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

Class PhylipWriter<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.phylip.PhylipWriter<S,C>

All Implemented Interfaces:

AlignmentWriter<S,C>

public class PhylipWriter<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 file in PHYLIP format. (This class is based on the implementation of the BioJava 1.8 class PHYLIPFileFormat written by Richard Holland, Tobias Thierer and Jim Balhoff, who provided the source code under LGPL.)

Author:

Ben Stöver

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_MAX_NAME_LENGTH

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

WHITESPACE_REPLACEMENT

Constructor Summary

Constructors

Constructor and Description
PhylipWriter()
PhylipWriter(boolean replaceWhiteSpace)
PhylipWriter(boolean replaceWhiteSpace, int maxNameLength)
PhylipWriter(UniqueNameMap nameMap) Note that certain parameter sets for the specified name map might lead to an invalid output of this class.

Method Summary

Modifier and Type	Method and Description
void	write(Alignment<S,C> alignment, java.io.OutputStream stream) Writes the specified alignment in sequential Phylip format.

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

DEFAULT_MAX_NAME_LENGTH

public static final int DEFAULT_MAX_NAME_LENGTH

See Also:

Constant Field Values

Constructor Detail

PhylipWriter

public PhylipWriter()

PhylipWriter

public PhylipWriter(boolean replaceWhiteSpace)

PhylipWriter

public PhylipWriter(boolean replaceWhiteSpace,
                    int maxNameLength)

PhylipWriter

public PhylipWriter(UniqueNameMap nameMap)

Note that certain parameter sets for the specified name map might lead to an invalid output of this class.

Parameters:

nameMap -

Method Detail

write

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

Writes the specified alignment in sequential Phylip format.

Throws:

java.lang.Exception

See Also:

AlignmentWriter.write(info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment, java.io.OutputStream)