ScoringUtils.java

/*
 * Copyright 2015 MiLaboratory.com
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package com.milaboratory.core.alignment;

import com.milaboratory.core.sequence.Alphabet;
import com.milaboratory.core.sequence.Wildcard;
import gnu.trove.set.hash.TByteHashSet;

import java.util.Arrays;

/**
 * ScoringUtils - class which contains some useful helpers used in scoring systems
 */
public final class ScoringUtils {
    private ScoringUtils() {
    }

    /**
     * Returns simple substitution matrix
     *
     * @param match    match score
     * @param mismatch mismatch score
     * @param alphabet alphabet
     * @return simple substitution matrix
     */
    public static int[] getSymmetricMatrix(int match, int mismatch, Alphabet<?> alphabet) {
        int codes = alphabet.size();
        int[] matrix = new int[codes * codes];
        Arrays.fill(matrix, mismatch);
        for (int i = 0; i < codes; ++i)
            matrix[i + codes * i] = match;
        return fillWildcardScores(matrix, alphabet);
    }

    public static int[] setMismatchScore(Alphabet<?> alphabet, int[] matrix, int mismatch) {
        int size = (int) Math.round(Math.sqrt(matrix.length));
        if (size * size != matrix.length || alphabet.size() != size)
            throw new IllegalArgumentException();
        int[] result = matrix.clone();
        int basicSize = alphabet.basicSize();
        for (int i = 0; i < basicSize; ++i)
            for (int j = 0; j < basicSize; ++j)
                if (i != j)
                    result[i + size * j] = mismatch;
        return fillWildcardScores(result, alphabet);
    }

    public static int[] setMatchScore(Alphabet<?> alphabet, int[] matrix, int match) {
        int size = (int) Math.round(Math.sqrt(matrix.length));
        if (size * size != matrix.length || alphabet.size() != size)
            throw new IllegalArgumentException();
        int[] result = matrix.clone();
        int basicSize = alphabet.basicSize();
        for (int i = 0; i < basicSize; ++i)
            result[i + size * i] = match;
        return fillWildcardScores(result, alphabet);
    }

    /**
     * Fills up scores for wildcards by averaging scores for all their matching scores combinations.
     *
     * @param matrix   initial matrix (will be modified in-place)
     * @param alphabet alphabet
     * @param exclude  list of codes to exclude from this action
     * @return the same reference as matrix
     */
    public static int[] fillWildcardScores(int[] matrix, Alphabet<?> alphabet, byte... exclude) {
        int alSize = alphabet.size();

        if (matrix.length != alSize * alSize)
            throw new IllegalArgumentException("Wrong matrix size.");

        TByteHashSet excludeSet = new TByteHashSet(exclude);
        for (Wildcard wc1 : alphabet.getAllWildcards())
            for (Wildcard wc2 : alphabet.getAllWildcards()) {
                if ((wc1.isBasic() || excludeSet.contains(wc1.getCode())) && (wc2.isBasic() || excludeSet.contains(wc2.getCode())))
                    continue;
                int sumScore = 0;
                for (int i = 0; i < wc1.basicSize(); i++)
                    for (int j = 0; j < wc2.basicSize(); j++) {
                        sumScore += matrix[wc1.getMatchingCode(i) + wc2.getMatchingCode(j) * alSize];
                    }
                sumScore /= wc1.basicSize() * wc2.basicSize();
                matrix[wc1.getCode() + wc2.getCode() * alSize] = sumScore;
            }

        return matrix;
    }

    ///**
    // * Returns true if scores for wildcard symbols is the same as {@link #fillWildcardScores(int[], Alphabet, byte...)}
    // * with no exclude symbols would produce.
    // *
    // * @param matrix matrix to test
    // * @return {@literal true} if scores for wildcards are the same as would be calculated automatically by {@link
    // * #fillWildcardScores(int[], Alphabet, byte...)} method
    // */
    //public static boolean isDefaultWildcardScores(int[] matrix, Alphabet<?> alphabet) {
    //    int alSize = alphabet.size();
    //
    //    if (matrix.length != alSize * alSize)
    //        throw new IllegalArgumentException("Wrong matrix size.");
    //
    //    for (Wildcard wc1 : alphabet.getAllWildcards())
    //        for (Wildcard wc2 : alphabet.getAllWildcards()) {
    //            if (wc1.isBasic())
    //                continue;
    //            int sumScore = 0;
    //            for (int i = 0; i < wc1.count(); i++)
    //                for (int j = 0; j < wc2.count(); j++) {
    //                    sumScore += matrix[wc1.getMatchingCode(i) + wc2.getMatchingCode(j) * alSize];
    //                }
    //            sumScore /= wc1.count() * wc2.count();
    //
    //            if (matrix[wc1.getCode() + wc2.getCode() * alSize] != sumScore)
    //                return false;
    //        }
    //
    //    return true;
    //}
}