/**
 * @file contig_info.h
 * @brief ContigInfo Class.
 * @author Yu Peng (ypeng@cs.hku.hk)
 * @version 1.0.0
 * @date 2011-08-26
 */

#ifndef __GRAPH_CONTIG_INFO_H_

#define __GRAPH_CONTIG_INFO_H_

#include "graph/bit_edges.h"

#include <algorithm>
#include <deque>
#include <istream>
#include <ostream>
#include <string>


typedef uint32_t SequenceCountUnitType;
typedef std::basic_string<SequenceCountUnitType> SequenceCount;

class ContigBuilder;

/**
 * @brief It is used to store information of contigs, like k-mer counts, in-edges,
 * out-edges, etc.
 */
class ContigInfo
{
    friend class ContigBuilder; 
    friend std::istream &operator >>(std::istream &is, ContigInfo &contig_info);
    friend std::ostream &operator <<(std::ostream &os, const ContigInfo &contig_info);

public:
    ContigInfo()
    { kmer_count_ = 0; kmer_size_ = 0; }

    ContigInfo(const ContigInfo &contig_info)
    {
        in_edges_ = contig_info.in_edges_;
        out_edges_ = contig_info.out_edges_;
        kmer_count_ = contig_info.kmer_count_;
        kmer_size_ = contig_info.kmer_size_;
        counts_ = contig_info.counts_;
    }

    const ContigInfo &operator =(const ContigInfo &contig_info)
    {
        in_edges_ = contig_info.in_edges_;
        out_edges_ = contig_info.out_edges_;
        kmer_count_ = contig_info.kmer_count_;
        kmer_size_ = contig_info.kmer_size_;
        counts_ = contig_info.counts_;
        return *this;
    }

    const ContigInfo &ReverseComplement()
    { std::swap(in_edges_, out_edges_); std::reverse(counts_.begin(), counts_.end()); return *this; }

    BitEdges &in_edges() { return in_edges_; }
    const BitEdges &in_edges() const { return in_edges_; }

    BitEdges &out_edges() { return out_edges_; }
    const BitEdges &out_edges() const { return out_edges_; }

    uint32_t kmer_size() const { return kmer_size_; }
    void set_kmer_size(uint32_t kmer_size) { kmer_size_ = kmer_size; }

    uint32_t kmer_count() const { return kmer_count_; }
    void set_kmer_count(uint32_t kmer_count) { kmer_count_ = kmer_count; }

    const SequenceCount &counts() const { return counts_; }
    void set_counts(const SequenceCount &counts) { counts_ = counts; }

    void swap(ContigInfo &contig_info)
    { 
        if (this != &contig_info)
        {
            std::swap(in_edges_, contig_info.in_edges_);
            std::swap(out_edges_, contig_info.out_edges_);
            std::swap(kmer_size_, contig_info.kmer_size_);
            std::swap(kmer_count_, contig_info.kmer_count_);
            counts_.swap(contig_info.counts_);
        }
    }

    void clear()
    { in_edges_ = 0; out_edges_ = 0; kmer_size_ = 0; kmer_count_ = 0; counts_.clear(); }

private:
    BitEdges in_edges_;
    BitEdges out_edges_;
    uint16_t kmer_size_;
    uint32_t kmer_count_;
    SequenceCount counts_;
};

namespace std
{
template <> inline void swap(ContigInfo &x, ContigInfo &y) { x.swap(y); }
}

std::istream &operator >>(std::istream &is, ContigInfo &contig_info);
std::ostream &operator <<(std::ostream &os, const ContigInfo &contig_info);

void ReadContigInfo(const std::string &filename, std::deque<ContigInfo> &contig_infos);
void WriteContigInfo(const std::string &filename, const std::deque<ContigInfo> &contig_infos);

#endif