info.bioinfweb.libralign.dataarea.implementations.charset

Class CharSetDataAdapter

java.lang.Object

info.bioinfweb.libralign.dataarea.implementations.charset.CharSetDataAdapter

All Implemented Interfaces:

info.bioinfweb.jphyloio.dataadapters.ObjectListDataAdapter<info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent>

public class CharSetDataAdapter
extends java.lang.Object
implements info.bioinfweb.jphyloio.dataadapters.ObjectListDataAdapter<info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent>

JPhyloIO data adapter implementation to write the contents of a CharSetDataModel.

The color of a character set can be written as metadata.

Since:

0.6.0

Author:

Ben Stöver

Module:

info.bioinfweb.libralign.io

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	COLOR_METADATA_ID_SUFFIX
static java.lang.String	COLOR_METADATA_LABEL

Constructor Summary

Constructors

Constructor and Description
CharSetDataAdapter(java.lang.String idPrefix, CharSetDataModel model, java.lang.String linkedMatrixID) Creates a new instance of this class that will not write character set colors.
CharSetDataAdapter(java.lang.String idPrefix, CharSetDataModel model, java.lang.String linkedMatrixID, info.bioinfweb.jphyloio.events.meta.URIOrStringIdentifier colorPredicate, info.bioinfweb.jphyloio.events.meta.URIOrStringIdentifier colorDataType) Creates a new instance of this class.

Method Summary

Modifier and Type	Method and Description
long	getCount(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters)
java.util.Iterator<java.lang.String>	getIDIterator(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters)
info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent	getObjectStartEvent(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters, java.lang.String id)
void	writeContentData(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters, info.bioinfweb.jphyloio.dataadapters.JPhyloIOEventReceiver receiver, java.lang.String id)

Methods inherited from class java.lang.Object

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

Field Detail

COLOR_METADATA_ID_SUFFIX

public static final java.lang.String COLOR_METADATA_ID_SUFFIX

See Also:

Constant Field Values

COLOR_METADATA_LABEL

public static final java.lang.String COLOR_METADATA_LABEL

See Also:

Constant Field Values

Constructor Detail

CharSetDataAdapter

public CharSetDataAdapter(java.lang.String idPrefix,
                          CharSetDataModel model,
                          java.lang.String linkedMatrixID,
                          info.bioinfweb.jphyloio.events.meta.URIOrStringIdentifier colorPredicate,
                          info.bioinfweb.jphyloio.events.meta.URIOrStringIdentifier colorDataType)

Creates a new instance of this class.

Parameters:

idPrefix - the JPhyloIO ID prefix to be used for the character set events to be written (Maybe "".)

model - the model providing the data to be written

linkedMatrixID - the ID used by the start event of the associated matrix data

colorPredicate - the predicate to be used to write the color metadata event (Maybe null.)

colorDataType - the data type to be used to write the color metadata event (Maybe null only if colorPredicate is null as well.)

Throws:

java.lang.IllegalArgumentException - if idPrefix, model or linkedMatrixID are null or if colorDataType is null while colorPredicate is not

CharSetDataAdapter

public CharSetDataAdapter(java.lang.String idPrefix,
                          CharSetDataModel model,
                          java.lang.String linkedMatrixID)

Creates a new instance of this class that will not write character set colors.

Parameters:

idPrefix - the JPhyloIO ID prefix to be used for the character set events to be written (Maybe "".)

model - the model providing the data to be written

linkedMatrixID - the ID used by the start event of the associated matrix data

Throws:

java.lang.IllegalArgumentException - if idPrefix, model or linkedMatrixID are null

Method Detail

getObjectStartEvent

public info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent getObjectStartEvent(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters,
                                                                               java.lang.String id)
                                                                        throws java.lang.IllegalArgumentException

Specified by:

getObjectStartEvent in interface info.bioinfweb.jphyloio.dataadapters.ObjectListDataAdapter<info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent>

Throws:

java.lang.IllegalArgumentException

getCount

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

Specified by:

getCount in interface info.bioinfweb.jphyloio.dataadapters.ObjectListDataAdapter<info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent>

getIDIterator

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

Specified by:

getIDIterator in interface info.bioinfweb.jphyloio.dataadapters.ObjectListDataAdapter<info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent>

writeContentData

public void writeContentData(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters,
                             info.bioinfweb.jphyloio.dataadapters.JPhyloIOEventReceiver receiver,
                             java.lang.String id)
                      throws java.io.IOException,
                             java.lang.IllegalArgumentException

Specified by:

writeContentData in interface info.bioinfweb.jphyloio.dataadapters.ObjectListDataAdapter<info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent>

Throws:

java.io.IOException

java.lang.IllegalArgumentException