info.bioinfweb.jphyloio.formats.nexus

Class NexusFactory

java.lang.Object

info.bioinfweb.jphyloio.factory.AbstractSingleReaderWriterFactory

info.bioinfweb.jphyloio.factory.AbstractStartStringSingleFactory

info.bioinfweb.jphyloio.formats.nexus.NexusFactory

All Implemented Interfaces:

SingleReaderWriterFactory, JPhyloIOFormatIDs, NexusConstants

public class NexusFactory
extends AbstractStartStringSingleFactory
implements NexusConstants, JPhyloIOFormatIDs

Reader and writer factory for the Nexus format.

Since:

0.0.0

Author:

Ben Stöver

Field Summary

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

Fields inherited from interface info.bioinfweb.jphyloio.formats.JPhyloIOFormatIDs

FASTA_FORMAT_ID, FORMAT_ID_PREFIX, MEGA_FORMAT_ID, NEWICK_FORMAT_ID, NEXML_FORMAT_ID, NEXUS_FORMAT_ID, PDE_FORMAT_ID, PHYLIP_FORMAT_ID, PHYLOXML_FORMAT_ID, SEQUENTIAL_PHYLIP_FORMAT_ID, XTG_FORMAT_ID

Constructor Summary

Constructors

Constructor and Description
NexusFactory()

Method Summary

Modifier and Type	Method and Description
protected JPhyloIOFormatInfo	createFormatInfo()
JPhyloIOEventReader	getReader(java.io.InputStream stream, ReadWriteParameterMap parameters) Creates a new reader instance for the target format of this factory.
JPhyloIOEventReader	getReader(java.io.Reader reader, ReadWriteParameterMap parameters) Creates a new reader instance for the target format of this factory.
JPhyloIOEventWriter	getWriter() Creates a new writer instance for the target format of this factory.
boolean	hasReader() Determines whether this factory is able to create reader instances for its target format.
boolean	hasWriter() Determines whether this factory is able to create writer instances for its target format.

Methods inherited from class info.bioinfweb.jphyloio.factory.AbstractStartStringSingleFactory

checkFormat, getExpectedStart

Methods inherited from class info.bioinfweb.jphyloio.factory.AbstractSingleReaderWriterFactory

checkFormat, getFormatInfo

Methods inherited from class java.lang.Object

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

Methods inherited from interface info.bioinfweb.jphyloio.factory.SingleReaderWriterFactory

checkFormat, getFormatInfo

Constructor Detail

NexusFactory

public NexusFactory()

Method Detail

getReader

public JPhyloIOEventReader getReader(java.io.InputStream stream,
                                     ReadWriteParameterMap parameters)
                              throws java.io.IOException

Description copied from interface: SingleReaderWriterFactory

Creates a new reader instance for the target format of this factory.

Specified by:

getReader in interface SingleReaderWriterFactory

Parameters:

stream - the stream to provide the content for the reader

parameters - the parameter map for the new reader instance

Returns:

the new reader instance

Throws:

java.io.IOException

getReader

public JPhyloIOEventReader getReader(java.io.Reader reader,
                                     ReadWriteParameterMap parameters)
                              throws java.io.IOException

Description copied from interface: SingleReaderWriterFactory

Creates a new reader instance for the target format of this factory.

Specified by:

getReader in interface SingleReaderWriterFactory

parameters - the parameter map for the new reader instance

Returns:

the new reader instance or null if this factory is not able to create readers

Throws:

java.io.IOException

See Also:

SingleReaderWriterFactory.hasReader()

getWriter

public JPhyloIOEventWriter getWriter()

Description copied from interface: SingleReaderWriterFactory

Creates a new writer instance for the target format of this factory.

Specified by:

getWriter in interface SingleReaderWriterFactory

Returns:

the new writer instance or null if this factory is not able to create writers

See Also:

SingleReaderWriterFactory.hasWriter()

hasReader

public boolean hasReader()

Description copied from interface: SingleReaderWriterFactory

Determines whether this factory is able to create reader instances for its target format.

Specified by:

hasReader in interface SingleReaderWriterFactory

Returns:

true if creating readers is supported or false otherwise

hasWriter

public boolean hasWriter()

Description copied from interface: SingleReaderWriterFactory

Determines whether this factory is able to create writer instances for its target format.

Specified by:

hasWriter in interface SingleReaderWriterFactory

Returns:

true if creating writers is supported or false otherwise

createFormatInfo

protected JPhyloIOFormatInfo createFormatInfo()

Specified by:

createFormatInfo in class AbstractSingleReaderWriterFactory