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

Class StrCompAlignment

java.lang.Object

org.biojava.nbio.structure.align.pairwise.StrCompAlignment

All Implemented Interfaces:

Alignable

public class StrCompAlignment
extends Object
implements Alignable

Constructor Summary

Constructors

Constructor	Description
StrCompAlignment(int rows, int cols)

Method Summary

Modifier and Type	Method	Description
AligMatEl[][]	getAligMat()
AligMatEl	getAligMat(int i, int j)
int	getCols()
float	getGapExtCol()
float	getGapExtRow()
float	getGapOpenCol()
float	getGapOpenRow()
IndexPair[]	getPath()
int	getPathSize()
int	getRows()
float	getScore()
void	setAligMat(int i, int j, AligMatEl el)
void	setAligMat(AligMatEl[][] al)
void	setGapExtCol(float gapExtCol)
void	setGapExtRow(float gapExtRow)
void	setGapOpenCol(float gapOpenCol)
void	setGapOpenRow(float gapOpenRow)
void	setPath(IndexPair[] path)
void	setPathSize(int pathSize)
void	setScore(float score)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

StrCompAlignment

public StrCompAlignment(int rows,
 int cols)

Method Details

getRows

public int getRows()

Specified by:

getRows in interface Alignable

getCols

public int getCols()

Specified by:

getCols in interface Alignable

setAligMat

public void setAligMat(int i,
 int j,
 AligMatEl el)

getAligMat

public AligMatEl getAligMat(int i,
 int j)

getAligMat

public AligMatEl[][] getAligMat()

Specified by:

getAligMat in interface Alignable

setAligMat

public void setAligMat(AligMatEl[][] al)

Specified by:

setAligMat in interface Alignable

getGapExtCol

public float getGapExtCol()

Specified by:

getGapExtCol in interface Alignable

setGapExtCol

public void setGapExtCol(float gapExtCol)

Specified by:

setGapExtCol in interface Alignable

getGapExtRow

public float getGapExtRow()

Specified by:

getGapExtRow in interface Alignable

setGapExtRow

public void setGapExtRow(float gapExtRow)

Specified by:

setGapExtRow in interface Alignable

getGapOpenCol

public float getGapOpenCol()

Specified by:

getGapOpenCol in interface Alignable

setGapOpenCol

public void setGapOpenCol(float gapOpenCol)

Specified by:

setGapOpenCol in interface Alignable

getGapOpenRow

public float getGapOpenRow()

Specified by:

getGapOpenRow in interface Alignable

setGapOpenRow

public void setGapOpenRow(float gapOpenRow)

Specified by:

setGapOpenRow in interface Alignable

getScore

public float getScore()

Specified by:

getScore in interface Alignable

setScore

public void setScore(float score)

Specified by:

setScore in interface Alignable

getPath

public IndexPair[] getPath()

Specified by:

getPath in interface Alignable

setPath

public void setPath(IndexPair[] path)

Specified by:

setPath in interface Alignable

getPathSize

public int getPathSize()

Specified by:

getPathSize in interface Alignable

setPathSize

public void setPathSize(int pathSize)

Specified by:

setPathSize in interface Alignable