// -*- mode: c++; indent-tabs-mode: nil; -*-
//
// Copyright 2009 Illumina, Inc.
//
// This software is covered by the "Illumina Genome Analyzer Software
// License Agreement" and the "Illumina Source Code License Agreement",
// and certain third party copyright/licenses, and any user of this
// source file is bound by the terms therein (see accompanying files
// Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
// Illumina_Source_Code_License_Agreement.pdf and third party
// copyright/license notices).
//
//

/// \file

/// \author Chris Saunders
///

#ifndef __QSCORE_CACHE_HH
#define __QSCORE_CACHE_HH

#include <stdint.h>

#include <cassert>


struct qphred_cache {

    static
    double
    get_error_prob(const int qscore) {
        return qc().get_error_prob_imp(qscore);
    }

    static
    double
    get_lncompe(const int qscore) {
        return qc().get_lncompe_imp(qscore);
    }

    static
    double
    get_lne(const int qscore) {
        return qc().get_lne_imp(qscore);
    }

    static
    int
    get_mapped_qscore(const int basecall_qscore,
                      const int mapping_qscore) {
        return qc().get_mapped_qscore_imp(basecall_qscore,mapping_qscore);
    }

private:
    qphred_cache();

    static
    const qphred_cache&
    qc() {
        static const qphred_cache qc;
        return qc;
    }

    void qscore_error(const int qscore) const;

    void qscore_check(const int qscore) const {
        if((qscore < 0) or (qscore > MAX_QSCORE)) qscore_error(qscore);
    }

    double
    get_error_prob_imp(const int qscore) const {
        qscore_check(qscore);
        return q2p[qscore];
    }

    double
    get_lncompe_imp(const int qscore) const {
        qscore_check(qscore);
        return q2lncompe[qscore];
    }

    double
    get_lne_imp(const int qscore) const {
        qscore_check(qscore);
        return q2lne[qscore];
    }
    
    int
    get_mapped_qscore_imp(const int basecall_qscore,
                          int mapping_qscore) const {
        qscore_check(basecall_qscore);
        assert(mapping_qscore>=0);
        if(mapping_qscore>MAX_MAP) { mapping_qscore=MAX_MAP; }
        return mappedq[mapping_qscore][basecall_qscore];
    }

    enum { MAX_QSCORE = 70,
           MAX_MAP = 90 };

    double q2p[MAX_QSCORE+1];
    double q2lncompe[MAX_QSCORE+1];
    double q2lne[MAX_QSCORE+1];
    uint8_t mappedq[MAX_MAP+1][MAX_QSCORE+1];
};


struct qlogodds_cache {

    static
    double
    get_error_prob(const int qscore) {
        static const qlogodds_cache qc;
        return qc.get_error_prob_imp(qscore);
    }

private:
    qlogodds_cache();
 
    void qscore_error(const int qscore) const;

    double
    get_error_prob_imp(const int qscore) const {
        if((qscore < MIN_QSCORE) or (qscore > MAX_QSCORE)) qscore_error(qscore);
        return q2p[qscore];
    }

    enum { MIN_QSCORE = -40, MAX_QSCORE = 70 };

    double q2p_base[MAX_QSCORE+1-MIN_QSCORE];
    double* const q2p;
};

#endif