com.milaboratory.core.alignment

Class ScoringUtils

java.lang.Object

com.milaboratory.core.alignment.ScoringUtils

public final class ScoringUtils
extends Object

ScoringUtils - class which contains some useful helpers used in scoring systems

Method Summary

Methods

Modifier and Type	Method and Description
static int[]	fillWildcardScores(int[] matrix, Alphabet<?> alphabet, byte... exclude) Fills up scores for wildcards by averaging scores for all their matching scores combinations.
static int[]	getSymmetricMatrix(int match, int mismatch, Alphabet<?> alphabet) Returns simple substitution matrix
static int[]	setMatchScore(Alphabet<?> alphabet, int[] matrix, int match)
static int[]	setMismatchScore(Alphabet<?> alphabet, int[] matrix, int mismatch)

Methods inherited from class java.lang.Object

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

Method Detail

getSymmetricMatrix

public static int[] getSymmetricMatrix(int match,
                       int mismatch,
                       Alphabet<?> alphabet)

Returns simple substitution matrix

Parameters:

match - match score

mismatch - mismatch score

alphabet - alphabet

Returns:

simple substitution matrix

setMismatchScore

public static int[] setMismatchScore(Alphabet<?> alphabet,
                     int[] matrix,
                     int mismatch)

setMatchScore

public static int[] setMatchScore(Alphabet<?> alphabet,
                  int[] matrix,
                  int match)

fillWildcardScores

public static int[] fillWildcardScores(int[] matrix,
                       Alphabet<?> alphabet,
                       byte... exclude)

Fills up scores for wildcards by averaging scores for all their matching scores combinations.

Parameters:

matrix - initial matrix (will be modified in-place)

alphabet - alphabet

exclude - list of codes to exclude from this action

Returns:

the same reference as matrix