public class NeXMLCollectTokenSetDefinitionDataReceiver extends NeXMLCollectNamespaceReceiver
The CharacterStateSetType of the token set will be different from the one given in the start event of the according set,
if a SingleTokenDefinitionEvent defines a token that is not allowed under the current type of token set
or if the original token set type was CharacterStateSetType.NUCLEOTIDE.
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 and Description |
|---|
NeXMLCollectTokenSetDefinitionDataReceiver(NeXMLWriterStreamDataProvider streamDataProvider,
ReadWriteParameterMap parameterMap,
java.lang.String tokenSetDefinitionID) |
| 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. |
handleComment, handleLiteralContentMeta, handleLiteralMetaStart, handleMetaEndEvent, handleResourceMetaStartadd, addIgnoredComments, addIgnoredLiteralMetadata, addIgnoredResourceMetadata, addIgnoreLogMessage, didIgnoreComments, didIgnoreLiteralMetadata, didIgnoreMetadata, didIgnoreResourceMetadata, getIgnoredComments, getIgnoredLiteralMetadata, getIgnoredMetadata, getIgnoredResourceMetadata, getLogger, getParameterMap, getParentEvent, getParentEvents, getStreamDataProvider, isInCommentpublic NeXMLCollectTokenSetDefinitionDataReceiver(NeXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameterMap, java.lang.String tokenSetDefinitionID)
protected boolean doAdd(JPhyloIOEvent event) throws java.io.IOException, javax.xml.stream.XMLStreamException
BasicEventReceiverBasicEventReceiver.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.
doAdd in class BasicEventReceiver<NeXMLWriterStreamDataProvider>event - the event to be processedtrue if more events can be written to this acceptor or false if writing should
be abortedjava.io.IOException - if an I/O error occurs when writing to the underlying streamjavax.xml.stream.XMLStreamException - if an XML stream error occurs when writing to the underlying stream