info.bioinfweb.jphyloio.formats.nexml

Class NeXMLWriterAlignmentInformation

java.lang.Object

info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterAlignmentInformation

All Implemented Interfaces:

NeXMLConstants

public class NeXMLWriterAlignmentInformation
extends java.lang.Object
implements NeXMLConstants

Class that is used by NeXMLEventWriter to store information about an alignment.

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
NeXMLWriterAlignmentInformation()

Method Summary

Modifier and Type	Method and Description
long	getAlignmentLength()
CharacterStateSetType	getAlignmentType()
java.util.Map<java.lang.String,java.util.SortedSet<java.lang.Long>>	getCharSets()
java.util.Map<java.lang.Long,java.lang.String>	getColumnIndexToIDMap()
java.util.Map<java.lang.Long,java.lang.String>	getColumnIndexToStatesMap()
java.lang.String	getDefaultTokenSetID()
java.util.Set<java.lang.String>	getDefinedTokens()
java.util.Map<java.lang.String,NeXMLWriterTokenSetInformation>	getIDToTokenSetInfoMap()
CharacterStateSetType	getTokenSetType()
CharacterStateSetType	getTokenType()
boolean	hasTokenDefinitionSet()
boolean	isWriteAlignment()
boolean	isWriteCellsTags()
boolean	isWriteDefaultTokenSet()
void	setAlignmentLength(long alignmentLength)
void	setAlignmentType(CharacterStateSetType alignmentType)
void	setDefaultTokenSetID(java.lang.String defaultTokenSetID)
void	setTokenSetType(CharacterStateSetType tokenSetType)
void	setTokenType(CharacterStateSetType tokenType)
void	setWriteAlignment(boolean writeAlignment)
void	setWriteCellsTags(boolean writeCellsTags)
void	setWriteDefaultTokenSet(boolean writeDefaultTokenSet)

Methods inherited from class java.lang.Object

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

Constructor Detail

NeXMLWriterAlignmentInformation

public NeXMLWriterAlignmentInformation()

Method Detail

isWriteAlignment

public boolean isWriteAlignment()

setWriteAlignment

public void setWriteAlignment(boolean writeAlignment)

isWriteCellsTags

public boolean isWriteCellsTags()

setWriteCellsTags

public void setWriteCellsTags(boolean writeCellsTags)

getAlignmentLength

public long getAlignmentLength()

setAlignmentLength

public void setAlignmentLength(long alignmentLength)

getAlignmentType

public CharacterStateSetType getAlignmentType()

setAlignmentType

public void setAlignmentType(CharacterStateSetType alignmentType)
                      throws JPhyloIOWriterException

Throws:

JPhyloIOWriterException

getTokenSetType

public CharacterStateSetType getTokenSetType()

setTokenSetType

public void setTokenSetType(CharacterStateSetType tokenSetType)

getTokenType

public CharacterStateSetType getTokenType()

setTokenType

public void setTokenType(CharacterStateSetType tokenType)

isWriteDefaultTokenSet

public boolean isWriteDefaultTokenSet()

setWriteDefaultTokenSet

public void setWriteDefaultTokenSet(boolean writeDefaultTokenSet)

hasTokenDefinitionSet

public boolean hasTokenDefinitionSet()

getIDToTokenSetInfoMap

public java.util.Map<java.lang.String,NeXMLWriterTokenSetInformation> getIDToTokenSetInfoMap()

getDefaultTokenSetID

public java.lang.String getDefaultTokenSetID()

setDefaultTokenSetID

public void setDefaultTokenSetID(java.lang.String defaultTokenSetID)

getCharSets

public java.util.Map<java.lang.String,java.util.SortedSet<java.lang.Long>> getCharSets()

getColumnIndexToIDMap

public java.util.Map<java.lang.Long,java.lang.String> getColumnIndexToIDMap()

getColumnIndexToStatesMap

public java.util.Map<java.lang.Long,java.lang.String> getColumnIndexToStatesMap()

getDefinedTokens

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