ReadWriteParameterNames

All Known Implementing Classes:

ReadWriteParameterMap
```
public interface ReadWriteParameterNames
```
Provides the names of parameters supported by one or more readers or writers included in JPhyloIO. Such names are used as keys in instances of ReadWriteParameterMap. Different readers and writers support different sets of parameters. Which are supported is defined in the documentation of each reader and writer and can also be programmatically determined using JPhyloIOFormatInfo.getSupportedParameters(boolean).
All parameter names defined here start with the prefix "info.bioinfweb.jphyloio." as defined by KEY_PREFIX. Developers of third party readers or writers may define additional parameters, but must make sure that these are globally unique by using their own reverse domain name as an unique prefix.

Since:

0.1.0

Author:

Ben Stöver

Field Summary

Fields
Modifier and Type	Field and Description
`static java.lang.String`	`KEY_ALLOW_DEFAULT_NAMESPACE` This parameter can be used to specify whether readers of XML formats shall also accept tags of their target format without any namespace definition.
`static java.lang.String`	`KEY_ALLOW_INTERLEAVED_PARSING` Parameter which determines whether interleaved input files (currently only in Phylip) shall be supported by this parser instance.
`static java.lang.String`	`KEY_ALWAYS_WRITE_NEXUS_NODE_LABELS` 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.
`static java.lang.String`	`KEY_APPLICATION_NAME` Identifies the name of the application generating the output.
`static java.lang.String`	`KEY_APPLICATION_URL` Identifies the URL of the application generating the output.
`static java.lang.String`	`KEY_APPLICATION_VERSION` Identifies the version number of the application generating the output.
`static java.lang.String`	`KEY_CREATE_UNKNOWN_COMMAND_EVENTS` This parameter can be used to specify whether special events shall be fired if the reader encounters unknown commands (e.g.
`static java.lang.String`	`KEY_CUSTOM_XML_NAMESPACE_HANDLING` 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.
`static java.lang.String`	`KEY_EXPECT_E_NEWICK` This parameter will only be used by `NexusEventReader` and `NewickEventReader` and allows to specify whether the eNewick extension of Newick strings is supported.
`static java.lang.String`	`KEY_GENERATE_NEXUS_TRANSLATION_TABLE` This parameter can be used to specify whether a `TRANSLATE` command should be included in the `TREES` block of a Nexus document.
`static java.lang.String`	`KEY_IGNORE_COMMENTS` This parameter is reserved for future use and currently not supported by any reader or writer in JPhyloIO.
`static java.lang.String`	`KEY_LABEL_EDITING_REPORTER` Writers may have to edit names of OTUs, sequences or tree/network nodes according to the limitations of a specific format.
`static java.lang.String`	`KEY_LINE_LENGTH` Specifies the preferred line length for writers that support this.
`static java.lang.String`	`KEY_LINE_SEPARATOR` 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.
`static java.lang.String`	`KEY_LOGGER` Identifies an application logger to write log messages to.
`static java.lang.String`	`KEY_MATCH_TOKEN` Parameter used with instances of `JPhyloIOEventReader` that specifies the match token in the sequences to be read.
`static java.lang.String`	`KEY_MAXIMUM_COMMENT_LENGTH` Parameter used with instances of `JPhyloIOEventReader` that specifies the maximal length of the text in a `CommentEvent`.
`static java.lang.String`	`KEY_MAXIMUM_NAME_LENGTH` This parameter can be used to specify a custom maximum lengths for element names.
`static java.lang.String`	`KEY_MAXIMUM_TOKENS_TO_READ` Parameter used with instances of `JPhyloIOEventReader` that specifies the maximal number of tokens to be included in a single `SequenceTokensEvent`.
`static java.lang.String`	`KEY_NEXML_TOKEN_DEFINITION_LABEL` 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`.
`static java.lang.String`	`KEY_NEXML_TOKEN_DEFINITION_LABEL_METADATA` 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`.
`static java.lang.String`	`KEY_NEXML_TOKEN_TRANSLATION_STRATEGY` 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.
`static java.lang.String`	`KEY_NEXUS_BLOCK_HANDLER_MAP` This parameter will only be used by `NexusEventReader` and allows to define a custom block handler map.
`static java.lang.String`	`KEY_NEXUS_COMMAND_READER_FACTORY` This parameter will only be used by `NexusEventReader` and allows to define a custom command reader factory.
`static java.lang.String`	`KEY_OBJECT_TRANSLATOR_FACTORY` 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.
`static java.lang.String`	`KEY_PHYLOXML_CONSIDER_PHYLOGENY_AS_TREE` 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.
`static java.lang.String`	`KEY_PHYLOXML_EVENT_ID_TRANSLATION_MAP` 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.
`static java.lang.String`	`KEY_PHYLOXML_METADATA_TREATMENT` This parameter will only be used by `PhyloXMLEventWriter` and allows to define which metadata events from an adapter should be written.
`static java.lang.String`	`KEY_PREFIX` The prefix of all keys used in JPhyloIO for parameter maps.
`static java.lang.String`	`KEY_RELAXED_PHYLIP` Parameter which determines whether Phylip readers should consider the input as relaxed Phylip (allowing longer taxon names).
`static java.lang.String`	`KEY_REPLACE_MATCH_TOKENS` Parameter used with instances of `JPhyloIOEventReader` that specifies whether possibly encountered match tokens shall be replaced by the according tokens from the first sequence.
`static java.lang.String`	`KEY_SEQUENCE_EXTENSION_TOKEN` 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.
`static java.lang.String`	`KEY_TRANSLATE_INTERNAL_NODE_NAMES` 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.
`static java.lang.String`	`KEY_USE_OTU_LABEL` 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.
`static java.lang.String`	`KEY_WRITER_INSTANCE` This key is used by implementations of `JPhyloIOEventWriter` to provide a reference to the currently active instance.

- Field Detail
  - KEY_PREFIX
```
static final java.lang.String KEY_PREFIX
```
    The prefix of all keys used in JPhyloIO for parameter maps.
    Application or third party library developers who implement additional readers or writers using additional parameter keys should define keys according to the reverse domain name pattern that do not start with this prefix ("info.bioinfweb.jphyloio.").
    
    See Also:
    
    Constant Field Values
  - KEY_WRITER_INSTANCE
```
static final java.lang.String KEY_WRITER_INSTANCE
```
    This key is used by implementations of JPhyloIOEventWriter to provide a reference to the currently active instance. The according entry is useful for implementations of a data adapter, if they wish to obtain information on the writer requesting data from them.
    Note that this key identifies a return value of a writer implementation and not a parameter for the writer. Entries provided by the implementation prior to calling a write method of a writer will be directly overwritten by the actual target format.
    The value must have the type JPhyloIOEventWriter.
    
    See Also:
    
    Constant Field Values
  - KEY_LOGGER
```
static final java.lang.String KEY_LOGGER
```
    Identifies an application logger to write log messages to.
    The value should have the type ApplicationLogger.
    
    See Also:
    
    Constant Field Values
  - KEY_MAXIMUM_TOKENS_TO_READ
```
static final java.lang.String KEY_MAXIMUM_TOKENS_TO_READ
```
    Parameter used with instances of JPhyloIOEventReader that specifies the maximal number of tokens to be included in a single SequenceTokensEvent. Some readers may ignore this parameter. (Refer to the documentations of the single readers for details on which parameters each of them supports.)
    The value should be an integer value (e.g. Integer).
    
    See Also:
    
    Constant Field Values
  - KEY_MAXIMUM_COMMENT_LENGTH
```
static final java.lang.String KEY_MAXIMUM_COMMENT_LENGTH
```
    Parameter used with instances of JPhyloIOEventReader that specifies the maximal length of the text in a CommentEvent. Readers that support this parameter will separate longer comments into separate events. (Refer to the documentations of the single readers for details on which parameters each of them supports.)
    The value should be an integer value (e.g. Integer).
    
    See Also:
    
    Constant Field Values
  - KEY_REPLACE_MATCH_TOKENS
```
static final java.lang.String KEY_REPLACE_MATCH_TOKENS
```
    Parameter used with instances of JPhyloIOEventReader that specifies whether possibly encountered match tokens shall be replaced by the according tokens from the first sequence. Some readers may ignore this parameter and always show a default behavior. (Refer to the documentations of the single readers for details on which parameters each of them supports.)
    The value should have the type Boolean. If true is specified, match tokens will be replaced, if false is specified match tokens will be treated as valid tokens and directly by passed to the sequence token events.
    
    See Also:
    
    KEY_MATCH_TOKEN, Constant Field Values
  - KEY_MATCH_TOKEN
```
static final java.lang.String KEY_MATCH_TOKEN
```
    Parameter used with instances of JPhyloIOEventReader that specifies the match token in the sequences to be read. Note that this parameter is only relevant if no match token is directly defined in the format. (Refer to the documentations of the single readers for details on which parameters each of them supports.)
    The value should have the type String. If it is omitted, readers supporting this parameter will use "." as the default match token.
    
    See Also:
    
    KEY_REPLACE_MATCH_TOKENS, Constant Field Values
  - KEY_RELAXED_PHYLIP
```
static final java.lang.String KEY_RELAXED_PHYLIP
```
    Parameter which determines whether Phylip readers should consider the input as relaxed Phylip (allowing longer taxon names).
    The value must have the type Boolean. If true is specified, relaxed Phylip will be expected. If false is specified or this parameter is omitted, strict Phylip will be expected.
    
    See Also:
    
    Constant Field Values
  - KEY_ALLOW_INTERLEAVED_PARSING
```
static final java.lang.String KEY_ALLOW_INTERLEAVED_PARSING
```
    Parameter which determines whether interleaved input files (currently only in Phylip) shall be supported by this parser instance. (In order to support this feature some readers need to keep a list of all sequence names. To parse files with a very large number of sequences which are not interleaved, this feature can be switched off to save memory. If this switch is set to true non-interleaved files can also still be parsed.)
    Note that not all readers for possibly interleaved formats will make use of this parameter. (Refer to the single reader documentations for details.)
    The value must have the type Boolean. If true is specified or this parameter is omitted, parsing interleaved files will be possible. If false is specified parsing interleaved files will not be possible.
    
    See Also:
    
    Constant Field Values
  - KEY_EXPECT_E_NEWICK
```
static final java.lang.String KEY_EXPECT_E_NEWICK
```
    This parameter will only be used by NexusEventReader and NewickEventReader and allows to specify whether the eNewick extension of Newick strings is supported. As a consequence, all trees will be considered as networks when reading Newick and Nexus files, when this option is activated.
    In Nexus this parameter only influences how Newick strings in TREE commands in TREES blocks are handled. Support for custom NETWORKS blocks containing eNewick strings can be added independently using NexusEventReader.addENewickNetworksBlockSupport().
    It must have the type Boolean. If it is omitted eNewick will not be expected. Network nodes will appear twice and labels will still contain possible network information.
    
    See Also:
    
    NexusEventReader.addENewickNetworksBlockSupport(), Constant Field Values
  - KEY_NEXUS_BLOCK_HANDLER_MAP
```
static final java.lang.String KEY_NEXUS_BLOCK_HANDLER_MAP
```
    This parameter will only be used by NexusEventReader and allows to define a custom block handler map.
    It must have the type NexusBlockHandler. If it is omitted a block handler for all blocks supported in JPhyloIO will be used.
    
    See Also:
    
    Constant Field Values
  - KEY_TRANSLATE_INTERNAL_NODE_NAMES
```
static final java.lang.String KEY_TRANSLATE_INTERNAL_NODE_NAMES
```
    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.
    It must have the type Boolean. If true is specified, all names are translated. If false is specified or this parameter is omitted, only terminal nodes will be translated. That latter can be useful if internal node names are used to represent support values instead of indices in the taxon list.
    
    See Also:
    
    Constant Field Values
  - KEY_NEXUS_COMMAND_READER_FACTORY
```
static final java.lang.String KEY_NEXUS_COMMAND_READER_FACTORY
```
    This parameter will only be used by NexusEventReader and allows to define a custom command reader factory.
    It must have the type NexusCommandReaderFactory. If it is omitted a factory providing all command readers available in JPhyloIO will be used.
    
    See Also:
    
    Constant Field Values
  - KEY_CREATE_UNKNOWN_COMMAND_EVENTS
```
static final java.lang.String KEY_CREATE_UNKNOWN_COMMAND_EVENTS
```
    This parameter can be used to specify whether special events shall be fired if the reader encounters unknown commands (e.g. NEXUS commands).
    The value should have the type Boolean. If false or no value is specified, no such events will be fired. If true is specified, an event for each unknown command will be created.
    
    See Also:
    
    Constant Field Values
  - KEY_NEXML_TOKEN_TRANSLATION_STRATEGY
```
static final java.lang.String KEY_NEXML_TOKEN_TRANSLATION_STRATEGY
```
    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.
    It must have the type TokenTranslationStrategy. If it is omitted TokenTranslationStrategy.SYMBOL_TO_LABEL will be used as the default.
    
    See Also:
    
    Constant Field Values
  - KEY_NEXML_TOKEN_DEFINITION_LABEL
```
static final java.lang.String KEY_NEXML_TOKEN_DEFINITION_LABEL
```
    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.
    The value should have the type Boolean. If false or no value is specified, the events' label will always be written to the label attribute. If true is specified, the token name defined in the event will be used.
    
    See Also:
    
    Constant Field Values
  - KEY_NEXML_TOKEN_DEFINITION_LABEL_METADATA
```
static final java.lang.String KEY_NEXML_TOKEN_DEFINITION_LABEL_METADATA
```
    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.
    It must have the type TokenDefinitionLabelHandling. If it is omitted TokenDefinitionLabelHandling.NEITHER will be used as the default.
    
    See Also:
    
    Constant Field Values
  - KEY_USE_OTU_LABEL
```
static final java.lang.String KEY_USE_OTU_LABEL
```
    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.
    (This parameter is not recognized by NexusEventReader, since the NEXUS format does not differentiate between labels and IDs and requires OTUs and linked sequences or tree nodes to have identical labels.)
    The value should have the type Boolean. If false or no value is specified, the events' label will remain null if no label was present in the element. If true is specified, the OTU label will be used, if present.
    
    See Also:
    
    Constant Field Values
  - KEY_APPLICATION_NAME
```
static final java.lang.String KEY_APPLICATION_NAME
```
    Identifies the name of the application generating the output. This information, as well as the application URL and version, shall be added at the beginning of formats that support this.
    The value should be a String.
    
    See Also:
    
    Constant Field Values
  - KEY_APPLICATION_VERSION
```
static final java.lang.String KEY_APPLICATION_VERSION
```
    Identifies the version number of the application generating the output. This information, as well as the application name and URL, shall be added at the beginning of formats that support this.
    The value should be an Object.
    
    See Also:
    
    Constant Field Values
  - KEY_APPLICATION_URL
```
static final java.lang.String KEY_APPLICATION_URL
```
    Identifies the URL of the application generating the output. This information, as well as the application name and version, shall be added at the beginning of formats that support this.
    The value should be a String.
    
    See Also:
    
    Constant Field Values
  - KEY_LINE_SEPARATOR
```
static final java.lang.String KEY_LINE_SEPARATOR
```
    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. (Note that writers for XML formats will not necessarily make use of this parameter.)
    The value should be a String.
    
    See Also:
    
    Constant Field Values
  - KEY_LINE_LENGTH
```
static final java.lang.String KEY_LINE_LENGTH
```
    Specifies the preferred line length for writers that support this.
    The value should have an integer type (e.g. Integer).
    
    See Also:
    
    Constant Field Values
  - KEY_SEQUENCE_EXTENSION_TOKEN
```
static final java.lang.String KEY_SEQUENCE_EXTENSION_TOKEN
```
    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.
    The value should have the type String and define the token to be used to fill up sequences. If this parameter is omitted or null is specified, sequences will not be filled up. Note that the specified string should only be longer than one character, if it is only used with MatrixDataAdapters that provide long tokens. (MatrixDataAdapter.containsLongTokens(ReadWriteParameterMap) must return true.)
    Note that this parameter is valid for all alignments. It is not possible to extend only a subset alignments of the same file using this parameter.
    
    See Also:
    
    Constant Field Values
  - KEY_IGNORE_COMMENTS
```
static final java.lang.String KEY_IGNORE_COMMENTS
```
    This parameter is reserved for future use and currently not supported by any reader or writer in JPhyloIO. It will specify whether comment events should generated by readers or comments should be ignored. If a file contains very large comments, ignoring them may lead to a performance increase.
    The value should have the type Boolean. If true is specified, comment events will be ignored by writers supporting this parameter. If false is specified or this parameter is omitted, comments will be written to the output at all supported positions.
    
    See Also:
    
    Constant Field Values
  - KEY_ALLOW_DEFAULT_NAMESPACE
```
static final java.lang.String KEY_ALLOW_DEFAULT_NAMESPACE
```
    This parameter can be used to specify whether readers of XML formats shall also accept tags of their target format without any namespace definition.
    The value should have the type Boolean. If true or no value is specified, tags without the target format namespace declaration will be supported, if their local part fits. If false is specified, the correct namespace is required.
    
    See Also:
    
    Constant Field Values
  - KEY_MAXIMUM_NAME_LENGTH
```
static final java.lang.String KEY_MAXIMUM_NAME_LENGTH
```
    This parameter can be used to specify a custom maximum lengths for element names. An example would be the length of sequence names in Phylip, which may be customized using this parameter.
    The value should have an integer type (e.g. Integer). Note that some formats may define a fixed maximum length and specifying this parameter may lead to a deviation from the standards of this format. Refer to the documentation of the according writer for details in that.
    
    See Also:
    
    Constant Field Values
  - KEY_GENERATE_NEXUS_TRANSLATION_TABLE
```
static final java.lang.String KEY_GENERATE_NEXUS_TRANSLATION_TABLE
```
    This parameter can be used to specify whether a TRANSLATE command should be included in the TREES block of a Nexus document.
    The value should have the type Boolean. If true is specified, a TRANSLATE command will be written and references to will be used as node labels in the following tree(s). If false or no value is specified, the full node labels will included in the tree(s).
    
    See Also:
    
    Constant Field Values
  - KEY_ALWAYS_WRITE_NEXUS_NODE_LABELS
```
static final java.lang.String KEY_ALWAYS_WRITE_NEXUS_NODE_LABELS
```
    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.
    The value should have the type Boolean. If false or no value is specified, labels will be replaced by indices, whenever possible. If true is specified, the full labels will always be used.
    
    See Also:
    
    Constant Field Values
  - KEY_LABEL_EDITING_REPORTER
```
static final java.lang.String KEY_LABEL_EDITING_REPORTER
```
    Writers may have to edit names of OTUs, sequences or tree/network nodes according to the limitations of a specific format. In such cases, the generated names used in the output will be registered in an information object, which will be stored in the parameter map under this key.
    The value will have the type LabelEditingReporter. If no instance is specified, writers supporting this key will create a new one and put it in their parameter map. If a reporter is specified, its previous contents will be cleared by the writer. If an object of another type is specified using this key, it will be replaced.
    
    See Also:
    
    #getLabelEditingReporter(), Constant Field Values
  - KEY_OBJECT_TRANSLATOR_FACTORY
```
static final java.lang.String KEY_OBJECT_TRANSLATOR_FACTORY
```
    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. Specifying a custom factory allows to provide translators for custom data types or to overwrite default translators for common types.
    
    See Also:
    
    ReadWriteParameterMap.getObjectTranslatorFactory(), Constant Field Values
  - KEY_PHYLOXML_CONSIDER_PHYLOGENY_AS_TREE
```
static final java.lang.String KEY_PHYLOXML_CONSIDER_PHYLOGENY_AS_TREE
```
    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. In the first case, "clade relation" tags contained in a phylogeny will only be represented as meta information, not as additional edge events.
    The value should have the type Boolean. If false or no value is specified, a phylogeny will always be considered as a network. If true is specified, it will always be considered as a tree.
    
    See Also:
    
    Constant Field Values
  - KEY_PHYLOXML_METADATA_TREATMENT
```
static final java.lang.String KEY_PHYLOXML_METADATA_TREATMENT
```
    This parameter will only be used by PhyloXMLEventWriter and allows to define which metadata events from an adapter should be written.
    The value must have the type PhyloXMLMetadataTreatment. If no value is specified, all metadata events will be written sequentially. A possible hierarchical structure will be lost.
    
    See Also:
    
    Constant Field Values
  - KEY_PHYLOXML_EVENT_ID_TRANSLATION_MAP
```
static final java.lang.String KEY_PHYLOXML_EVENT_ID_TRANSLATION_MAP
```
    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.
    The value will have the type Map.
    
    See Also:
    
    Constant Field Values
  - KEY_CUSTOM_XML_NAMESPACE_HANDLING
```
static final java.lang.String KEY_CUSTOM_XML_NAMESPACE_HANDLING
```
    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. Managing may include changing the prefix a namespace is bound to.
    The value should have the type Boolean. If false or no value is specified, the JPhyloIO writer will not manage namespaces within custom XML elements. If true is specified, it will manage them.
    
    See Also:
    
    Constant Field Values

Interface ReadWriteParameterNames

Field Summary

Field Detail

KEY_PREFIX

KEY_WRITER_INSTANCE

KEY_LOGGER

KEY_MAXIMUM_TOKENS_TO_READ

KEY_MAXIMUM_COMMENT_LENGTH

KEY_REPLACE_MATCH_TOKENS

KEY_MATCH_TOKEN

KEY_RELAXED_PHYLIP

KEY_ALLOW_INTERLEAVED_PARSING

KEY_EXPECT_E_NEWICK

KEY_NEXUS_BLOCK_HANDLER_MAP

KEY_TRANSLATE_INTERNAL_NODE_NAMES

KEY_NEXUS_COMMAND_READER_FACTORY

KEY_CREATE_UNKNOWN_COMMAND_EVENTS

KEY_NEXML_TOKEN_TRANSLATION_STRATEGY

KEY_NEXML_TOKEN_DEFINITION_LABEL

KEY_NEXML_TOKEN_DEFINITION_LABEL_METADATA

KEY_USE_OTU_LABEL

KEY_APPLICATION_NAME

KEY_APPLICATION_VERSION

KEY_APPLICATION_URL

KEY_LINE_SEPARATOR

KEY_LINE_LENGTH

KEY_SEQUENCE_EXTENSION_TOKEN

KEY_IGNORE_COMMENTS

KEY_ALLOW_DEFAULT_NAMESPACE

KEY_MAXIMUM_NAME_LENGTH

KEY_GENERATE_NEXUS_TRANSLATION_TABLE

KEY_ALWAYS_WRITE_NEXUS_NODE_LABELS

KEY_LABEL_EDITING_REPORTER

KEY_OBJECT_TRANSLATOR_FACTORY

KEY_PHYLOXML_CONSIDER_PHYLOGENY_AS_TREE

KEY_PHYLOXML_METADATA_TREATMENT

KEY_PHYLOXML_EVENT_ID_TRANSLATION_MAP

KEY_CUSTOM_XML_NAMESPACE_HANDLING