/*
Copyright (c) 2006-2018 Elmar Pruesse <elmar.pruesse@ucdenver.edu>

This file is part of SINA.
SINA 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.

SINA is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
for more details.

You should have received a copy of the GNU General Public License
along with SINA.  If not, see <http://www.gnu.org/licenses/>.

Additional permission under GNU GPL version 3 section 7

If you modify SINA, or any covered work, by linking or combining it
with components of ARB (or a modified version of that software),
containing parts covered by the terms of the
ARB-public-library-license, the licensors of SINA grant you additional
permission to convey the resulting work. Corresponding Source for a
non-source form of such a combination shall include the source code
for the parts of ARB used as well as that of the covered work.
*/

#ifndef _QUERY_ARB_H_
#define _QUERY_ARB_H_

#include <string>
#include <utility>
#include <vector>
#include <list>
#include <memory>

#include <boost/filesystem.hpp>

#include "cseq.h"
#include "alignment_stats.h"

struct GBDATA;

namespace sina {

/**
 * Base exception thrown by query_arb
 */
class query_arb_exception : public std::exception
{
public:
    query_arb_exception(std::string& what): m_what(what) {}
    query_arb_exception(std::string  what): m_what(std::move(what)) {}
    query_arb_exception(const char* what): m_what(what) {}
    query_arb_exception() = default;
    const char* what() const noexcept override { return m_what.c_str(); }
    ~query_arb_exception() noexcept override = default;

private:
    std::string m_what;
};


class query_arb{
    query_arb(const boost::filesystem::path& arbfile);
    ~query_arb();

 public:
    /**
     * Factory method.
     * @param file_name ...
     * @returns one instance per database file. If the method is called multiple times on the same file the same instance is returned.
     */
    static query_arb* getARBDB(const boost::filesystem::path& file_name);
    static void closeOpenARBDBs();

    static const char* fn_turn;
    static const char* fn_acc;
    static const char* fn_start;
    static const char* fn_qual;
    static const char* fn_head;
    static const char* fn_tail;
    static const char* fn_date;
    static const char* fn_astart;
    static const char* fn_astop;
    static const char* fn_idty;
    static const char* fn_family;
    static const char* fn_nuc;
    static const char* fn_nuc_gene;
    static const char* fn_bpscore;
    static const char* fn_used_rels;
    static const char* fn_fullname;
    static const char* fn_align_log;
    static const char* fn_filter;
    static const char* fn_nearest;

    /**
     * Saves the database using the default filename in binary format.
     * @note The filename is specified in init().
     *       Do not call this method before init() has been called.
     *
     * @see saveAs(const char* fname, const char* type="b")
     */
    void save();

    /**
     * Saves the database using the specified filename.
     * @param fname the filename.
     * @param type Defines how the database should be saved.
     *        The value is a combination of one or more of the following
     *        values:
     *        * 'a' ascii
     *        * 'b' binary
     *        * 'm' save mapfile (only together with binary)
     *        * 'f' force saving even in disabled path to a different directory (out of order save)
     *        * 'S' save to stdout (for debugging)
     *        @note Either 'a' or 'b' must be defined.
     */
    void saveAs(const boost::filesystem::path& fname, const char* type="b");

    /**
     * Returns filename of underlying ARB database file
     */
    const boost::filesystem::path& getFileName() const;

    void setProtectionLevel(int p);

    int getSeqCount() const;
    std::vector<std::string> getSequenceNames();

    const cseq& getCseq(const std::string& name);
    cseq getCseqUncached(const std::string& name);
    void putCseq(const cseq& seq);

    /**
     * Loads a meta data entry from ARB into the Cseq
     * Note that this will only load missing keys, and not update
     * changed keys unless relpad=true
     */
    void loadKey(const cseq& c, const std::string& key, bool reload=false, bool warnMissingField = true);
    void storeKey(cseq& c, const std::string& key);
    std::vector<std::tuple<std::string, std::string, int>> listKeys();

    long getAlignmentWidth() const;
    static void override_default_alignment(const std::string& ali_name);

    std::string getFilter(const std::string& name);
    std::vector<int> getPairs();
    std::vector<alignment_stats> getAlignmentStats();

    void loadCache();
    void loadCache(std::vector<std::string>& keys);
    std::vector<cseq*> getCacheContents();

    void copySequence(query_arb& source, const std::string& name, bool mark);
private:
    void setMark();
    void setMark(const std::string& name);
    void setMark(const cseq& cs);


    // make query_arb non-copyable
    query_arb(const query_arb&) = delete;
    query_arb& operator=(const query_arb&) = delete;

    struct priv_data;
    std::unique_ptr<priv_data> data;
    static std::map<boost::filesystem::path, query_arb*> open_arb_dbs;

};

inline void
query_arb::setMark(const cseq& cs) {
    setMark(cs.getName());
}

inline void
query_arb::loadCache() {
  std::vector<std::string> vs; loadCache(vs);
}


} // namespace sina

#endif // _QUERY_ARB_H_

/*
  Local Variables:
  mode:c++
  c-file-style:"stroustrup"
  c-file-offsets:((innamespace . 0)(inline-open . 0)(case-label . +))
  indent-tabs-mode:nil
  fill-column:99
  End:
*/
// vim: filetype=cpp:expandtab:shiftwidth=4:tabstop=8:softtabstop=4:encoding=utf-8:textwidth=99 :