public class NeXMLWriterAlignmentInformation extends Object implements NeXMLConstants
NeXMLEventWriter
to store information about an alignment.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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NeXMLWriterAlignmentInformation() |
public NeXMLWriterAlignmentInformation()
public boolean isWriteAlignment()
public void setWriteAlignment(boolean writeAlignment)
public boolean isWriteCellsTags()
public void setWriteCellsTags(boolean writeCellsTags)
public long getAlignmentLength()
public void setAlignmentLength(long alignmentLength)
public CharacterStateSetType getAlignmentType()
public void setAlignmentType(CharacterStateSetType alignmentType) throws JPhyloIOWriterException
JPhyloIOWriterException
public CharacterStateSetType getTokenSetType()
public void setTokenSetType(CharacterStateSetType tokenSetType)
public CharacterStateSetType getTokenType()
public void setTokenType(CharacterStateSetType tokenType)
public boolean isWriteDefaultTokenSet()
public void setWriteDefaultTokenSet(boolean writeDefaultTokenSet)
public boolean hasTokenDefinitionSet()
public Map<String,NeXMLWriterTokenSetInformation> getIDToTokenSetInfoMap()
public String getDefaultTokenSetID()
public void setDefaultTokenSetID(String defaultTokenSetID)
public Map<String,SortedSet<Long>> getCharSets()
public Map<Long,String> getColumnIndexToIDMap()
public Map<Long,String> getColumnIndexToStatesMap()
public Set<String> getDefinedTokens()