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

## C

changeMetaLevel(long) - Method in class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLPredicateMetaReceiver
CHARACTER_NAME_STATES_SEPARATOR - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
CharacterDefinitionEvent - Class in info.bioinfweb.jphyloio.events
  Event that indicates a defined character (alignment column).
CharacterDefinitionEvent(String, String, long) - Constructor for class info.bioinfweb.jphyloio.events.CharacterDefinitionEvent
CharactersDataUnalignedBlockHandler - Class in info.bioinfweb.jphyloio.formats.nexus.blockhandlers
  A Nexus block handler to read sequence data from the `CHARACTERS`, `DATA` or `UNALIGNED` blocks.
CharactersDataUnalignedBlockHandler() - Constructor for class info.bioinfweb.jphyloio.formats.nexus.blockhandlers.CharactersDataUnalignedBlockHandler
CharacterSetEventReceiver - Class in info.bioinfweb.jphyloio.formats.nexus.receivers
CharacterSetEventReceiver(NexusWriterStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.receivers.CharacterSetEventReceiver
CharacterSetIntervalEvent - Class in info.bioinfweb.jphyloio.events
  Event that indicates that new information on a character set has been read.
CharacterSetIntervalEvent(long, long) - Constructor for class info.bioinfweb.jphyloio.events.CharacterSetIntervalEvent
  Creates a new instance of this class.
CharLabelsReader - Class in info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters
  Nexus reader for the `CHARLABELS` command that produces `CharacterDefinitionEvent`s.
CharLabelsReader(NexusReaderStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.CharLabelsReader
CharSetReader - Class in info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets
  Parser for the `CHARSET` command in the `SETS` block.
CharSetReader(NexusReaderStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets.CharSetReader
CharStateLabelsReader - Class in info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters
  Nexus reader for the `CHARSTATELABELS` command that produces `CharacterDefinitionEvent`s.
CharStateLabelsReader(NexusReaderStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.CharStateLabelsReader
checkFormat(InputStream, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.factory.AbstractSingleReaderWriterFactory
checkFormat(Reader, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.factory.AbstractStartStringSingleFactory
checkFormat(InputStream, ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.factory.SingleReaderWriterFactory
  Implementations should read the start of the stream here and determine whether the content could be valid according to the target format.
checkFormat(Reader, ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.factory.SingleReaderWriterFactory
  Implementations should read the start of the characters returned by the reader here and determine whether the content could be valid according to the target format.
checkFormat(Reader, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.formats.newick.NewickFactory
  Since there is no real characteristic starting string for any Newick file, it is just checked whether at least five events (if available) can be created from the input without an exception.
checkFormat(Reader, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipFactory
checkFormat(Reader, ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.formats.xml.AbstractXMLFactory
  Tests whether the specified reader provides an XML document and whether the local part of the start tag of it equals to the local part of `AbstractXMLFactory.getRootTag()`.
checkID(String, String) - Method in class info.bioinfweb.jphyloio.events.LabeledIDEvent
checkLiteralContentMeta(NeXMLWriterStreamDataProvider, ReadWriteParameterMap, LiteralMetadataContentEvent) - Static method in class info.bioinfweb.jphyloio.formats.nexml.receivers.AbstractNeXMLDataReceiverMixin
checkLiteralMeta(NeXMLWriterStreamDataProvider, LiteralMetadataEvent) - Static method in class info.bioinfweb.jphyloio.formats.nexml.receivers.AbstractNeXMLDataReceiverMixin
checkResourceMeta(NeXMLWriterStreamDataProvider, ResourceMetadataEvent) - Static method in class info.bioinfweb.jphyloio.formats.nexml.receivers.AbstractNeXMLDataReceiverMixin
checkRootTag(StartElement) - Method in class info.bioinfweb.jphyloio.formats.xml.AbstractXMLFactory
  Implementations can overwrite this method in order to perform further tests on the root tag of the XML document.
clear() - Method in class info.bioinfweb.jphyloio.formats.newick.NewickNodeEdgeEventReceiver
clear() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees.NexusTranslationTable
clear() - Method in class info.bioinfweb.jphyloio.formats.nexus.receivers.TokenSetEventReceiver
clear() - Method in class info.bioinfweb.jphyloio.utils.LabelEditingReporter
  Removes all mappings from this instance.
clearBlockInformation() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider
clearCurrentRowInformation() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderStreamDataProvider
  Method used for reading cell tags that clears the map of buffered cell informations (`NeXMLReaderStreamDataProvider.getCurrentCellsBuffer()`) and resets the columns ID iterator used by `NeXMLReaderStreamDataProvider.nextCharID()`.
close() - Method in class info.bioinfweb.jphyloio.AbstractEventReader
close() - Method in class info.bioinfweb.jphyloio.formats.text.AbstractTextEventReader
close() - Method in class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader
close() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.AbstractMetaXMLReader
  This method has no effect in this reader.
close() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLEventWriter
  This method has no effect in this writer.
close() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamWriter
  This method has no effect in this writer.
close() - Method in interface info.bioinfweb.jphyloio.JPhyloIOEventReader
  Closes the underlying document source (usually a stream).
collectEvents(JPhyloIOEventReader, Set<EventType>, Class<E>) - Static method in class info.bioinfweb.jphyloio.utils.JPhyloIOReadingUtils
  Reads all (remaining) events from the specified reader and adds events that implement the specified class and have a type that is contained in the specified set to the returned list.
collectEvents(JPhyloIOEventReader, Set<EventType>) - Static method in class info.bioinfweb.jphyloio.utils.JPhyloIOReadingUtils
  Reads all (remaining) events from the specified reader and adds events that have a type that is contained in the # specified set to the returned list.
ColorTranslator - Class in info.bioinfweb.jphyloio.objecttranslation.implementations
  An object translator that converts between a `Color` instance and its hexadecimal representation.
ColorTranslator() - Constructor for class info.bioinfweb.jphyloio.objecttranslation.implementations.ColorTranslator
COMMAND_END - Static variable in interface info.bioinfweb.jphyloio.formats.mega.MEGAConstants
COMMAND_END - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
COMMAND_NAME_CHAR_LABELS - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
COMMAND_NAME_CHAR_SET - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
COMMAND_NAME_CHAR_STATE_LABELS - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
COMMAND_NAME_DESCRIPTION - Static variable in interface info.bioinfweb.jphyloio.formats.mega.MEGAConstants
COMMAND_NAME_DIMENSIONS - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
COMMAND_NAME_DOMAIN - Static variable in interface info.bioinfweb.jphyloio.formats.mega.MEGAConstants
COMMAND_NAME_FORMAT - Static variable in interface info.bioinfweb.jphyloio.formats.mega.MEGAConstants
COMMAND_NAME_FORMAT - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
COMMAND_NAME_GENE - Static variable in interface info.bioinfweb.jphyloio.formats.mega.MEGAConstants
COMMAND_NAME_LABEL - Static variable in interface info.bioinfweb.jphyloio.formats.mega.MEGAConstants
COMMAND_NAME_LINK - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
COMMAND_NAME_MATRIX - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
COMMAND_NAME_NETWORK - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
  This command name is not part of the initial Nexus standard and used by `ENewickNetworkReader`.
COMMAND_NAME_TAX_LABELS - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
COMMAND_NAME_TAXON_SET - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
COMMAND_NAME_TITLE - Static variable in interface info.bioinfweb.jphyloio.formats.mega.MEGAConstants
COMMAND_NAME_TITLE - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
COMMAND_NAME_TRANSLATE - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
COMMAND_NAME_TREE - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
COMMAND_NAME_TREE_SET - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
COMMAND_START - Static variable in interface info.bioinfweb.jphyloio.formats.mega.MEGAConstants
COMMENT_END - Static variable in interface info.bioinfweb.jphyloio.formats.mega.MEGAConstants
COMMENT_END - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants
COMMENT_END - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
COMMENT_START - Static variable in interface info.bioinfweb.jphyloio.formats.mega.MEGAConstants
COMMENT_START - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants
COMMENT_START - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
COMMENT_START_CHAR - Static variable in interface info.bioinfweb.jphyloio.formats.fasta.FASTAConstants
CommentElementReader<P extends XMLReaderStreamDataProvider<? extends AbstractXMLEventReader<P>>> - Class in info.bioinfweb.jphyloio.formats.xml.elementreaders
  Element reader that is commonly used by `JPhyloIOXMLEventReader`s to process comments.
CommentElementReader() - Constructor for class info.bioinfweb.jphyloio.formats.xml.elementreaders.CommentElementReader
CommentEvent - Class in info.bioinfweb.jphyloio.events
  Event that indicates that a comment has been parsed at the current position or within the data the last non-comment event has been parsed from.
CommentEvent(String, boolean) - Constructor for class info.bioinfweb.jphyloio.events.CommentEvent
  Creates a new instance of this class.
CommentEvent(String) - Constructor for class info.bioinfweb.jphyloio.events.CommentEvent
  Creates a new instance of this class that is not continued in the next event.
compareTo(EventType) - Method in class info.bioinfweb.jphyloio.events.type.EventType
ConcreteJPhyloIOEvent - Class in info.bioinfweb.jphyloio.events
  Implements basic functionality for `JPhyloIOEvent`s.
ConcreteJPhyloIOEvent(EventContentType, EventTopologyType) - Constructor for class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
  Creates a new instance of this class.
consumeWhiteSpaceAndComments() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventReader
  Calls `AbstractTextEventReader.consumeWhiteSpaceAndComments(char, char)` with according parameters and ensures visibility for `NexusReaderStreamDataProvider`.
consumeWhiteSpaceAndComments() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider
  Calls `#consumeWhiteSpaceAndComments(char, char)` with according parameters and ensures visibility for `NexusReaderStreamDataProvider`.
consumeWhiteSpaceAndComments(char, char) - Method in class info.bioinfweb.jphyloio.formats.text.AbstractTextEventReader
consumeWhiteSpaceAndCommentsToBuffer(Collection<JPhyloIOEvent>) - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.AbstractNexusCommandEventReader
containsLongTokens(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreMatrixDataAdapter
containsLongTokens(ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter
  Returns whether tokens longer than one character are contained in the matrix modeled by this instance.
ContinuedEvent - Class in info.bioinfweb.jphyloio.events
  Base class for events that have a content that may be split across separate subsequent events, if it is large.
ContinuedEvent(EventContentType, boolean) - Constructor for class info.bioinfweb.jphyloio.events.ContinuedEvent
  Returns a new instance of this class with the topology type `EventTopologyType.SOLE`.
createEndEvent(EventContentType) - Static method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
  Creates a new instance of this class with the topology type `EventTopologyType.END`-
createEvent(String, List<String>) - Method in class info.bioinfweb.jphyloio.utils.SequenceTokensEventManager
  Creates a sequence character event object from the provided data and manages the replacement of match tokens by tokens of the first sequence.
createEventsForInterval(long, long) - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets.AbstractNexusSetReader
  Creates the event(s) representing the specified interval in the current set type
createEventsForInterval(long, long) - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets.CharSetReader
createEventsForInterval(long, long) - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets.IDBasedSetsReader
createFileFilter(ContentExtensionFileFilter.TestStrategy) - Method in class info.bioinfweb.jphyloio.formatinfo.DefaultFormatInfo
createFileFilter(ContentExtensionFileFilter.TestStrategy) - Method in interface info.bioinfweb.jphyloio.formatinfo.JPhyloIOFormatInfo
  Creates a new file filter instance that is associated with the modeled format.
createFormatInfo() - Method in class info.bioinfweb.jphyloio.factory.AbstractSingleReaderWriterFactory
createFormatInfo() - Method in class info.bioinfweb.jphyloio.formats.fasta.FASTAFactory
  Returns the FASTA format info including a file filter that specifies the file extensions listed here.
createFormatInfo() - Method in class info.bioinfweb.jphyloio.formats.mega.MEGAFactory
createFormatInfo() - Method in class info.bioinfweb.jphyloio.formats.newick.NewickFactory
createFormatInfo() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLFactory
createFormatInfo() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusFactory
createFormatInfo() - Method in class info.bioinfweb.jphyloio.formats.pde.PDEFactory
createFormatInfo(String, String, Set<String>, Set<String>, String) - Method in class info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipFactory
createFormatInfo() - Method in class info.bioinfweb.jphyloio.formats.phylip.PhylipFactory
createFormatInfo() - Method in class info.bioinfweb.jphyloio.formats.phylip.SequentialPhylipFactory
createFormatInfo() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLFactory
createFormatInfo() - Method in class info.bioinfweb.jphyloio.formats.xtg.XTGFactory
createIntervalEvents(NeXMLReaderStreamDataProvider, String[]) - Method in class info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractNeXMLElementReader
  Creates a series of `CharacterSetIntervalEvent`s from an array of IDs referencing `CharacterDefinitionEvent`s and adds them to the current event collection.
createMetaXMLEventReader() - Method in class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader
createMetaXMLEventReader() - Method in interface info.bioinfweb.jphyloio.formats.xml.JPhyloIOXMLEventReader
  Creates a new `XMLEventReader` that allows to read events of XML content of literal metadata from this JPhyloIO event reader instance through that interface.
createMetaXMLEventWriter(JPhyloIOEventReceiver) - Method in class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventWriter
createMetaXMLEventWriter(JPhyloIOEventReceiver) - Method in interface info.bioinfweb.jphyloio.formats.xml.JPhyloIOXMLEventWriter
  Creates a new `XMLEventWriter` that allows to write events of XML content of literal metadata to this JPhyloIO event writer instance through that interface.
createMetaXMLStreamReader() - Method in class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader
createMetaXMLStreamReader() - Method in interface info.bioinfweb.jphyloio.formats.xml.JPhyloIOXMLEventReader
  Creates a `XMLStreamReader` that allows to read events of XML content of literal metadata from this JPhyloIO event reader instance through that interface.
createMetaXMLStreamWriter(JPhyloIOEventReceiver) - Method in class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventWriter
createMetaXMLStreamWriter(JPhyloIOEventReceiver) - Method in interface info.bioinfweb.jphyloio.formats.xml.JPhyloIOXMLEventWriter
  Creates a new `XMLStreamWriter` that allows to write events of XML content of literal metadata to this JPhyloIO event writer instance through that interface.
createNewID(String) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
createNodeName(LinkedLabeledIDEvent) - Method in class info.bioinfweb.jphyloio.formats.newick.DefaultNewickWriterNodeLabelProcessor
createNodeName(LinkedLabeledIDEvent) - Method in interface info.bioinfweb.jphyloio.formats.newick.NewickWriterNodeLabelProcessor
createNodeName(LinkedLabeledIDEvent) - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusNewickWriterNodeLabelProcessor
createReader(String, String, NexusReaderStreamDataProvider) - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.NexusCommandReaderFactory
  Creates a new reader instance that is able to parse the specified command in the specified block, if an according class was registered in this factory instance.
createStreamDataProvider() - Method in class info.bioinfweb.jphyloio.AbstractEventReader
  This method is called in the constructor of `AbstractEventReader` to initialize the stream data provider that will be returned by `AbstractEventReader.getStreamDataProvider()`.
createStreamDataProvider() - Method in class info.bioinfweb.jphyloio.AbstractEventWriter
  This method is called in the constructor of `AbstractEventWriter` to initialize the stream data provider that will be returned by `AbstractEventWriter.getStreamDataProvider()`.
createStreamDataProvider() - Method in class info.bioinfweb.jphyloio.formats.fasta.FASTAEventWriter
createStreamDataProvider() - Method in class info.bioinfweb.jphyloio.formats.newick.NewickEventWriter
createStreamDataProvider() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLEventReader
createStreamDataProvider() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLEventWriter
createStreamDataProvider() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventReader
createStreamDataProvider() - Method in class info.bioinfweb.jphyloio.formats.nexus.NexusEventWriter
createStreamDataProvider() - Method in class info.bioinfweb.jphyloio.formats.pde.PDEEventReader
createStreamDataProvider() - Method in class info.bioinfweb.jphyloio.formats.phylip.PhylipEventWriter
createStreamDataProvider() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLEventReader
createStreamDataProvider() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLEventWriter
createStreamDataProvider() - Method in class info.bioinfweb.jphyloio.formats.text.AbstractTextEventReader
createStreamDataProvider() - Method in class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader
createTokenList(CharSequence) - Method in class info.bioinfweb.jphyloio.formats.text.AbstractTextEventReader
createUniqueLabel(ReadWriteParameterMap, AbstractEventWriter.UniqueLabelHandler, String, String, String, String) - Static method in class info.bioinfweb.jphyloio.AbstractEventWriter
createUniqueLabel(ReadWriteParameterMap, AbstractEventWriter.UniqueLabelHandler, LabeledIDEvent) - Static method in class info.bioinfweb.jphyloio.AbstractEventWriter
createUniqueLabel(ReadWriteParameterMap, LabeledIDEvent) - Static method in class info.bioinfweb.jphyloio.AbstractEventWriter
createUniqueLinkedOTULabel(ReadWriteParameterMap, AbstractEventWriter.UniqueLabelHandler, LinkedLabeledIDEvent, OTUListDataAdapter, boolean) - Static method in class info.bioinfweb.jphyloio.AbstractEventWriter
currentSequenceName - Variable in class info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipEventReader

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