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

Class FastaWriter<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.fasta.FastaWriter<S,C>

All Implemented Interfaces:

AlignmentWriter<S,C>

public class FastaWriter<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 FASTA file. (Note that no character set information will be written because the FASTA format does not support this.)

Author:

Ben Stöver

Field Summary

Fields

Modifier and Type	Field and Description
static int	LINE_LENGTH

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

WHITESPACE_REPLACEMENT

Constructor Summary

Constructors

Constructor and Description
FastaWriter()
FastaWriter(UniqueNameMap nameMap)

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

LINE_LENGTH

public static final int LINE_LENGTH

See Also:

Constant Field Values

Constructor Detail

FastaWriter

public FastaWriter()

FastaWriter

public FastaWriter(UniqueNameMap nameMap)

Method Detail

write

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

Throws:

java.lang.Exception