IdGroup
, java.io.Serializable
AnnotationAlignment
AbstractAlignment
, AlignmentReaders.PhylipClustalAlignment
, AlignmentReaders.UnalignedAlignment
, BootstrappedAlignment
, ConcatenatedAlignment
, ConcatenatedAnnotatedAlignment
, GapBalancedAlignment
, IndelAlignment
, IndelAnnotatedAlignment
, JumbledAlignment
, MultiLocusAnnotatedAlignment
, ReadAlignment
, ReadAlignmentOld
, SimpleAlignment
, SimpleAnnotatedAlignment
, SimulatedAlignment
, SitePattern
, StrippedAlignment
, StrippedAnnotatedAlignment
public interface Alignment extends java.io.Serializable, IdGroup
IdGroup.Utils
Modifier and Type | Field | Description |
---|---|---|
static char |
GAP |
character used to designate gaps
|
static java.lang.String |
GAP_TLA |
A three letter acronym version of a gap.
|
static java.lang.String |
GAPS |
Characters that might be used as gaps
|
static char |
UNKNOWN |
character used to designate unknown characters
|
static java.lang.String |
UNKNOWN_TLA |
character used to designate unknown characters
|
Modifier and Type | Method | Description |
---|---|---|
java.lang.String |
getAlignedSequenceString(int sequence) |
Returns string representation of single sequence in
alignment with gap characters included.
|
char |
getData(int seq,
int site) |
sequence alignment at (sequence, site)
|
DataType |
getDataType() |
Return DataType of this alignment.
|
int |
getSequenceCount() |
Return number of sequences in this alignment
|
int |
getSiteCount() |
getIdCount, getIdentifier, setIdentifier, whichIdNumber
static final char GAP
static final char UNKNOWN
static final java.lang.String UNKNOWN_TLA
static final java.lang.String GAP_TLA
static final java.lang.String GAPS
char getData(int seq, int site)
int getSiteCount()
int getSequenceCount()
DataType getDataType()
java.lang.String getAlignedSequenceString(int sequence)