info.bioinfweb.jphyloio.formats.nexus

Class NexusEventWriter

java.lang.Object

info.bioinfweb.jphyloio.AbstractEventWriter<P>

info.bioinfweb.jphyloio.formats.text.AbstractTextEventWriter<NexusWriterStreamDataProvider>

info.bioinfweb.jphyloio.formats.nexus.NexusEventWriter

All Implemented Interfaces:

NexusConstants, JPhyloIOEventWriter, JPhyloIOFormatSpecificObject

public class NexusEventWriter
extends AbstractTextEventWriter<NexusWriterStreamDataProvider>
implements NexusConstants

Event based writer for the Nexus format.

This writer is able to write OTU, sequence and tree data to Nexus formatted streams. It will ignore any data for phylogenetic networks that are provided by DocumentDataAdapter#getTreeNetworkIterator(ReadWriteParameterMap), because the Nexus format only supports trees.

Comments and metadata

Comments nested in any of the supported elements will usually be written. Metadata is only supported nested in tree node or edge definitions and is written into hot comments as they are supported by NewickStringWriter. Metadata nested into other elements will be ignored.

Labels and IDs

Note that the Nexus format does not differentiate between labels and IDs and because of this, labels of OTUs and labels of sequences or nodes linked to them must have identical names in Nexus. Therefore this writer will always use the OTU label of the linked OTU, also for writing sequences and nodes. Labels of sequences and nodes will be ignored (which does not make a difference, of they are identical with the labels of their linked OTUs).

Sequence labels will be used though, if no OTU is linked. In such cases the NEWTAXA subcommand will be specified in the DIMENSIONS command.

If an OTU event without a defined label is provided by the data adapter, this writer will use the OTU ID as the taxon name in Nexus instead. If two OTUs with identical labels are provided, the Nexus name of the second will be a combination of the ID and the label, while the first will be represented as the unchanged label as usual. If additional conflicts occur (e.g. if an ID of an OTU without a label is equal to the label of a previous OTU) an index will be added to the end of the label, until it is unique labels. The elements (ID, label, index) of edited Nexus names will be separated by AbstractEventWriter.EDITED_LABEL_SEPARATOR.

The Nexus names that have actually been used in the output can be obtained from the LabelEditingReporter added to the parameter map using ReadWriteParameterMap.getLabelEditingReporter(). (A reference to the parameter map passed to one of the #writeDocument() methods must be kept by the application code, in order to access the label editing reporter after the document has been written.)

Token sets

Note that this writer (and the Nexus format) does not support multiple token sets for a single matrix. If multiple sets are provided, only the first one will be considered to determine the symbols to be declared in the FORMAT command. According warnings will be logged, if multiple token sets are found.

NexusEventReader supports an extension of the Nexus format introduced by MrBayes but this writer currently does not make use of that, since the output would not be conform with the Nexus standard and some applications may not be able to read it.

Recognized parameters

• ReadWriteParameterNames.KEY_WRITER_INSTANCE
• ReadWriteParameterNames.KEY_LOGGER
• ReadWriteParameterNames.KEY_APPLICATION_NAME
• ReadWriteParameterNames.KEY_APPLICATION_VERSION
• ReadWriteParameterNames.KEY_APPLICATION_URL
• ReadWriteParameterNames.KEY_LINE_SEPARATOR
• ReadWriteParameterNames.KEY_SEQUENCE_EXTENSION_TOKEN
• ReadWriteParameterNames.KEY_MAXIMUM_NAME_LENGTH (If this parameter is omitted, any name length is possible.)
• ReadWriteParameterNames.KEY_ALWAYS_WRITE_NEXUS_NODE_LABELS
• ReadWriteParameterNames.KEY_GENERATE_NEXUS_TRANSLATION_TABLE
• ReadWriteParameterNames.KEY_LABEL_EDITING_REPORTER
• ReadWriteParameterNames.KEY_OBJECT_TRANSLATOR_FACTORY

Since:

0.0.0

Author:

Ben Stöver

See Also:

Metadata demo application

Nested Class Summary

Nested classes/interfaces inherited from class info.bioinfweb.jphyloio.AbstractEventWriter

AbstractEventWriter.NoEditUniqueLabelHandler, AbstractEventWriter.UniqueLabelHandler

Field Summary

Fields inherited from class info.bioinfweb.jphyloio.AbstractEventWriter

EDITED_LABEL_SEPARATOR

Fields inherited from interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants

ALTERNATIVE_END_COMMAND, BEGIN_COMMAND, BLOCK_NAME_CHARACTERS, BLOCK_NAME_DATA, BLOCK_NAME_NETWORKS, BLOCK_NAME_SETS, BLOCK_NAME_TAXA, BLOCK_NAME_TREES, BLOCK_NAME_UNALIGNED, CHARACTER_NAME_STATES_SEPARATOR, COMMAND_END, COMMAND_NAME_CHAR_LABELS, COMMAND_NAME_CHAR_SET, COMMAND_NAME_CHAR_STATE_LABELS, COMMAND_NAME_DIMENSIONS, COMMAND_NAME_FORMAT, COMMAND_NAME_LINK, COMMAND_NAME_MATRIX, COMMAND_NAME_NETWORK, COMMAND_NAME_TAX_LABELS, COMMAND_NAME_TAXON_SET, COMMAND_NAME_TITLE, COMMAND_NAME_TRANSLATE, COMMAND_NAME_TREE, COMMAND_NAME_TREE_SET, COMMENT_END, COMMENT_START, DIMENSIONS_SUBCOMMAND_NCHAR, DIMENSIONS_SUBCOMMAND_NEW_TAXA, DIMENSIONS_SUBCOMMAND_NTAX, ELEMENT_SEPARATOR, END_COMMAND, FIRST_LINE, FORMAT_NAME_STANDARD, FORMAT_NAME_VECTOR, FORMAT_SUBCOMMAND_DATA_TYPE, FORMAT_SUBCOMMAND_GAP_CHAR, FORMAT_SUBCOMMAND_INTERLEAVE, FORMAT_SUBCOMMAND_MATCH_CHAR, FORMAT_SUBCOMMAND_MISSING_CHAR, FORMAT_SUBCOMMAND_NO_LABELS, FORMAT_SUBCOMMAND_NO_TOKENS, FORMAT_SUBCOMMAND_SYMBOLS, FORMAT_SUBCOMMAND_TOKENS, FORMAT_SUBCOMMAND_TRANSPOSE, FORMAT_VALUE_CONTINUOUS_DATA_TYPE, FORMAT_VALUE_DNA_DATA_TYPE, FORMAT_VALUE_MIXED_DATA_TYPE, FORMAT_VALUE_NUCLEOTIDE_DATA_TYPE, FORMAT_VALUE_PROTEIN_DATA_TYPE, FORMAT_VALUE_RNA_DATA_TYPE, FORMAT_VALUE_STANDARD_DATA_TYPE, KEY_VALUE_SEPARATOR, MATRIX_POLYMORPHIC_TOKEN_END, MATRIX_POLYMORPHIC_TOKEN_START, MATRIX_UNCERTAINS_TOKEN_END, MATRIX_UNCERTAINS_TOKEN_START, NEXUS_FORMAT_NAME, NEXUS_NAMESPACE_PREFIX, NEXUS_PREDICATE_NAMESPACE, SET_END_INDEX_SYMBOL, SET_KEY_WORD_ALL, SET_KEY_WORD_REMAINING, SET_REGULAR_INTERVAL_SYMBOL, SET_TO_SYMBOL, SET_VECTOR_CONTAINED, SET_VECTOR_NOT_CONTAINED, UNTIL_WHITESPACE_COMMENT_COMMAND_EQUAL_PATTERN, UNTIL_WHITESPACE_COMMENT_COMMAND_PATTERN, VALUE_DELIMITER, WORD_DELIMITER

Constructor Summary

Constructors

Constructor and Description
NexusEventWriter()

Method Summary

Modifier and Type	Method and Description
protected NexusWriterStreamDataProvider	createStreamDataProvider() This method is called in the constructor of AbstractEventWriter to initialize the stream data provider that will be returned by AbstractEventWriter.getStreamDataProvider().
protected void	doWriteDocument(DocumentDataAdapter document, java.io.Writer writer, ReadWriteParameterMap parameters)
static java.lang.String	formatToken(java.lang.String token)
java.lang.String	getFormatID() Returns a string ID uniquely identifying the target format of this instance.
protected ApplicationLogger	getLogger()
protected java.util.Map<java.lang.String,NexusMatrixWriteResult>	getMatrixIDToBlockTypeMap()
protected ReadWriteParameterMap	getParameters()
protected void	writeBlockEnd()
protected void	writeBlockStart(java.lang.String name)
protected void	writeCommandEnd()
static void	writeKeyValueExpression(java.io.Writer writer, java.lang.String key, java.lang.String value)
protected void	writeLineStart(java.io.Writer writer, java.lang.String text)
protected void	writeLinkCommand(java.lang.String linkedID, java.lang.String linkedBlockName, EventContentType linkedContentType)

Methods inherited from class info.bioinfweb.jphyloio.formats.text.AbstractTextEventWriter

getWriter

Methods inherited from class info.bioinfweb.jphyloio.AbstractEventWriter

createUniqueLabel, createUniqueLabel, createUniqueLabel, createUniqueLinkedOTULabel, decreaseIndention, determineMaxSequenceLength, extendSequence, getFileStartInfo, getIndention, getLabeledIDName, getLinkedOTUNameOTUFirst, getLinkedOTUNameOwnFirst, getReferencedOTUList, getStreamDataProvider, increaseIndention, logIngnoredOTULists, writeDocument, writeDocument, writeDocument, writeLineBreak

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

NexusEventWriter

public NexusEventWriter()

Method Detail

getFormatID

public java.lang.String getFormatID()

Description copied from interface: JPhyloIOFormatSpecificObject

Returns a string ID uniquely identifying the target format of this instance. Additional information on the format can be retrieved by passing the returned ID to JPhyloIOReaderWriterFactory.getFormatInfo(String).

Third party developers that create readers or writers for additional formats must make sure to use a globally unique format ID. It is strongly recommended to use owned reverse domain names for this (e.g. org.example.additionalformat).

Specified by:

getFormatID in interface JPhyloIOFormatSpecificObject

Returns:

the ID of the target format of this instance

See Also:

JPhyloIOReaderWriterFactory.getFormatInfo(String)

createStreamDataProvider

protected NexusWriterStreamDataProvider createStreamDataProvider()

Description copied from class: AbstractEventWriter

This method is called in the constructor of AbstractEventWriter to initialize the stream data provider that will be returned by AbstractEventWriter.getStreamDataProvider(). Inheriting classes that use their own stream data provider implementation should overwrite this method.

This default implementation creates a new instance of WriterStreamDataProvider.

Overrides:

createStreamDataProvider in class AbstractEventWriter<NexusWriterStreamDataProvider>

Returns:

the stream data provider to be used with this instance

getParameters

protected ReadWriteParameterMap getParameters()

getLogger

protected ApplicationLogger getLogger()

getMatrixIDToBlockTypeMap

protected java.util.Map<java.lang.String,NexusMatrixWriteResult> getMatrixIDToBlockTypeMap()

writeLineStart

protected void writeLineStart(java.io.Writer writer,
                              java.lang.String text)
                       throws java.io.IOException

Overrides:

writeLineStart in class AbstractEventWriter<NexusWriterStreamDataProvider>

Throws:

java.io.IOException

formatToken

public static java.lang.String formatToken(java.lang.String token)

writeCommandEnd

protected void writeCommandEnd()
                        throws java.io.IOException

Throws:

java.io.IOException

writeBlockStart

protected void writeBlockStart(java.lang.String name)
                        throws java.io.IOException

Throws:

java.io.IOException

writeBlockEnd

protected void writeBlockEnd()
                      throws java.io.IOException

Throws:

java.io.IOException

writeKeyValueExpression

public static void writeKeyValueExpression(java.io.Writer writer,
                                           java.lang.String key,
                                           java.lang.String value)
                                    throws java.io.IOException

Throws:

java.io.IOException

writeLinkCommand

protected void writeLinkCommand(java.lang.String linkedID,
                                java.lang.String linkedBlockName,
                                EventContentType linkedContentType)
                         throws java.io.IOException

Throws:

java.io.IOException

doWriteDocument

protected void doWriteDocument(DocumentDataAdapter document,
                               java.io.Writer writer,
                               ReadWriteParameterMap parameters)
                        throws java.io.IOException

Overrides:

doWriteDocument in class AbstractTextEventWriter<NexusWriterStreamDataProvider>

Throws:

java.io.IOException