smueller.alignment

Class Alignment

java.lang.Object

smueller.alignment.Alignment

Direct Known Subclasses:

AffineAlignment, OneAffineAlignment

public class Alignment
extends Object

Author:

Soeren Mueller, smueller@cebitec.uni-bielefeld.de

Constructor Summary

Constructors

Constructor and Description
Alignment(IFileFragment ref1, IFileFragment query1)

Method Summary

Methods

Modifier and Type	Method and Description
void	ausgabe()
int	chartoNumber(char a)
void	cloneAl()
void	computeMatrix(String u, String v)
void	createAlignments(String u, String v)
void	drawMatrix()
void	drawPathway()
Vector<OptimalAlignmentVector>	getAllalignments()
double[][]	getMatrix()
double[][]	getPairwiseDistance()
int[][][]	getPathway()
IFileFragment	getQuery()
IFileFragment	getRef()
String	getSeq1()
String	getSeq2()
double	mini(double a, double b, double c)
void	setKostenfunktion(double[][] kostenfunktion1)
void	setQuery(IFileFragment query1)
void	setRef(IFileFragment ref1)
void	setSeq1(String seq11)
void	setSeq2(String seq21)
double	vergleiche(int i, int j)

Methods inherited from class java.lang.Object

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

Constructor Detail

Alignment

public Alignment(IFileFragment ref1,
         IFileFragment query1)

Parameters:

ref1 -

query1 -

Method Detail

ausgabe

public void ausgabe()

chartoNumber

public int chartoNumber(char a)

Parameters:

a -

Returns:

cloneAl

public void cloneAl()

computeMatrix

public void computeMatrix(String u,
                 String v)

Parameters:

u -

v -

createAlignments

public void createAlignments(String u,
                    String v)

Parameters:

u -

v -

drawMatrix

public void drawMatrix()

drawPathway

public void drawPathway()

getAllalignments

public Vector<OptimalAlignmentVector> getAllalignments()

Returns:

getMatrix

public double[][] getMatrix()

Returns:

getPairwiseDistance

public double[][] getPairwiseDistance()

Returns:

getPathway

public int[][][] getPathway()

Returns:

getQuery

public IFileFragment getQuery()

Returns:

getRef

public IFileFragment getRef()

Returns:

getSeq1

public String getSeq1()

Returns:

getSeq2

public String getSeq2()

Returns:

mini

public double mini(double a,
          double b,
          double c)

Parameters:

a -

b -

c -

Returns:

setKostenfunktion

public void setKostenfunktion(double[][] kostenfunktion1)

Parameters:

kostenfunktion1 -

setQuery

public void setQuery(IFileFragment query1)

Parameters:

query1 -

setRef

public void setRef(IFileFragment ref1)

Parameters:

ref1 -

setSeq1

public void setSeq1(String seq11)

Parameters:

seq11 -

setSeq2

public void setSeq2(String seq21)

Parameters:

seq21 -

vergleiche

public double vergleiche(int i,
                int j)

Parameters:

i -

j -

Returns: