyloio.JPhyloIOFormatSpecificObject

getFormatID

Constructor Detail

AbstractSingleMatrixEventWriter

public AbstractSingleMatrixEventWriter(java.lang.String formatName)

Creates a new instance of this class.

Parameters:

formatName - the name of the format the inherited implementation writes to, which will be used for the log messages generated by this abstract implementation.

Method Detail

writeSingleMatrix

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

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

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

writer - the writer to write the data to

parameters - the parameter map for the writer implementation

Throws:

java.lang.Exception - if the implementing writer throws an exception

java.io.IOException

editSequenceOrNodeLabel

protected java.lang.String editSequenceOrNodeLabel(LinkedLabeledIDEvent event,
                                                   ReadWriteParameterMap parameters,
                                                   OTUListDataAdapter otuList)

maskReservedLabelCharacters

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

doWriteDocument

protected void doWriteDocument(DocumentDataAdapter document,
                               java.io.Writer writer,
                               ReadWriteParameterMap parameters)
                        throws java.io.IOException

Overrides:

doWriteDocument in class AbstractTextEventWriter<P extends TextWriterStreamDataProvider<? extends AbstractTextEventWriter<P>>>

Throws:

java.io.IOException