src/model/Marker.cpp

/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2021 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 "Marker.h"

#include <U2Core/DNASequence.h>
#include <U2Core/QVariantUtils.h>

#include <U2Lang/MarkerUtils.h>
#include <U2Lang/WorkflowEnv.h>

static const QString LENGTH_SLOT_ID("length-marker");
static const QString ANN_COUNT_SLOT_ID("ann-count-marker");
static const QString ANN_VALUE_SLOT_ID("ann-value-marker");
static const QString FILENAME_SLOT_ID("filename-marker");

namespace U2 {

const QString MarkerTypes::SEQ_LENGTH_MARKER_ID("sequence-length");
const QString MarkerTypes::SEQ_NAME_MARKER_ID("sequence-name");
const QString MarkerTypes::ANNOTATION_COUNT_MARKER_ID("annotations-count");
const QString MarkerTypes::ANNOTATION_LENGTH_MARKER_ID("annotation-length");
const QString MarkerTypes::QUAL_INT_VALUE_MARKER_ID("qualifier-int-value");
const QString MarkerTypes::QUAL_TEXT_VALUE_MARKER_ID("qualifier-text-value");
const QString MarkerTypes::QUAL_FLOAT_VALUE_MARKER_ID("qualifier-float-value");
const QString MarkerTypes::TEXT_MARKER_ID("text");

MarkerDataType MarkerTypes::getDataTypeById(const QString &typeId) {
    if (SEQ_LENGTH_MARKER_ID == typeId) {
        return INTEGER;
    } else if (ANNOTATION_COUNT_MARKER_ID == typeId) {
        return INTEGER;
    } else if (ANNOTATION_LENGTH_MARKER_ID == typeId) {
        return INTEGER;
    } else if (QUAL_INT_VALUE_MARKER_ID == typeId) {
        return INTEGER;
    } else if (QUAL_TEXT_VALUE_MARKER_ID == typeId) {
        return STRING;
    } else if (QUAL_FLOAT_VALUE_MARKER_ID == typeId) {
        return FLOAT;
    } else if (TEXT_MARKER_ID == typeId) {
        return STRING;
    } else if (SEQ_NAME_MARKER_ID == typeId) {
        return STRING;
    } else {
        assert(0);
        return MarkerDataType();
    }
}

const Descriptor MarkerTypes::SEQ_LENGTH() {
    return Descriptor(MarkerTypes::SEQ_LENGTH_MARKER_ID, tr("Length markers"), tr("Length markers group."));
}
const Descriptor MarkerTypes::SEQ_NAME() {
    return Descriptor(MarkerTypes::SEQ_NAME_MARKER_ID, tr("Sequence name markers"), tr("Sequence name markers group."));
}
const Descriptor MarkerTypes::ANNOTATION_COUNT() {
    return Descriptor(MarkerTypes::ANNOTATION_COUNT_MARKER_ID, tr("Annotation count markers"), tr("Annotation count markers group."));
}
const Descriptor MarkerTypes::ANNOTATION_LENGTH() {
    return Descriptor(MarkerTypes::ANNOTATION_LENGTH_MARKER_ID, tr("Annotation length markers"), tr("Annotation length markers group."));
}
const Descriptor MarkerTypes::QUAL_INT_VALUE() {
    return Descriptor(MarkerTypes::QUAL_INT_VALUE_MARKER_ID, tr("Qualifier integer value markers"), tr("Qualifier integer value markers group."));
}
const Descriptor MarkerTypes::QUAL_FLOAT_VALUE() {
    return Descriptor(MarkerTypes::QUAL_FLOAT_VALUE_MARKER_ID, tr("Qualifier float value markers"), tr("Qualifier float value markers group."));
}
const Descriptor MarkerTypes::QUAL_TEXT_VALUE() {
    return Descriptor(MarkerTypes::QUAL_TEXT_VALUE_MARKER_ID, tr("Qualifier text value markers"), tr("Qualifier text value markers group."));
}
const Descriptor MarkerTypes::TEXT() {
    return Descriptor(MarkerTypes::TEXT_MARKER_ID, tr("Text markers"), tr("Text markers group."));
}

const Descriptor MarkerSlots::getSlotByMarkerType(const QString &markerId, const QString &slotName) {
    if (markerId == MarkerTypes::SEQ_LENGTH_MARKER_ID) {
        return Descriptor(slotName, slotName, tr("Sequence length marker."));
    } else if (markerId == MarkerTypes::ANNOTATION_COUNT_MARKER_ID) {
        return Descriptor(slotName, slotName, tr("Annotation count marker."));
    } else if (markerId == MarkerTypes::ANNOTATION_LENGTH_MARKER_ID) {
        return Descriptor(slotName, slotName, tr("Annotation length marker."));
    } else if (markerId == MarkerTypes::QUAL_INT_VALUE_MARKER_ID) {
        return Descriptor(slotName, slotName, tr("Qualifier integer value marker."));
    } else if (markerId == MarkerTypes::QUAL_TEXT_VALUE_MARKER_ID) {
        return Descriptor(slotName, slotName, tr("Qualifier text value marker."));
    } else if (markerId == MarkerTypes::QUAL_FLOAT_VALUE_MARKER_ID) {
        return Descriptor(slotName, slotName, tr("Qualifier float value marker."));
    } else if (markerId == MarkerTypes::TEXT_MARKER_ID) {
        return Descriptor(slotName, slotName, tr("Text marker."));
    } else if (markerId == MarkerTypes::SEQ_NAME_MARKER_ID) {
        return Descriptor(slotName, slotName, tr("Sequence name marker."));
    } else {
        assert(0);
        return Descriptor();
    }
}

const QString MarkerPorts::IN_MARKER_SEQ_PORT() {
    return "in-marked-seq";
}
const QString MarkerPorts::OUT_MARKER_SEQ_PORT() {
    return "out-marked-seq";
}

Marker *MarkerFactory::createInstanse(const QString &type, const QVariant &additionalParam) {
    Marker *m = nullptr;
    if (type == MarkerTypes::QUAL_INT_VALUE_MARKER_ID || type == MarkerTypes::QUAL_TEXT_VALUE_MARKER_ID || type == MarkerTypes::QUAL_FLOAT_VALUE_MARKER_ID) {
        m = new QualifierMarker(type, "NewQualMarker", additionalParam.toString());
    } else if (MarkerTypes::ANNOTATION_LENGTH_MARKER_ID == type || MarkerTypes::ANNOTATION_COUNT_MARKER_ID == type) {
        m = new AnnotationMarker(type, "NewQualMarker", additionalParam.toString());
    } else if (MarkerTypes::TEXT_MARKER_ID == type) {
        m = new TextMarker(type, "NewTextMarker");
    } else {
        m = new SequenceMarker(type, "NewSequenceMarker");
    }

    if (NONE != m->hasAdditionalParameter()) {
        m->setAdditionalParameter(additionalParam);
    }

    return m;
}

/************************************************************************/
/* Marker */
/************************************************************************/
Marker::Marker(const QString &markerType, const QString &markerName)
    : type(markerType), name(markerName) {
    dataType = MarkerTypes::getDataTypeById(markerType);
    values.insert(MarkerUtils::REST_OPERATION, tr("Rest"));
}

Marker::Marker(const Marker &m)
    : QObject(), type(m.type), name(m.name), dataType(m.dataType), values(m.values) {
}

void Marker::addValue(QString name, QString value) {
    values.insert(name, value);
}

ParameterState Marker::hasAdditionalParameter() {
    return NONE;
}

void Marker::setAdditionalParameter(const QVariant &) {
}

QVariant Marker::getAdditionalParameter() {
    return QVariant();
}

QString Marker::getAdditionalParameterName() {
    return "";
}

QString Marker::getMarkingResult(const QVariant &object) {
    foreach (QString val, values.keys()) {
        if (MarkerUtils::REST_OPERATION == val) {
            continue;
        }
        QVariantList expr;
        bool res = MarkerUtils::stringToValue(dataType, val, expr);
        if (!res) {
            continue;
        }

        bool marked = false;
        switch (dataType) {
            case INTEGER:
                marked = getMarkerIntResult(object, expr);
                break;
            case FLOAT:
                marked = getMarkerFloatResult(object, expr);
                break;
            case BOOLEAN:
                // marked = getMarkerBooleanResult(object, expr);
                break;
            case STRING:
                marked = getMarkerStringResult(object, expr);
                break;
        }
        if (marked) {
            return values.value(val);
        }
    }

    return values.value(MarkerUtils::REST_OPERATION);
}

bool Marker::getMarkerIntResult(const QVariant &object, QVariantList &expr) {
    int obj = object.toInt();
    QString operation = expr.at(0).toString();

    if (MarkerUtils::LESS_OPERATION == operation) {
        int val = expr.at(1).toInt();
        if (obj <= val) {
            return true;
        }
    } else if (MarkerUtils::GREATER_OPERATION == operation) {
        int val = expr.at(1).toInt();
        if (obj >= val) {
            return true;
        }
    } else if (MarkerUtils::INTERVAL_OPERATION == operation) {
        int val1 = expr.at(1).toInt();
        int val2 = expr.at(2).toInt();

        if (obj >= val1 && obj <= val2) {
            return true;
        }
    }

    return false;
}

bool Marker::getMarkerFloatResult(const QVariant &object, QVariantList &expr) {
    float obj = object.toFloat();
    QString operation = expr.at(0).toString();

    if (MarkerUtils::LESS_OPERATION == operation) {
        float val = expr.at(1).toFloat();
        if (obj <= val) {
            return true;
        }
    } else if (MarkerUtils::GREATER_OPERATION == operation) {
        float val = expr.at(1).toFloat();
        if (obj >= val) {
            return true;
        }
    } else if (MarkerUtils::INTERVAL_OPERATION == operation) {
        float val1 = expr.at(1).toFloat();
        float val2 = expr.at(2).toFloat();

        if (obj >= val1 && obj <= val2) {
            return true;
        }
    }

    return false;
}

bool Marker::getMarkerStringResult(const QVariant &object, QVariantList &expr) {
    QString obj = object.toString();
    QString operation = expr.at(0).toString();
    QString val = expr.at(1).toString();

    if (MarkerUtils::STARTS_OPERATION == operation) {
        return obj.startsWith(val);
    } else if (MarkerUtils::ENDS_OPERATION == operation) {
        return obj.endsWith(val);
    } else if (MarkerUtils::CONTAINS_OPERATION == operation) {
        return obj.contains(val);
    } else if (MarkerUtils::REGEXP_OPERATION == operation) {
        QRegExp rx(val);
        rx.setPatternSyntax(QRegExp::Wildcard);

        return rx.exactMatch(obj);
    }

    return false;
}

const QString &Marker::getName() const {
    return name;
}

const QString &Marker::getType() const {
    return type;
}

const QMap<QString, QString> &Marker::getValues() const {
    return values;
}

QMap<QString, QString> &Marker::getValues() {
    return values;
}

void Marker::setName(const QString &newName) {
    name = newName;
}

const QString Marker::toString() const {
    QString res;

    foreach (QString key, values.keys()) {
        res += key + " : " + values.value(key) + "; ";
    }
    return res;
}

/************************************************************************/
/* SequencerMarker */
/************************************************************************/
QString SequenceMarker::getMarkingResult(const QVariant &object) {
    DNASequence seq = object.value<DNASequence>();

    if (MarkerTypes::SEQ_LENGTH_MARKER_ID == type) {
        return Marker::getMarkingResult(seq.length());
    } else if (MarkerTypes::SEQ_NAME_MARKER_ID == type) {
        return Marker::getMarkingResult(seq.getName());
    } else {
        assert(0);
        return values.value(MarkerUtils::REST_OPERATION);
    }
}

MarkerGroup SequenceMarker::getGroup() {
    return SEQUENCE;
}

Marker *SequenceMarker::clone() {
    return new SequenceMarker(*this);
}

/************************************************************************/
/* QualifierMarker */
/************************************************************************/
QString QualifierMarker::getMarkingResult(const QVariant &object) {
    const QString rest = values.value(MarkerUtils::REST_OPERATION);

    QList<SharedAnnotationData> anns;
    foreach (const QVariant &ann, object.toList()) {
        SAFE_POINT(ann.canConvert<SharedAnnotationData>(), "Invalid annotation data encountered!", QString());
        anns << ann.value<SharedAnnotationData>();
    }

    for (const SharedAnnotationData &ann : qAsConst(anns)) {
        foreach (const U2Qualifier &qual, ann->qualifiers) {
            if (qual.name == qualName) {
                bool ok = false;
                QVariant value;
                if (MarkerTypes::QUAL_INT_VALUE_MARKER_ID == type) {
                    value = qVariantFromValue(qual.value.toInt(&ok));
                } else if (MarkerTypes::QUAL_FLOAT_VALUE_MARKER_ID == type) {
                    value = qVariantFromValue(qual.value.toFloat(&ok));
                } else if (MarkerTypes::QUAL_TEXT_VALUE_MARKER_ID == type) {
                    value = qVariantFromValue(qual.value);
                    ok = true;
                } else {
                    FAIL("Unexpected marker type!", rest);
                }
                SAFE_POINT(ok, "Variant conversion error!", QString());
                QString mark = Marker::getMarkingResult(value);
                if (rest != mark) {
                    return mark;
                }
            }
        }
    }
    return rest;
}

MarkerGroup QualifierMarker::getGroup() {
    return QUALIFIER;
}

const QString &QualifierMarker::getQualifierName() const {
    return qualName;
}

Marker *QualifierMarker::clone() {
    return new QualifierMarker(*this);
}

ParameterState QualifierMarker::hasAdditionalParameter() {
    return REQUIRED;
}

void QualifierMarker::setAdditionalParameter(const QVariant &param) {
    qualName = param.toString();
}

QVariant QualifierMarker::getAdditionalParameter() {
    return qualName;
}

QString QualifierMarker::getAdditionalParameterName() {
    return tr("Qualifier name");
}

/************************************************************************/
/* AnnotationMarker */
/************************************************************************/
QString AnnotationMarker::getMarkingResult(const QVariant &object) {
    QList<SharedAnnotationData> anns;
    foreach (const QVariant &ann, object.toList()) {
        SAFE_POINT(ann.canConvert<SharedAnnotationData>(), "Invalid annotation data encountered!", QString());
        anns << ann.value<SharedAnnotationData>();
    }

    if (MarkerTypes::ANNOTATION_COUNT_MARKER_ID == type) {
        int count = 0;
        if (annName.isEmpty()) {
            count = anns.size();
        } else {
            foreach (const SharedAnnotationData &ann, anns) {
                if (ann->name == annName) {
                    count++;
                }
            }
        }
        return Marker::getMarkingResult(qVariantFromValue(count));
    } else if (MarkerTypes::ANNOTATION_LENGTH_MARKER_ID == type) {
        return values.value(MarkerUtils::REST_OPERATION);
    } else {
        assert(0);
    }

    return values.value(MarkerUtils::REST_OPERATION);
}

MarkerGroup AnnotationMarker::getGroup() {
    return ANNOTATION;
}

const QString &AnnotationMarker::getAnnotationName() const {
    return annName;
}

Marker *AnnotationMarker::clone() {
    return new AnnotationMarker(*this);
}

ParameterState AnnotationMarker::hasAdditionalParameter() {
    return NOT_REQUIRED;
}

void AnnotationMarker::setAdditionalParameter(const QVariant &param) {
    annName = param.toString();
}

QVariant AnnotationMarker::getAdditionalParameter() {
    return annName;
}

QString AnnotationMarker::getAdditionalParameterName() {
    return tr("Annotation name");
}

/************************************************************************/
/* TextMarker */
/************************************************************************/
QString TextMarker::getMarkingResult(const QVariant &object) {
    if (MarkerTypes::TEXT_MARKER_ID == type) {
        return Marker::getMarkingResult(object);
    } else {
        assert(0);
    }

    return values.value(MarkerUtils::REST_OPERATION);
}

MarkerGroup TextMarker::getGroup() {
    return TEXT;
}

Marker *TextMarker::clone() {
    return new TextMarker(*this);
}

}  // namespace U2