info.bioinfweb.jphyloio.formats.nexml.receivers

Class NeXMLIgnoreCertainMetadataReceiver

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.NeXMLPredicateMetaReceiver

info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLIgnoreCertainMetadataReceiver

All Implemented Interfaces:

JPhyloIOEventReceiver, NeXMLConstants

public class NeXMLIgnoreCertainMetadataReceiver
extends NeXMLPredicateMetaReceiver

Receiver that is able to ignore metadata events with certain predicates, e.g. if they were already processed by NeXMLAttributeMetadataReceiver to be written as attributes. The content of the ignored events will not be written to the file by this receiver.

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
NeXMLIgnoreCertainMetadataReceiver(NeXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameterMap, boolean writePredicateMetadata, javax.xml.namespace.QName... predicates) Creates a new instance of this class.

Method Summary

Modifier and Type	Method and Description
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.formats.nexml.receivers.NeXMLPredicateMetaReceiver

changeMetaLevel, getMetaLevel, getPredicates, isUnderPredicate, setMetaLevel, setUnderPredicate

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, getStreamDataProvider, isInComment

Methods inherited from class java.lang.Object

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

Constructor Detail

NeXMLIgnoreCertainMetadataReceiver

public NeXMLIgnoreCertainMetadataReceiver(NeXMLWriterStreamDataProvider streamDataProvider,
                                          ReadWriteParameterMap parameterMap,
                                          boolean writePredicateMetadata,
                                          javax.xml.namespace.QName... predicates)

Creates a new instance of this class.

Parameters:

writer - the XML writer of the calling NeXMLEventWriter

parameterMap - the parameter map of the calling NeXMLEventWriter

streamDataProvider - the stream data provider of the calling NeXMLEventReader

writePredicateMetadata - specify {code true} here if only metadata nested under the specified predicates should be written or false if metadata under these predicates should be ignored

predicates - the predicates to be processed in a special way

Method Detail

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

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

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