IntronList.h

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/*
 * 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 3 of the License, or
 * (at your option) any later version.
 *
 * Written (W) 2009 Jonas Behr
 * Copyright (C) 2009 Fraunhofer Institute FIRST and Max-Planck-Society
 */

#ifndef __INTRON_LIST__
#define __INTRON_LIST__

#include <shogun/lib/common.h>
#include <shogun/base/SGObject.h>

namespace shogun
{
class CIntronList : public CSGObject
{
    public:

        CIntronList();

        virtual ~CIntronList();

        void init_list(int32_t* all_pos, int32_t len);

        void read_introns(int32_t* start_pos, int32_t* end_pos, int32_t* quality, int32_t len);

        void get_intron_support(int32_t* values, int32_t from_pos, int32_t to_pos);

        inline virtual const char* get_name() const { return "IntronList"; }
    protected:
        int32_t m_length;

        int32_t* m_all_pos;

        int32_t** m_intron_list;

        int32_t** m_quality_list;
};
}
#endif