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/*****************************************************************

* Unipro UGENE - Integrated Bioinformatics Suite

* Copyright (C) 2008 Unipro, Russia (http://ugene.unipro.ru)

* All Rights Reserved

* 

*     This source code is distributed under the terms of the

*     GNU General Public License. See the files COPYING and LICENSE

*     for details.

*****************************************************************/

 

#ifndef _GB2_HMMSEARCH_TASK_H_

#define _GB2_HMMSEARCH_TASK_H_

 

#include "uhmmsearch.h"

 

#include <core_api/LRegion.h>

#include <core_api/Task.h>

#include <datatype/DNASequence.h>

#include <datatype/AnnotationData.h>

#include <util_tasks/SequenceWalkerTask.h>

 

struct plan7_s;

 

namespace GB2 {

 

class DNATranslation;

 

class HMMSearchTaskResult {

public:

    HMMSearchTaskResult() : evalue(0), score(0), onCompl(false), onAmino(false){} 

    float   evalue;

    float   score;

    bool    onCompl;

    bool    onAmino;

    LRegion r;

 

};

 

class HMMSearchTaskCachedResult : public HMMSearchTaskResult {

public:

        HMMSearchTaskCachedResult() {}

    LRegion globalReg;

 

};

 

class HMMSearchTask: public Task, SequenceWalkerCallback {

    Q_OBJECT

public:

    HMMSearchTask(plan7_s* hmm, const DNASequence& seq, const UHMMSearchSettings& s);

 

    virtual void prepare();

    

    const QList<HMMSearchTaskResult>& getResults() const {return results;}

 

    virtual void onRegion(SequenceWalkerSubtask* t, TaskStateInfo& stateInfo);

 

        Task::ReportResult report();

 

    QList<SharedAnnotationData> getResultsAsAnnotations(const QString& name) const;

 

private:

    bool checkAlphabets(int hmmAl, DNAAlphabet* seqAl, DNATranslation*& complTrans, DNATranslation*& aminoTrans);

private:

    plan7_s*                    hmm;

    DNASequence                 seq;

    UHMMSearchSettings          settings;

    DNATranslation*             complTrans;

    DNATranslation*             aminoTrans;

    QList<HMMSearchTaskResult>  results;

        QList<HMMSearchTaskResult>  resultsCompl;

        QList<HMMSearchTaskCachedResult>  cacheDirect;

        QList<HMMSearchTaskCachedResult>  cacheCompl;

};

 

 

 

}//namespace

#endif