jaligner
Class Alignment

java.lang.Object
  jaligner.Alignment

public final class Alignment

extends java.lang.Object

Holds the output of a pairwise sequences alignment.

Author:

Ahmed Moustafa (ahmed@users.sf.net)

Field Summary

static char

GAP Gap character

Constructor Summary

Alignment()
Constructor for Alignment

Method Summary

float	calculateScore() Calculate the score of the alignment, not using the score field (the function only uses sequence1, sequence2, matrix and gap penalties).
boolean	checkScore() Check if the calculated score matches the field score.
float	getExtend()
int	getGaps()
int	getIdentity()
char[]	getMarkupLine()
Matrix	getMatrix()
java.lang.String	getName1()
java.lang.String	getName2()
float	getOpen()
Sequence	getOriginalSequence1() Returns original Sequence #1
Sequence	getOriginalSequence2() Returns original Sequence #2
float	getScore()
char[]	getSequence1()
char[]	getSequence2()
int	getSimilarity()
int	getStart1()
int	getStart2()
java.lang.String	getSummary() Returns a summary for alignment
void	setExtend(float extend)
void	setGaps(int gaps)
void	setIdentity(int identity)
void	setMarkupLine(char[] markupLine)
void	setMatrix(Matrix matrix)
void	setName1(java.lang.String name1)
void	setName2(java.lang.String name2)
void	setOpen(float open)
void	setOriginalSequence1(Sequence originalSequence1)
void	setOriginalSequence2(Sequence originalSequence2)
void	setScore(float score)
void	setSequence1(char[] sequence1)
void	setSequence2(char[] sequence2)
void	setSimilarity(int similarity)
void	setStart1(int start1)
void	setStart2(int start2)

Methods inherited from class java.lang.Object

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

Field Detail

GAP

public static final char GAP

Gap character

See Also:

Constant Field Values

Constructor Detail

Alignment

public Alignment()

Constructor for Alignment

Method Detail

getExtend

public float getExtend()

Returns:

Returns the extend.

setExtend

public void setExtend(float extend)

Parameters:

extend - The extend to set.

getMatrix

public Matrix getMatrix()

Returns:

Returns the matrix.

setMatrix

public void setMatrix(Matrix matrix)

Parameters:

matrix - The matrix to set.

getName1

public java.lang.String getName1()

Returns:

Returns the name1.

setName1

public void setName1(java.lang.String name1)

Parameters:

name1 - The name1 to set.

getName2

public java.lang.String getName2()

Returns:

Returns the name2.

setName2

public void setName2(java.lang.String name2)

Parameters:

name2 - The name2 to set.

getOpen

public float getOpen()

Returns:

Returns the open.

setOpen

public void setOpen(float open)

Parameters:

open - The open to set.

getScore

public float getScore()

Returns:

Returns the score.

setScore

public void setScore(float score)

Parameters:

score - The score to set.

getSequence1

public char[] getSequence1()

Returns:

Returns the sequence1.

setSequence1

public void setSequence1(char[] sequence1)

Parameters:

sequence1 - The sequence1 to set.

getSequence2

public char[] getSequence2()

Returns:

Returns the sequence2.

setSequence2

public void setSequence2(char[] sequence2)

Parameters:

sequence2 - The sequence2 to set.

getStart1

public int getStart1()

Returns:

Returns the start1.

setStart1

public void setStart1(int start1)

Parameters:

start1 - The start1 to set.

getStart2

public int getStart2()

Returns:

Returns the start2.

setStart2

public void setStart2(int start2)

Parameters:

start2 - The start2 to set.

getGaps

public int getGaps()

Returns:

Returns the gaps.

setGaps

public void setGaps(int gaps)

Parameters:

gaps - The gaps to set.

getIdentity

public int getIdentity()

Returns:

Returns the identity.

setIdentity

public void setIdentity(int identity)

Parameters:

identity - The identity to set.

getMarkupLine

public char[] getMarkupLine()

Returns:

Returns the markupLine.

setMarkupLine

public void setMarkupLine(char[] markupLine)

Parameters:

markupLine - The markupLine to set.

getSimilarity

public int getSimilarity()

Returns:

Returns the similarity.

setSimilarity

public void setSimilarity(int similarity)

Parameters:

similarity - The similarity to set.

getSummary

public java.lang.String getSummary()

Returns a summary for alignment

Returns:

String alignment summary

calculateScore

public float calculateScore()

Calculate the score of the alignment, not using the score field (the function only uses sequence1, sequence2, matrix and gap penalties).

Returns:

the calculated score (By: Bram Minnaert)

checkScore

public boolean checkScore()

Check if the calculated score matches the field score.

Returns:

true if equal, else false. (By: Bram Minnaert)

getOriginalSequence1

public Sequence getOriginalSequence1()

Returns original Sequence #1

Returns:

original Sequence #1

setOriginalSequence1

public void setOriginalSequence1(Sequence originalSequence1)

Parameters:

originalSequence1 -

getOriginalSequence2

public Sequence getOriginalSequence2()

Returns original Sequence #2

Returns:

original Sequence #2

setOriginalSequence2

public void setOriginalSequence2(Sequence originalSequence2)

Parameters:

originalSequence2 -