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

A

AbstractCharLabelsReader - Class in info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters
Implements shared functionality for Nexus command readers that process character (alignment column) definitions.
AbstractCharLabelsReader - Class in info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters
Implements shared functionality for Nexus command readers that process character (alignment column) definitions.
AbstractCharLabelsReader(String, NexusReaderStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.AbstractCharLabelsReader
 
AbstractCharLabelsReader(String, NexusReaderStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.AbstractCharLabelsReader
 
AbstractEventReader<P extends ReaderStreamDataProvider<? extends AbstractEventReader<P>>> - Class in info.bioinfweb.jphyloio
Basic implementation for event readers in PhyloIO.
AbstractEventReader<P extends ReaderStreamDataProvider<? extends AbstractEventReader<P>>> - Class in info.bioinfweb.jphyloio
Basic implementation for event readers in PhyloIO.
AbstractEventReader(ReadWriteParameterMap, String) - Constructor for class info.bioinfweb.jphyloio.AbstractEventReader
 
AbstractEventReader(ReadWriteParameterMap, String) - Constructor for class info.bioinfweb.jphyloio.AbstractEventReader
 
AbstractEventWriter<P extends WriterStreamDataProvider<? extends AbstractEventWriter<P>>> - Class in info.bioinfweb.jphyloio
Implements shared functionality for JPhyloIO event writers.
AbstractEventWriter<P extends WriterStreamDataProvider<? extends AbstractEventWriter<P>>> - Class in info.bioinfweb.jphyloio
Implements shared functionality for JPhyloIO event writers.
AbstractEventWriter() - Constructor for class info.bioinfweb.jphyloio.AbstractEventWriter
 
AbstractEventWriter() - Constructor for class info.bioinfweb.jphyloio.AbstractEventWriter
 
AbstractEventWriter.NoEditUniqueLabelHandler - Class in info.bioinfweb.jphyloio
 
AbstractEventWriter.NoEditUniqueLabelHandler - Class in info.bioinfweb.jphyloio
 
AbstractEventWriter.UniqueLabelHandler - Interface in info.bioinfweb.jphyloio
 
AbstractEventWriter.UniqueLabelHandler - Interface in info.bioinfweb.jphyloio
 
AbstractIDLinkSetElementReader - Class in info.bioinfweb.jphyloio.formats.nexml.elementreader
Element reader for NeXML sets that are represented as a sequence of EventContentType.SET_ELEMENT events.
AbstractIDLinkSetElementReader - Class in info.bioinfweb.jphyloio.formats.nexml.elementreader
Element reader for NeXML sets that are represented as a sequence of EventContentType.SET_ELEMENT events.
AbstractIDLinkSetElementReader(EventContentType, EventContentType, QName...) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractIDLinkSetElementReader
Creates a new instance of this class.
AbstractIDLinkSetElementReader(EventContentType, EventContentType, QName...) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractIDLinkSetElementReader
Creates a new instance of this class.
AbstractKeyValueCommandReader - Class in info.bioinfweb.jphyloio.formats.nexus.commandreaders
 
AbstractKeyValueCommandReader - Class in info.bioinfweb.jphyloio.formats.nexus.commandreaders
 
AbstractKeyValueCommandReader(String, String[], NexusReaderStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.AbstractKeyValueCommandReader
 
AbstractKeyValueCommandReader(String, String[], NexusReaderStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.AbstractKeyValueCommandReader
 
AbstractMetaXMLReader - Class in info.bioinfweb.jphyloio.formats.xml.stax
Implements shared functionality for custom XML readers.
AbstractMetaXMLReader - Class in info.bioinfweb.jphyloio.formats.xml.stax
Implements shared functionality for custom XML readers.
AbstractMetaXMLReader(XMLReaderStreamDataProvider<?>) - Constructor for class info.bioinfweb.jphyloio.formats.xml.stax.AbstractMetaXMLReader
 
AbstractMetaXMLReader(XMLReaderStreamDataProvider<?>) - Constructor for class info.bioinfweb.jphyloio.formats.xml.stax.AbstractMetaXMLReader
 
AbstractMetaXMLWriter - Class in info.bioinfweb.jphyloio.formats.xml.stax
Implements shared functionality for the StAX adapter writers of JPhyloIO.
AbstractMetaXMLWriter - Class in info.bioinfweb.jphyloio.formats.xml.stax
Implements shared functionality for the StAX adapter writers of JPhyloIO.
AbstractMetaXMLWriter(JPhyloIOEventReceiver, XMLStreamWriter) - Constructor for class info.bioinfweb.jphyloio.formats.xml.stax.AbstractMetaXMLWriter
 
AbstractMetaXMLWriter(JPhyloIOEventReceiver, XMLStreamWriter) - Constructor for class info.bioinfweb.jphyloio.formats.xml.stax.AbstractMetaXMLWriter
 
AbstractNeXMLDataReceiver - Class in info.bioinfweb.jphyloio.formats.nexml.receivers
Implements basic functionality for event receivers writing NeXML.
AbstractNeXMLDataReceiver - Class in info.bioinfweb.jphyloio.formats.nexml.receivers
Implements basic functionality for event receivers writing NeXML.
AbstractNeXMLDataReceiver(NeXMLWriterStreamDataProvider, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.receivers.AbstractNeXMLDataReceiver
 
AbstractNeXMLDataReceiver(NeXMLWriterStreamDataProvider, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.receivers.AbstractNeXMLDataReceiver
 
AbstractNeXMLDataReceiverMixin - Class in info.bioinfweb.jphyloio.formats.nexml.receivers
Provides a set of static methods to be used as static imports when needed across multiple NeXML data receivers.
AbstractNeXMLDataReceiverMixin - Class in info.bioinfweb.jphyloio.formats.nexml.receivers
Provides a set of static methods to be used as static imports when needed across multiple NeXML data receivers.
AbstractNeXMLDataReceiverMixin() - Constructor for class info.bioinfweb.jphyloio.formats.nexml.receivers.AbstractNeXMLDataReceiverMixin
 
AbstractNeXMLDataReceiverMixin() - Constructor for class info.bioinfweb.jphyloio.formats.nexml.receivers.AbstractNeXMLDataReceiverMixin
 
AbstractNeXMLElementReader - Class in info.bioinfweb.jphyloio.formats.nexml.elementreader
Processes a NeXML tag without any of its subelements.
AbstractNeXMLElementReader - Class in info.bioinfweb.jphyloio.formats.nexml.elementreader
Processes a NeXML tag without any of its subelements.
AbstractNeXMLElementReader() - Constructor for class info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractNeXMLElementReader
 
AbstractNeXMLElementReader() - Constructor for class info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractNeXMLElementReader
 
AbstractNeXMLElementReader.LabeledIDEventInformation - Class in info.bioinfweb.jphyloio.formats.nexml.elementreader
Contains information about a LabeledIDEvent.
AbstractNeXMLElementReader.LabeledIDEventInformation - Class in info.bioinfweb.jphyloio.formats.nexml.elementreader
Contains information about a LabeledIDEvent.
AbstractNeXMLElementReader.OTUorOTUsEventInformation - Class in info.bioinfweb.jphyloio.formats.nexml.elementreader
Contains information about a LinkedLabeledIDEvent.
AbstractNeXMLElementReader.OTUorOTUsEventInformation - Class in info.bioinfweb.jphyloio.formats.nexml.elementreader
Contains information about a LinkedLabeledIDEvent.
AbstractNexusBlockHandler - Class in info.bioinfweb.jphyloio.formats.nexus.blockhandlers
Abstract implementation of NexusBlockHandler that stores a set of block names in an unmodifiable collection.
AbstractNexusBlockHandler - Class in info.bioinfweb.jphyloio.formats.nexus.blockhandlers
Abstract implementation of NexusBlockHandler that stores a set of block names in an unmodifiable collection.
AbstractNexusBlockHandler(String[]) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.blockhandlers.AbstractNexusBlockHandler
Creates a new instance of this class.
AbstractNexusBlockHandler(String[]) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.blockhandlers.AbstractNexusBlockHandler
Creates a new instance of this class.
AbstractNexusCommandEventReader - Class in info.bioinfweb.jphyloio.formats.nexus.commandreaders
Implements shared functionality for classes implementing NexusCommandEventReader.
AbstractNexusCommandEventReader - Class in info.bioinfweb.jphyloio.formats.nexus.commandreaders
Implements shared functionality for classes implementing NexusCommandEventReader.
AbstractNexusCommandEventReader(String, String[], NexusReaderStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.AbstractNexusCommandEventReader
Creates a new instance of this class.
AbstractNexusCommandEventReader(String, String[], NexusReaderStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.AbstractNexusCommandEventReader
Creates a new instance of this class.
AbstractNexusEventReceiver - Class in info.bioinfweb.jphyloio.formats.nexus.receivers
Implements basic functionality for event receivers writing Nexus.
AbstractNexusEventReceiver - Class in info.bioinfweb.jphyloio.formats.nexus.receivers
Implements basic functionality for event receivers writing Nexus.
AbstractNexusEventReceiver(NexusWriterStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.receivers.AbstractNexusEventReceiver
 
AbstractNexusEventReceiver(NexusWriterStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.receivers.AbstractNexusEventReceiver
 
AbstractNexusSetReader - Class in info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets
General reader implementation to read the Nexus commands that define different kinds of sets.
AbstractNexusSetReader - Class in info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets
General reader implementation to read the Nexus commands that define different kinds of sets.
AbstractNexusSetReader(EventContentType, String, String[], NexusReaderStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets.AbstractNexusSetReader
 
AbstractNexusSetReader(EventContentType, String, String[], NexusReaderStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.commandreaders.sets.AbstractNexusSetReader
 
AbstractNexusSetsEventReceiver - Class in info.bioinfweb.jphyloio.formats.nexus.receivers
General implementation for event receivers writing Nexus set commands.
AbstractNexusSetsEventReceiver - Class in info.bioinfweb.jphyloio.formats.nexus.receivers
General implementation for event receivers writing Nexus set commands.
AbstractNexusSetsEventReceiver(NexusWriterStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.receivers.AbstractNexusSetsEventReceiver
Creates a new instance of this class.
AbstractNexusSetsEventReceiver(NexusWriterStreamDataProvider) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.receivers.AbstractNexusSetsEventReceiver
Creates a new instance of this class.
AbstractNexusSetWriter - Class in info.bioinfweb.jphyloio.formats.nexus
Customizable implementation for writing different kinds of Nexus sets.
AbstractNexusSetWriter - Class in info.bioinfweb.jphyloio.formats.nexus
Customizable implementation for writing different kinds of Nexus sets.
AbstractNexusSetWriter(NexusWriterStreamDataProvider, String, EventContentType, Iterator<? extends ElementDataAdapter<? extends LabeledIDEvent>>, AbstractNexusEventReceiver) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.AbstractNexusSetWriter
 
AbstractNexusSetWriter(NexusWriterStreamDataProvider, String, EventContentType, Iterator<? extends ElementDataAdapter<? extends LabeledIDEvent>>, AbstractNexusEventReceiver) - Constructor for class info.bioinfweb.jphyloio.formats.nexus.AbstractNexusSetWriter
 
AbstractObjectTranslator<O> - Class in info.bioinfweb.jphyloio.objecttranslation.implementations
AbstractObjectTranslator<O> - Class in info.bioinfweb.jphyloio.objecttranslation.implementations
AbstractObjectTranslator() - Constructor for class info.bioinfweb.jphyloio.objecttranslation.implementations.AbstractObjectTranslator
 
AbstractObjectTranslator() - Constructor for class info.bioinfweb.jphyloio.objecttranslation.implementations.AbstractObjectTranslator
 
AbstractPhylipEventReader<P extends TextReaderStreamDataProvider<? extends AbstractPhylipEventReader<P>>> - Class in info.bioinfweb.jphyloio.formats.phylip
Implements shared functionality of Phylip event readers.
AbstractPhylipEventReader<P extends TextReaderStreamDataProvider<? extends AbstractPhylipEventReader<P>>> - Class in info.bioinfweb.jphyloio.formats.phylip
Implements shared functionality of Phylip event readers.
AbstractPhylipEventReader(PeekReader, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipEventReader
 
AbstractPhylipEventReader(Reader, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipEventReader
 
AbstractPhylipEventReader(InputStream, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipEventReader
 
AbstractPhylipEventReader(File, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipEventReader
 
AbstractPhylipEventReader(PeekReader, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipEventReader
 
AbstractPhylipEventReader(Reader, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipEventReader
 
AbstractPhylipEventReader(InputStream, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipEventReader
 
AbstractPhylipEventReader(File, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipEventReader
 
AbstractPhylipFactory - Class in info.bioinfweb.jphyloio.formats.phylip
Implements shared functionality for Phylip factories.
AbstractPhylipFactory - Class in info.bioinfweb.jphyloio.formats.phylip
Implements shared functionality for Phylip factories.
AbstractPhylipFactory() - Constructor for class info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipFactory
 
AbstractPhylipFactory() - Constructor for class info.bioinfweb.jphyloio.formats.phylip.AbstractPhylipFactory
 
AbstractSequenceContentReceiver<P extends WriterStreamDataProvider<? extends AbstractEventWriter<P>>> - Class in info.bioinfweb.jphyloio.dataadapters.implementations.receivers
 
AbstractSequenceContentReceiver<P extends WriterStreamDataProvider<? extends AbstractEventWriter<P>>> - Class in info.bioinfweb.jphyloio.dataadapters.implementations.receivers
 
AbstractSequenceContentReceiver(P, ReadWriteParameterMap, boolean) - Constructor for class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.AbstractSequenceContentReceiver
 
AbstractSequenceContentReceiver(P, ReadWriteParameterMap, boolean) - Constructor for class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.AbstractSequenceContentReceiver
 
AbstractSetElementReader - Class in info.bioinfweb.jphyloio.formats.nexml.elementreader
Abstract element reader that processes NeXML set tags that contain one or more attributes of the type xs:IDREFS.
AbstractSetElementReader - Class in info.bioinfweb.jphyloio.formats.nexml.elementreader
Abstract element reader that processes NeXML set tags that contain one or more attributes of the type xs:IDREFS.
AbstractSetElementReader(EventContentType, EventContentType, QName...) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractSetElementReader
 
AbstractSetElementReader(EventContentType, EventContentType, QName...) - Constructor for class info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractSetElementReader
 
AbstractSingleMatrixEventWriter<P extends TextWriterStreamDataProvider<? extends AbstractTextEventWriter<P>>> - Class in info.bioinfweb.jphyloio
Default implementation for writers that can only write a single matrix (multiple sequence alignment) to their target format, because that format does not support additional data.
AbstractSingleMatrixEventWriter<P extends TextWriterStreamDataProvider<? extends AbstractTextEventWriter<P>>> - Class in info.bioinfweb.jphyloio
Default implementation for writers that can only write a single matrix (multiple sequence alignment) to their target format, because that format does not support additional data.
AbstractSingleMatrixEventWriter(String) - Constructor for class info.bioinfweb.jphyloio.AbstractSingleMatrixEventWriter
Creates a new instance of this class.
AbstractSingleMatrixEventWriter(String) - Constructor for class info.bioinfweb.jphyloio.AbstractSingleMatrixEventWriter
Creates a new instance of this class.
AbstractSingleReaderWriterFactory - Class in info.bioinfweb.jphyloio.factory
 
AbstractSingleReaderWriterFactory - Class in info.bioinfweb.jphyloio.factory
 
AbstractSingleReaderWriterFactory() - Constructor for class info.bioinfweb.jphyloio.factory.AbstractSingleReaderWriterFactory
 
AbstractSingleReaderWriterFactory() - Constructor for class info.bioinfweb.jphyloio.factory.AbstractSingleReaderWriterFactory
 
AbstractStartStringSingleFactory - Class in info.bioinfweb.jphyloio.factory
Abstract single format factory that implements the checkFormat() methods by testing of the read content start with a certain string, determined by AbstractStartStringSingleFactory.getExpectedStart().
AbstractStartStringSingleFactory - Class in info.bioinfweb.jphyloio.factory
Abstract single format factory that implements the checkFormat() methods by testing of the read content start with a certain string, determined by AbstractStartStringSingleFactory.getExpectedStart().
AbstractStartStringSingleFactory(String) - Constructor for class info.bioinfweb.jphyloio.factory.AbstractStartStringSingleFactory
Creates a new instance of this class.
AbstractStartStringSingleFactory(String) - Constructor for class info.bioinfweb.jphyloio.factory.AbstractStartStringSingleFactory
Creates a new instance of this class.
AbstractTextEventReader<P extends TextReaderStreamDataProvider<? extends AbstractTextEventReader<P>>> - Class in info.bioinfweb.jphyloio.formats.text
Abstract base class for all readers that read their data from a file using a PeekReader.
AbstractTextEventReader<P extends TextReaderStreamDataProvider<? extends AbstractTextEventReader<P>>> - Class in info.bioinfweb.jphyloio.formats.text
Abstract base class for all readers that read their data from a file using a PeekReader.
AbstractTextEventReader(PeekReader, ReadWriteParameterMap, String) - Constructor for class info.bioinfweb.jphyloio.formats.text.AbstractTextEventReader
Creates a new instance of this class.
AbstractTextEventReader(Reader, ReadWriteParameterMap, String) - Constructor for class info.bioinfweb.jphyloio.formats.text.AbstractTextEventReader
Creates a new instance of this class.
AbstractTextEventReader(InputStream, ReadWriteParameterMap, String) - Constructor for class info.bioinfweb.jphyloio.formats.text.AbstractTextEventReader
Creates a new instance of this class.
AbstractTextEventReader(File, ReadWriteParameterMap, String) - Constructor for class info.bioinfweb.jphyloio.formats.text.AbstractTextEventReader
Creates a new instance of this class.
AbstractTextEventReader(PeekReader, ReadWriteParameterMap, String) - Constructor for class info.bioinfweb.jphyloio.formats.text.AbstractTextEventReader
Creates a new instance of this class.
AbstractTextEventReader(Reader, ReadWriteParameterMap, String) - Constructor for class info.bioinfweb.jphyloio.formats.text.AbstractTextEventReader
Creates a new instance of this class.
AbstractTextEventReader(InputStream, ReadWriteParameterMap, String) - Constructor for class info.bioinfweb.jphyloio.formats.text.AbstractTextEventReader
Creates a new instance of this class.
AbstractTextEventReader(File, ReadWriteParameterMap, String) - Constructor for class info.bioinfweb.jphyloio.formats.text.AbstractTextEventReader
Creates a new instance of this class.
AbstractTextEventWriter<P extends TextWriterStreamDataProvider<? extends AbstractTextEventWriter<P>>> - Class in info.bioinfweb.jphyloio.formats.text
 
AbstractTextEventWriter<P extends TextWriterStreamDataProvider<? extends AbstractTextEventWriter<P>>> - Class in info.bioinfweb.jphyloio.formats.text
 
AbstractTextEventWriter() - Constructor for class info.bioinfweb.jphyloio.formats.text.AbstractTextEventWriter
 
AbstractTextEventWriter() - Constructor for class info.bioinfweb.jphyloio.formats.text.AbstractTextEventWriter
 
AbstractXMLDataReceiver<P extends XMLWriterStreamDataProvider<? extends AbstractXMLEventWriter<P>>> - Class in info.bioinfweb.jphyloio.formats.xml.receivers
Abstract implementation of a data receiver that can be used to write XML formats.
AbstractXMLDataReceiver<P extends XMLWriterStreamDataProvider<? extends AbstractXMLEventWriter<P>>> - Class in info.bioinfweb.jphyloio.formats.xml.receivers
Abstract implementation of a data receiver that can be used to write XML formats.
AbstractXMLDataReceiver(P, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.xml.receivers.AbstractXMLDataReceiver
 
AbstractXMLDataReceiver(P, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.xml.receivers.AbstractXMLDataReceiver
 
AbstractXMLElementReader<P extends XMLReaderStreamDataProvider<? extends AbstractXMLEventReader<P>>> - Class in info.bioinfweb.jphyloio.formats.xml.elementreaders
Abstract implementation of an element reader that is used to process parts of an XML document.
AbstractXMLElementReader<P extends XMLReaderStreamDataProvider<? extends AbstractXMLEventReader<P>>> - Class in info.bioinfweb.jphyloio.formats.xml.elementreaders
Abstract implementation of an element reader that is used to process parts of an XML document.
AbstractXMLElementReader() - Constructor for class info.bioinfweb.jphyloio.formats.xml.elementreaders.AbstractXMLElementReader
 
AbstractXMLElementReader() - Constructor for class info.bioinfweb.jphyloio.formats.xml.elementreaders.AbstractXMLElementReader
 
AbstractXMLEventReader<P extends XMLReaderStreamDataProvider<? extends AbstractXMLEventReader<P>>> - Class in info.bioinfweb.jphyloio.formats.xml
Implements shared functionality for reading XML formats.
AbstractXMLEventReader<P extends XMLReaderStreamDataProvider<? extends AbstractXMLEventReader<P>>> - Class in info.bioinfweb.jphyloio.formats.xml
Implements shared functionality for reading XML formats.
AbstractXMLEventReader(File, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader
 
AbstractXMLEventReader(InputStream, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader
 
AbstractXMLEventReader(XMLEventReader, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader
 
AbstractXMLEventReader(Reader, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader
 
AbstractXMLEventReader(File, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader
 
AbstractXMLEventReader(InputStream, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader
 
AbstractXMLEventReader(XMLEventReader, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader
 
AbstractXMLEventReader(Reader, ReadWriteParameterMap) - Constructor for class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader
 
AbstractXMLEventWriter<P extends XMLWriterStreamDataProvider<? extends AbstractXMLEventWriter<P>>> - Class in info.bioinfweb.jphyloio.formats.xml
Implements shared functionality for writing XML formats.
AbstractXMLEventWriter<P extends XMLWriterStreamDataProvider<? extends AbstractXMLEventWriter<P>>> - Class in info.bioinfweb.jphyloio.formats.xml
Implements shared functionality for writing XML formats.
AbstractXMLEventWriter() - Constructor for class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventWriter
 
AbstractXMLEventWriter() - Constructor for class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventWriter
 
AbstractXMLFactory - Class in info.bioinfweb.jphyloio.formats.xml
Implements shared functionality for reader and writer factories of XML formats.
AbstractXMLFactory - Class in info.bioinfweb.jphyloio.formats.xml
Implements shared functionality for reader and writer factories of XML formats.
AbstractXMLFactory(QName) - Constructor for class info.bioinfweb.jphyloio.formats.xml.AbstractXMLFactory
Creates a new instance of this class.
AbstractXMLFactory(QName) - Constructor for class info.bioinfweb.jphyloio.formats.xml.AbstractXMLFactory
Creates a new instance of this class.
AbstractXMLObjectTranslator<O> - Class in info.bioinfweb.jphyloio.objecttranslation.implementations
Abstract implementation for object translators that need XML tags to represent their object and do not support simple string representations.
AbstractXMLObjectTranslator<O> - Class in info.bioinfweb.jphyloio.objecttranslation.implementations
Abstract implementation for object translators that need XML tags to represent their object and do not support simple string representations.
AbstractXMLObjectTranslator() - Constructor for class info.bioinfweb.jphyloio.objecttranslation.implementations.AbstractXMLObjectTranslator
 
AbstractXMLObjectTranslator() - Constructor for class info.bioinfweb.jphyloio.objecttranslation.implementations.AbstractXMLObjectTranslator
 
acceptContent(FileInputStream) - Method in class info.bioinfweb.jphyloio.factory.JPhyloIOContentExtensionFileFilter
 
acceptContent(FileInputStream) - Method in class info.bioinfweb.jphyloio.factory.JPhyloIOContentExtensionFileFilter
 
add(JPhyloIOEvent) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver
 
add(JPhyloIOEvent) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver
 
add(JPhyloIOEvent) - Method in interface info.bioinfweb.jphyloio.dataadapters.JPhyloIOEventReceiver
Adds a new event to the sequence written to this receiver.
add(JPhyloIOEvent) - Method in interface info.bioinfweb.jphyloio.dataadapters.JPhyloIOEventReceiver
Adds a new event to the sequence written to this receiver.
add(String, String) - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees.NexusTranslationTable
 
add(String, String) - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.trees.NexusTranslationTable
 
add(XMLEvent) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLEventWriter
 
add(XMLEventReader) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLEventWriter
 
add(XMLEvent) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLEventWriter
 
add(XMLEventReader) - Method in class info.bioinfweb.jphyloio.formats.xml.stax.MetaXMLEventWriter
 
add(JPhyloIOEvent) - Method in class info.bioinfweb.jphyloio.ParentEventInformation
 
add(JPhyloIOEvent) - Method in class info.bioinfweb.jphyloio.ParentEventInformation
 
addCharacterDefinition(String, long) - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.AbstractCharLabelsReader
 
addCharacterDefinition(String, long) - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.AbstractCharLabelsReader
 
addEdit(EventContentType, String, String, boolean) - Method in class info.bioinfweb.jphyloio.utils.LabelEditingReporter
Adds a new mapping from an element ID to the label used for it in the target document to this instance.
addEdit(LabeledIDEvent, String) - Method in class info.bioinfweb.jphyloio.utils.LabelEditingReporter
Adds a new mapping from an element ID to the label used for it in the target document to this instance.
addEdit(EventContentType, String, String, boolean) - Method in class info.bioinfweb.jphyloio.utils.LabelEditingReporter
Adds a new mapping from an element ID to the label used for it in the target document to this instance.
addEdit(LabeledIDEvent, String) - Method in class info.bioinfweb.jphyloio.utils.LabelEditingReporter
Adds a new mapping from an element ID to the label used for it in the target document to this instance.
addEventListener(JPhyloIOEventListener) - Method in class info.bioinfweb.jphyloio.AbstractEventReader
 
addEventListener(JPhyloIOEventListener) - Method in class info.bioinfweb.jphyloio.AbstractEventReader
 
addEventListener(JPhyloIOEventListener) - Method in interface info.bioinfweb.jphyloio.JPhyloIOEventReader
Adds a JPhyloIOEventListener to the reader.
addEventListener(JPhyloIOEventListener) - Method in interface info.bioinfweb.jphyloio.JPhyloIOEventReader
Adds a JPhyloIOEventListener to the reader.
addFactory(SingleReaderWriterFactory) - Method in class info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory
Allows to add additional or replace existing single format factories to be used by this instance.
addFactory(SingleReaderWriterFactory) - Method in class info.bioinfweb.jphyloio.factory.JPhyloIOReaderWriterFactory
Allows to add additional or replace existing single format factories to be used by this instance.
addHandler(NexusBlockHandler) - Method in class info.bioinfweb.jphyloio.formats.nexus.blockhandlers.NexusBlockHandlerMap
Adds a new handler to this map.
addHandler(NexusBlockHandler) - Method in class info.bioinfweb.jphyloio.formats.nexus.blockhandlers.NexusBlockHandlerMap
Adds a new handler to this map.
addIgnoredComments(long) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver
 
addIgnoredComments(long) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver
 
addIgnoredLiteralMetadata(long) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver
 
addIgnoredLiteralMetadata(long) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver
 
addIgnoredResourceMetadata(long) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver
 
addIgnoredResourceMetadata(long) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver
 
addIgnoreLogMessage(ApplicationLogger, String, String) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver
 
addIgnoreLogMessage(ApplicationLogger, String, String) - Method in class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver
 
addJPhyloIOHandlers() - Method in class info.bioinfweb.jphyloio.formats.nexus.blockhandlers.NexusBlockHandlerMap
Adds all handlers that are available in JPhyloIO to this instance.
addJPhyloIOHandlers() - Method in class info.bioinfweb.jphyloio.formats.nexus.blockhandlers.NexusBlockHandlerMap
Adds all handlers that are available in JPhyloIO to this instance.
addJPhyloIOReaders() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.NexusCommandReaderFactory
Adds all Nexus command readers available in JPhyloIO to this instance.
addJPhyloIOReaders() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.NexusCommandReaderFactory
Adds all Nexus command readers available in JPhyloIO to this instance.
addJPhyloIOTranslators(boolean) - Method in class info.bioinfweb.jphyloio.objecttranslation.ObjectTranslatorFactory
Adds all translators for custom types defined in JPhyloIO.
addJPhyloIOTranslators(boolean) - Method in class info.bioinfweb.jphyloio.objecttranslation.ObjectTranslatorFactory
Adds all translators for custom types defined in JPhyloIO.
addNextEvents() - Method in class info.bioinfweb.jphyloio.formats.newick.NewickStringReader
Creates the next JPhyloIO event(s) from the Newick string provided by the underlying reader.
addNextEvents() - Method in class info.bioinfweb.jphyloio.formats.newick.NewickStringReader
Creates the next JPhyloIO event(s) from the Newick string provided by the underlying reader.
addReaderClass(Class<? extends NexusCommandEventReader>) - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.NexusCommandReaderFactory
Adds a new type of reader to this factory instance.
addReaderClass(Class<? extends NexusCommandEventReader>) - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.NexusCommandReaderFactory
Adds a new type of reader to this factory instance.
addRemainingEvents(CharacterStateSetType) - Method in class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLMolecularDataTokenDefinitionReceiver
Determines the type of alignment to which additional token definitions need to be add.
addRemainingEvents(CharacterStateSetType) - Method in class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLMolecularDataTokenDefinitionReceiver
Determines the type of alignment to which additional token definitions need to be add.
addStoredEvents() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.AbstractKeyValueCommandReader
Implementations that need to store events, until all generated events are known should add such events to the queue, when this method is called.
addStoredEvents() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.AbstractKeyValueCommandReader
Implementations that need to store events, until all generated events are known should add such events to the queue, when this method is called.
addStoredEvents() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.all.LinkReader
 
addStoredEvents() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.all.LinkReader
 
addStoredEvents() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.DimensionsReader
 
addStoredEvents() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.DimensionsReader
 
addStoredEvents() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.FormatReader
Adds the stored token set event with nested single token definition events to the queue, if present.
addStoredEvents() - Method in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.characters.FormatReader
Adds the stored token set event with nested single token definition events to the queue, if present.
addToDocumentIDs(String) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
 
addToDocumentIDs(String) - Method in class info.bioinfweb.jphyloio.formats.nexml.NeXMLWriterStreamDataProvider
 
addTranslator(ObjectTranslator<?>, boolean, QName, QName...) - Method in class info.bioinfweb.jphyloio.objecttranslation.ObjectTranslatorFactory
Registers a new translator in this factory for one or more data types.
addTranslator(ObjectTranslator<?>, boolean, QName, QName...) - Method in class info.bioinfweb.jphyloio.objecttranslation.ObjectTranslatorFactory
Registers a new translator in this factory for one or more data types.
addXSDTranslators(boolean) - Method in class info.bioinfweb.jphyloio.objecttranslation.ObjectTranslatorFactory
Adds all translators for XSD types available in JPhyloIO.
addXSDTranslators(boolean) - Method in class info.bioinfweb.jphyloio.objecttranslation.ObjectTranslatorFactory
Adds all translators for XSD types available in JPhyloIO.
ALIGN_LEFT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ALIGN_LEFT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ALIGN_RIGHT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ALIGN_RIGHT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ALIGN_TREE_WIDTH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ALIGN_TREE_WIDTH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ALL_BLOCKS_IDENTIFIER - Static variable in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.NexusCommandReaderFactory
 
ALL_BLOCKS_IDENTIFIER - Static variable in class info.bioinfweb.jphyloio.formats.nexus.commandreaders.NexusCommandReaderFactory
 
ALLOCATION_SEPARATOR_SYMBOL - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants
 
ALLOCATION_SEPARATOR_SYMBOL - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants
 
ALLOCATION_SYMBOL - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants
 
ALLOCATION_SYMBOL - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants
 
ALTERNATIVE_END_COMMAND - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
 
ALTERNATIVE_END_COMMAND - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
 
ALTERNATIVE_NAME_DELIMITER - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants
 
ALTERNATIVE_NAME_DELIMITER - Static variable in interface info.bioinfweb.jphyloio.formats.newick.NewickConstants
 
AMINO_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
 
AMINO_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
 
AnnotatedDataAdapter - Interface in info.bioinfweb.jphyloio.dataadapters
Superinterface for all data adapters providing metadata to the object they model.
AnnotatedDataAdapter - Interface in info.bioinfweb.jphyloio.dataadapters
Superinterface for all data adapters providing metadata to the object they model.
anyLabelEdited(EventContentType) - Method in class info.bioinfweb.jphyloio.utils.LabelEditingReporter
Determines whether any label of data elements of the specified content type was edited.
anyLabelEdited(EventContentType) - Method in class info.bioinfweb.jphyloio.utils.LabelEditingReporter
Determines whether any label of data elements of the specified content type was edited.
APPLIES_TO_ANNOTATION - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
APPLIES_TO_ANNOTATION - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
APPLIES_TO_CLADE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
APPLIES_TO_CLADE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
APPLIES_TO_NODE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
APPLIES_TO_NODE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
APPLIES_TO_OTHER - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
APPLIES_TO_OTHER - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
APPLIES_TO_PARENT_BRANCH - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
APPLIES_TO_PARENT_BRANCH - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
APPLIES_TO_PHYLOGENY - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
APPLIES_TO_PHYLOGENY - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
asCharacterDefinitionEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asCharacterDefinitionEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asCharacterDefinitionEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a character definition event.
asCharacterDefinitionEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a character definition event.
asCharacterSetIntervalEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asCharacterSetIntervalEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asCharacterSetIntervalEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a character set event.
asCharacterSetIntervalEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a character set event.
asCommentEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asCommentEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asCommentEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a comment event.
asCommentEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a comment event.
asEdgeEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asEdgeEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asEdgeEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a tree or graph edge event.
asEdgeEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a tree or graph edge event.
asLabeledIDEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asLabeledIDEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asLabeledIDEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a labeled ID event.
asLabeledIDEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a labeled ID event.
asLinkedLabeledIDEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asLinkedLabeledIDEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asLinkedLabeledIDEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a basic OTU event.
asLinkedLabeledIDEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a basic OTU event.
asLiteralMetadataContentEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asLiteralMetadataContentEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asLiteralMetadataContentEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a literal content metadata event.
asLiteralMetadataContentEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a literal content metadata event.
asLiteralMetadataEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asLiteralMetadataEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asLiteralMetadataEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a literal metadata event.
asLiteralMetadataEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a literal metadata event.
asNodeEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asNodeEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asNodeEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a tree or graph node event.
asNodeEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a tree or graph node event.
asPartEndEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asPartEndEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asPartEndEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a part end event.
asPartEndEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a part end event.
asResourceMetadataEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asResourceMetadataEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asResourceMetadataEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a resource metadata event.
asResourceMetadataEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a resource metadata event.
asSequenceTokensEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asSequenceTokensEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asSequenceTokensEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a tokens event.
asSequenceTokensEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a tokens event.
asSetElementEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asSetElementEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asSetElementEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a set element event.
asSetElementEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a set element event.
asSingleSequenceTokenEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asSingleSequenceTokenEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asSingleSequenceTokenEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a single token event.
asSingleSequenceTokenEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a single token event.
asSingleTokenDefinitionEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asSingleTokenDefinitionEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asSingleTokenDefinitionEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a single character state symbol definition event.
asSingleTokenDefinitionEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a single character state symbol definition event.
asTokenSetDefinitionEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asTokenSetDefinitionEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asTokenSetDefinitionEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a character state set definition event.
asTokenSetDefinitionEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to a character state set definition event.
asUnknownCommandEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asUnknownCommandEvent() - Method in class info.bioinfweb.jphyloio.events.ConcreteJPhyloIOEvent
 
asUnknownCommandEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to an unknown command event.
asUnknownCommandEvent() - Method in interface info.bioinfweb.jphyloio.events.JPhyloIOEvent
Casts this event to an unknown command event.
ATTR_ABOUT - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_ABOUT - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_ABSENT_COUNT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_ABSENT_COUNT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_ADAPTER_ID - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_ADAPTER_ID - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_ADAPTER_NAME - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_ADAPTER_NAME - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_ADAPTER_PURPOSE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_ADAPTER_PURPOSE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_ALIGN_TO_SUBTREE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_ALIGN_TO_SUBTREE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_ALIGNMENT_LENGTH - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
 
ATTR_ALIGNMENT_LENGTH - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
 
ATTR_ALT_UNIT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_ALT_UNIT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_ANCHOR_0 - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_ANCHOR_0 - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_ANCHOR_1 - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_ANCHOR_1 - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_APPLIES_TO - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_APPLIES_TO - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_BG_COLOR - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_BG_COLOR - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_BOTTOM - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_BOTTOM - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_BRANCH_LENGTH - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_BRANCH_LENGTH - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_BRANCH_LENGTH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_BRANCH_LENGTH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_BRANCH_LENGTH_SCALE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_BRANCH_LENGTH_SCALE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_BRANCH_LENGTH_UNIT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_BRANCH_LENGTH_UNIT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_CELL_SET_LINKED_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_CELL_SET_LINKED_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_CHAR_SET_LINKED_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_CHAR_SET_LINKED_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_CHARSET_LABEL - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
 
ATTR_CHARSET_LABEL - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
 
ATTR_CODON_POSITION - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_CODON_POSITION - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_COLLAPSE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_COLLAPSE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_COLOR - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
 
ATTR_COLOR - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
 
ATTR_COMMENT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_COMMENT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_CONFIDENCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_CONFIDENCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_CONSTANT_WIDTH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_CONSTANT_WIDTH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_CONTENT - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_CONTENT - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_DATATYPE - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_DATATYPE - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_DATATYPE - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
 
ATTR_DATATYPE - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
 
ATTR_DATATYPE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_DATATYPE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_DECIMAL_FORMAT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_DECIMAL_FORMAT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_DESC - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_DESC - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_DISTANCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_DISTANCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_DOI - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_DOI - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_EDGE_RADIUS - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_EDGE_RADIUS - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_EVIDENCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_EVIDENCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_FONT_FAMILY - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_FONT_FAMILY - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_FROM - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_FROM - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_GAINED_COUNT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_GAINED_COUNT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_GENERATOR - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_GENERATOR - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_GEO_DATUM - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_GEO_DATUM - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_HEIGHT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_HEIGHT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_HREF - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_HREF - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_ICON - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_ICON - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_ICON_FILLED - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_ICON_FILLED - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_ICON_HEIGHT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_ICON_HEIGHT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_ICON_WIDTH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_ICON_WIDTH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_ID - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_ID - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_ID - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
 
ATTR_ID - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
 
ATTR_ID - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_ID - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_ID - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_ID - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_ID_PROVIDER - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_ID_PROVIDER - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_ID_REF - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_ID_REF - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_ID_REF_0 - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_ID_REF_0 - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_ID_REF_1 - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_ID_REF_1 - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_ID_SOURCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_ID_SOURCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_IS_ALIGNED - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_IS_ALIGNED - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_LABEL - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_LABEL - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_LABEL_ABOVE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LABEL_ABOVE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LABEL_HEIGHT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LABEL_HEIGHT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LABEL_SPACING - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LABEL_SPACING - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LABEL_WIDTH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LABEL_WIDTH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LEFT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LEFT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LEGEND_POS - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LEGEND_POS - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LEGEND_SPACING - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LEGEND_SPACING - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LEGEND_STYLE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LEGEND_STYLE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LENGTH - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_LENGTH - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_LENGTH - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_LENGTH - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_LINE_COLOR - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LINE_COLOR - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LINE_NO - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LINE_NO - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LINE_POS - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LINE_POS - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LINE_WIDTH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LINE_WIDTH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LOCALE_COUNTRY - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LOCALE_COUNTRY - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LOCALE_LANG - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LOCALE_LANG - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LOCALE_VARIANT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LOCALE_VARIANT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LONG_INTERVAL - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LONG_INTERVAL - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_LOST_COUNT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_LOST_COUNT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_MIN_BRANCH_LENGTH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_MIN_BRANCH_LENGTH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_MIN_SPACE_ABOVE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_MIN_SPACE_ABOVE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_MIN_SPACE_BELOW - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_MIN_SPACE_BELOW - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_MIN_TREE_DISTANCE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_MIN_TREE_DISTANCE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_NODE_EDGE_SET_LINKED_EDGE_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_NODE_EDGE_SET_LINKED_EDGE_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_NODE_EDGE_SET_LINKED_NODE_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_NODE_EDGE_SET_LINKED_NODE_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_NODE_EDGE_SET_LINKED_ROOTEDGE_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_NODE_EDGE_SET_LINKED_ROOTEDGE_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_OTU_SET_LINKED_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_OTU_SET_LINKED_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_OTUS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_OTUS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_PIE_COLOR - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_PIE_COLOR - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_POSITION_LABELS_TO_LEFT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_POSITION_LABELS_TO_LEFT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_PRESENT_COUNT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_PRESENT_COUNT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_PROPERTY - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_PROPERTY - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_REF - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_REF - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_REL - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_REL - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_REROOTABLE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_REROOTABLE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_RIGHT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_RIGHT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_ROOT - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_ROOT - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_ROOTED - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_ROOTED - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_SCALE_BAR_ALIGN - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_SCALE_BAR_ALIGN - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_SCALE_BAR_DISTANCE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_SCALE_BAR_DISTANCE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_SCALE_BAR_HEIGHT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_SCALE_BAR_HEIGHT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_SCALE_BAR_INCREASE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_SCALE_BAR_INCREASE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_SCALE_BAR_START - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_SCALE_BAR_START - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_SCALE_BAR_WIDTH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_SCALE_BAR_WIDTH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_SEQUENCE_COUNT - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
 
ATTR_SEQUENCE_COUNT - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
 
ATTR_SEQUENCE_INDEX - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
 
ATTR_SEQUENCE_INDEX - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
 
ATTR_SEQUENCE_SET_LINKED_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_SEQUENCE_SET_LINKED_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_SHOW_INTERNAL_LINES - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_SHOW_INTERNAL_LINES - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_SHOW_NULL_LINES - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_SHOW_NULL_LINES - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_SHOW_ROOTED - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_SHOW_ROOTED - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_SHOW_SCALE_BAR - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_SHOW_SCALE_BAR - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_SINGLE_CHAR_LINK - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_SINGLE_CHAR_LINK - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_SINGLE_OTU_LINK - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_SINGLE_OTU_LINK - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_SINGLE_STATE_LINK - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_SINGLE_STATE_LINK - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_SMALL_INTERVAL - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_SMALL_INTERVAL - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_SOURCE - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_SOURCE - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_SOURCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_SOURCE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_STANDARD_DEVIATION - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_STANDARD_DEVIATION - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_STATE_SET_LINKED_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_STATE_SET_LINKED_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_STATES - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_STATES - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_SYMBOL - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_SYMBOL - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_TARGET - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_TARGET - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_TEXT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_TEXT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_TEXT_COLOR - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_TEXT_COLOR - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_TEXT_HEIGHT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_TEXT_HEIGHT - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_TEXT_IS_DECIMAL - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_TEXT_IS_DECIMAL - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_TEXT_ORIENTATION - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_TEXT_ORIENTATION - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_TEXT_STYLE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_TEXT_STYLE - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_TO - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_TO - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_TOKENS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_TOKENS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_TOP - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_TOP - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_TREE_SET_LINKED_NETWORK_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_TREE_SET_LINKED_NETWORK_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_TREE_SET_LINKED_TREE_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_TREE_SET_LINKED_TREE_IDS - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_UNIQUE_NAME - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_UNIQUE_NAME - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_UNIT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_UNIT - Static variable in interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants
 
ATTR_VERSION - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_VERSION - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_VERSION - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
 
ATTR_VERSION - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
 
ATTR_VISIBILITY - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
 
ATTR_VISIBILITY - Static variable in interface info.bioinfweb.jphyloio.formats.pde.PDEConstants
 
ATTR_WIDTH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_WIDTH - Static variable in interface info.bioinfweb.jphyloio.formats.xtg.XTGConstants
 
ATTR_XSI_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTR_XSI_TYPE - Static variable in interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants
 
ATTRIBUTE_STRING_KEY - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants
 
ATTRIBUTE_STRING_KEY - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants
 
AttributeInfo - Class in info.bioinfweb.jphyloio.formats.xml
This class models an XML attribute.
AttributeInfo - Class in info.bioinfweb.jphyloio.formats.xml
This class models an XML attribute.
AttributeInfo(QName, QName, QName) - Constructor for class info.bioinfweb.jphyloio.formats.xml.AttributeInfo
 
AttributeInfo(QName, QName, QName) - Constructor for class info.bioinfweb.jphyloio.formats.xml.AttributeInfo
 
ATTRIBUTES_NAMESPACE_FOLDER - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants
 
ATTRIBUTES_NAMESPACE_FOLDER - Static variable in interface info.bioinfweb.jphyloio.ReadWriteConstants
 
A B C D E F G H I J K L M N O P Q R S T U V W X 
Skip navigation links