A B C D E F G H I J K L M N O P Q R S T U V W X

## S

SCHEMA_LOCATION - Static variable in class info.bioinfweb.jphyloio.formats.xml.XMLReadWriteUtils
SEQUENCE_END - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
SequenceTokensEvent - Class in info.bioinfweb.jphyloio.events
  Indicates that one or more sequence tokens have been read from an alignment.
SequenceTokensEvent(List<String>) - Constructor for class info.bioinfweb.jphyloio.events.SequenceTokensEvent
SequenceTokensEventManager - Class in info.bioinfweb.jphyloio.utils
  Class used by implementations of `JPhyloIOEventReader` to keep track of the current alignment position and replacing match tokens by the according tokens from the first sequence.
SequenceTokensEventManager(JPhyloIOEventReader, String) - Constructor for class info.bioinfweb.jphyloio.utils.SequenceTokensEventManager
  Creates a new instance of this class.
SEQUENTIAL_PHYLIP_FORMAT_ID - Static variable in interface info.bioinfweb.jphyloio.formats.JPhyloIOFormatIDs
SEQUENTIAL_PHYLIP_FORMAT_NAME - Static variable in interface info.bioinfweb.jphyloio.formats.phylip.PhylipConstants
SequentialPhylipEventReader - Class in info.bioinfweb.jphyloio.formats.phylip
  Event based reader for sequential Phylip alignment files.
SequentialPhylipEventReader(BufferedReader, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.phylip.SequentialPhylipEventReader
  Creates a new instance of this class.
SequentialPhylipEventReader(File, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.phylip.SequentialPhylipEventReader
  Creates a new instance of this class.
SequentialPhylipEventReader(InputStream, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.phylip.SequentialPhylipEventReader
  Creates a new instance of this class.
SequentialPhylipEventReader(Reader, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.phylip.SequentialPhylipEventReader
  Creates a new instance of this class.
SequentialPhylipFactory - Class in info.bioinfweb.jphyloio.formats.phylip
  Reader and writer factory for the sequential Phylip format.
SequentialPhylipFactory() - Constructor for class info.bioinfweb.jphyloio.formats.phylip.SequentialPhylipFactory
SET_END_INDEX_SYMBOL - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
SET_KEY_WORD_ALL - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
SET_KEY_WORD_REMAINING - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
SET_REGULAR_INTERVAL_SYMBOL - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
SET_TO_SYMBOL - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
SET_VECTOR_CONTAINED - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
SET_VECTOR_NOT_CONTAINED - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
setAdditionalResourceMetaRel(URIOrStringIdentifier) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderStreamDataProvider
setAfferentBranchID(String) - Method in class info.bioinfweb.jphyloio.utils.TopoplogicalNodeInfo
setAlignmentLength(long) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterAlignmentInformation
setAlignmentLength(int) - Method in class info.bioinfweb.jphyloio.formats.pde.PDEReaderStreamDataProvider
setAlignmentType(CharacterStateSetType) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterAlignmentInformation
setAllDataProcessed(boolean) - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.AbstractNexusCommandEventReader
setAllowLongTokens(boolean) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderStreamDataProvider
setAlternativeStringRepresentation(String) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderStreamDataProvider
setCharacterSetType(CharacterStateSetType) - Method in class info.bioinfweb.jphyloio.formats.xml.XMLReaderStreamDataProvider
setCreateAlignmentEnd(boolean) - Method in class info.bioinfweb.jphyloio.formats.pde.PDEReaderStreamDataProvider
setCreateAlignmentStart(boolean) - Method in class info.bioinfweb.jphyloio.formats.pde.PDEReaderStreamDataProvider
setCreateNodeStart(boolean) - Method in class info.bioinfweb.jphyloio.formats.xml.XMLReaderStreamDataProvider
setCreatePhylogenyStart(boolean) - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLReaderStreamDataProvider
setCreateTreeGroupEnd(boolean) - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLReaderStreamDataProvider
setCreateTreeGroupStart(boolean) - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLReaderStreamDataProvider
setCurrentAlignmentID(String) - Method in class info.bioinfweb.jphyloio.formats.pde.PDEReaderStreamDataProvider
setCurrentAlignmentInfo(NeXMLWriterAlignmentInformation) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
setCurrentCellBuffered(boolean) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderStreamDataProvider
  Allow to specify whether the contents of the current `cell` tag are buffered or not.
setCurrentCladeIDSource(String) - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLWriterStreamDataProvider
setCurrentEventCollection(Collection<JPhyloIOEvent>) - Method in class info.bioinfweb.jphyloio.AbstractEventReader
  Adds a new current event collection to the stack.
setCurrentEventCollection(Collection<JPhyloIOEvent>) - Method in class info.bioinfweb.jphyloio.ReaderStreamDataProvider
  Adds a new current event collection to the stack.
setCurrentLiteralContentSequenceType(LiteralContentSequenceType) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderStreamDataProvider
setCurrentLiteralMetaDatatype(URIOrStringIdentifier) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
setCurrentLiteralMetaSequenceType(LiteralContentSequenceType) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
setCurrentSequenceID(String) - Method in class info.bioinfweb.jphyloio.formats.pde.PDEReaderStreamDataProvider
setCurrentSequenceIndex(int) - Method in class info.bioinfweb.jphyloio.formats.pde.PDEReaderStreamDataProvider
setCurrentSequenceLength(int) - Method in class info.bioinfweb.jphyloio.formats.pde.PDEReaderStreamDataProvider
setCurrentSetIsSupported(boolean) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderStreamDataProvider
setCurrentSingleTokenDefinition(NeXMLSingleTokenDefinitionInformation) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderStreamDataProvider
setCurrentTokenSetInfo(NeXMLWriterTokenSetInformation) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
setCustomXMLStartWritten(boolean) - Method in class info.bioinfweb.jphyloio.formats.xml.XMLReaderStreamDataProvider
setDefaultNamespace(String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLEventWriter
setDefaultNamespace(String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
setDefaultTokenSetID(String) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterAlignmentInformation
setDelimited(boolean) - Method in class info.bioinfweb.jphyloio.formats.newick.NewickToken
setDocumentHasMetadata(boolean) - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLWriterStreamDataProvider
setDocumentHasPhylogeny(boolean) - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLWriterStreamDataProvider
SetElementEvent - Class in info.bioinfweb.jphyloio.events
  Event object that models an ID-based link to an object that is contained in set.
SetElementEvent(String, EventContentType) - Constructor for class info.bioinfweb.jphyloio.events.SetElementEvent
  Creates a new instance of this class.
setElementName(String) - Method in class info.bioinfweb.jphyloio.formats.xml.XMLReaderStreamDataProvider
setEndDocumentFired(boolean) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.AbstractMetaXMLReader
setEndReached() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.AbstractMetaXMLReader
setFirstContentEvent(boolean) - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLReaderStreamDataProvider
setHasOTUList(boolean) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
setIDIndex(int) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
setIncompleteToken(String) - Method in class info.bioinfweb.jphyloio.formats.xml.XMLReaderStreamDataProvider
setIsRoot(boolean) - Method in class info.bioinfweb.jphyloio.formats.NodeEdgeInfo
setLabel(String) - Method in class info.bioinfweb.jphyloio.formats.NodeEdgeInfo
setLastNodeID(String) - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLReaderStreamDataProvider
setLength(double) - Method in class info.bioinfweb.jphyloio.formats.newick.NewickToken
setLength(double) - Method in class info.bioinfweb.jphyloio.formats.NodeEdgeInfo
setListStartEvent(LabeledIDEvent) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreOTUListDataAdapter
setLiteralContentIsContinued(boolean) - Method in class info.bioinfweb.jphyloio.formats.xml.XMLWriterStreamDataProvider
setMatchToken(String) - Method in class info.bioinfweb.jphyloio.utils.SequenceTokensEventManager
setMetaLevel(long) - Method in class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLPredicateMetaReceiver
setNamespaceContext(NamespaceContext) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLEventWriter
setNamespaceContext(NamespaceContext) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
setNamespacePrefix(String, String) - Method in class info.bioinfweb.jphyloio.formats.xml.XMLWriterStreamDataProvider
setNestedUnderSingleToken(boolean) - Method in class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLHandleSequenceDataReceiver
setNucleotideType(boolean) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterTokenSetInformation
setObjectStartEvent(E) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreObjectData
setObjectStartEvent(E) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreObjectListDataAdapter
setOtuListID(String) - Method in class info.bioinfweb.jphyloio.formats.pde.PDEReaderStreamDataProvider
setParentName(String) - Method in class info.bioinfweb.jphyloio.formats.xml.XMLReaderStreamDataProvider
setParentNodeID(String) - Method in class info.bioinfweb.jphyloio.utils.TopoplogicalNodeInfo
setPhylogenyID(String) - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLWriterStreamDataProvider
setPhylogenyIDProvider(String) - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLWriterStreamDataProvider
setPrefix(String, String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLEventWriter
setPrefix(String, String) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
setPropertyHasResource(boolean) - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLReaderStreamDataProvider
setPropertyIsURI(boolean) - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLReaderStreamDataProvider
setReadAheadLimit(int) - Method in class info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory
  Allows to specify the maximal number of bytes this factory will read to determine the format of an input in the `#guess*()` methods.
setResetEventCollection(boolean) - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLReaderStreamDataProvider
setRootedPhylogeny(boolean) - Method in class info.bioinfweb.jphyloio.formats.xml.XMLReaderStreamDataProvider
setSequenceCount(int) - Method in class info.bioinfweb.jphyloio.formats.pde.PDEReaderStreamDataProvider
setSingleToken(String) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
setSource(String) - Method in class info.bioinfweb.jphyloio.formats.NodeEdgeInfo
setStartDocumentEvent(StartDocument) - Method in class info.bioinfweb.jphyloio.formats.xml.XMLReaderStreamDataProvider
setStartDocumentFired(boolean) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.AbstractMetaXMLReader
setTarget(String) - Method in class info.bioinfweb.jphyloio.formats.NodeEdgeInfo
setText(String) - Method in class info.bioinfweb.jphyloio.formats.newick.NewickToken
setTokenIndex(long) - Method in class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLHandleSequenceDataReceiver
setTokenSetType(CharacterStateSetType) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterAlignmentInformation
setTokenType(CharacterStateSetType) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterAlignmentInformation
setTreeGroupHasMetadata(boolean) - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLWriterStreamDataProvider
setTreeLabel(String) - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLReaderStreamDataProvider
setUndefinedOTUID(String) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
setUndefinedOTUsID(String) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
setUnderPredicate(boolean) - Method in class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLPredicateMetaReceiver
setWriteAlignment(boolean) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterAlignmentInformation
setWriteCellsTags(boolean) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterAlignmentInformation
setWriteDefaultTokenSet(boolean) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterAlignmentInformation
setWriteUndefinedOTU(boolean) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
setWriteUndefinedOtuList(boolean) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
SEUQUENCE_START - Static variable in interface info.bioinfweb.jphyloio.formats.mega.MEGAConstants
SHARED_EMPTY_OBJECT_LIST_ADAPTER - Static variable in class info.bioinfweb.jphyloio.dataadapters.implementations.EmptyObjectListDataAdapter
ShortTranslator - Class in info.bioinfweb.jphyloio.objecttranslation.implementations
  An object translator from and to `Short`.
ShortTranslator() - Constructor for class info.bioinfweb.jphyloio.objecttranslation.implementations.ShortTranslator
SimpleValueTranslator<O> - Class in info.bioinfweb.jphyloio.objecttranslation.implementations
  Abstract base class for converting simple types that can be described by strings and do not need a more complex XML representation.
SimpleValueTranslator() - Constructor for class info.bioinfweb.jphyloio.objecttranslation.implementations.SimpleValueTranslator
SingleReaderWriterFactory - Interface in info.bioinfweb.jphyloio.factory
  Implementations of this interface are used internally by `JPhyloIOReaderWriterFactory` to create reader and writer instances of a specific format.
SingleSequenceTokenEvent - Class in info.bioinfweb.jphyloio.events
SingleSequenceTokenEvent(String, String) - Constructor for class info.bioinfweb.jphyloio.events.SingleSequenceTokenEvent
SingleTokenDefinitionEvent - Class in info.bioinfweb.jphyloio.events
  Event that indicates the definition of a single new valid token that could be contained in a sequence of the current alignment.
SingleTokenDefinitionEvent(String, String, String, CharacterSymbolMeaning, CharacterSymbolType, Collection<String>) - Constructor for class info.bioinfweb.jphyloio.events.SingleTokenDefinitionEvent
  Creates a new instance of this class.
SingleTokenDefinitionEvent(String, String, String, CharacterSymbolMeaning, CharacterSymbolType) - Constructor for class info.bioinfweb.jphyloio.events.SingleTokenDefinitionEvent
  Creates a new instance of this class without a constituents collection.
size() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees.NexusTranslationTable
size() - Method in class info.bioinfweb.jphyloio.ParentEventInformation
standaloneSet() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader
StartDocumentElementReader<P extends XMLReaderStreamDataProvider<? extends AbstractXMLEventReader<P>>> - Class in info.bioinfweb.jphyloio.formats.xml.elementreaders
  This element reader implements basic functionality for reading the start document event of an XML document.
StartDocumentElementReader() - Constructor for class info.bioinfweb.jphyloio.formats.xml.elementreaders.StartDocumentElementReader
StoreAnnotatedDataAdapter<E extends JPhyloIOEvent> - Class in info.bioinfweb.jphyloio.dataadapters.implementations.store
StoreAnnotatedDataAdapter(List<JPhyloIOEvent>) - Constructor for class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreAnnotatedDataAdapter
StoreDocumentDataAdapter - Class in info.bioinfweb.jphyloio.dataadapters.implementations.store
StoreDocumentDataAdapter(List<JPhyloIOEvent>, OrderedMap<String, OTUListDataAdapter>, List<MatrixDataAdapter>, List<TreeNetworkGroupDataAdapter>) - Constructor for class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreDocumentDataAdapter
StoreDocumentDataAdapter() - Constructor for class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreDocumentDataAdapter
  Creates a new instance of this class with empty array lists for all properties.
StoreMatrixDataAdapter - Class in info.bioinfweb.jphyloio.dataadapters.implementations.store
StoreMatrixDataAdapter(LinkedLabeledIDEvent, boolean, List<JPhyloIOEvent>) - Constructor for class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreMatrixDataAdapter
StoreObjectData<E extends JPhyloIOEvent> - Class in info.bioinfweb.jphyloio.dataadapters.implementations.store
StoreObjectData(E) - Constructor for class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreObjectData
StoreObjectData(E, List<JPhyloIOEvent>) - Constructor for class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreObjectData
StoreObjectListDataAdapter<E extends LabeledIDEvent> - Class in info.bioinfweb.jphyloio.dataadapters.implementations.store
StoreObjectListDataAdapter() - Constructor for class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreObjectListDataAdapter
StoreOTUListDataAdapter - Class in info.bioinfweb.jphyloio.dataadapters.implementations.store
StoreOTUListDataAdapter(LabeledIDEvent, List<JPhyloIOEvent>) - Constructor for class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreOTUListDataAdapter
StoreTreeNetworkDataAdapter - Class in info.bioinfweb.jphyloio.dataadapters.implementations.store
StoreTreeNetworkDataAdapter(LabeledIDEvent, boolean, List<JPhyloIOEvent>) - Constructor for class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreTreeNetworkDataAdapter
StoreTreeNetworkGroupDataAdapter - Class in info.bioinfweb.jphyloio.dataadapters.implementations.store
StoreTreeNetworkGroupDataAdapter(LinkedLabeledIDEvent, List<JPhyloIOEvent>) - Constructor for class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreTreeNetworkGroupDataAdapter
STRING_DELEMITER_REPLACEMENT - Static variable in class info.bioinfweb.jphyloio.formats.newick.NewickNodeEdgeEventReceiver
StringTranslator - Class in info.bioinfweb.jphyloio.objecttranslation.implementations
  An object translator from and to `String`.
StringTranslator() - Constructor for class info.bioinfweb.jphyloio.objecttranslation.implementations.StringTranslator
STYLE_BOLD - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
STYLE_BRACE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
STYLE_BRACKET - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
STYLE_ITALIC - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
STYLE_UNDERLINE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
SUBTREE_END - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants
SUBTREE_START - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants

A B C D E F G H I J K L M N O P Q R S T U V W X