gene.h

/**************************************************************************
 * Copyright (c) 2002-2011 T. M. Murali                                   *
 * Copyright (c) 2010-2011 Christopher L. Poirel                          *
 *                                                                        *
 * This file is part of Biorithm.                                         *
 *                                                                        *
 * Biorithm 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.                                    *
 *                                                                        *
 * Biorithm 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 Biorithm.  If not, see <http://www.gnu.org/licenses/>.      *
 *                                                                        *
 **************************************************************************/

#ifndef _GENE_H
#define _GENE_H

#include "global.h"
#include "read.h"

// class for storing points.
class MyAffyGene: public MyInfo
{
public:
  // constructors and destructors.
  MyAffyGene(MyString id = "", MyString sid = "")
      : MyInfo(id, sid)
    {}

  MyAffyGene(const MyAffyGene& copy)
      : MyInfo(copy)
    {}

  virtual ~MyAffyGene()
    {}
  
  // return a clone of MyAffyGene.
  virtual MyInfo* clone() const
    {
      MyAffyGene* clone = new MyAffyGene(*this);
      return(clone);
    }

  // numNames is a hacky way of specifying how many names the input
  // file contains for each gene. there must be a cleaner way of
  // passing the expected format of a line.
  void read(istream &istr, char delim = '\t', int numNames = 1);  
  void read(istream &istr, vector< MyNT >& coords, unsigned int& dimension, 
                  char delim = '\t', int numNames = 1, bool hasCallData = false);
  bool read(istream &istr, vector< MyNT >& coords, unsigned int& dimension,
                  const MyAffyFileFormat &format, 
                  set< unsigned int > &missing);
  
  void write(ostream &ostr) const
    {
      ostr << "Name = " << getName() << endl;
      ostr << "Short name = " << getShortName() << endl;
    }

  // add an index for which the expression value is missing.
  void addMissingIndex(unsigned int i)
  {
    missingIndices.insert(i);
  }
  
  // check if the expression value for an index is missing.
  bool isMissing(unsigned int i) const
  {
    return(missingIndices.end() != missingIndices.find(i));
  }

private:
  set< unsigned int > missingIndices;
};

inline istream& operator>>(istream& istr, MyAffyGene &gene)
{
  gene.read(istr);
  return istr;
}

inline ostream& operator<<(ostream& ostr, const MyAffyGene& gene)
{
  gene.write(ostr);
  return ostr;
}


#endif // _GENE_H