org.forester.msa
Interface Msa

All Known Implementing Classes:

BasicMsa, ResampleableMsa

public interface Msa

Method Summary

java.util.List<java.lang.Character>	getColumnAt(int col)
java.lang.Object	getIdentifier(int row)
int	getLength()
int	getNumberOfSequences()
char	getResidueAt(int row, int col)
java.lang.StringBuffer	getSequenceAsString(int row)
Sequence.TYPE	getType()
void	setIdentifier(int row, java.lang.Object identifier)
void	setResidueAt(int row, int col, char residue)
void	write(java.io.Writer w)

Method Detail

getIdentifier

java.lang.Object getIdentifier(int row)

setIdentifier

void setIdentifier(int row,
                   java.lang.Object identifier)

getLength

int getLength()

getNumberOfSequences

int getNumberOfSequences()

getResidueAt

char getResidueAt(int row,
                  int col)

getColumnAt

java.util.List<java.lang.Character> getColumnAt(int col)

getSequenceAsString

java.lang.StringBuffer getSequenceAsString(int row)

getType

Sequence.TYPE getType()

setResidueAt

void setResidueAt(int row,
                  int col,
                  char residue)

write

void write(java.io.Writer w)
           throws java.io.IOException

Throws:

java.io.IOException