info.bioinfweb.libralign.model.io

Class AlignmentModelDataAdapter<T>

java.lang.Object

info.bioinfweb.jphyloio.dataadapters.implementations.EmptyAnnotatedDataAdapter<info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent>

info.bioinfweb.jphyloio.dataadapters.implementations.NoCharDefsNoSetsMatrixDataAdapter

info.bioinfweb.libralign.model.io.AlignmentModelDataAdapter<T>

Type Parameters:

T - the type of sequence elements (tokens) used by the underlying alignment model object

All Implemented Interfaces:

info.bioinfweb.jphyloio.dataadapters.AnnotatedDataAdapter, info.bioinfweb.jphyloio.dataadapters.ElementDataAdapter<info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent>, info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter

public class AlignmentModelDataAdapter<T>
extends info.bioinfweb.jphyloio.dataadapters.implementations.NoCharDefsNoSetsMatrixDataAdapter
implements info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter

An JPhyloIO data adapter that allows writing the contents of an implementation of AlignmentModel to an implementation of JPhyloIOEventWriter.

Whether the sequence start events link an associated OTU or not can be defined by the constructor parameter linkOTUs. If OTUs shall be linked, it will be assumed that such an OTU will have an ID consisting of the concatenation of ReadWriteConstants.DEFAULT_OTU_ID_PREFIX and the sequence ID used in the underlying AlignmentModel. If a more complex OTU linking is necessary, the method #getLinkedOTUID(int) can be overwritten accordingly.

This implementation does not write any metadata associated with sequences or the alignment as a whole. If such data shall be written the methods #writeMetadata(JPhyloIOEventReceiver) or writeSequenceMetadata(JPhyloIOEventReceiver, String) should be overwritten accordingly. If character definitions or sets shall be written, the according methods need to be overwritten as well.

Author:

Ben Stöver

Constructor Summary

Constructors

Constructor and Description
AlignmentModelDataAdapter(java.lang.String idPrefix, info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent startEvent, AlignmentModel<T> model, boolean linkOTUs) Creates a new instance of this class.

Method Summary

Modifier and Type	Method and Description
boolean	containsLongTokens(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters)
long	getColumnCount(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters) Returns the number of columns in the underlying AlignmentModel instance if all sequences have an equal length.
java.lang.String	getIDPrefix() Returns the ID prefix used by this instance.
protected java.lang.String	getLinkedOTUID(java.lang.String sequenceID) Returns the ID of the JPhyloIO OTU that shall be linked with the specified sequence.
long	getSequenceCount(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters)
java.util.Iterator<java.lang.String>	getSequenceIDIterator(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters)
long	getSequenceLength(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters, java.lang.String sequenceID)
info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent	getSequenceStartEvent(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters, java.lang.String sequenceID)
info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent	getStartEvent(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters)
info.bioinfweb.jphyloio.dataadapters.ObjectListDataAdapter<info.bioinfweb.jphyloio.events.TokenSetDefinitionEvent>	getTokenSets(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters)
boolean	isLinkOTUs()
protected java.lang.String	jPhyloIOByModelSequenceID(java.lang.String modelSequenceID) Returns the JPhyloIO sequence ID to be used for the specified sequence ID used in the underlying model.
protected java.lang.String	modelByJPhyloIOSequenceID(java.lang.String jPhyloIOsequenceID) Returns the LibrAlign model sequence ID associated with the specified JPhyloIO sequence ID.
protected void	writeSequenceMetadata(info.bioinfweb.jphyloio.dataadapters.JPhyloIOEventReceiver receiver, java.lang.String sequenceID) Can be used to write metadata associated with a sequence.
void	writeSequencePartContentData(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters, info.bioinfweb.jphyloio.dataadapters.JPhyloIOEventReceiver receiver, java.lang.String sequenceID, long startColumn, long endColumn)

Methods inherited from class info.bioinfweb.jphyloio.dataadapters.implementations.NoCharDefsNoSetsMatrixDataAdapter

getCharacterDefinitions, getCharacterSets, getSequenceSets

Methods inherited from class info.bioinfweb.jphyloio.dataadapters.implementations.EmptyAnnotatedDataAdapter

writeMetadata

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.dataadapters.MatrixDataAdapter

getCharacterDefinitions, getCharacterSets, getSequenceSets

Methods inherited from interface info.bioinfweb.jphyloio.dataadapters.AnnotatedDataAdapter

writeMetadata

Constructor Detail

AlignmentModelDataAdapter

public AlignmentModelDataAdapter(java.lang.String idPrefix,
                                 info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent startEvent,
                                 AlignmentModel<T> model,
                                 boolean linkOTUs)

Creates a new instance of this class.

Parameters:

idPrefix - the ID prefix to be used for all generated JPhyloIO IDs of sequences and token sets. (Must be a valid NCName or an empty string. See getIDPrefix() for further details.)

startEvent - the JPhyloIO alignment start event to be used

model - the LibrAlign alignment model which shall be the source for this adapter

linkOTUs - Specify true here, if each sequence shall link an OTU or false otherwise. (See #getLinkedOTUID(int) for details on how OTU IDs are generated.)

Method Detail

getIDPrefix

public java.lang.String getIDPrefix()

Returns the ID prefix used by this instance.

The prefix is added to LibrAlign sequence IDs to create JPhyloIO sequences IDs from them. It may be an empty string, otherwise it needs to be a valid NCName. If multiple instance of this class are combined to write a file containing multiple alignments (e.g. possible in NeXML or Nexus) the prefixes of each instance need to be different in order to avoid ID conflicts.

Returns:

the ID prefix of this instance as it was specified in the constructor

isLinkOTUs

public boolean isLinkOTUs()

getStartEvent

public info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent getStartEvent(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters)

Specified by:

getStartEvent in interface info.bioinfweb.jphyloio.dataadapters.ElementDataAdapter<info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent>

getSequenceCount

public long getSequenceCount(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters)

Specified by:

getSequenceCount in interface info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter

getColumnCount

public long getColumnCount(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters)

Returns the number of columns in the underlying AlignmentModel instance if all sequences have an equal length. If at least two of these sequences differ in their length, -1 is returned.

Specified by:

getColumnCount in interface info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter

Returns:

the column count or -1

See Also:

MatrixDataAdapter.getColumnCount(info.bioinfweb.jphyloio.ReadWriteParameterMap)

containsLongTokens

public boolean containsLongTokens(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters)

Specified by:

containsLongTokens in interface info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter

getTokenSets

public info.bioinfweb.jphyloio.dataadapters.ObjectListDataAdapter<info.bioinfweb.jphyloio.events.TokenSetDefinitionEvent> getTokenSets(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters)

Specified by:

getTokenSets in interface info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter

Overrides:

getTokenSets in class info.bioinfweb.jphyloio.dataadapters.implementations.NoCharDefsNoSetsMatrixDataAdapter

jPhyloIOByModelSequenceID

protected java.lang.String jPhyloIOByModelSequenceID(java.lang.String modelSequenceID)

Returns the JPhyloIO sequence ID to be used for the specified sequence ID used in the underlying model.

This default implementation returns the concatenation of getIDPrefix() and sequenceID. It can be overwritten to use a different pattern.

Parameters:

modelSequenceID - the ID of the sequence used in the underlying AlignmentModel instance

Returns:

the JPhyloIO sequence ID

modelByJPhyloIOSequenceID

protected java.lang.String modelByJPhyloIOSequenceID(java.lang.String jPhyloIOsequenceID)
                                              throws java.lang.IllegalArgumentException

Returns the LibrAlign model sequence ID associated with the specified JPhyloIO sequence ID.

This default implementation extracts the integer ID that was used to create such an ID using #jPhyloIOByModelSequenceID(int). If #jPhyloIOByModelSequenceID(int) was overwritten this method must be overwritten accordingly.

Note that this method does not test, if the extracted ID actually exists in the underlying LibrAlign alignment model.

Parameters:

jPhyloIOsequenceID - the sequence ID used by JPhyloIO

Returns:

the sequence ID used by the underlying alignment model

Throws:

java.lang.IllegalArgumentException - if no integer ID can be extracted from the specified ID

getLinkedOTUID

protected java.lang.String getLinkedOTUID(java.lang.String sequenceID)

Returns the ID of the JPhyloIO OTU that shall be linked with the specified sequence.

This default implementation returns the concatenation of ReadWriteConstants.DEFAULT_OTU_ID_PREFIX and sequenceID if isLinkOTUs() returns true or null if isLinkOTUs() returns false.

Note that the ID prefix for sequences and token sets, which can be specified in the constructor will not be used for IDs creates by this method.

This method can be overwritten to use a different pattern of OTU linking.

Parameters:

sequenceID - the ID of the sequence used in the underlying AlignmentModel instance

Returns:

the linked OTU or null if no OTU shall be linked.

getSequenceIDIterator

public java.util.Iterator<java.lang.String> getSequenceIDIterator(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters)

Specified by:

getSequenceIDIterator in interface info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter

getSequenceStartEvent

public info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent getSequenceStartEvent(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters,
                                                                                 java.lang.String sequenceID)

Specified by:

getSequenceStartEvent in interface info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter

getSequenceLength

public long getSequenceLength(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters,
                              java.lang.String sequenceID)
                       throws java.lang.IllegalArgumentException

Specified by:

getSequenceLength in interface info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter

Throws:

java.lang.IllegalArgumentException

writeSequenceMetadata

protected void writeSequenceMetadata(info.bioinfweb.jphyloio.dataadapters.JPhyloIOEventReceiver receiver,
                                     java.lang.String sequenceID)
                              throws java.io.IOException,
                                     java.lang.IllegalArgumentException

Can be used to write metadata associated with a sequence.

This default implementation is empty, but can be overwritten by inherited classes.

Parameters:

receiver - the receiver to write the events to

sequenceID - the ID of the sequence carrying the metadata

Throws:

java.io.IOException - if an I/O error occurs while receiver is trying to write the data

java.lang.IllegalArgumentException - if not sequence with the specified ID exists

writeSequencePartContentData

public void writeSequencePartContentData(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters,
                                         info.bioinfweb.jphyloio.dataadapters.JPhyloIOEventReceiver receiver,
                                         java.lang.String sequenceID,
                                         long startColumn,
                                         long endColumn)
                                  throws java.io.IOException,
                                         java.lang.IllegalArgumentException

Specified by:

writeSequencePartContentData in interface info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter

Throws:

java.io.IOException

java.lang.IllegalArgumentException