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 CharacterDefinitionEvents.

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 CharacterDefinitionEvents.

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 JPhyloIOXMLEventReaders 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 JPhyloIOEvents.

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 CharacterSetIntervalEvents from an array of IDs referencing CharacterDefinitionEvents 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