info.bioinfweb.commons.bio

Class AmbiguityBaseScore

java.lang.Object

info.bioinfweb.commons.bio.AmbiguityBaseScore

All Implemented Interfaces:

java.lang.Cloneable, java.lang.Comparable<AmbiguityBaseScore>

public class AmbiguityBaseScore
extends java.lang.Object
implements java.lang.Comparable<AmbiguityBaseScore>, java.lang.Cloneable

Field Summary

Fields

Modifier and Type	Field and Description
static int	ADENINE_INDEX
static int	CYTOSINE_INDEX
static int	GUANINE_INDEX
static int	THYMINE_INDEX

Constructor Summary

Constructors

Constructor and Description
AmbiguityBaseScore(double[] scores) Note that no deep copy of the array will be made.
AmbiguityBaseScore(double adenine, double thymine, double cytosine, double guanine) Creates a new instance of this class.
AmbiguityBaseScore(double adenine, double thymine, double cytosine, double guanine, double sum) Creates a new instance of this class and directly scales is to the specified sum.

Method Summary

Modifier and Type	Method and Description
void	add(AmbiguityBaseScore other)
protected java.lang.Object	clone()
int	compareTo(AmbiguityBaseScore other)
boolean	equals(java.lang.Object other)
double	getAdenineScore()
char	getConsensusBase()
double	getCytosineScore()
double	getGuanineScore()
double	getMaxScore()
double	getScoreByIndex(int index)
double	getSum() Returns the sum of all scores.
double	getThymineScore()
void	rescale(double sum) Scales all scores with the same linear factor so that the sum of all scores is equal to sum.
void	setAdeninScore(double score)
void	setCytosinScore(double score)
void	setGuaninScore(double score)
void	setScoreByIndex(int index, double score)
void	setThyminScore(double score)

Methods inherited from class java.lang.Object

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

Field Detail

ADENINE_INDEX

public static final int ADENINE_INDEX

See Also:

Constant Field Values

THYMINE_INDEX

public static final int THYMINE_INDEX

See Also:

Constant Field Values

CYTOSINE_INDEX

public static final int CYTOSINE_INDEX

See Also:

Constant Field Values

GUANINE_INDEX

public static final int GUANINE_INDEX

See Also:

Constant Field Values

Constructor Detail

AmbiguityBaseScore

public AmbiguityBaseScore(double[] scores)

Note that no deep copy of the array will be made.

Parameters:

scores -

AmbiguityBaseScore

public AmbiguityBaseScore(double adenine,
                          double thymine,
                          double cytosine,
                          double guanine)

Creates a new instance of this class.

Parameters:

adenine - the score for adenine

thymine - the score for thymin

cytosine - the score for cytosin

guanine - the score for guanine

AmbiguityBaseScore

public AmbiguityBaseScore(double adenine,
                          double thymine,
                          double cytosine,
                          double guanine,
                          double sum)

Creates a new instance of this class and directly scales is to the specified sum.

Parameters:

adenine - the score for adenine

thymine - the score for thymin

cytosine - the score for cytosin

guanine - the score for guanine

sum - the sum all scroes together shall have

Method Detail

getAdenineScore

public double getAdenineScore()

getThymineScore

public double getThymineScore()

getCytosineScore

public double getCytosineScore()

getGuanineScore

public double getGuanineScore()

setAdeninScore

public void setAdeninScore(double score)

setThyminScore

public void setThyminScore(double score)

setCytosinScore

public void setCytosinScore(double score)

setGuaninScore

public void setGuaninScore(double score)

getScoreByIndex

public double getScoreByIndex(int index)

setScoreByIndex

public void setScoreByIndex(int index,
                            double score)

add

public void add(AmbiguityBaseScore other)

getMaxScore

public double getMaxScore()

getSum

public double getSum()

Returns the sum of all scores.

rescale

public void rescale(double sum)

Scales all scores with the same linear factor so that the sum of all scores is equal to sum. If the current sum of all scores is zero calling this method will have no effect.

Parameters:

sum - the sum all scored together shall have

getConsensusBase

public char getConsensusBase()

clone

protected java.lang.Object clone()
                          throws java.lang.CloneNotSupportedException

Overrides:

clone in class java.lang.Object

Throws:

java.lang.CloneNotSupportedException

equals

public boolean equals(java.lang.Object other)

Overrides:

equals in class java.lang.Object

compareTo

public int compareTo(AmbiguityBaseScore other)

Specified by:

compareTo in interface java.lang.Comparable<AmbiguityBaseScore>