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

Class AbstractAlignmentWriter<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>

All Implemented Interfaces:

AlignmentWriter<S,C>

Direct Known Subclasses:

FastaWriter, Hennig86Writer, MEGAWriter, NexusWriter, PhylipWriter

public abstract class AbstractAlignmentWriter<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>
extends java.lang.Object
implements AlignmentWriter<S,C>

Field Summary

Fields

Modifier and Type	Field and Description
static char	WHITESPACE_REPLACEMENT

Constructor Summary

Constructors

Constructor and Description
AbstractAlignmentWriter()
AbstractAlignmentWriter(UniqueNameMap nameMap)

Method Summary

Modifier and Type	Method and Description
UniqueNameMap	getNameMap()
void	write(Alignment<S,C> alignment, java.io.File file)

Methods inherited from class java.lang.Object

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

Methods inherited from interface info.bioinfweb.commons.bio.biojava3.alignment.io.AlignmentWriter

write

Field Detail

WHITESPACE_REPLACEMENT

public static final char WHITESPACE_REPLACEMENT

See Also:

Constant Field Values

Constructor Detail

AbstractAlignmentWriter

public AbstractAlignmentWriter(UniqueNameMap nameMap)

AbstractAlignmentWriter

public AbstractAlignmentWriter()

Method Detail

getNameMap

public UniqueNameMap getNameMap()

Specified by:

getNameMap in interface AlignmentWriter<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

write

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

Specified by:

write in interface AlignmentWriter<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound>

Throws:

java.lang.Exception