info.bioinfweb.commons.bio.biojava3.alignment.io.hennig86

Class Hennig86Writer<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.hennig86.Hennig86Writer<S,C>

All Implemented Interfaces:

AlignmentWriter<S,C>

public class Hennig86Writer<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 Hennig86 file. (Note that no character set information will be written.) Optionally a nstates command for TNT can be written depending on the constructor that is used.

Author:

Ben Stöver

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	COMMAND_TERMINATOR
static java.lang.String	DATATYPE_DNA
static java.lang.String	DATATYPE_PROTEIN
static java.lang.String	MATRIX_COMMAND
static java.lang.String	NO_OF_STATES_COMMAND
static char	WHITESPACE_REPLACEMENT

Constructor Summary

Constructors

Constructor and Description
Hennig86Writer()
Hennig86Writer(int noOfStates)
Hennig86Writer(java.lang.String noOfStates)

Method Summary

Modifier and Type	Method and Description
int	getMaxTaxonNameLength()
java.lang.String	getNoOfStates()
void	setMaxTaxonNameLength(int maxTaxonNameLength)
void	setNoOfStates(java.lang.String noOfStates)
void	write(Alignment<S,C> alignment, java.io.File file, java.lang.String title)
void	write(Alignment<S,C> alignment, java.io.OutputStream stream)
void	write(Alignment<S,C> alignment, java.io.OutputStream stream, java.lang.String title)

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

NO_OF_STATES_COMMAND

public static final java.lang.String NO_OF_STATES_COMMAND

See Also:

Constant Field Values

MATRIX_COMMAND

public static final java.lang.String MATRIX_COMMAND

See Also:

Constant Field Values

DATATYPE_DNA

public static final java.lang.String DATATYPE_DNA

See Also:

Constant Field Values

DATATYPE_PROTEIN

public static final java.lang.String DATATYPE_PROTEIN

See Also:

Constant Field Values

WHITESPACE_REPLACEMENT

public static final char WHITESPACE_REPLACEMENT

See Also:

Constant Field Values

Constructor Detail

Hennig86Writer

public Hennig86Writer()

Hennig86Writer

public Hennig86Writer(java.lang.String noOfStates)

Hennig86Writer

public Hennig86Writer(int noOfStates)

Method Detail

getNoOfStates

public java.lang.String getNoOfStates()

setNoOfStates

public void setNoOfStates(java.lang.String noOfStates)

getMaxTaxonNameLength

public int getMaxTaxonNameLength()

setMaxTaxonNameLength

public void setMaxTaxonNameLength(int maxTaxonNameLength)

write

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

Throws:

java.lang.Exception

write

public void write(Alignment<S,C> alignment,
                  java.io.File file,
                  java.lang.String title)
           throws java.lang.Exception

Throws:

java.lang.Exception

write

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

Throws:

java.lang.Exception