source: trunk/yat/omic/GFF.h @ 2482

#ifndef theplu_yat_omic_gff
#define theplu_yat_omic_gff

/*
  $Id: GFF.h 2482 2011-04-24 22:17:19Z peter $

  Copyright (C) 2011 Peter Johansson

  This file is part of the yat library, http://dev.thep.lu.se/yat

  The yat library 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.

  The yat library 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 yat. If not, see <http://www.gnu.org/licenses/>.
*/

#include <iosfwd>
#include <map>
#include <string>
#include <vector>

namespace theplu {
namespace yat {
namespace omic {

  /**
     Abstract class for GFF2 and GFF3

     \since New in yat 0.8
   */
  class GFF
  {
  public:
    /**
       \brief Default Constructor

       Constructs an empty GFF. Class need to be loaded with function
       getline before calling any other functions.

       \see getline(std::istream& is, GFF& gff);
     */
    GFF(void);

    /**
       \brief Destructor
     */
    virtual ~GFF(void);

    /**
       \return attribute value for attribute \a key

       If attribute with key \a key has several values, the values are
       given appended together comma-separated as it appears in file.
     */
    const std::string& attribute(const std::string& key) const;

    /**
       \return map containing all attributes

       \see attribute(const std::string& key) const
     */
    const std::map<std::string, std::string>& attributes(void) const;

    /**
       \return end string
     */
    const std::string& end(void) const;

    /**
       \return phase string
     */
    const std::string& phase(void) const;

    /**
       \return score string
     */
    const std::string& score(void) const;

    /**
       \return seqid string
     */
    const std::string& seqid(void) const;

    /**
       \return source string
     */
    const std::string& source(void) const;

    /**
       \return start string
     */
    const std::string& start(void) const;

    /**
       \return strand string
     */
    const std::string& strand(void) const;

    /**
       \return type string
     */
    const std::string& type(void) const;
  protected:
    /**
       \return vector with the 9 elements
     */
    const std::vector<std::string>& vec(void) const;
    friend std::ostream& operator<<(std::ostream&, const GFF&);
    // user compiler generated copy
    //GFF(const GFF& other) {};
    //GFFBase& operator=(const GFF&);
  private:
    friend bool getline(std::istream&, GFF&);
    virtual void add_attribute(std::map<std::string, std::string>& m,
                               const std::string&) const=0;

    void create_attributes(std::map<std::string, std::string>& m) const;
    std::vector<std::string> vec_;
    std::map<std::string, std::string> attributes_;
  };

  /**
     \return true iff a GFF object was loaded successfully

     Empty lines and lines starting with '#' are ignored.

     \relates GFF
     \since New in yat 0.8
   */
  bool getline(std::istream& is, GFF& gff);

  /**
     \brief output operator for GFF

     \relates GFF
     \since New in yat 0.8
   */
  std::ostream& operator<<(std::ostream& os, const GFF& gff);

}}}
#endif