info.bioinfweb.jphyloio.formats.nexml.receivers

Class NeXMLHandleSequenceDataReceiver

java.lang.Object

info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver<P>

info.bioinfweb.jphyloio.dataadapters.implementations.receivers.AbstractSequenceContentReceiver<NeXMLWriterStreamDataProvider>

info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLHandleSequenceDataReceiver

All Implemented Interfaces:

JPhyloIOEventReceiver, NeXMLConstants

Direct Known Subclasses:

NeXMLCollectSequenceDataReceiver, NeXMLSequenceTokensReceiver

public abstract class NeXMLHandleSequenceDataReceiver
extends AbstractSequenceContentReceiver<NeXMLWriterStreamDataProvider>
implements NeXMLConstants

General implementation of a receiver that processes sequence tokens.

Author:

Sarah Wiechers

Field Summary

Fields inherited from interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants

ATTR_ABOUT, ATTR_CELL_SET_LINKED_IDS, ATTR_CHAR_SET_LINKED_IDS, ATTR_CODON_POSITION, ATTR_CONTENT, ATTR_DATATYPE, ATTR_GENERATOR, ATTR_HREF, ATTR_ID, ATTR_LABEL, ATTR_LENGTH, ATTR_NODE_EDGE_SET_LINKED_EDGE_IDS, ATTR_NODE_EDGE_SET_LINKED_NODE_IDS, ATTR_NODE_EDGE_SET_LINKED_ROOTEDGE_IDS, ATTR_OTU_SET_LINKED_IDS, ATTR_OTUS, ATTR_PROPERTY, ATTR_REL, ATTR_ROOT, ATTR_SEQUENCE_SET_LINKED_IDS, ATTR_SINGLE_CHAR_LINK, ATTR_SINGLE_OTU_LINK, ATTR_SINGLE_STATE_LINK, ATTR_SOURCE, ATTR_STATE_SET_LINKED_IDS, ATTR_STATES, ATTR_SYMBOL, ATTR_TARGET, ATTR_TOKENS, ATTR_TREE_SET_LINKED_NETWORK_IDS, ATTR_TREE_SET_LINKED_TREE_IDS, ATTR_VERSION, ATTR_XSI_TYPE, DEFAULT_TOKEN_DEFINITION_SET_ID_PREFIX, NEXML_DEFAULT_NAMESPACE_PREFIX, NEXML_FORMAT_NAME, NEXML_NAMESPACE, NEXML_NAMESPACE_PREFIX, NEXML_PREDICATE_NAMESPACE, NEXML_VERSION, PREDICATE_CHAR_ATTR_CODON_POSITION, PREDICATE_CHAR_ATTR_TOKENS, PREDICATE_FORMAT, PREDICATE_MATRIX, PREDICATE_ORIGINAL_LABEL, PREDICATE_ORIGINAL_TOKEN_NAME, TAG_CELL, TAG_CHAR, TAG_CHARACTERS, TAG_EDGE, TAG_FORMAT, TAG_MATRIX, TAG_MEMBER, TAG_META, TAG_NETWORK, TAG_NODE, TAG_OTU, TAG_OTUS, TAG_POLYMORPHIC, TAG_ROOT, TAG_ROOTEDGE, TAG_ROW, TAG_SEQ, TAG_SET, TAG_STATE, TAG_STATES, TAG_TREE, TAG_TREES, TAG_UNCERTAIN, TYPE_CONTIN_CELLS, TYPE_CONTIN_SEQ, TYPE_DNA_CELLS, TYPE_DNA_SEQS, TYPE_FLOAT_NETWORK, TYPE_FLOAT_TREE, TYPE_INT_NETWORK, TYPE_INT_TREE, TYPE_LITERAL_META, TYPE_PROTEIN_CELLS, TYPE_PROTEIN_SEQS, TYPE_RESOURCE_META, TYPE_RESTRICTION_CELLS, TYPE_RESTRICTION_SEQS, TYPE_RNA_CELLS, TYPE_RNA_SEQS, TYPE_STANDARD_CELLS, TYPE_STANDARD_SEQ, UNDEFINED_OTU_ID_PREFIX, UNDEFINED_OTU_LABEL, UNDEFINED_OTUS_ID_PREFIX, UNDEFINED_OTUS_LABEL

Constructor Summary

Constructors

Constructor and Description
NeXMLHandleSequenceDataReceiver(NeXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameterMap, boolean longTokens)

Method Summary

Modifier and Type	Method and Description
protected boolean	doAdd(JPhyloIOEvent event) This method is called internally by BasicEventReceiver.add(JPhyloIOEvent) to process events that do not model metadata or comments.
long	getTokenIndex() Returns the index of the alignment character the currently handled token belongs to.
protected void	handleTokenEnd()
boolean	isNestedUnderSingleToken() Determines whether the current event is nested under a SingleTokenDefinitionEvent or not.
void	setNestedUnderSingleToken(boolean nestedUnderSingleToken)
void	setTokenIndex(long tokenIndex)

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

handleToken, isLongTokens

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

add, addIgnoredComments, addIgnoredLiteralMetadata, addIgnoredResourceMetadata, addIgnoreLogMessage, didIgnoreComments, didIgnoreLiteralMetadata, didIgnoreMetadata, didIgnoreResourceMetadata, getIgnoredComments, getIgnoredLiteralMetadata, getIgnoredMetadata, getIgnoredResourceMetadata, getLogger, getParameterMap, getParentEvent, getParentEvents, getStreamDataProvider, handleComment, handleLiteralContentMeta, handleLiteralMetaStart, handleMetaEndEvent, handleResourceMetaStart, isInComment

Methods inherited from class java.lang.Object

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

Constructor Detail

NeXMLHandleSequenceDataReceiver

public NeXMLHandleSequenceDataReceiver(NeXMLWriterStreamDataProvider streamDataProvider,
                                       ReadWriteParameterMap parameterMap,
                                       boolean longTokens)

Method Detail

isNestedUnderSingleToken

public boolean isNestedUnderSingleToken()

Determines whether the current event is nested under a SingleTokenDefinitionEvent or not.

Returns:

true if the current event is nested under a SingleTokenDefinitionEvent

setNestedUnderSingleToken

public void setNestedUnderSingleToken(boolean nestedUnderSingleToken)

getTokenIndex

public long getTokenIndex()

Returns the index of the alignment character the currently handled token belongs to.

Returns:

the character index of the currently handled token

setTokenIndex

public void setTokenIndex(long tokenIndex)

handleTokenEnd

protected void handleTokenEnd()
                       throws javax.xml.stream.XMLStreamException

Throws:

javax.xml.stream.XMLStreamException

doAdd

protected boolean doAdd(JPhyloIOEvent event)
                 throws java.io.IOException,
                        javax.xml.stream.XMLStreamException

Description copied from class: BasicEventReceiver

This method is called internally by BasicEventReceiver.add(JPhyloIOEvent) to process events that do not model metadata or comments. (Such events are treated by the according special methods of this class).

This default implementation just throws an IllegalEventException. Inherited classes that need to support other events then these modeling metadata or comments, must overwrite this method.

Overrides:

doAdd in class AbstractSequenceContentReceiver<NeXMLWriterStreamDataProvider>

Parameters:

event - the event to be processed

Returns:

true if more events can be written to this acceptor or false if writing should be aborted

Throws:

java.io.IOException - if an I/O error occurs when writing to the underlying stream

javax.xml.stream.XMLStreamException - if an XML stream error occurs when writing to the underlying stream