info.bioinfweb.jphyloio.formats.pde

Class PDEReaderStreamDataProvider

java.lang.Object

info.bioinfweb.jphyloio.ReaderStreamDataProvider<R>

info.bioinfweb.jphyloio.formats.xml.XMLReaderStreamDataProvider<PDEEventReader>

info.bioinfweb.jphyloio.formats.pde.PDEReaderStreamDataProvider

public class PDEReaderStreamDataProvider
extends XMLReaderStreamDataProvider<PDEEventReader>

The XML stream data provider used by PDEEventReader.

Since:

0.0.0

Author:

Ben Stöver

Constructor Summary

Constructors

Constructor and Description
PDEReaderStreamDataProvider(PDEEventReader eventReader)

Method Summary

Modifier and Type	Method and Description
int	getAlignmentLength()
java.lang.String	getCurrentAlignmentID() Returns the ID of the characters element (representing an alignment) that is currently read.
protected java.lang.String	getCurrentSequenceID()
int	getCurrentSequenceIndex()
protected int	getCurrentSequenceLength()
java.util.Map<java.lang.Integer,PDEMetaColumnDefintion>	getMetaColumns()
java.lang.String	getOtuListID()
protected int	getSequenceCount()
java.util.Map<java.lang.Integer,java.lang.String>	getSequenceIndexToOTUID()
java.util.List<java.util.Map<java.lang.Integer,java.lang.String>>	getSequenceInformations()
protected boolean	isCreateAlignmentEnd()
protected boolean	isCreateAlignmentStart()
void	setAlignmentLength(int alignmentLength)
protected void	setCreateAlignmentEnd(boolean createAlignmentEnd)
protected void	setCreateAlignmentStart(boolean createAlignmentStart)
void	setCurrentAlignmentID(java.lang.String currentAlignmentID)
protected void	setCurrentSequenceID(java.lang.String currentSequenceID)
void	setCurrentSequenceIndex(int currentSequenceIndex)
protected void	setCurrentSequenceLength(int currentSequenceLength)
void	setOtuListID(java.lang.String otuListID)
protected void	setSequenceCount(int sequenceCount)

Methods inherited from class info.bioinfweb.jphyloio.formats.xml.XMLReaderStreamDataProvider

getCharacterSetType, getEdgeInfos, getElementName, getIncompleteToken, getNestedMetaNames, getParentName, getSourceNode, getStartDocumentEvent, getXMLReader, hasIncompleteToken, isCreateNodeStart, isCustomXMLStartWritten, isRootedPhylogeny, setCharacterSetType, setCreateNodeStart, setCustomXMLStartWritten, setElementName, setIncompleteToken, setParentName, setRootedPhylogeny, setStartDocumentEvent

Methods inherited from class info.bioinfweb.jphyloio.ReaderStreamDataProvider

eventsUpcoming, getCurrentEventCollection, getEventReader, getIDManager, getParameters, getSequenceTokensEventManager, hasSpecialEventCollection, resetCurrentEventCollection, setCurrentEventCollection

Methods inherited from class java.lang.Object

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

Constructor Detail

PDEReaderStreamDataProvider

public PDEReaderStreamDataProvider(PDEEventReader eventReader)

Method Detail

getAlignmentLength

public int getAlignmentLength()

setAlignmentLength

public void setAlignmentLength(int alignmentLength)

getSequenceCount

protected int getSequenceCount()

setSequenceCount

protected void setSequenceCount(int sequenceCount)

getOtuListID

public java.lang.String getOtuListID()

setOtuListID

public void setOtuListID(java.lang.String otuListID)

getCurrentAlignmentID

public java.lang.String getCurrentAlignmentID()

Returns the ID of the characters element (representing an alignment) that is currently read.

Returns:

the current alignment ID

setCurrentAlignmentID

public void setCurrentAlignmentID(java.lang.String currentAlignmentID)

isCreateAlignmentStart

protected boolean isCreateAlignmentStart()

setCreateAlignmentStart

protected void setCreateAlignmentStart(boolean createAlignmentStart)

isCreateAlignmentEnd

protected boolean isCreateAlignmentEnd()

setCreateAlignmentEnd

protected void setCreateAlignmentEnd(boolean createAlignmentEnd)

getCurrentSequenceID

protected java.lang.String getCurrentSequenceID()

setCurrentSequenceID

protected void setCurrentSequenceID(java.lang.String currentSequenceID)

getSequenceIndexToOTUID

public java.util.Map<java.lang.Integer,java.lang.String> getSequenceIndexToOTUID()

getCurrentSequenceIndex

public int getCurrentSequenceIndex()

setCurrentSequenceIndex

public void setCurrentSequenceIndex(int currentSequenceIndex)

getCurrentSequenceLength

protected int getCurrentSequenceLength()

setCurrentSequenceLength

protected void setCurrentSequenceLength(int currentSequenceLength)

getSequenceInformations

public java.util.List<java.util.Map<java.lang.Integer,java.lang.String>> getSequenceInformations()

getMetaColumns

public java.util.Map<java.lang.Integer,PDEMetaColumnDefintion> getMetaColumns()