public class NeXMLWriterStreamDataProvider extends XMLWriterStreamDataProvider<NeXMLEventWriter> implements NeXMLConstants
AbstractNeXMLDataReceiver
and the writer instance that uses them.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 |
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NeXMLWriterStreamDataProvider(NeXMLEventWriter eventWriter) |
getCommentContent, getNamespacePrefixes, getWriter, isLiteralContentContinued, setLiteralContentIsContinued, setNamespacePrefix
getEventWriter
public NeXMLWriterStreamDataProvider(NeXMLEventWriter eventWriter)
public Set<String> getDocumentIDs()
public int getIDIndex()
public void setIDIndex(int idIndex)
public void addToDocumentIDs(String id) throws JPhyloIOWriterException
JPhyloIOWriterException
public boolean hasOTUList()
public void setHasOTUList(boolean hasOTUList)
public LiteralContentSequenceType getCurrentLiteralMetaSequenceType()
public void setCurrentLiteralMetaSequenceType(LiteralContentSequenceType currentLiteralMetaType)
public URIOrStringIdentifier getCurrentLiteralMetaDatatype()
public void setCurrentLiteralMetaDatatype(URIOrStringIdentifier currentLiteralMetaDatatype)
public Map<String,EnumMap<EventContentType,Set<String>>> getSetIDToSetElementsMap()
public NeXMLWriterAlignmentInformation getCurrentAlignmentInfo()
public void setCurrentAlignmentInfo(NeXMLWriterAlignmentInformation currentAlignmentInfo)
public Map<String,NeXMLWriterAlignmentInformation> getIdToAlignmentInfo()
public NeXMLWriterTokenSetInformation getCurrentTokenSetInfo()
public void setCurrentTokenSetInfo(NeXMLWriterTokenSetInformation currentTokenSetInfo)
public String getSingleToken()
public void setSingleToken(String singleToken)
public boolean isWriteUndefinedOTU()
public void setWriteUndefinedOTU(boolean writeUndefinedOTU)
public boolean isWriteUndefinedOtuList()
public void setWriteUndefinedOtuList(boolean writeUndefinedOtuList)
public String getUndefinedOTUID()
public void setUndefinedOTUID(String undefinedOTUID)
public String getUndefinedOTUsID()
public void setUndefinedOTUsID(String undefinedOTUsID)
public String createNewID(String prefix)
public void writeLabeledIDAttributes(LabeledIDEvent event) throws XMLStreamException, JPhyloIOWriterException
public void writeLabeledIDAttributes(LabeledIDEvent event, String about) throws XMLStreamException, JPhyloIOWriterException
public void writeLinkedLabeledIDAttributes(LinkedLabeledIDEvent event, QName linkAttribute, boolean forceOTULink) throws XMLStreamException, JPhyloIOWriterException
public String getNeXMLPrefix(XMLStreamWriter writer) throws XMLStreamException
XMLStreamException