jebl.evolution.align.scores
Class Scores

java.lang.Object
  jebl.evolution.align.scores.Scores

All Implemented Interfaces:

ScoreMatrix

Direct Known Subclasses:

AminoAcidScores, NucleotideScores, SubstScoreMatrix

public abstract class Scores
extends Object
implements ScoreMatrix

Base class for all score matrices in the package.

Author:

Alexei Drummond

Field Summary

float[][]

score

Constructor Summary

Scores()

Method Summary

protected void	buildScores(float[][] scores)
static Scores	duplicate(Scores scores)
protected String	getExtraResidues()
float	getScore(char x, char y)
static Scores	includeAdditionalCharacters(Scores scores, String characters) includes additional characters in the score matrix which will all have scored zero when compared to other characters.
static Scores	includeGaps(Scores scores, float gapVersusResidueCost, float gapVersusGapCost)
String	toString()

Methods inherited from class java.lang.Object

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

Methods inherited from interface jebl.evolution.align.scores.ScoreMatrix

getAlphabet, getName

Field Detail

score

public float[][] score

Constructor Detail

Scores

public Scores()

Method Detail

buildScores

protected void buildScores(float[][] scores)

getScore

public final float getScore(char x,
                            char y)

Specified by:

getScore in interface ScoreMatrix

Returns:

the score for matching char x with char y

toString

public String toString()

Overrides:

toString in class Object

duplicate

public static Scores duplicate(Scores scores)

includeGaps

public static Scores includeGaps(Scores scores,
                                 float gapVersusResidueCost,
                                 float gapVersusGapCost)

Parameters:

scores -

gapVersusResidueCost - should be a negative value

gapVersusGapCost - should be a positive value

includeAdditionalCharacters

public static Scores includeAdditionalCharacters(Scores scores,
                                                 String characters)

includes additional characters in the score matrix which will all have scored zero when compared to other characters. Current system does not handle special characters well, such as ? Or "R" for NucleotideSequences, which represents a "A" or "G". Currently, we just add all characters to the allowed set of characters, and they are scored as zero cost when comparing to other characters, including themselves. One-day, we should probably introduce better scoring system so that "R" is a positive score compared to "A" or "G", but a negative score compared to "C" or "T". example usage: scores = Scores.includeAdditionalCharacters(scores, "?ABCDEFGHIJKLMNOPQRSTUVWXYZ");

Parameters:

scores -

characters -

Returns:

a new score matrix.

getExtraResidues

protected String getExtraResidues()