/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2017 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.
 */

#ifndef _U2_WORKFLOW_DOC_WORKERS_H_
#define _U2_WORKFLOW_DOC_WORKERS_H_

#include "BaseDocWriter.h"
#include "CoreLib.h"
#include <U2Lang/CoreLibConstants.h>
#include <U2Core/IOAdapter.h>


namespace U2 {

class DatasetFilesIterator;

namespace LocalWorkflow {

// generic sequence writer
class SeqWriter : public BaseDocWriter {
    Q_OBJECT
public:
    SeqWriter(Actor *a);
    SeqWriter(Actor *a, const DocumentFormatId &fid);

    static bool hasSequence(const QVariantMap &data);
    static bool hasSequenceOrAnns(const QVariantMap &data);
    static GObject * getSeqObject(const QVariantMap &data, WorkflowContext *context);
    static GObject * getAnnObject(const QVariantMap &data, WorkflowContext *context);

protected:
    int numSplitSequences;
    int currentSplitSequence;

    virtual void data2doc(Document*, const QVariantMap&);
    virtual bool hasDataToWrite(const QVariantMap &data) const;
    virtual QSet<GObject *> getObjectsToWrite(const QVariantMap &data) const;
    virtual void storeEntry(IOAdapter *io, const QVariantMap &data, int entryNum);

    virtual void takeParameters(U2OpStatus &os);
    virtual QStringList takeUrlList(const QVariantMap &data, int metadataId, U2OpStatus &os);
    virtual bool isStreamingSupport() const;
};

class MSAWriter : public BaseDocWriter {
    Q_OBJECT
public:
    MSAWriter(Actor* a, const DocumentFormatId& fid) : BaseDocWriter(a, fid){}
    MSAWriter(Actor * a) : BaseDocWriter(a){}
protected:
    virtual void data2doc(Document*, const QVariantMap&);
    virtual bool isStreamingSupport() const;
    virtual bool hasDataToWrite(const QVariantMap &data) const;
    virtual QSet<GObject *> getObjectsToWrite(const QVariantMap &data) const;
public:
    static void data2document(Document*, const QVariantMap&, WorkflowContext*);
};

class TextReader : public BaseWorker {
    Q_OBJECT
public:
    TextReader(Actor *a);

    void init();
    Task * tick();
    void cleanup();

private:
    DataTypePtr mtype;
    CommunicationChannel* ch;
    IOAdapter *io;
    DatasetFilesIterator *urls;
    QString url;

    static const int MAX_LINE_LEN;
    static const int READ_BLOCK_SIZE;

private:
    void sendMessage(const QByteArray &data);
    void processNextLine();
    Task * processUrlEntity(const QString &url);
    Task * processFile(const QString &url);
    Task * processDbObject(const QString &url);
    Task * createDbObjectReadFailTask(const QString &url);
};

class TextWriter : public BaseDocWriter {
    Q_OBJECT
public:
    TextWriter(Actor* a) : BaseDocWriter(a, BaseDocumentFormats::PLAIN_TEXT){}
protected:
    virtual void data2doc(Document*, const QVariantMap&);
    virtual bool isStreamingSupport() const;
    virtual bool isSupportedSeveralMessages() const;
    virtual bool hasDataToWrite(const QVariantMap &data) const;
    virtual QSet<GObject *> getObjectsToWrite(const QVariantMap &data) const;
};

class FastaWriter : public SeqWriter {
    Q_OBJECT
public:
    FastaWriter(Actor* a) : SeqWriter(a, BaseDocumentFormats::FASTA){}
protected:
    virtual void data2doc(Document*, const QVariantMap&);
    virtual void storeEntry(IOAdapter *io, const QVariantMap &data, int entryNum);
    virtual bool hasDataToWrite(const QVariantMap &data) const;
public:
    static void data2document(Document*, const QVariantMap&, WorkflowContext*, int numSplitSequences, int currentSplit);
    static U2Region getSplitRegion(int numSplitSequences, int currentSplit, qint64 seqLen);
    static void streamingStoreEntry(DocumentFormat* format, IOAdapter *io, const QVariantMap &data, WorkflowContext *context, int entryNum);
};

class GenbankWriter : public BaseDocWriter {
    Q_OBJECT
public:
    GenbankWriter(Actor* a) : BaseDocWriter(a, BaseDocumentFormats::PLAIN_GENBANK){}
protected:
    virtual void data2doc(Document*, const QVariantMap&);
    virtual void storeEntry(IOAdapter *io, const QVariantMap &data, int entryNum);
    virtual bool hasDataToWrite(const QVariantMap &data) const;
    virtual QSet<GObject *> getObjectsToWrite(const QVariantMap &data) const;
public:
    static void data2document(Document*, const QVariantMap&, WorkflowContext*);
    static void streamingStoreEntry(DocumentFormat* format, IOAdapter *io, const QVariantMap &data, WorkflowContext *context, int entryNum);
};

class FastQWriter : public BaseDocWriter {
    Q_OBJECT
public:
    FastQWriter(Actor* a) : BaseDocWriter(a, BaseDocumentFormats::FASTQ){}
protected:
    virtual void data2doc(Document*, const QVariantMap&);
    virtual void storeEntry(IOAdapter *io, const QVariantMap &data, int entryNum);
    virtual bool hasDataToWrite(const QVariantMap &data) const;
    virtual QSet<GObject *> getObjectsToWrite(const QVariantMap &data) const;
public:
    static void data2document(Document*, const QVariantMap&, WorkflowContext*);
    static void streamingStoreEntry(DocumentFormat* format, IOAdapter *io, const QVariantMap &data, WorkflowContext *context, int entryNum);
};

class RawSeqWriter : public BaseDocWriter {
    Q_OBJECT
public:
    RawSeqWriter(Actor* a) : BaseDocWriter(a, BaseDocumentFormats::RAW_DNA_SEQUENCE){}
protected:
    virtual void data2doc(Document*, const QVariantMap&);
    virtual void storeEntry(IOAdapter *io, const QVariantMap &data, int entryNum);
    virtual bool hasDataToWrite(const QVariantMap &data) const;
    virtual GObject * getObjectToWrite(const QVariantMap &data) const;
public:
    static void data2document(Document*, const QVariantMap&, WorkflowContext*);
    static void streamingStoreEntry(DocumentFormat* format, IOAdapter *io, const QVariantMap &data, WorkflowContext *context, int entryNum);
};

class GFFWriter : public BaseDocWriter {
    Q_OBJECT
public:
    GFFWriter(Actor* a) : BaseDocWriter(a, BaseDocumentFormats::GFF){}
protected:
    virtual void data2doc(Document*, const QVariantMap&);
    virtual bool hasDataToWrite(const QVariantMap &data) const;
    virtual QSet<GObject *> getObjectsToWrite(const QVariantMap &data) const;
public:
    static void data2document(Document*, const QVariantMap&, WorkflowContext*);
};

class DataWorkerFactory : public DomainFactory {
public:
    DataWorkerFactory(const Descriptor& d) : DomainFactory(d) {}
    virtual ~DataWorkerFactory() {}
    virtual Worker* createWorker(Actor*);
    static void init();
};

} // Workflow namespace
} // U2 namespace

#endif

