info.bioinfweb.jphyloio.formats.newick

Class NewickNodeEdgeEventReceiver<E extends JPhyloIOEvent>

java.lang.Object

info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver

info.bioinfweb.jphyloio.formats.newick.NewickNodeEdgeEventReceiver<E>

All Implemented Interfaces:

JPhyloIOEventReceiver, NewickConstants

public class NewickNodeEdgeEventReceiver<E extends JPhyloIOEvent>
extends BasicEventReceiver
implements NewickConstants

Field Summary

Fields

Modifier and Type	Field and Description
static char	STRING_DELEMITER_REPLACEMENT

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
NewickNodeEdgeEventReceiver(TextWriterStreamDataProvider<?> streamDataProvider, ReadWriteParameterMap parameterMap)

Method Summary

Modifier and Type	Method and Description
void	clear()
TextWriterStreamDataProvider	getStreamDataProvider()
protected void	handleComment(CommentEvent event)
protected void	handleLiteralContentMeta(LiteralMetadataContentEvent event)
protected void	handleLiteralMetaStart(LiteralMetadataEvent event)
protected void	handleMetaEndEvent(JPhyloIOEvent event)
boolean	hasMetadataToWrite() Determines whether this receiver currently stores metadata to be written into a Newick/Nexus hot comment.
boolean	isIgnoredXMLMetadata()
void	writeComments()
void	writeMetadata() Write the metadata stored in this receiver into a Newick/Nexus hot comment.

Methods inherited from class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver

add, addIgnoredComments, addIgnoredLiteralMetadata, addIgnoredResourceMetadata, addIgnoreLogMessage, didIgnoreComments, didIgnoreLiteralMetadata, didIgnoreMetadata, didIgnoreResourceMetadata, doAdd, getIgnoredComments, getIgnoredLiteralMetadata, getIgnoredMetadata, getIgnoredResourceMetadata, getLogger, getParameterMap, getParentEvent, getParentEvents, handleResourceMetaStart, isInComment

Methods inherited from class java.lang.Object

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

Field Detail

STRING_DELEMITER_REPLACEMENT

public static final char STRING_DELEMITER_REPLACEMENT

See Also:

Constant Field Values

Constructor Detail

NewickNodeEdgeEventReceiver

public NewickNodeEdgeEventReceiver(TextWriterStreamDataProvider<?> streamDataProvider,
                                   ReadWriteParameterMap parameterMap)

Method Detail

getStreamDataProvider

public TextWriterStreamDataProvider getStreamDataProvider()

Overrides:

getStreamDataProvider in class BasicEventReceiver

isIgnoredXMLMetadata

public boolean isIgnoredXMLMetadata()

clear

public void clear()

handleLiteralMetaStart

protected void handleLiteralMetaStart(LiteralMetadataEvent event)
                               throws java.io.IOException,
                                      javax.xml.stream.XMLStreamException

Overrides:

handleLiteralMetaStart in class BasicEventReceiver

Throws:

java.io.IOException

javax.xml.stream.XMLStreamException

handleLiteralContentMeta

protected void handleLiteralContentMeta(LiteralMetadataContentEvent event)
                                 throws java.io.IOException,
                                        javax.xml.stream.XMLStreamException

Overrides:

handleLiteralContentMeta in class BasicEventReceiver

Throws:

java.io.IOException

javax.xml.stream.XMLStreamException

handleMetaEndEvent

protected void handleMetaEndEvent(JPhyloIOEvent event)
                           throws java.io.IOException,
                                  javax.xml.stream.XMLStreamException

Overrides:

handleMetaEndEvent in class BasicEventReceiver

Throws:

java.io.IOException

javax.xml.stream.XMLStreamException

handleComment

protected void handleComment(CommentEvent event)

Overrides:

handleComment in class BasicEventReceiver

hasMetadataToWrite

public boolean hasMetadataToWrite()

Determines whether this receiver currently stores metadata to be written into a Newick/Nexus hot comment.

Returns:

true if any data can be written, false otherwise

writeMetadata

public void writeMetadata()
                   throws java.io.IOException

Write the metadata stored in this receiver into a Newick/Nexus hot comment.

Throws:

java.io.IOException

writeComments

public void writeComments()
                   throws java.io.IOException

Throws:

java.io.IOException