- 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
-
