- 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
-
- 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
-
- 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
-
- 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
JPhyloIOEventReaders 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
-
