info.bioinfweb.jphyloio.formats.nexml

Class NeXMLWriterStreamDataProvider

java.lang.Object

info.bioinfweb.jphyloio.WriterStreamDataProvider<R>

info.bioinfweb.jphyloio.formats.xml.XMLWriterStreamDataProvider<NeXMLEventWriter>

info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider

All Implemented Interfaces:

NeXMLConstants

public class NeXMLWriterStreamDataProvider
extends XMLWriterStreamDataProvider<NeXMLEventWriter>
implements NeXMLConstants

Stores data that shall be shared among different implementations of AbstractNeXMLDataReceiver and the writer instance that uses them.

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
NeXMLWriterStreamDataProvider(NeXMLEventWriter eventWriter)

Method Summary

Modifier and Type	Method and Description
void	addToDocumentIDs(java.lang.String id)
java.lang.String	createNewID(java.lang.String prefix)
java.util.Map<java.lang.String,NeXMLWriterAlignmentInformation>	getAlignmentInfoByIDMap()
NeXMLWriterAlignmentInformation	getCurrentAlignmentInfo()
URIOrStringIdentifier	getCurrentLiteralMetaDatatype()
LiteralContentSequenceType	getCurrentLiteralMetaSequenceType()
NeXMLWriterTokenSetInformation	getCurrentTokenSetInfo()
java.util.Set<java.lang.String>	getDocumentIDs()
int	getIDIndex()
java.lang.String	getNeXMLPrefix(javax.xml.stream.XMLStreamWriter writer)
java.util.Map<java.lang.String,java.util.EnumMap<EventContentType,java.util.Set<java.lang.String>>>	getSetIDToSetElementsMap()
java.lang.String	getSingleToken()
java.lang.String	getUndefinedOTUID()
java.lang.String	getUndefinedOTUsID()
boolean	hasOTUList()
boolean	isWriteUndefinedOTU()
boolean	isWriteUndefinedOtuList()
void	setCurrentAlignmentInfo(NeXMLWriterAlignmentInformation currentAlignmentInfo)
void	setCurrentLiteralMetaDatatype(URIOrStringIdentifier currentLiteralMetaDatatype)
void	setCurrentLiteralMetaSequenceType(LiteralContentSequenceType currentLiteralMetaType)
void	setCurrentTokenSetInfo(NeXMLWriterTokenSetInformation currentTokenSetInfo)
void	setHasOTUList(boolean hasOTUList)
void	setIDIndex(int idIndex)
void	setSingleToken(java.lang.String singleToken)
void	setUndefinedOTUID(java.lang.String undefinedOTUID)
void	setUndefinedOTUsID(java.lang.String undefinedOTUsID)
void	setWriteUndefinedOTU(boolean writeUndefinedOTU)
void	setWriteUndefinedOtuList(boolean writeUndefinedOtuList)
void	writeLabeledIDAttributes(LabeledIDEvent event)
void	writeLabeledIDAttributes(LabeledIDEvent event, java.lang.String about)
void	writeLinkedLabeledIDAttributes(LinkedLabeledIDEvent event, javax.xml.namespace.QName linkAttribute, boolean forceOTULink)

Methods inherited from class info.bioinfweb.jphyloio.formats.xml.XMLWriterStreamDataProvider

getCommentContent, getNamespacePrefixes, getWriter, isLiteralContentContinued, setLiteralContentIsContinued, setNamespacePrefix

Methods inherited from class info.bioinfweb.jphyloio.WriterStreamDataProvider

getEventWriter

Methods inherited from class java.lang.Object

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

Constructor Detail

NeXMLWriterStreamDataProvider

public NeXMLWriterStreamDataProvider(NeXMLEventWriter eventWriter)

Method Detail

getDocumentIDs

public java.util.Set<java.lang.String> getDocumentIDs()

getIDIndex

public int getIDIndex()

setIDIndex

public void setIDIndex(int idIndex)

addToDocumentIDs

public void addToDocumentIDs(java.lang.String id)
                      throws JPhyloIOWriterException

Throws:

JPhyloIOWriterException

hasOTUList

public boolean hasOTUList()

setHasOTUList

public void setHasOTUList(boolean hasOTUList)

getCurrentLiteralMetaSequenceType

public LiteralContentSequenceType getCurrentLiteralMetaSequenceType()

setCurrentLiteralMetaSequenceType

public void setCurrentLiteralMetaSequenceType(LiteralContentSequenceType currentLiteralMetaType)

getCurrentLiteralMetaDatatype

public URIOrStringIdentifier getCurrentLiteralMetaDatatype()

setCurrentLiteralMetaDatatype

public void setCurrentLiteralMetaDatatype(URIOrStringIdentifier currentLiteralMetaDatatype)

getSetIDToSetElementsMap

public java.util.Map<java.lang.String,java.util.EnumMap<EventContentType,java.util.Set<java.lang.String>>> getSetIDToSetElementsMap()

getCurrentAlignmentInfo

public NeXMLWriterAlignmentInformation getCurrentAlignmentInfo()

setCurrentAlignmentInfo

public void setCurrentAlignmentInfo(NeXMLWriterAlignmentInformation currentAlignmentInfo)

getAlignmentInfoByIDMap

public java.util.Map<java.lang.String,NeXMLWriterAlignmentInformation> getAlignmentInfoByIDMap()

getCurrentTokenSetInfo

public NeXMLWriterTokenSetInformation getCurrentTokenSetInfo()

setCurrentTokenSetInfo

public void setCurrentTokenSetInfo(NeXMLWriterTokenSetInformation currentTokenSetInfo)

getSingleToken

public java.lang.String getSingleToken()

setSingleToken

public void setSingleToken(java.lang.String singleToken)

isWriteUndefinedOTU

public boolean isWriteUndefinedOTU()

setWriteUndefinedOTU

public void setWriteUndefinedOTU(boolean writeUndefinedOTU)

isWriteUndefinedOtuList

public boolean isWriteUndefinedOtuList()

setWriteUndefinedOtuList

public void setWriteUndefinedOtuList(boolean writeUndefinedOtuList)

getUndefinedOTUID

public java.lang.String getUndefinedOTUID()

setUndefinedOTUID

public void setUndefinedOTUID(java.lang.String undefinedOTUID)

getUndefinedOTUsID

public java.lang.String getUndefinedOTUsID()

setUndefinedOTUsID

public void setUndefinedOTUsID(java.lang.String undefinedOTUsID)

createNewID

public java.lang.String createNewID(java.lang.String prefix)

writeLabeledIDAttributes

public void writeLabeledIDAttributes(LabeledIDEvent event)
                              throws javax.xml.stream.XMLStreamException,
                                     JPhyloIOWriterException

Throws:

javax.xml.stream.XMLStreamException

JPhyloIOWriterException

writeLabeledIDAttributes

public void writeLabeledIDAttributes(LabeledIDEvent event,
                                     java.lang.String about)
                              throws javax.xml.stream.XMLStreamException,
                                     JPhyloIOWriterException

Throws:

javax.xml.stream.XMLStreamException

JPhyloIOWriterException

writeLinkedLabeledIDAttributes

public void writeLinkedLabeledIDAttributes(LinkedLabeledIDEvent event,
                                           javax.xml.namespace.QName linkAttribute,
                                           boolean forceOTULink)
                                    throws javax.xml.stream.XMLStreamException,
                                           JPhyloIOWriterException

Throws:

javax.xml.stream.XMLStreamException

JPhyloIOWriterException

getNeXMLPrefix

public java.lang.String getNeXMLPrefix(javax.xml.stream.XMLStreamWriter writer)
                                throws javax.xml.stream.XMLStreamException

Throws:

javax.xml.stream.XMLStreamException