info.bioinfweb.jphyloio.formats.newick

Class NewickEventWriter

java.lang.Object

info.bioinfweb.jphyloio.AbstractEventWriter<P>

info.bioinfweb.jphyloio.formats.text.AbstractTextEventWriter<TextWriterStreamDataProvider<NewickEventWriter>>

info.bioinfweb.jphyloio.formats.newick.NewickEventWriter

All Implemented Interfaces:

NewickConstants, JPhyloIOEventWriter, JPhyloIOFormatSpecificObject

public class NewickEventWriter
extends AbstractTextEventWriter<TextWriterStreamDataProvider<NewickEventWriter>>
implements NewickConstants

Event writer for the Newick format.

Recognized parameters

• ReadWriteParameterNames.KEY_WRITER_INSTANCE
• ReadWriteParameterNames.KEY_LOGGER
• ReadWriteParameterNames.KEY_LINE_SEPARATOR
• ReadWriteParameterNames.KEY_MAXIMUM_NAME_LENGTH (If this parameter is omitted, any name length is possible.)
• ReadWriteParameterNames.KEY_LABEL_EDITING_REPORTER
• ReadWriteParameterNames.KEY_OBJECT_TRANSLATOR_FACTORY

Author:

Ben Stöver

See Also:

0.0.0, Metadata demo application

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

Fields inherited from interface info.bioinfweb.jphyloio.formats.newick.NewickConstants

ALLOCATION_SEPARATOR_SYMBOL, ALLOCATION_SYMBOL, ALTERNATIVE_NAME_DELIMITER, COMMENT_END, COMMENT_START, DATA_TYPE_NEWICK_ARRAY, E_NEWICK_EDGE_TYPE_HYBRIDIZATION, E_NEWICK_EDGE_TYPE_LATERAL_GENE_TRANSFER, E_NEWICK_EDGE_TYPE_RECOMBINATION, E_NEWICK_NAMESPACE_PREFIX, E_NEWICK_NETWORK_DATA_SEPARATOR, ELEMENT_SEPERATOR, FIELD_END_SYMBOL, FIELD_START_SYMBOL, FIELD_VALUE_SEPARATOR_SYMBOL, FREE_NAME_BLANK, HOT_COMMENT_START_SYMBOL, INDEX_END_SYMBOL, INDEX_START_SYMBOL, LENGTH_SEPERATOR, NAME_DELIMITER, NEWICK_DATA_TYPE_NAMESPACE, NEWICK_FORMAT_NAME, NEWICK_NAMESPACE_PREFIX, NHX_KEY_CONFIDENCE, NHX_KEY_EVENT, NHX_KEY_GENE_NAME, NHX_KEY_PREFIX, NHX_KEY_SCIENTIFIC_NAME, NHX_KEY_SEQUENCE_ACCESSION, NHX_KEY_TAXONOMY_ID, NHX_START, NHX_VALUE_SEPARATOR_SYMBOL, PREDICATE_E_NEWICK_EDGE_TYPE, ROOTED_HOT_COMMENT, SUBTREE_END, SUBTREE_START, TERMINAL_SYMBOL, UNROOTED_HOT_COMMENT

Constructor Summary

Constructors

Constructor and Description
NewickEventWriter()

Method Summary

Modifier and Type	Method and Description
protected TextWriterStreamDataProvider<NewickEventWriter>	createStreamDataProvider() This method is called in the constructor of AbstractEventWriter to initialize the stream data provider that will be returned by AbstractEventWriter.getStreamDataProvider().
protected void	doWriteDocument(DocumentDataAdapter document, java.io.Writer writer, ReadWriteParameterMap parameters)
java.lang.String	getFormatID() Returns a string ID uniquely identifying the target format of this instance.

Methods inherited from class info.bioinfweb.jphyloio.formats.text.AbstractTextEventWriter

getWriter

Methods inherited from class info.bioinfweb.jphyloio.AbstractEventWriter

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

Constructor Detail

NewickEventWriter

public NewickEventWriter()

Method Detail

getFormatID

public java.lang.String getFormatID()

Description copied from interface: JPhyloIOFormatSpecificObject

Returns a string ID uniquely identifying the target format of this instance. Additional information on the format can be retrieved by passing the returned ID to JPhyloIOReaderWriterFactory.getFormatInfo(String).

Third party developers that create readers or writers for additional formats must make sure to use a globally unique format ID. It is strongly recommended to use owned reverse domain names for this (e.g. org.example.additionalformat).

Specified by:

getFormatID in interface JPhyloIOFormatSpecificObject

Returns:

the ID of the target format of this instance

See Also:

JPhyloIOReaderWriterFactory.getFormatInfo(String)

createStreamDataProvider

protected TextWriterStreamDataProvider<NewickEventWriter> createStreamDataProvider()

Description copied from class: AbstractEventWriter

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

This default implementation creates a new instance of WriterStreamDataProvider.

Overrides:

createStreamDataProvider in class AbstractEventWriter<TextWriterStreamDataProvider<NewickEventWriter>>

Returns:

the stream data provider to be used with this instance

doWriteDocument

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

Overrides:

doWriteDocument in class AbstractTextEventWriter<TextWriterStreamDataProvider<NewickEventWriter>>

Throws:

java.io.IOException