pal.alignment
public interface Alignment extends java.io.Serializable, IdGroup
IdGroup.Utils
Modifier and Type | Field and 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 and 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)