/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2024 UniPro <ugene@unipro.ru>
 * http://ugene.net
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
 * MA 02110-1301, USA.
 */
#include "ReadShortReadsSubTask.h"

#include <U2Core/AppContext.h>
#include <U2Core/DNATranslation.h>
#include <U2Core/TextUtils.h>
#include <U2Core/Timer.h>
#include <U2Core/U2SafePoints.h>

#include "GenomeAlignerTask.h"

namespace U2 {

#define DROP_BUNCH_DATA_SIZE 1000000

static bool isDnaQualityAboveThreshold(const DNAQuality& dna, int threshold) {
    assert(!dna.isEmpty());
    for (int i = 0; i < dna.qualCodes.length(); ++i) {
        int qValue = dna.getValue(i);
        if (qValue < threshold) {
            return false;
        }
    }

    return true;
}

static bool checkDnaQuality(SearchQuery* query, int qualityThreshold) {
    if (!(qualityThreshold > 0 && query->hasQuality())) {
        return true;
    }

    // simple quality filtering
    return isDnaQualityAboveThreshold(query->getQuality(), qualityThreshold);
}

static void updateMinMaxReadLengths(AlignContext& alignContext, int l) {
    if (GenomeAlignerTask::MIN_SHORT_READ_LENGTH <= l) {
        if (alignContext.minReadLength > l) {
            alignContext.minReadLength = l;
        }
        if (alignContext.maxReadLength < l) {
            alignContext.maxReadLength = l;
        }
    }
}

static SearchQuery* createRevComplQuery(SearchQuery* query, DNATranslation* transl) {
    SAFE_POINT(query != nullptr, "Query is null", nullptr);
    SAFE_POINT(transl != nullptr, "Transl is null", nullptr);

    QByteArray reversed(query->constSequence());
    TextUtils::reverse(reversed.data(), reversed.count());

    DNASequence dnaSeq(QString("%1_rev").arg(query->getName()), reversed, nullptr);
    SearchQuery* rQu = new SearchQuery(&dnaSeq, query);
    transl->translate(const_cast<char*>(rQu->constData()), rQu->length());

    if (rQu->constSequence() == query->constSequence()) {
        delete rQu;
        rQu = nullptr;
        return nullptr;
    }

    query->setRevCompl(rQu);
    return rQu;
}

ReadShortReadsSubTask::ReadShortReadsSubTask(GenomeAlignerReader* _seqReader,
                                             const DnaAssemblyToRefTaskSettings& _settings,
                                             AlignContext& _alignContext,
                                             qint64 m)
    : Task("ReadShortReadsSubTask", TaskFlag_None),
      seqReader(_seqReader), settings(_settings), alignContext(_alignContext),
      freeMemorySize(m), prevMemoryHint(0), dataBunch(nullptr) {
}

void ReadShortReadsSubTask::readingFinishedWakeAll() {
    taskLog.trace("Wake all");

    delete dataBunch;
    dataBunch = nullptr;

    QMutexLocker lock(&alignContext.readingStatusMutex);
    alignContext.isReadingFinished = true;
    alignContext.readShortReadsWait.wakeAll();
}

void ReadShortReadsSubTask::dropToAlignContext() {
    alignContext.listM.lockForWrite();

    algoLog.trace("ReadShortReadsSubTask::dropToAlignContext");
    dataBunch->squeeze();
    prevMemoryHint += dataBunch->memoryHint();
    if (!dataBunch->empty()) {
        alignContext.data.append(dataBunch);
    }
    dataBunch = new DataBunch();

    alignContext.listM.unlock();
}

void ReadShortReadsSubTask::run() {
    stateInfo.setProgress(0);
    GTIMER(cvar, tvar, "ReadSubTask");
    auto parent = static_cast<GenomeAlignerTask*>(getParentTask());
    if (!alignContext.bestMode) {
        parent->pWriteTask->flush();
    }

    alignContext.cleanVectors();
    dataBunch = new DataBunch();

    if (isCanceled()) {
        readingFinishedWakeAll();
        return;
    }
    qint64 m = freeMemorySize;
    taskLog.details(QString("Memory size is %1").arg(m));
    bool alignReversed = settings.getCustomValue(GenomeAlignerTask::OPTION_ALIGN_REVERSED, true).toBool();
    int qualityThreshold = settings.getCustomValue(GenomeAlignerTask::OPTION_QUAL_THRESHOLD, 0).toInt();

    DNATranslation* transl = AppContext::getDNATranslationRegistry()->lookupTranslation(BaseDNATranslationIds::NUCL_DNA_DEFAULT_COMPLEMENT);

    alignContext.isReadingStarted = true;
    bunchSize = 0;
    int readNum = 0;
    while (!seqReader->isEnd()) {
        if (isCanceled()) {
            readingFinishedWakeAll();
            return;
        }
        SearchQuery* query = seqReader->read();
        if (query == nullptr) {
            if (!seqReader->isEnd()) {
                setError("Short-reads object type must be a sequence, but not a multiple alignment");
                readingFinishedWakeAll();
                return;
            }
            break;
        }
        ++bunchSize;

        if (!checkDnaQuality(query, qualityThreshold)) {
            continue;
        }
        updateMinMaxReadLengths(alignContext, query->length());

        int W = 0, q = 0;
        int CMAX = alignContext.nMismatches;
        if (!add(CMAX, W, q, readNum, query, parent)) {
            delete query;
            continue;
        }
        m -= query->memoryHint();

        if (alignReversed) {
            SearchQuery* rQu = createRevComplQuery(query, transl);
            if (rQu) {
                add(CMAX, W, q, readNum, rQu, parent);
                m -= rQu->memoryHint();
            }
        }

        qint64 alignContextMemoryHint = dataBunch->memoryHint();
        if (m <= alignContextMemoryHint + prevMemoryHint) {
            break;
        }

        SAFE_POINT(dataBunch != nullptr, "No dataBunch", );
        if (dataBunch->bitValuesV.size() > DROP_BUNCH_DATA_SIZE) {
            dropToAlignContext();
            readNum = 0;
            alignContext.readShortReadsWait.wakeOne();
        }
    }

    dropToAlignContext();
    readingFinishedWakeAll();
}

inline bool ReadShortReadsSubTask::add(int& CMAX, int& W, int& q, int& readNum, SearchQuery* query, GenomeAlignerTask* parent) {
    SAFE_POINT(dataBunch != nullptr, "No dataBunch", false);
    SAFE_POINT(query != nullptr, "No query", false);

    W = query->length();
    if (!alignContext.absMismatches) {
        CMAX = (W * alignContext.ptMismatches) / MAX_PERCENTAGE;
    }
    q = W / (CMAX + 1);
    CHECK_EXT(0 != q, , false);

    const char* querySeq = query->constData();
    SAFE_POINT(querySeq != nullptr, "No querySeq", false);

    int win = query->length() < GenomeAlignerTask::MIN_SHORT_READ_LENGTH ? GenomeAlignerTask::calculateWindowSize(alignContext.absMismatches,
                                                                                                                  alignContext.nMismatches,
                                                                                                                  alignContext.ptMismatches,
                                                                                                                  query->length(),
                                                                                                                  query->length())
                                                                         : GenomeAlignerTask::calculateWindowSize(alignContext.absMismatches,
                                                                                                                  alignContext.nMismatches,
                                                                                                                  alignContext.ptMismatches,
                                                                                                                  alignContext.minReadLength,
                                                                                                                  alignContext.maxReadLength);

    for (int i = 0; i < W - q + 1; i += q) {
        const char* seq = querySeq + i;
        BMType bv = parent->index->getBitValue(seq, qMin(GenomeAlignerIndex::charsInMask, W - i));

        dataBunch->bitValuesV.append(bv);
        dataBunch->readNumbersV.append(readNum);
        dataBunch->positionsAtReadV.append(i);
        dataBunch->windowSizes.append(win);
    }
    readNum++;
    dataBunch->queries.append(query);

    return true;
}

}  // namespace U2
