info.bioinfweb.jphyloio.formats.nexml.elementreader

Class AbstractSetElementReader

java.lang.Object

info.bioinfweb.jphyloio.formats.xml.elementreaders.AbstractXMLElementReader<NeXMLReaderStreamDataProvider>

info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractNeXMLElementReader

info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractSetElementReader

All Implemented Interfaces:

NeXMLConstants, XMLElementReader<NeXMLReaderStreamDataProvider>, ReadWriteConstants

Direct Known Subclasses:

AbstractIDLinkSetElementReader

public abstract class AbstractSetElementReader
extends AbstractNeXMLElementReader

Abstract element reader that processes NeXML set tags that contain one or more attributes of the type xs:IDREFS.

Since:

0.0.0

Author:

Ben Stöver

Nested Class Summary

Nested classes/interfaces inherited from class info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractNeXMLElementReader

AbstractNeXMLElementReader.LabeledIDEventInformation, AbstractNeXMLElementReader.OTUorOTUsEventInformation

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

Fields inherited from interface info.bioinfweb.jphyloio.ReadWriteConstants

ATTRIBUTE_STRING_KEY, ATTRIBUTES_NAMESPACE_FOLDER, DATA_TYPE_NAMESPACE_FOLDER, DATA_TYPE_SIMPLE_VALUE_LIST, DEFAULT_CHAR_SET_ID_PREFIX, DEFAULT_CHARACTER_DEFINITION_ID_PREFIX, DEFAULT_EDGE_ID_PREFIX, DEFAULT_GENERAL_ID_PREFIX, DEFAULT_MATRIX_ID_PREFIX, DEFAULT_MAX_COMMENT_LENGTH, DEFAULT_MAX_TOKENS_TO_READ, DEFAULT_META_ID_PREFIX, DEFAULT_NETWORK_ID_PREFIX, DEFAULT_NODE_EDGE_SET_ID_PREFIX, DEFAULT_NODE_ID_PREFIX, DEFAULT_OTU_ID_PREFIX, DEFAULT_OTU_LIST_ID_PREFIX, DEFAULT_OTU_SET_ID_PREFIX, DEFAULT_SEQUENCE_ID_PREFIX, DEFAULT_SEQUENCE_SET_ID_PREFIX, DEFAULT_TOKEN_DEFINITION_ID_PREFIX, DEFAULT_TOKEN_SET_ID_PREFIX, DEFAULT_TREE_ID_PREFIX, DEFAULT_TREE_NETWORK_GROUP_ID_PREFIX, DEFAULT_TREE_NETWORK_SET_ID_PREFIX, JPHYLOIO_ATTRIBUTES_NAMESPACE, JPHYLOIO_ATTRIBUTES_PREFIX, JPHYLOIO_DATA_TYPE_NAMESPACE, JPHYLOIO_DATA_TYPE_PREFIX, JPHYLOIO_FORMATS_NAMESPACE_PREFIX, JPHYLOIO_GENERAL_NAMESPACE, JPHYLOIO_NAMESPACE_PREFIX, JPHYLOIO_PREDICATE_NAMESPACE, JPHYLOIO_PREDICATE_PREFIX, PREDICATE_CHARACTER_COUNT, PREDICATE_EDGE_LENGTH, PREDICATE_EDGE_SOURCE_NODE, PREDICATE_EDGE_TARGET_NODE, PREDICATE_HAS_CUSTOM_XML, PREDICATE_HAS_LITERAL_METADATA, PREDICATE_HAS_RESOURCE_METADATA, PREDICATE_IS_CROSSLINK, PREDICATE_NAMESPACE_FOLDER, PREDICATE_PART_SEPERATOR, PREDICATE_SEQUENCE_COUNT, RESERVED_ID_PREFIX

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AbstractSetElementReader(EventContentType setType, EventContentType linkedIDType, javax.xml.namespace.QName... linkedIDsAttributes)

Method Summary

Modifier and Type	Method and Description
EventContentType	getSetType()
protected abstract void	processIDs(NeXMLReaderStreamDataProvider streamDataProvider, java.lang.String[] linkedIDs, javax.xml.namespace.QName attribute) Method that is called to process a list of IDs that has been found in an according attribute of the tag processed by this instance.
void	readEvent(NeXMLReaderStreamDataProvider streamDataProvider, javax.xml.stream.events.XMLEvent event)

Methods inherited from class info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractNeXMLElementReader

createIntervalEvents, getLabeledIDEventInformation, getOTUorOTUsEventInformation, parseStateMeaning, readSequence

Methods inherited from class info.bioinfweb.jphyloio.formats.xml.elementreaders.AbstractXMLElementReader

readAttributes, readAttributes

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractSetElementReader

protected AbstractSetElementReader(EventContentType setType,
                                   EventContentType linkedIDType,
                                   javax.xml.namespace.QName... linkedIDsAttributes)

Method Detail

getSetType

public EventContentType getSetType()

readEvent

public void readEvent(NeXMLReaderStreamDataProvider streamDataProvider,
                      javax.xml.stream.events.XMLEvent event)
               throws java.io.IOException,
                      javax.xml.stream.XMLStreamException

Throws:

java.io.IOException

javax.xml.stream.XMLStreamException

processIDs

protected abstract void processIDs(NeXMLReaderStreamDataProvider streamDataProvider,
                                   java.lang.String[] linkedIDs,
                                   javax.xml.namespace.QName attribute)
                            throws JPhyloIOReaderException,
                                   javax.xml.stream.XMLStreamException

Method that is called to process a list of IDs that has been found in an according attribute of the tag processed by this instance.

Parameters:

streamDataProvider - the stream data provider of the associated event reader

linkedIDs - the list of IDs linked by the read tag

attribute - the attribute that contained the linked IDs

Throws:

JPhyloIOReaderException

javax.xml.stream.XMLStreamException