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public interface Alignment
interface for any alignment data.
Nested Class Summary |
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Nested classes/interfaces inherited from interface pal.misc.IdGroup |
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IdGroup.Utils |
Field Summary | |
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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 |
Method Summary | |
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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()
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Methods inherited from interface pal.misc.IdGroup |
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getIdCount, getIdentifier, setIdentifier, whichIdNumber |
Field Detail |
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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
Method Detail |
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char getData(int seq, int site)
int getSiteCount()
int getSequenceCount()
DataType getDataType()
java.lang.String getAlignedSequenceString(int sequence)
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