read.h

/**************************************************************************
 * Copyright (c) 2002-2011 T. M. Murali                                   *
 *                                                                        *
 * 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 _READ_H
#define _READ_H

#include <algorithm>

using namespace std;

//#include "cog.h"
#include "format.h"
#include "interval.h"
#include "params.h"
#include "point.h"


void readAffyData(const string& inputFile, const string& genesFile,
                  int numPointsToRead,
                  MyPointSet& points,
                  vector< MyDimInfo >& dimInfo,
                  unsigned int& numDims, 
                           const MyAffyFileFormat &format
                  // i need this argument for calling _setUpFormat().
                           //                  const MyClusterParams *params = NULL
                  );

void readAffyData(//const 
                           MyClusterParams &params,
                  MyPointSet& points,
                  vector< MyDimInfo >& dimInfo,
                  unsigned int& numDims,
                           // when params can have multiple input files, i need
                           // some variable to say which one to read!
                           unsigned int whichPointSet
                           );

void readData(const MyClusterParams& params, MyPointSet& points,
              vector< MyDimInfo >& dimInfo,
              unsigned int& numDims,
                    // when params can have multiple input files, i need
                    // some variable to say which one to read!
                    unsigned int whichPointSet
                    );
void readWidths(const string &widthFile, int numDims, vector< MyNT >& widths);

void readWidthRanges(const string &widthFile, unsigned int numDims,
                     vector< map< MyNT, MyWidthRange > >& widths);

void createIntervals(const MyPointSet &points, MyNT maxLower, MyNT minUpper,
                                 vector< vector< MyInterval > >& intervals);
void readIntervals(const string &intervalFile, unsigned int numDims,
                   MyNT maxPValue, int maxCount,
                   vector< vector< MyInterval > >& intervals,//);
                   vector< MyNT >& widths);
void readClasses(const string& classFile, MyClassesType& classes,
                 MyClassNamesType& classNames);



#endif // _READ_H