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

I

id - Variable in class info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractNeXMLElementReader.LabeledIDEventInformation

IDBasedSetsReader - Class in info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets

Base class for all Nexus readers that create set event streams that consist of SetElementEvents.

IDBasedSetsReader(EventContentType, String, String, EventContentType, NexusReaderStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets.IDBasedSetsReader

IDENTIFIER_ANY_PREDICATE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLPrivateConstants

IDENTIFIER_CUSTOM_XML - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLPrivateConstants

IDENTIFIER_EDGE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLPrivateConstants

IDENTIFIER_NODE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLPrivateConstants

IDENTIFIER_PHYLOGENY - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLPrivateConstants

IDToNameManager - Class in info.bioinfweb.jphyloio.utils

Allows to assign IDs to labels, without having multiple IDs for the same label.

IDToNameManager(String) - Constructor for class info.bioinfweb.jphyloio.utils.IDToNameManager

IllegalArgumentExceptionSimpleValueTranslator<O> - Class in info.bioinfweb.jphyloio.objecttranslation.implementations

IllegalArgumentExceptionSimpleValueTranslator() - Constructor for class info.bioinfweb.jphyloio.objecttranslation.implementations.IllegalArgumentExceptionSimpleValueTranslator

IllegalEventException - Exception in info.bioinfweb.jphyloio.exception

This exception in thrown by implementations of JPhyloIOEventReceiver and indicates that a data adapter passed an event that is illegal at the current position according to the grammar defined in the documentation of JPhyloIOEventReader.

IllegalEventException(String, JPhyloIOEventReceiver, JPhyloIOEvent, JPhyloIOEvent) - Constructor for exception info.bioinfweb.jphyloio.exception.IllegalEventException

InconsistentAdapterDataException - Exception in info.bioinfweb.jphyloio.exception

Exception which is thrown by an instance of JPhyloIOEventWriter if the data in the specified DocumentDataAdapter or one of its nested adapter classes is inconsistent.

InconsistentAdapterDataException() - Constructor for exception info.bioinfweb.jphyloio.exception.InconsistentAdapterDataException

InconsistentAdapterDataException(String, Throwable) - Constructor for exception info.bioinfweb.jphyloio.exception.InconsistentAdapterDataException

InconsistentAdapterDataException(String) - Constructor for exception info.bioinfweb.jphyloio.exception.InconsistentAdapterDataException

InconsistentAdapterDataException(Throwable) - Constructor for exception info.bioinfweb.jphyloio.exception.InconsistentAdapterDataException

increaseIndention() - Method in class info.bioinfweb.jphyloio.AbstractEventWriter

INDEX_END_SYMBOL - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants

INDEX_START_SYMBOL - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants

info.bioinfweb.jphyloio - package info.bioinfweb.jphyloio

The main package of JPhyloIO.

info.bioinfweb.jphyloio.dataadapters - package info.bioinfweb.jphyloio.dataadapters

Contains adapter interfaces that should be implemented by adapters mediating between the business model of an application and implementations of JPhyloIOEventWriter.

info.bioinfweb.jphyloio.dataadapters.implementations - package info.bioinfweb.jphyloio.dataadapters.implementations

Contains some basic (abstract) implementations of JPhyloIOEventWriter.

info.bioinfweb.jphyloio.dataadapters.implementations.receivers - package info.bioinfweb.jphyloio.dataadapters.implementations.receivers

Contains some basic (abstract) implementations of JPhyloIOEventReceiver to be used by implementations of JPhyloIOEventWriter.

info.bioinfweb.jphyloio.dataadapters.implementations.store - package info.bioinfweb.jphyloio.dataadapters.implementations.store

Contains implementations of data adapters that directly store their modeled data in mutable lists or maps instead of delegating to an application business model.

info.bioinfweb.jphyloio.events - package info.bioinfweb.jphyloio.events

Contains implementations of JPhyloIO events, triggered during event based parsing.

info.bioinfweb.jphyloio.events.meta - package info.bioinfweb.jphyloio.events.meta

Contains event classes that model metadata, as well as related implementations.

info.bioinfweb.jphyloio.events.type - package info.bioinfweb.jphyloio.events.type

Contains classes used to indentify the type of an JPhyloIO event.

info.bioinfweb.jphyloio.exception - package info.bioinfweb.jphyloio.exception

Contains exceptions that are of general use in JPhyloIO.

info.bioinfweb.jphyloio.factory - package info.bioinfweb.jphyloio.factory

Contains interfaces and general implementations for creating JPhyloIO readers and writers related to JPhyloIOReaderWriterFactory.

info.bioinfweb.jphyloio.formatinfo - package info.bioinfweb.jphyloio.formatinfo

Contains JPhyloIOFormatInfo and related classes that describe a format supported by JPhyloIO.

info.bioinfweb.jphyloio.formats - package info.bioinfweb.jphyloio.formats

The subpackages of this package contain implementations of JPhyloIO readers and writers for different formats.

info.bioinfweb.jphyloio.formats.fasta - package info.bioinfweb.jphyloio.formats.fasta

Contains classes for reading from and writing to streams/files in FASTA format.

info.bioinfweb.jphyloio.formats.mega - package info.bioinfweb.jphyloio.formats.mega

Contains classes for reading from and writing to streams/files in MEGA format.

info.bioinfweb.jphyloio.formats.newick - package info.bioinfweb.jphyloio.formats.newick

Contains classes for reading from and writing to streams/files in Newick tree format.

info.bioinfweb.jphyloio.formats.nexml - package info.bioinfweb.jphyloio.formats.nexml

Contains classes for reading from and writing to streams/files in NeXML format.

info.bioinfweb.jphyloio.formats.nexml.elementreader - package info.bioinfweb.jphyloio.formats.nexml.elementreader

Contains implementations of XMLElementReader used by NeXMLEventReader.

info.bioinfweb.jphyloio.formats.nexml.receivers - package info.bioinfweb.jphyloio.formats.nexml.receivers

Contains implementations for JPhyloIOEventReceiver necessary for writing NeXML.

info.bioinfweb.jphyloio.formats.nexus - package info.bioinfweb.jphyloio.formats.nexus

Contains classes for reading from and writing to streams/files in Nexus format.

info.bioinfweb.jphyloio.formats.nexus.blockhandlers - package info.bioinfweb.jphyloio.formats.nexus.blockhandlers

Contains implementations of NexusCommandEventReader for commands that are valid in all Nexus blocks.

info.bioinfweb.jphyloio.formats.nexus.commandreaders - package info.bioinfweb.jphyloio.formats.nexus.commandreaders

Contains general classes for reading Nexus commands.

info.bioinfweb.jphyloio.formats.nexus.commandreaders.all - package info.bioinfweb.jphyloio.formats.nexus.commandreaders.all

Contains implementations of NexusCommandEventReader for commands that are valid in all Nexus blocks.

info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters - package info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters

Contains classes for reading Nexus commands in a CHARACTERS, UNALIGNED or DATA block.

info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets - package info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets

Contains classes for reading Nexus commands in a SETS block.

info.bioinfweb.jphyloio.formats.nexus.commandreaders.taxa - package info.bioinfweb.jphyloio.formats.nexus.commandreaders.taxa

Contains classes for reading Nexus commands in a TAXA block.

info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees - package info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees

Contains classes for reading Nexus commands in a TREES block.

info.bioinfweb.jphyloio.formats.nexus.receivers - package info.bioinfweb.jphyloio.formats.nexus.receivers

Contains implementations of JPhyloIOEventReceiver used internally by NexusEventReader.

info.bioinfweb.jphyloio.formats.pde - package info.bioinfweb.jphyloio.formats.pde

Contains classes for reading from streams/files in PDE format.

info.bioinfweb.jphyloio.formats.phylip - package info.bioinfweb.jphyloio.formats.phylip

Contains classes for reading from and writing to streams/files in Phylip format.

info.bioinfweb.jphyloio.formats.phyloxml - package info.bioinfweb.jphyloio.formats.phyloxml

Contains classes for reading from and writing to streams/files in PhyloXML format.

info.bioinfweb.jphyloio.formats.phyloxml.elementreader - package info.bioinfweb.jphyloio.formats.phyloxml.elementreader

Contains implementations of XMLElementReader used by PhyloXMLEventReader.

info.bioinfweb.jphyloio.formats.phyloxml.receivers - package info.bioinfweb.jphyloio.formats.phyloxml.receivers

Contains implementations for JPhyloIOEventReceiver necessary for writing PhyloXML.

info.bioinfweb.jphyloio.formats.text - package info.bioinfweb.jphyloio.formats.text

Contains classes implementing shared functionality for reading from and writing to streams/files in text formats.

info.bioinfweb.jphyloio.formats.xml - package info.bioinfweb.jphyloio.formats.xml

Contains classes implementing shared functionality for reading from and writing to streams/files in XML formats.

info.bioinfweb.jphyloio.formats.xml.elementreaders - package info.bioinfweb.jphyloio.formats.xml.elementreaders

Contains general (abstract) implementations of XMLElementReader used by readers of XML formats.

info.bioinfweb.jphyloio.formats.xml.receivers - package info.bioinfweb.jphyloio.formats.xml.receivers

Contains general (abstract) implementations for JPhyloIOEventReceiver necessary for writing XML formats.

info.bioinfweb.jphyloio.formats.xml.stax - package info.bioinfweb.jphyloio.formats.xml.stax

Contains implementations that allow StAX based reading and writing of XML metadata.

info.bioinfweb.jphyloio.formats.xtg - package info.bioinfweb.jphyloio.formats.xtg

Contains classes for reading from and writing to streams/files in XTG format.

info.bioinfweb.jphyloio.objecttranslation - package info.bioinfweb.jphyloio.objecttranslation

Contains classes used by readers and writers that convert between (complex) Java objects and their text or XML representation.

info.bioinfweb.jphyloio.objecttranslation.implementations - package info.bioinfweb.jphyloio.objecttranslation.implementations

Contains implementations of ObjectTranslator.

info.bioinfweb.jphyloio.push - package info.bioinfweb.jphyloio.push

Contains classes that allow push-parsing.

info.bioinfweb.jphyloio.utils - package info.bioinfweb.jphyloio.utils

Contains general tool classes of JPhyloIO.

INFO_CHARACTER_NAME_TO_INDEX_MAP - Static variable in class info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider

INFO_KEY_BLOCK_ID_MAP - Static variable in class info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider

INFO_KEY_BLOCK_LINKS - Static variable in class info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider

INFO_KEY_BLOCK_START_EVENT_FIRED - Static variable in class info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider

INFO_KEY_BLOCK_TITLE - Static variable in class info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider

Used to store the title of the current block if specified by a TITLE command.

INFO_KEY_CHAR - Static variable in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.DimensionsReader

INFO_KEY_CURRENT_BLOCK_ID - Static variable in class info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider

Used to store the ID of the according JPhyloIO event to the current Nexus block (if one exists).

INFO_KEY_ELEMENT_LIST - Static variable in class info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider

INFO_KEY_INTERLEAVE - Static variable in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.FormatReader

INFO_KEY_LABELS - Static variable in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.FormatReader

INFO_KEY_MATRIX_WIDTHS_MAP - Static variable in class info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider

Used to Determine the lengths of character set intervals that shall reach until the end of a matrix.

INFO_KEY_NEXUS_NAME_TO_ID_MAP - Static variable in class info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider

INFO_KEY_NTAX - Static variable in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.DimensionsReader

INFO_KEY_TOKENS_FORMAT - Static variable in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.FormatReader

INFO_KEY_TRANSPOSE - Static variable in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.FormatReader

INFO_KEY_TREES_TRANSLATION - Static variable in class info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider

IntegerTranslator - Class in info.bioinfweb.jphyloio.objecttranslation.implementations

An object translator from and to Integer.

IntegerTranslator() - Constructor for class info.bioinfweb.jphyloio.objecttranslation.implementations.IntegerTranslator

INTERNAL_USE_NAMESPACE - Static variable in class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader

InvalidObjectSourceDataException - Exception in info.bioinfweb.jphyloio.objecttranslation

Exception that indicates that an an instance of ObjectTranslator was not able to use the provided source data (string or XML events) to create an instance of the handled object type (e.g.

InvalidObjectSourceDataException() - Constructor for exception info.bioinfweb.jphyloio.objecttranslation.InvalidObjectSourceDataException

InvalidObjectSourceDataException(String, Throwable) - Constructor for exception info.bioinfweb.jphyloio.objecttranslation.InvalidObjectSourceDataException

InvalidObjectSourceDataException(String) - Constructor for exception info.bioinfweb.jphyloio.objecttranslation.InvalidObjectSourceDataException

InvalidObjectSourceDataException(Throwable) - Constructor for exception info.bioinfweb.jphyloio.objecttranslation.InvalidObjectSourceDataException

isAllDataProcessed() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.AbstractNexusCommandEventReader

Returns true if the whole command this instance was created on has been parsed or false if another events can be generated by the next call of AbstractNexusCommandEventReader.readNextEvent().

isAllowDefaultNamespace() - Method in class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader

isAllowLongTokens() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderStreamDataProvider

isAttributeSpecified(int) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader

isBeforeFirstAccess() - Method in class info.bioinfweb.jphyloio.AbstractEventReader

Indicates whether there have been any previous calls of AbstractEventReader.readNextEvent() since the last call of #reset().

isCharacters() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader

isCharAfterLength(char) - Static method in class info.bioinfweb.jphyloio.formats.newick.NewickScanner

isContinuedInNextEvent() - Method in class info.bioinfweb.jphyloio.events.ContinuedEvent

Returns whether this event only contains a part of a long text (e.g.

isCreateAlignmentEnd() - Method in class info.bioinfweb.jphyloio.formats.pde.PDEReaderStreamDataProvider

isCreateAlignmentStart() - Method in class info.bioinfweb.jphyloio.formats.pde.PDEReaderStreamDataProvider

isCreateNodeStart() - Method in class info.bioinfweb.jphyloio.formats.xml.XMLReaderStreamDataProvider

isCreatePhylogenyStart() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLReaderStreamDataProvider

isCreateTreeGroupEnd() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLReaderStreamDataProvider

isCreateTreeGroupStart() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLReaderStreamDataProvider

isCurrentCellBuffered() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderStreamDataProvider

Determines whether the contents of the current cell tag are buffered or not.

isCurrentSetSupported() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLReaderStreamDataProvider

Returns true if the set element that is currently read can be interpreted as a series of JPhyloIOEvents or false if the set and all its contents will be ignored.

isCustomXMLStartWritten() - Method in class info.bioinfweb.jphyloio.formats.xml.XMLReaderStreamDataProvider

isDocumentHasMetadata() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLWriterStreamDataProvider

isDocumentHasPhylogeny() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLWriterStreamDataProvider

isEdgeMeta() - Method in class info.bioinfweb.jphyloio.formats.xml.elementreaders.XMLStartElementReader

isElementModeled(EventContentType, boolean) - Method in class info.bioinfweb.jphyloio.formatinfo.DefaultFormatInfo

isElementModeled(EventContentType, boolean) - Method in interface info.bioinfweb.jphyloio.formatinfo.JPhyloIOFormatInfo

Determines whether the represented format allows to model the specified data element (content type).

isEmpty() - Method in class info.bioinfweb.jphyloio.ParentEventInformation

isEndDocumentFired() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.AbstractMetaXMLReader

isEndElement() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader

isEndReached() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.AbstractMetaXMLReader

isFirstContentEvent() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLReaderStreamDataProvider

isFreeNameChar(char) - Static method in class info.bioinfweb.jphyloio.formats.newick.NewickScanner

isFreeNameCharForWriting(char) - Static method in class info.bioinfweb.jphyloio.formats.newick.NewickStringWriter

isIgnoredXMLMetadata() - Method in class info.bioinfweb.jphyloio.formats.newick.NewickNodeEdgeEventReceiver

isInComment() - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver

Determines whether the last event was a continued comment event and the next event is expected to be the continuing comment event.

isLabelUsed(EventContentType, String) - Method in class info.bioinfweb.jphyloio.utils.LabelEditingReporter

Checks whether the specified label was already used for the specified content type.

isLiteralContentContinued() - Method in class info.bioinfweb.jphyloio.formats.xml.XMLWriterStreamDataProvider

isLongTokens() - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.AbstractSequenceContentReceiver

isNestedUnderSingleToken() - Method in class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLHandleSequenceDataReceiver

Determines whether the current event is nested under a SingleTokenDefinitionEvent or not.

isNucleotideType() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterTokenSetInformation

isParentSequence(EventContentType...) - Method in class info.bioinfweb.jphyloio.ParentEventInformation

Checks whether the current parent events have the specified content type(s).

isPropertyHasResource() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLReaderStreamDataProvider

isPropertyIsURI() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLReaderStreamDataProvider

isRelaxedPhylip() - Method in class info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipEventReader

isResetEventCollection() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLReaderStreamDataProvider

isRoot() - Method in class info.bioinfweb.jphyloio.formats.NodeEdgeInfo

isRootedPhylogeny() - Method in class info.bioinfweb.jphyloio.formats.xml.XMLReaderStreamDataProvider

isRootNode() - Method in class info.bioinfweb.jphyloio.events.NodeEvent

Indicates whether this node is a root of its tree or network.

isStandalone() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader

isStartDocumentFired() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.AbstractMetaXMLReader

isStartElement() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader

isTerminated() - Method in class info.bioinfweb.jphyloio.events.PartEndEvent

Specifies whether another part of the same sequence or character set definition may follow.

isTopLevel() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLMetaEventInfo

isTree(ReadWriteParameterMap) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.store.StoreTreeNetworkDataAdapter

isTree(ReadWriteParameterMap) - Method in interface info.bioinfweb.jphyloio.dataadapters.TreeNetworkDataAdapter

Determines whether this instance represents a phylogenetic tree or a phylogenetic network.

isUnderPredicate() - Method in class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLPredicateMetaReceiver

isUnique(String) - Method in interface info.bioinfweb.jphyloio.AbstractEventWriter.UniqueLabelHandler

isWhiteSpace() - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLStreamReader

isWriteAlignment() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterAlignmentInformation

isWriteCellsTags() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterAlignmentInformation

isWriteContent() - Method in class info.bioinfweb.jphyloio.formats.phyloxml.receivers.PhyloXMLMetaDataReceiver

isWriteDefaultTokenSet() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterAlignmentInformation

isWriteUndefinedOTU() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider

isWriteUndefinedOtuList() - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider

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