info.bioinfweb.commons.bio.biojava3.alignment.io.nexus

Class NexusWriter<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

java.lang.Object

info.bioinfweb.commons.bio.biojava3.alignment.io.AbstractAlignmentWriter<S,C>

info.bioinfweb.commons.bio.biojava3.alignment.io.nexus.NexusWriter<S,C>

All Implemented Interfaces:

AlignmentWriter<S,C>

public class NexusWriter<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>
extends AbstractAlignmentWriter<S,C>

Writes an Alignment to a stream in Nexus format. The result contains a TAXA, a CHARACTERS and a SETS block (if the specified alignment contains any character set).

Author:

Ben Stöver

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	COMMAND_TERMINATOR
static java.lang.String	COMMENT_END
static java.lang.String	COMMENT_START
static java.lang.String	DATATYPE_CONTINUOUS
static java.lang.String	DATATYPE_DNA
static java.lang.String	DATATYPE_NUCLEOTIDE
static java.lang.String	DATATYPE_PROTEIN
static java.lang.String	DATATYPE_RNA
static java.lang.String	DATATYPE_STANDARD

Fields inherited from class info.bioinfweb.commons.bio.biojava3.alignment.io.AbstractAlignmentWriter

WHITESPACE_REPLACEMENT

Constructor Summary

Constructors

Constructor and Description
NexusWriter(java.lang.String matrixDataType) Creates a new instance of this class with "-" as gap data and "? as missing data character.
NexusWriter(java.lang.String matrixDataType, char gapCharacter, char missingCharacter) Creates a new instance of this class.
NexusWriter(java.lang.String matrixDataType, char gapCharacter, char missingCharacter, UniqueNameMap nameMap) Creates a new instance of this class.
NexusWriter(java.lang.String matrixDataType, UniqueNameMap nameMap) Creates a new instance of this class with "-" as gap data and "? as missing data character.

Method Summary

Modifier and Type	Method and Description
void	write(Alignment<S,C> alignment, java.io.OutputStream stream)

Methods inherited from class info.bioinfweb.commons.bio.biojava3.alignment.io.AbstractAlignmentWriter

getNameMap, write

Methods inherited from class java.lang.Object

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

Field Detail

COMMAND_TERMINATOR

public static final java.lang.String COMMAND_TERMINATOR

See Also:

Constant Field Values

COMMENT_START

public static final java.lang.String COMMENT_START

See Also:

Constant Field Values

COMMENT_END

public static final java.lang.String COMMENT_END

See Also:

Constant Field Values

DATATYPE_STANDARD

public static final java.lang.String DATATYPE_STANDARD

See Also:

Constant Field Values

DATATYPE_DNA

public static final java.lang.String DATATYPE_DNA

See Also:

Constant Field Values

DATATYPE_RNA

public static final java.lang.String DATATYPE_RNA

See Also:

Constant Field Values

DATATYPE_NUCLEOTIDE

public static final java.lang.String DATATYPE_NUCLEOTIDE

See Also:

Constant Field Values

DATATYPE_PROTEIN

public static final java.lang.String DATATYPE_PROTEIN

See Also:

Constant Field Values

DATATYPE_CONTINUOUS

public static final java.lang.String DATATYPE_CONTINUOUS

See Also:

Constant Field Values

Constructor Detail

NexusWriter

public NexusWriter(java.lang.String matrixDataType,
                   char gapCharacter,
                   char missingCharacter,
                   UniqueNameMap nameMap)

Creates a new instance of this class.

Parameters:

matrixDataType - the data type specified in the Nexus FORMAT command (Nexus allows STANDARD, DNA, , NUCLEOTIDE, PROTEIN or CONTINUOUS.)

gapCharacter - the character coding a gap in the alignment

missingCharacter - the character coding missing data in the alignment

nameMap - used to translate sequence names, if necessary

NexusWriter

public NexusWriter(java.lang.String matrixDataType,
                   UniqueNameMap nameMap)

Creates a new instance of this class with "-" as gap data and "? as missing data character.

Parameters:

matrixDataType - the data type specified in the Nexus FORMAT command (Nexus allows STANDARD, DNA, , NUCLEOTIDE, PROTEIN or CONTINUOUS.)

nameMap - used to translate sequence names, if necessary

NexusWriter

public NexusWriter(java.lang.String matrixDataType,
                   char gapCharacter,
                   char missingCharacter)

Creates a new instance of this class.

Parameters:

matrixDataType - the data type specified in the Nexus FORMAT command (Nexus allows STANDARD, DNA, , NUCLEOTIDE, PROTEIN or CONTINUOUS.)

gapCharacter - the character coding a gap in the alignment

missingCharacter - the character coding missing data in the alignment

NexusWriter

public NexusWriter(java.lang.String matrixDataType)

Creates a new instance of this class with "-" as gap data and "? as missing data character.

Parameters:

matrixDataType - the data type specified in the Nexus FORMAT command (Nexus allows STANDARD, DNA, , NUCLEOTIDE, PROTEIN or CONTINUOUS.)

Method Detail

write

public void write(Alignment<S,C> alignment,
                  java.io.OutputStream stream)
           throws java.lang.Exception

Throws:

java.lang.Exception