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 `SetElementEvent`s.
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 `JPhyloIOEvent`s 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