info.bioinfweb.jphyloio.formats.nexml.receivers

Class NeXMLCollectSetMetadataReceiver

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.NeXMLCollectNamespaceReceiver

info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLCollectSetMetadataReceiver

All Implemented Interfaces:

JPhyloIOEventReceiver, NeXMLConstants

public class NeXMLCollectSetMetadataReceiver
extends NeXMLCollectNamespaceReceiver

Receiver that collects information about sets contained in a document.

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
NeXMLCollectSetMetadataReceiver(NeXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameterMap, java.lang.String setID, boolean ignoreMetadata)

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.
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

NeXMLCollectSetMetadataReceiver

public NeXMLCollectSetMetadataReceiver(NeXMLWriterStreamDataProvider streamDataProvider,
                                       ReadWriteParameterMap parameterMap,
                                       java.lang.String setID,
                                       boolean ignoreMetadata)

Method Detail

handleLiteralMetaStart

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

Overrides:

handleLiteralMetaStart in class NeXMLCollectNamespaceReceiver

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 NeXMLCollectNamespaceReceiver

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 NeXMLCollectNamespaceReceiver

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 NeXMLCollectNamespaceReceiver

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 NeXMLCollectNamespaceReceiver

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