/**
 * 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.
 */

#pragma once

#include <U2Core/AnnotationData.h>
#include <U2Core/BaseDocumentFormats.h>
#include <U2Core/DocumentModel.h>
#include <U2Core/U2Region.h>

#include "TextDocumentFormat.h"

namespace U2 {

/** Validates a line from a file in FPKM Tracking Format */
class FpkmTrackingLineValidateFlags {
public:
    FpkmTrackingLineValidateFlags();

    void setFlagEmptyField() {
        emptyField = true;
    }
    void setFlagIncorrectNumberOfFields() {
        incorrectNumberOfFields = true;
    }
    void setFlagIncorrectCoordinates() {
        incorrectCoordinates = true;
    }
    void setFlagEmptyTrackingId() {
        emptyTrackingId = true;
    }
    void setFlagIncorrectLength() {
        incorrectLength = true;
    }
    void setFlagIncorrectCoverage() {
        incorrectCoverage = true;
    }

    FormatDetectionScore getFormatDetectionScore();

    bool isFileInvalid() {
        return emptyField ||
               incorrectNumberOfFields ||
               incorrectCoordinates ||
               emptyTrackingId ||
               incorrectLength ||
               incorrectCoverage;
    }

    bool isEmptyField() {
        return emptyField;
    }
    bool isIncorrectNumberOfFields() {
        return incorrectNumberOfFields;
    }
    bool isIncorrectCoordinates() {
        return incorrectCoordinates;
    }
    bool isEmptyTrackingId() {
        return emptyTrackingId;
    }
    bool isIncorrectLength() {
        return incorrectLength;
    }
    bool isIncorrectCoverage() {
        return incorrectCoverage;
    }

private:
    bool emptyField;
    bool incorrectNumberOfFields;  // must be equal to the number of columns in the header line
    bool incorrectCoordinates;  // coordinates are parsed from locus
    bool emptyTrackingId;  // must be a unique string, but it is only verified that it is not '-'
    bool incorrectLength;  // must be '-' or an integer value
    bool incorrectCoverage;  // must be '-' or a double value
};

struct FpkmTrackingLineData {
    QString trackingId;
    QString classCode;
    QString nearestRefId;
    QString geneId;
    QString geneShortName;
    QString tssId;
    QString locus;
    QString seqName;  // from locus
    U2Region region;  // from locus
    QString length;
    QString coverage;
    QMap<QString, QString> otherFields;
};

class IOAdapter;

enum FpkmTrackingLineFieldsIndeces { FPKM_TRACKING_ID_INDEX = 0,
                                     FPKM_CLASS_CODE_INDEX = 1,
                                     FPKM_NEAREST_REF_ID_INDEX = 2,
                                     FPKM_GENE_ID_INDEX = 3,
                                     FPKM_GENE_SHORT_NAME_INDEX = 4,
                                     FPKM_TSS_ID_INDEX = 5,
                                     FPKM_LOCUS_INDEX = 6,
                                     FPKM_LENGTH_INDEX = 7,
                                     FPKM_COVERAGE_INDEX = 8,
                                     FPKM_FIELDS_FIRST_INDEX = 9 };

/**
 * Description of the format from the Cufflinks manual was used:
 * http://cufflinks.cbcb.umd.edu/manual.html#fpkm_tracking_format
 */
class U2FORMATS_EXPORT FpkmTrackingFormat : public TextDocumentFormatDeprecated {
    Q_OBJECT

public:
    FpkmTrackingFormat(QObject* parent);

    void storeDocument(Document* doc, IOAdapter* io, U2OpStatus& os) override;

protected:
    FormatCheckResult checkRawTextData(const QByteArray& rawData, const GUrl& = GUrl()) const override;

    Document* loadTextDocument(IOAdapter* io, const U2DbiRef& dbiRef, const QVariantMap& hints, U2OpStatus& os) override;

    QList<SharedAnnotationData> parseDocument(IOAdapter* io, QString& seqName, QString annotName, U2OpStatus& os);

    void load(IOAdapter* io, QList<GObject*>& objects, const U2DbiRef& dbiRef, const QVariantMap& hints, U2OpStatus& os);

private:
    FpkmTrackingLineData parseAndValidateLine(QString line, QStringList columns, FpkmTrackingLineValidateFlags& status) const;

    static const QString NO_VALUE_STR;
    static const QString TRACKING_ID_COLUMN;
    static const QString CLASS_CODE_COLUMN;
    static const QString NEAREST_REF_ID_COLUMN;
    static const QString GENE_ID_COLUMN;
    static const QString GENE_SHORT_NAME_COLUMN;
    static const QString TSS_ID_COLUMN;
    static const QString LOCUS_COLUMN;
    static const QString LENGTH_COLUMN;
    static const QString COVERAGE_COLUMN;

    /**
     * Parses and validates the header line.
     * If the header is appropriate returns true and the columns list contains the columns names.
     * Otherwise returns "false".
     */
    bool parseHeader(const QString& headerLine, QStringList& columns) const;

    /**
     * Qualifiers from the FIRST FOUND annotation are used to restore names of "additional"
     * columns in the FPKM Tracking Format file (like "FPKM status", etc.).
     * Also:
     * 1) Only qualifiers that contain "FPKM" or that equal to "status" are taken into account,
     * other values are ignored.
     * 2) It is verified that a "samplename_FPKM_lo" (or "samplename_FPKM_conf_lo") column
     * goes before a "samplename_FPKM_hi" (or "samplename_FPKM_conf_hi") column.
     * The function returns the list of all columns names.
     */
    QStringList writeHeader(QList<GObject*> annotTables, Document* doc, IOAdapter* io, U2OpStatus& os);

    void addQualifierIfValuePresent(SharedAnnotationData& annotData, const QString& name, const QString& val);
};

}  // namespace U2
