info.bioinfweb.jphyloio.formats.nexml.receivers

Class NeXMLMolecularDataTokenDefinitionReceiver

java.lang.Object

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

info.bioinfweb.jphyloio.formats.xml.receivers.AbstractXMLDataReceiver<NeXMLWriterStreamDataProvider>

info.bioinfweb.jphyloio.formats.nexml.receivers.AbstractNeXMLDataReceiver

info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLMetaDataReceiver

info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLMolecularDataTokenDefinitionReceiver

All Implemented Interfaces:

JPhyloIOEventReceiver, NeXMLConstants

public class NeXMLMolecularDataTokenDefinitionReceiver
extends NeXMLMetaDataReceiver

Receiver that writes token definitions for molecular data, such as DNA, RNA or protein sequences.

Author:

Sarah Wiechers, Ben Stöver

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
NeXMLMolecularDataTokenDefinitionReceiver(NeXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameterMap, java.lang.String tokenSetID)

Method Summary

Modifier and Type	Method and Description
void	addRemainingEvents(CharacterStateSetType type) Determines the type of alignment to which additional token definitions need to be add.
protected boolean	doAdd(JPhyloIOEvent event) This method is called internally by BasicEventReceiver.add(JPhyloIOEvent) to process events that do not model metadata or comments.
protected void	handleComment(CommentEvent event)
protected void	handleLiteralContentMeta(LiteralMetadataContentEvent event)
protected void	handleLiteralMetaStart(LiteralMetadataEvent event)
protected void	handleMetaEndEvent(JPhyloIOEvent event)
protected void	handleResourceMetaStart(ResourceMetadataEvent event)

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, isInComment

Methods inherited from class java.lang.Object

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

Constructor Detail

NeXMLMolecularDataTokenDefinitionReceiver

public NeXMLMolecularDataTokenDefinitionReceiver(NeXMLWriterStreamDataProvider streamDataProvider,
                                                 ReadWriteParameterMap parameterMap,
                                                 java.lang.String tokenSetID)

Method Detail

addRemainingEvents

public void addRemainingEvents(CharacterStateSetType type)
                        throws java.io.IOException,
                               javax.xml.stream.XMLStreamException

Determines the type of alignment to which additional token definitions need to be add.

Parameters:

type - the CharacterStateSetType of the current token set

Throws:

java.io.IOException

javax.xml.stream.XMLStreamException

handleLiteralMetaStart

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

Overrides:

handleLiteralMetaStart in class NeXMLMetaDataReceiver

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 NeXMLMetaDataReceiver

Throws:

java.io.IOException

javax.xml.stream.XMLStreamException

handleResourceMetaStart

protected void handleResourceMetaStart(ResourceMetadataEvent event)
                                throws java.io.IOException,
                                       javax.xml.stream.XMLStreamException

Overrides:

handleResourceMetaStart in class NeXMLMetaDataReceiver

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 NeXMLMetaDataReceiver

Throws:

java.io.IOException

javax.xml.stream.XMLStreamException

handleComment

protected void handleComment(CommentEvent event)
                      throws java.io.IOException,
                             javax.xml.stream.XMLStreamException

Overrides:

handleComment in class NeXMLMetaDataReceiver

Throws:

java.io.IOException

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 BasicEventReceiver<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