read_summary.h

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#pragma once

#include <vector>
#include "interop/util/exception.h"
#include "interop/util/assert.h"
#include "interop/model/summary/lane_summary.h"
#include "interop/model/summary/metric_summary.h"
#include "interop/model/run/read_info.h"
#include "interop/model/model_exceptions.h"
#include "interop/io/format/generic_layout.h"

namespace illumina { namespace interop { namespace model { namespace summary
{

    class read_summary
    {
        typedef std::vector<lane_summary> lane_summary_vector_t;
    public:
        typedef lane_summary_vector_t::reference reference;
        typedef lane_summary_vector_t::const_reference const_reference;
        typedef lane_summary_vector_t::iterator iterator;
        typedef lane_summary_vector_t::const_iterator const_iterator;
        typedef lane_summary_vector_t::size_type size_type;
    public:
        read_summary(const run::read_info &read = run::read_info(), const size_t channel_count=0) :
                m_read(read), m_metric_summary(channel_count)
        {
        }

    public:
        lane_summary & operator[](const size_type n) INTEROP_THROW_SPEC((model::index_out_of_bounds_exception))
        {
            INTEROP_BOUNDS_CHECK(n, m_summary_by_lane.size(), "Lane index exceeds lane count");
            return m_summary_by_lane[n];
        }

        lane_summary &at(const size_type n) INTEROP_THROW_SPEC((model::index_out_of_bounds_exception))
        {
            INTEROP_BOUNDS_CHECK(n, m_summary_by_lane.size(), "Lane index exceeds lane count");
            return m_summary_by_lane[n];
        }

        iterator begin()
        {
            return m_summary_by_lane.begin();
        }

        iterator end()
        {
            return m_summary_by_lane.end();
        }

        void resize(const size_type n)
        {
            m_summary_by_lane.resize(n);
        }

        run::read_info &read()
        {
            return m_read;
        }

        metric_summary &summary()
        {
            return m_metric_summary;
        }

        void summary(const metric_summary &summary)
        {
            m_metric_summary = summary;
        }

    public:
        const lane_summary& operator[](const size_t n) const INTEROP_THROW_SPEC((model::index_out_of_bounds_exception))
        {
            INTEROP_BOUNDS_CHECK(n, m_summary_by_lane.size(), "Lane index exceeds lane count");
            return m_summary_by_lane[n];
        }

        const_reference at(const size_type n) const INTEROP_THROW_SPEC((model::index_out_of_bounds_exception))
        {
            INTEROP_BOUNDS_CHECK(n, m_summary_by_lane.size(), "Lane index exceeds lane count");
            return m_summary_by_lane[n];
        }

        size_t size() const
        {
            return m_summary_by_lane.size();
        }

        size_t lane_count() const
        {
            return m_summary_by_lane.size();
        }

        const_iterator begin() const
        {
            return m_summary_by_lane.begin();
        }

        const_iterator end() const
        {
            return m_summary_by_lane.end();
        }

    public:
        const run::read_info &read() const
        {
            return m_read;
        }

        const metric_summary &summary() const
        {
            return m_metric_summary;
        }
    private:
        run::read_info m_read;
        metric_summary m_metric_summary;

    private:
        lane_summary_vector_t m_summary_by_lane;
        template<class MetricType, int Version>
        friend struct io::generic_layout;
    };

}}}}