public class NexusWriter<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound> extends AbstractAlignmentWriter<S,C>
Alignment
to a stream in Nexus format. The result contains a TAXA, a CHARACTERS and
a SETS block (if the specified alignment contains any character set).Modifier and Type | Field and Description |
---|---|
static String |
COMMAND_TERMINATOR |
static String |
COMMENT_END |
static String |
COMMENT_START |
static String |
DATATYPE_CONTINUOUS |
static String |
DATATYPE_DNA |
static String |
DATATYPE_NUCLEOTIDE |
static String |
DATATYPE_PROTEIN |
static String |
DATATYPE_RNA |
static String |
DATATYPE_STANDARD |
WHITESPACE_REPLACEMENT
Constructor and Description |
---|
NexusWriter(String matrixDataType)
Creates a new instance of this class with "
- " as gap data and "? as missing data character. |
NexusWriter(String matrixDataType,
char gapCharacter,
char missingCharacter)
Creates a new instance of this class.
|
NexusWriter(String matrixDataType,
char gapCharacter,
char missingCharacter,
UniqueNameMap nameMap)
Creates a new instance of this class.
|
NexusWriter(String matrixDataType,
UniqueNameMap nameMap)
Creates a new instance of this class with "
- " as gap data and "? as missing data character. |
Modifier and Type | Method and Description |
---|---|
void |
write(Alignment<S,C> alignment,
OutputStream stream) |
getNameMap, write
public static final String COMMAND_TERMINATOR
public static final String COMMENT_START
public static final String COMMENT_END
public static final String DATATYPE_STANDARD
public static final String DATATYPE_DNA
public static final String DATATYPE_RNA
public static final String DATATYPE_NUCLEOTIDE
public static final String DATATYPE_PROTEIN
public static final String DATATYPE_CONTINUOUS
public NexusWriter(String matrixDataType, char gapCharacter, char missingCharacter, UniqueNameMap nameMap)
matrixDataType
- the data type specified in the Nexus FORMAT
command (Nexus allows
STANDARD
, DNA
, , NUCLEOTIDE
, PROTEIN
or CONTINUOUS
.)gapCharacter
- the character coding a gap in the alignmentmissingCharacter
- the character coding missing data in the alignmentnameMap
- used to translate sequence names, if necessarypublic NexusWriter(String matrixDataType, UniqueNameMap nameMap)
-
" as gap data and "?
as missing data character.matrixDataType
- the data type specified in the Nexus FORMAT
command (Nexus allows
STANDARD
, DNA
, , NUCLEOTIDE
, PROTEIN
or CONTINUOUS
.)nameMap
- used to translate sequence names, if necessarypublic NexusWriter(String matrixDataType, char gapCharacter, char missingCharacter)
matrixDataType
- the data type specified in the Nexus FORMAT
command (Nexus allows
STANDARD
, DNA
, , NUCLEOTIDE
, PROTEIN
or CONTINUOUS
.)gapCharacter
- the character coding a gap in the alignmentmissingCharacter
- the character coding missing data in the alignmentpublic NexusWriter(String matrixDataType)
-
" as gap data and "?
as missing data character.matrixDataType
- the data type specified in the Nexus FORMAT
command (Nexus allows
STANDARD
, DNA
, , NUCLEOTIDE
, PROTEIN
or CONTINUOUS
.)