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

## K

KEY_ALLOW_DEFAULT_NAMESPACE - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  This parameter can be used to specify whether readers of XML formats shall also accept tags of their target format without any namespace definition.
KEY_ALLOW_INTERLEAVED_PARSING - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  Parameter which determines whether interleaved input files (currently only in Phylip) shall be supported by this parser instance.
KEY_ALWAYS_WRITE_NEXUS_NODE_LABELS - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  This parameter can be used to specify whether a nodes in a Nexus TREE command should always be written as full labels of if their index in the associated TAXA block should be used, when possible.
KEY_APPLICATION_NAME - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  Identifies the name of the application generating the output.
KEY_APPLICATION_URL - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  Identifies the URL of the application generating the output.
KEY_APPLICATION_VERSION - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  Identifies the version number of the application generating the output.
KEY_CREATE_UNKNOWN_COMMAND_EVENTS - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  This parameter can be used to specify whether special events shall be fired if the reader encounters unknown commands (e.g.
KEY_CUSTOM_XML_NAMESPACE_HANDLING - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  This parameter will be used by XML writers to determine whether namespaces used or declared in customXML shall be managed together with other namespaces of the document by the used JPhyloIO writer.
KEY_EXPECT_E_NEWICK - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  This parameter will only be used by `NexusEventReader` and `NewickEventReader` and allows to specify whether the eNewick extension of Newick strings is supported.
KEY_GENERATE_NEXUS_TRANSLATION_TABLE - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  This parameter can be used to specify whether a `TRANSLATE` command should be included in the `TREES` block of a Nexus document.
KEY_IGNORE_COMMENTS - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  This parameter is reserved for future use and currently not supported by any reader or writer in JPhyloIO.
KEY_LABEL_EDITING_REPORTER - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  Writers may have to edit names of OTUs, sequences or tree/network nodes according to the limitations of a specific format.
KEY_LINE_LENGTH - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  Specifies the preferred line length for writers that support this.
KEY_LINE_SEPARATOR - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  If a line separator different from that of the current operating system shall be used by a writer, it can be specified using this key.
KEY_LOGGER - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  Identifies an application logger to write log messages to.
KEY_MATCH_TOKEN - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  Parameter used with instances of `JPhyloIOEventReader` that specifies the match token in the sequences to be read.
KEY_MAXIMUM_COMMENT_LENGTH - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  Parameter used with instances of `JPhyloIOEventReader` that specifies the maximal length of the text in a `CommentEvent`.
KEY_MAXIMUM_NAME_LENGTH - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  This parameter can be used to specify a custom maximum lengths for element names.
KEY_MAXIMUM_TOKENS_TO_READ - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  Parameter used with instances of `JPhyloIOEventReader` that specifies the maximal number of tokens to be included in a single `SequenceTokensEvent`.
KEY_NEXML_TOKEN_DEFINITION_LABEL - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  This parameter will only be used by `NeXMLEventWriter` and allows to define whether the token name or the label of a `SingleTokenDefinitionEvent` shall be written to the label-attribute of a state element in a NeXML characters block of type `standard` or `protein`.
KEY_NEXML_TOKEN_DEFINITION_LABEL_METADATA - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  This parameter will only be used by `NeXMLEventWriter` and allows to define whether the token name and the label of a `SingleTokenDefinitionEvent` shall be represented as metadata always, never or only if one of these properties could not be written to the label-attribute of a state element in a NeXML characters block of type `standard` or `protein`.
KEY_NEXML_TOKEN_TRANSLATION_STRATEGY - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  This parameter will only be used by `NeXMLEventReader` and allows to define the way tokens stored in a NeXML characters block of type `standard` should be parsed.
KEY_NEXUS_BLOCK_HANDLER_MAP - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  This parameter will only be used by `NexusEventReader` and allows to define a custom block handler map.
KEY_NEXUS_COMMAND_READER_FACTORY - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  This parameter will only be used by `NexusEventReader` and allows to define a custom command reader factory.
KEY_OBJECT_TRANSLATOR_FACTORY - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  This parameter can be used to specify a custom instance of `ObjectTranslatorFactory` that is used by readers to create literal meta object values and writers to obtain string and XML representations of objects.
KEY_PHYLOXML_CONSIDER_PHYLOGENY_AS_TREE - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  This parameter will only be used by `PhyloXMLEventReader` and allows to define if trees read from a PhyloXML file should always be considered as trees or networks.
KEY_PHYLOXML_EVENT_ID_TRANSLATION_MAP - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  This parameter will only be used by `PhyloXMLEventReader` and allows to obtain an object that maps the IDs used in a PhyloXML document to refer to specific elements to according JPhyloIO event IDs.
KEY_PHYLOXML_METADATA_TREATMENT - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  This parameter will only be used by `PhyloXMLEventWriter` and allows to define which metadata events from an adapter should be written.
KEY_PREFIX - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  The prefix of all keys used in JPhyloIO for parameter maps.
KEY_RELAXED_PHYLIP - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  Parameter which determines whether Phylip readers should consider the input as relaxed Phylip (allowing longer taxon names).
KEY_REPLACE_MATCH_TOKENS - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  Parameter used with instances of `JPhyloIOEventReader` that specifies whether possibly encountered match tokens shall be replaced by the according tokens from the first sequence.
KEY_SEQUENCE_EXTENSION_TOKEN - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  This parameter can be used to specify that sequences with unequal lengths (in character matrix data) shall be filled up with, until all have an equal length.
KEY_TRANSLATE_INTERNAL_NODE_NAMES - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  This parameter will only be used by `NexusEventReader` and allows to define whether internal node names should be translated using the taxon list from a `TAXA` block or a translation table.
KEY_USE_OTU_LABEL - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  This parameter will be used by some `JPhyloIOEventReader`s to determine whether the label of an associated OTU should be used as a label, if none was present in an element.
KEY_VALUE_SEPARATOR - Static variable in interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants
KEY_WRITER_INSTANCE - Static variable in interface info.bioinfweb.jphyloio.ReadWriteParameterNames
  This key is used by implementations of `JPhyloIOEventWriter` to provide a reference to the currently active instance.
keyByPredicate(QName) - Method in class info.bioinfweb.jphyloio.formats.newick.NHXUtils
  Returns the NHX key associated with the specified PhyloXML predicate.
KeyValueInformation - Class in info.bioinfweb.jphyloio.formats.text
  Used internally by `AbstractTextEventReader` and inherited classes to store contents of commands containing key value information.
KeyValueInformation(String, String, char) - Constructor for class info.bioinfweb.jphyloio.formats.text.KeyValueInformation

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