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SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
interface for any alignment data.
Field Summary | |
static char |
GAP
character used to designate gaps |
Method Summary | |
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. |
double[] |
getFrequency()
Returns frequency of character states. |
int |
getSequenceCount()
Return number of sequences in this alignment |
int |
getSiteCount()
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void |
setDataType(DataType dataType)
Sets the dataType of this alignment. |
void |
setFrequency(double[] frequencies)
Sets frequency of character states. |
Methods inherited from interface pal.misc.IdGroup |
getIdCount, getIdentifier, setIdentifier, whichIdNumber |
Field Detail |
public static final char GAP
Method Detail |
public char getData(int seq, int site)
public int getSiteCount()
public int getSequenceCount()
public DataType getDataType()
public void setDataType(DataType dataType)
public java.lang.String getAlignedSequenceString(int sequence)
public double[] getFrequency()
public void setFrequency(double[] frequencies)
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