SQ_helix.h

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//  ==================================================================== //
//                                                                       //
//    File      : SQ_helix.h                                             //
//    Purpose   : Class used for calculation of helix layout             //
//                                                                       //
//                                                                       //
//  Coded by Juergen Huber in July 2003 - February 2004                  //
//  Coded by Kai Bader (baderk@in.tum.de) in 2007 - 2008                 //
//  Copyright Department of Microbiology (Technical University Munich)   //
//                                                                       //
//  Visit our web site at: http://www.arb-home.de/                       //
//                                                                       //
//  ==================================================================== //

#ifndef _GLIBCXX_STRING
#include <string>
#endif
#ifndef _GLIBCXX_MAP
#include <map>
#endif

#ifndef BI_HELIX_HXX
#include <BI_helix.hxx>
#endif
#ifndef AP_FILTER_HXX
#include <AP_filter.hxx>
#endif
#ifndef ARBDB_H
#include <arbdb.h>
#endif


class SQ_helix : virtual Noncopyable {
    const char *sequence;
    int         count_strong_helix;
    int         count_weak_helix;
    int         count_no_helix;
    int         size;

    static SmartPtr<BI_helix>    helix;
    static SmartPtr<BI_pairdef>  pairdef;
    static GBDATA               *helix_gb_main;
    static std::string           helix_ali_name;

    static void updateHelixAndPairdef(GBDATA *gb_main, const char *ali_name);

public:
    SQ_helix(int size);
    ~SQ_helix();

    void SQ_calc_helix_layout(const char *sequence, GBDATA *gb_main, char *alignment_name, GBDATA *gb_quality, AP_filter *filter);

    int SQ_get_no_helix() const {
        return count_no_helix;
    }
    int SQ_get_weak_helix() const {
        return count_weak_helix;
    }
    int SQ_get_strong_helix() const {
        return count_strong_helix;
    }
};

// global data
SmartPtr<BI_helix>    SQ_helix::helix;
SmartPtr<BI_pairdef>  SQ_helix::pairdef;
GBDATA               *SQ_helix::helix_gb_main = NULp;
std::string           SQ_helix::helix_ali_name;

// SQ_helix implementation
void SQ_helix::updateHelixAndPairdef(GBDATA *gb_main, const char *ali_name) {
    if (helix.isNull() ||
        gb_main != helix_gb_main ||
        strcmp(helix_ali_name.c_str(), ali_name) != 0)
    {
        helix = new BI_helix;
        helix->init(gb_main, ali_name);

        pairdef = new BI_pairdef;

        helix_gb_main  = gb_main;
        helix_ali_name = ali_name;
    }
}

SQ_helix::SQ_helix(int size_) :
    sequence(NULp),
    count_strong_helix(0),
    count_weak_helix(0),
    count_no_helix(0),
    size(size_)
{}

SQ_helix::~SQ_helix() {
}

void SQ_helix::SQ_calc_helix_layout(const char *seq, GBDATA *gb_main, char *alignment_name, GBDATA *gb_quality, AP_filter *filter) {
    updateHelixAndPairdef(gb_main, alignment_name);

    size_t        filterLen          = filter->get_filtered_length();
    const size_t *filterpos_2_seqpos = filter->get_filterpos_2_seqpos();

    std::map<int, int> filterMap;
    for (size_t filter_pos = 0; filter_pos < filterLen; filter_pos++) {
        filterMap[filterpos_2_seqpos[filter_pos]] = filter_pos;
    }

    if (!helix->has_entries()) {
        count_strong_helix = 1;
        count_weak_helix = 1;
        count_no_helix = 1;
    }
    else {
        // calculate the number of strong, weak and no helixes
        std::map<int, int>::iterator it;

        for (size_t filter_pos = 0; filter_pos < filterLen; filter_pos++) {
            int seq_pos = filterpos_2_seqpos[filter_pos];

            if (helix->is_pairpos(seq_pos)) {
                int v_seq_pos = helix->opposite_position(seq_pos);

                if (v_seq_pos > seq_pos) { // ignore right helix positions
                    it = filterMap.find(v_seq_pos);

                    if (it != filterMap.end()) {
                        char left  = seq[filter_pos];
                        char right = seq[it->second];

                        int strength = pairdef->pair_strength(left, right);

                        switch (strength) {
                            case 3:
                            case 2:
                                count_strong_helix++;
                                break;
                            case 1:
                                count_weak_helix++;
                                break;
                            case 0:
                                if (!((left == '-') && (right == '-')))
                                    count_no_helix++;
                                break;
                            default:
                                seq_assert(0);
                                break;
                        }
                    }
                }
            }
        }
    }

    GBDATA *gb_result1 = GB_search(gb_quality, "number_of_no_helix", GB_INT);
    seq_assert(gb_result1);
    GB_write_int(gb_result1, count_no_helix);

    GBDATA *gb_result2 = GB_search(gb_quality, "number_of_weak_helix", GB_INT);
    seq_assert(gb_result2);
    GB_write_int(gb_result2, count_weak_helix);

    GBDATA *gb_result3 = GB_search(gb_quality, "number_of_strong_helix", GB_INT);
    seq_assert(gb_result3);
    GB_write_int(gb_result3, count_strong_helix);
}