root/trunk/FRII/gui/Feature.hh

/*
 * This file is part of the FamilyRelations II source distribution.
 *
 * FamilyRelations II is part of the FamilyJewels package for comparative
 * sequence analysis: http://family.caltech.edu/.
 *
 * Contact author: C. Titus Brown, titus@caltech.edu.
 *
 * This program and all associated source code files are Copyright (C) 2003,
 * 2004 the California Institute of Technology, Pasadena, CA, 91125 USA.  It
 * is under the Lesser GNU Public License; please see the included
 * LICENSE.txt file for more information, or contact Titus directly.
 *
 */

// Feature, on one sequence, possibly with a reference to another sequence
// and an attached alignment.

#ifndef FEATURE_HH // protect against multiple includes
#define FEATURE_HH

#include <string>

namespace gui {
  class Feature {
  protected:
    Feature * _other;
    std::string top_aln, bot_aln;
    std::string _info;
  public:
    const unsigned int start, end;
    const int orientation;
    Feature(unsigned int s, unsigned int e, int o) :
      _other(NULL), start(s), end(e), orientation(o)
           { ; }

    void other(int s, int e) {
      _other = new Feature(s, e, 1);
    }
    const Feature * other() const { return _other; }

    const std::string information() const { return _info; }
    void add_information(std::string i) { _info += i; }
    bool has_info() const { return (_info.length() > 0); }

    void set_alignment(std::string top, std::string bot) {
      top_aln = top;
      bot_aln = bot;
    }
    void get_alignment(std::string &top, std::string &bot) const {
      top = top_aln;
      bot = bot_aln;
    }

    Feature * copy_me() const {
      Feature * new_f = new Feature(start, end, orientation);
      if (_other) {
        new_f->_other = _other->copy_me();
      }
      new_f->set_alignment(top_aln, bot_aln);
      new_f->_info = _info;

      return new_f;
    }

    bool has_alignment() const {
      if (_other && top_aln.length() && bot_aln.length()) {
        return true;
      }
      return false;
    }

    virtual ~Feature() { if (_other) delete _other; }
  };
}

#endif // FEATURE_HH