Motif.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.motif;

import com.milaboratory.core.sequence.Alphabet;
import com.milaboratory.core.sequence.Sequence;
import com.milaboratory.core.sequence.Wildcard;
import com.milaboratory.util.BitArray;

import java.util.Arrays;

/**
 * Data structure for efficient exact and fuzzy matching/searching of sequences (wildcard-aware).
 *
 * @param <S> base sequence type
 */
public final class Motif<S extends Sequence<S>> implements java.io.Serializable {
    private final Alphabet<S> alphabet;
    private final int size;
    /**
     * data.get(code * size + position)
     */
    final BitArray data;
    final BitapPattern bitapPattern;

    Motif(Alphabet<S> alphabet, int size, BitArray data) {
        if (!dataConsistent(data, size))
            throw new IllegalArgumentException("Inconsistent data. Some positions in motif has no possible values.");
        this.alphabet = alphabet;
        this.size = size;
        this.data = data;
        this.bitapPattern = toBitapPattern();
    }

    /**
     * Creates motif from sequence.
     *
     * @param sequence sequence
     */
    public Motif(S sequence) {
        this.alphabet = sequence.getAlphabet();
        this.size = sequence.size();
        int alphabetSize = alphabet.size();
        this.data = new BitArray(alphabetSize * size);
        for (int i = 0; i < size; ++i) {
            Wildcard wildcard = this.alphabet.codeToWildcard(sequence.codeAt(i));
            for (int j = 0; j < wildcard.size(); j++)
                data.set(wildcard.getMatchingCode(j) * size + i);
        }
        this.bitapPattern = toBitapPattern();
    }

    /**
     * Returns per-position or of two motifs.
     *
     * <p>e.g. ATGC or TTCC = WTSC</p>
     *
     * @param other
     * @return
     */
    public Motif<S> or(Motif<S> other) {
        if (other.size != size)
            throw new IllegalArgumentException("Supports only motifs with the same size as this.");

        BitArray result = data.clone();
        result.or(other.data);

        return new Motif<>(alphabet, size, result);
    }

    public BitapPattern getBitapPattern() {
        if (size >= 64)
            throw new RuntimeException("Supports motifs with length less then 64.");
        return bitapPattern;
    }

    private BitapPattern toBitapPattern() {
        if (size >= 64)
            return null;
        int aSize = alphabet.size();
        long[] patternMask = new long[aSize],
                reversePatternMask = new long[aSize];
        Arrays.fill(patternMask, ~0);
        Arrays.fill(reversePatternMask, ~0);
        int p = 0;
        for (int i = 0; i < aSize; ++i)
            for (int j = 0; j < size; ++j)
                if (data.get(p++)) {
                    patternMask[i] &= ~(1L << j);
                    reversePatternMask[i] &= ~(1L << (size - j - 1));
                }
        return new BitapPattern(size, patternMask, reversePatternMask);
    }

    public int size() {
        return size;
    }

    public boolean allows(byte code, int position) {
        return data.get(code * size + position);
    }

    public boolean matches(S sequence, int from) {
        if (from < 0 || from + size > sequence.size())
            throw new IndexOutOfBoundsException();
        for (int i = 0; i < size; ++i)
            if (!allows(sequence.codeAt(from++), i))
                return false;
        return true;
    }

    @Override
    public boolean equals(Object o) {
        if (this == o) return true;
        if (o == null || getClass() != o.getClass()) return false;

        Motif<?> motif = (Motif<?>) o;

        if (size != motif.size) return false;
        if (!alphabet.equals(motif.alphabet)) return false;
        return data.equals(motif.data);
    }

    @Override
    public int hashCode() {
        int result = alphabet.hashCode();
        result = 31 * result + size;
        result = 31 * result + data.hashCode();
        return result;
    }

    private final static boolean dataConsistent(BitArray data, int size) {
        OUTER:
        for (int i = 0; i < size; i++) {
            for (int j = i; j < data.size(); j += size)
                if (data.get(j))
                    continue OUTER;
            return false;
        }
        return true;
    }

    //private final static boolean dataConsistent(BitArray data, int size) {
    //    int i = 0;
    //    while (i < data.size()) {
    //        if (data.get(i)) {
    //            i = ((i / size) + 1) * size;
    //            continue;
    //        }
    //        ++i;
    //        if (i % size == 0)
    //            return false;
    //    }
    //    return true;
    //}
}