info.bioinfweb.jphyloio

Class AbstractEventWriter<P extends WriterStreamDataProvider<? extends AbstractEventWriter<P>>>

java.lang.Object

info.bioinfweb.jphyloio.AbstractEventWriter<P>

All Implemented Interfaces:

JPhyloIOEventWriter, JPhyloIOFormatSpecificObject

Direct Known Subclasses:

AbstractTextEventWriter, AbstractXMLEventWriter

public abstract class AbstractEventWriter<P extends WriterStreamDataProvider<? extends AbstractEventWriter<P>>>
extends java.lang.Object
implements JPhyloIOEventWriter

Implements shared functionality for JPhyloIO event writers.

Author:

Ben Stöver

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	AbstractEventWriter.NoEditUniqueLabelHandler
static interface	AbstractEventWriter.UniqueLabelHandler

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	EDITED_LABEL_SEPARATOR

Constructor Summary

Constructors

Constructor and Description
AbstractEventWriter()

Method Summary

Modifier and Type	Method and Description
protected P	createStreamDataProvider() This method is called in the constructor of AbstractEventWriter to initialize the stream data provider that will be returned by getStreamDataProvider().
static java.lang.String	createUniqueLabel(ReadWriteParameterMap parameters, AbstractEventWriter.UniqueLabelHandler handler, LabeledIDEvent event)
static java.lang.String	createUniqueLabel(ReadWriteParameterMap parameters, AbstractEventWriter.UniqueLabelHandler handler, java.lang.String label1, java.lang.String id1, java.lang.String label2, java.lang.String id2)
static java.lang.String	createUniqueLabel(ReadWriteParameterMap parameters, LabeledIDEvent event)
static java.lang.String	createUniqueLinkedOTULabel(ReadWriteParameterMap parameters, AbstractEventWriter.UniqueLabelHandler handler, LinkedLabeledIDEvent event, OTUListDataAdapter otuList, boolean otuFirst)
protected void	decreaseIndention()
static long	determineMaxSequenceLength(MatrixDataAdapter matrix, ReadWriteParameterMap parameters) Calculates the maximum sequence length in matrix with unequal lengths.
protected abstract void	doWriteDocument(DocumentDataAdapter document, java.io.Writer writer, ReadWriteParameterMap parameters)
protected void	extendSequence(MatrixDataAdapter matrix, ReadWriteParameterMap parameters, java.lang.String sequenceID, long targetLength, java.lang.String extensionToken, JPhyloIOEventReceiver receiver)
protected java.lang.String	getFileStartInfo(ReadWriteParameterMap parameters)
protected java.lang.String	getIndention()
static java.lang.String	getLabeledIDName(LabeledIDEvent event) Returns a name for the specified event.
static java.lang.String	getLinkedOTUNameOTUFirst(LinkedLabeledIDEvent linkedOTUEvent, OTUListDataAdapter otuList, ReadWriteParameterMap parameters) Determines the name (label) to be used for the specified event when writing its data to a file.
static java.lang.String	getLinkedOTUNameOwnFirst(LinkedLabeledIDEvent linkedOTUEvent, OTUListDataAdapter otuList, ReadWriteParameterMap parameters) Determines the name (label) to be used for the specified event when writing its data to a file.
static OTUListDataAdapter	getReferencedOTUList(DocumentDataAdapter document, ElementDataAdapter<LinkedLabeledIDEvent> source, ReadWriteParameterMap parameters) Returns the OTU list found in document which is referenced by the specified event.
P	getStreamDataProvider()
protected void	increaseIndention()
static void	logIngnoredOTULists(DocumentDataAdapter document, ApplicationLogger logger, ReadWriteParameterMap parameters, java.lang.String formatName, java.lang.String labeledElements) Outputs a warning message, if the specified document data adapter provides one or more OTU lists.
void	writeDocument(DocumentDataAdapter document, java.io.File file, ReadWriteParameterMap parameters) Writes the data provided by the data adapter to a document in the according format of the implementing class.
void	writeDocument(DocumentDataAdapter document, java.io.OutputStream stream, ReadWriteParameterMap parameters) Writes the data provided by the data adapter to a document in the according format of the implementing class.
void	writeDocument(DocumentDataAdapter document, java.io.Writer writer, ReadWriteParameterMap parameters) Writes the data provided by the data adapter to a document in the according format of the implementing class.
static void	writeLineBreak(java.io.Writer writer, ReadWriteParameterMap parameters) Writes the line separator, as it is specified in the parameter map or the line separator of the current operating system, if the map contains no according entry.
protected void	writeLineStart(java.io.Writer writer, java.lang.String text)

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

Field Detail

EDITED_LABEL_SEPARATOR

public static final java.lang.String EDITED_LABEL_SEPARATOR

See Also:

Constant Field Values

Constructor Detail

AbstractEventWriter

public AbstractEventWriter()

Method Detail

createStreamDataProvider

protected P createStreamDataProvider()

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

This default implementation creates a new instance of WriterStreamDataProvider.

Returns:

the stream data provider to be used with this instance

getStreamDataProvider

public P getStreamDataProvider()

writeLineBreak

public static void writeLineBreak(java.io.Writer writer,
                                  ReadWriteParameterMap parameters)
                           throws java.io.IOException

Writes the line separator, as it is specified in the parameter map or the line separator of the current operating system, if the map contains no according entry.

Parameters:

writer - the writer to write the line break to

parameters - the parameter map possibly containing a line separator definition

Throws:

java.io.IOException - if an I/O error occurs while writing to the specified writer

logIngnoredOTULists

public static void logIngnoredOTULists(DocumentDataAdapter document,
                                       ApplicationLogger logger,
                                       ReadWriteParameterMap parameters,
                                       java.lang.String formatName,
                                       java.lang.String labeledElements)

Outputs a warning message, if the specified document data adapter provides one or more OTU lists.

Parameters:

document - the document data adapter to be checked for OTU lists

logger - the logger to write the warning to

formatName - the name of the format to which OTU lists cannot be written (will be included in the message)

labeledElements - the name of data elements (e.g. sequences or nodes) that may reference the OTU lists (The warning message will use this name for a hint that the OTU lists may still be used to label this type of elements.)

getLabeledIDName

public static java.lang.String getLabeledIDName(LabeledIDEvent event)

Returns a name for the specified event.

Parameters:

event - the event to get the name of

Returns:

either the label of the event or its ID, if it does not carry a label

getLinkedOTUNameOwnFirst

public static java.lang.String getLinkedOTUNameOwnFirst(LinkedLabeledIDEvent linkedOTUEvent,
                                                        OTUListDataAdapter otuList,
                                                        ReadWriteParameterMap parameters)

Determines the name (label) to be used for the specified event when writing its data to a file. The name is tried to be set by the following properties in decreasing priority:

1. the label of linkedOTUEvent if present
2. the label of the linked OTU event, if any is linked and carries a label
3. the ID of linkedOTUEvent

Parameters:

linkedOTUEvent - the event defining the name

otuList - the data adapter providing the OTU data

Returns:

a string representing the specified event as described

See Also:

#getLinkedOTUNameOTUFirst(LinkedLabeledIDEvent, OTUListDataAdapter)

getLinkedOTUNameOTUFirst

public static java.lang.String getLinkedOTUNameOTUFirst(LinkedLabeledIDEvent linkedOTUEvent,
                                                        OTUListDataAdapter otuList,
                                                        ReadWriteParameterMap parameters)

Determines the name (label) to be used for the specified event when writing its data to a file. The name is tried to be set by the following properties in decreasing priority:

1. the label of the linked OTU event, if any is linked and carries a label
2. the ID of the linked OTU event, if any is linked
3. the label of linkedOTUEvent if present
4. the ID of linkedOTUEvent

Parameters:

linkedOTUEvent - the event defining the name

otuList - the data adapter providing the OTU data

Returns:

a string representing the specified event as described

See Also:

#getLinkedOTUNameOwnFirst(LinkedLabeledIDEvent, OTUListDataAdapter)

getReferencedOTUList

public static OTUListDataAdapter getReferencedOTUList(DocumentDataAdapter document,
                                                      ElementDataAdapter<LinkedLabeledIDEvent> source,
                                                      ReadWriteParameterMap parameters)

Returns the OTU list found in document which is referenced by the specified event.

Parameters:

document - the document data adapter providing the OTU lists.

source - the event referencing the OTU list

Returns:

the referenced list or null, if the specified event does not reference any OTU

Throws:

java.lang.IllegalArgumentException - if no OTU list with the specified ID is available in document

determineMaxSequenceLength

public static long determineMaxSequenceLength(MatrixDataAdapter matrix,
                                              ReadWriteParameterMap parameters)

Calculates the maximum sequence length in matrix with unequal lengths. This method iterates over all sequences if MatrixDataAdapter.getColumnCount(ReadWriteParameterMap) returns -1, otherwise it will directly return the specified column count.

Parameters:

matrix - the matrix data adapter containing the sequences

Returns:

the maximal sequence length or -1, if the specified matrix data adapter does not declare any sequences

getIndention

protected java.lang.String getIndention()

writeLineStart

protected void writeLineStart(java.io.Writer writer,
                              java.lang.String text)
                       throws java.io.IOException

Throws:

java.io.IOException

increaseIndention

protected void increaseIndention()

decreaseIndention

protected void decreaseIndention()

createUniqueLabel

public static java.lang.String createUniqueLabel(ReadWriteParameterMap parameters,
                                                 AbstractEventWriter.UniqueLabelHandler handler,
                                                 java.lang.String label1,
                                                 java.lang.String id1,
                                                 java.lang.String label2,
                                                 java.lang.String id2)

createUniqueLabel

public static java.lang.String createUniqueLabel(ReadWriteParameterMap parameters,
                                                 AbstractEventWriter.UniqueLabelHandler handler,
                                                 LabeledIDEvent event)

createUniqueLabel

public static java.lang.String createUniqueLabel(ReadWriteParameterMap parameters,
                                                 LabeledIDEvent event)

createUniqueLinkedOTULabel

public static java.lang.String createUniqueLinkedOTULabel(ReadWriteParameterMap parameters,
                                                          AbstractEventWriter.UniqueLabelHandler handler,
                                                          LinkedLabeledIDEvent event,
                                                          OTUListDataAdapter otuList,
                                                          boolean otuFirst)

extendSequence

protected void extendSequence(MatrixDataAdapter matrix,
                              ReadWriteParameterMap parameters,
                              java.lang.String sequenceID,
                              long targetLength,
                              java.lang.String extensionToken,
                              JPhyloIOEventReceiver receiver)
                       throws java.io.IOException

Throws:

java.io.IOException

getFileStartInfo

protected java.lang.String getFileStartInfo(ReadWriteParameterMap parameters)

writeDocument

public void writeDocument(DocumentDataAdapter document,
                          java.io.File file,
                          ReadWriteParameterMap parameters)
                   throws java.io.IOException

Description copied from interface: JPhyloIOEventWriter

Writes the data provided by the data adapter to a document in the according format of the implementing class.

Specified by:

writeDocument in interface JPhyloIOEventWriter

Parameters:

document - the adapter providing the data to be written

file - the file to write the data to

parameters - a map of parameters to exchange information with the writer implementation (Care should be taken, if a parameter map is reused for multiple calls, since the writer implementation may add or changes entries in the map.)

Throws:

java.io.IOException

writeDocument

public void writeDocument(DocumentDataAdapter document,
                          java.io.OutputStream stream,
                          ReadWriteParameterMap parameters)
                   throws java.io.IOException

Description copied from interface: JPhyloIOEventWriter

Writes the data provided by the data adapter to a document in the according format of the implementing class.

Specified by:

writeDocument in interface JPhyloIOEventWriter

Parameters:

document - the adapter providing the data to be written

stream - the stream to write the data to

parameters - a map of parameters to exchange information with the writer implementation (Care should be taken, if a parameter map is reused for multiple calls, since the writer implementation may add or changes entries in the map.)

Throws:

java.io.IOException

writeDocument

public void writeDocument(DocumentDataAdapter document,
                          java.io.Writer writer,
                          ReadWriteParameterMap parameters)
                   throws java.io.IOException

Description copied from interface: JPhyloIOEventWriter

Writes the data provided by the data adapter to a document in the according format of the implementing class.

Specified by:

writeDocument in interface JPhyloIOEventWriter

Parameters:

document - the adapter providing the data to be written

writer - the writer to write the data to

parameters - a map of parameters to exchange information with the writer implementation (Care should be taken, if a parameter map is reused for multiple calls, since the writer implementation may add or changes entries in the map.)

Throws:

java.io.IOException

doWriteDocument

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

Throws:

java.io.IOException