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

Class MEGAWriter<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.mega.MEGAWriter<S,C>

All Implemented Interfaces:

AlignmentWriter<S,C>

public class MEGAWriter<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 MEGA file. (Note that no character set information will be written.)

Author:

Ben Stöver

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	DATATYPE_DNA
static java.lang.String	DATATYPE_PROTEIN
static char	DEFAULT_GAP_CHAR
static java.lang.String	DEFAULT_TITLE
static int	LINE_LENGTH
static byte[]	LINE_SEPARATOR

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

WHITESPACE_REPLACEMENT

Constructor Summary

Constructors

Constructor and Description
MEGAWriter(java.lang.String datatype)
MEGAWriter(java.lang.String datatype, char gapCharacter)

Method Summary

Modifier and Type	Method and Description
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

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

DEFAULT_TITLE

public static final java.lang.String DEFAULT_TITLE

See Also:

Constant Field Values

DEFAULT_GAP_CHAR

public static final char DEFAULT_GAP_CHAR

See Also:

Constant Field Values

LINE_LENGTH

public static final int LINE_LENGTH

See Also:

Constant Field Values

LINE_SEPARATOR

public static final byte[] LINE_SEPARATOR

Constructor Detail

MEGAWriter

public MEGAWriter(java.lang.String datatype,
                  char gapCharacter)

MEGAWriter

public MEGAWriter(java.lang.String datatype)

Method Detail

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