pal.alignment
Interface Alignment

All Superinterfaces:
IdGroup, java.io.Serializable
All Known Subinterfaces:
AnnotationAlignment
All Known Implementing Classes:
AbstractAlignment

public interface Alignment
extends java.io.Serializable, IdGroup

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()
           
 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

GAP

public static final char GAP
character used to designate gaps
Method Detail

getData

public char getData(int seq,
                    int site)
sequence alignment at (sequence, site)

getSiteCount

public int getSiteCount()
Returns:
number of sites for each sequence in this alignment

getSequenceCount

public int getSequenceCount()
Return number of sequences in this alignment

getDataType

public DataType getDataType()
Return DataType of this alignment.

setDataType

public void setDataType(DataType dataType)
Sets the dataType of this alignment.

getAlignedSequenceString

public java.lang.String getAlignedSequenceString(int sequence)
Returns string representation of single sequence in alignment with gap characters included.

getFrequency

public double[] getFrequency()
Returns frequency of character states.

setFrequency

public void setFrequency(double[] frequencies)
Sets frequency of character states.