Package org.biojava.nbio.structure.align.pairwise

Interface Alignable

All Known Implementing Classes:

StrCompAlignment

public interface Alignable

Method Summary

Modifier and Type	Method	Description
AligMatEl[][]	getAligMat()
int	getCols()
float	getGapExtCol()
float	getGapExtRow()
float	getGapOpenCol()
float	getGapOpenRow()
IndexPair[]	getPath()
int	getPathSize()
int	getRows()
float	getScore()
void	setAligMat(AligMatEl[][] alignmentMatrix)
void	setGapExtCol(float penalty)
void	setGapExtRow(float penalty)
void	setGapOpenCol(float penalty)
void	setGapOpenRow(float penalty)
void	setPath(IndexPair[] path)
void	setPathSize(int pathSize)
void	setScore(float score)

Method Details

getRows

int getRows()

getCols

int getCols()

getAligMat

AligMatEl[][] getAligMat()

setAligMat

void setAligMat(AligMatEl[][] alignmentMatrix)

getGapExtCol

float getGapExtCol()

setGapExtCol

void setGapExtCol(float penalty)

getGapExtRow

float getGapExtRow()

setGapExtRow

void setGapExtRow(float penalty)

getGapOpenCol

float getGapOpenCol()

setGapOpenCol

void setGapOpenCol(float penalty)

getGapOpenRow

float getGapOpenRow()

setGapOpenRow

void setGapOpenRow(float penalty)

setScore

void setScore(float score)

getScore

float getScore()

getPathSize

int getPathSize()

setPathSize

void setPathSize(int pathSize)

setPath

void setPath(IndexPair[] path)

getPath

IndexPair[] getPath()