tcparser.cc

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#include "tcparser.h"
#include <sstream>
#include <iostream>

using namespace std;

TcParser::TcParser() : pInFile(0)
{
//   cerr<<"NB: Due to (temporary) bug in time course files, parser skips last 4 values in each line"<<endl;
}

TcParser::~TcParser()
{
  if ( pInFile ) {
    pInFile->close();
    delete pInFile;
  }
}

void TcParser::set_file(string file_name)
{
  if ( pInFile ) {
    //Parsing a new file before previous one finished
    cleanup();
  }
  pInFile = new ifstream( file_name.c_str() );
  line_num = 0;
}

bool TcParser::parse_line(string& name, std::vector<double>& tc)
{
  if ( pInFile ) {//File handle open
    string line;
    if ( getline(*pInFile, line) ) {
      line_num++;
      istringstream is(line);
      
      if ( !(is>>name) ) {
        cerr<<"TcParser::parse_line(), input error"<<endl;
        cerr<<"line "<<line_num<<": "<<line<<"\nis ill formated"<<endl;
        cleanup();
        return false;
      }
      string tmp;
      double val;
      int num_parsed(0);//Temporary file bug fix
      while ( is>>tmp ) {

        if ( tmp == "NA" ) {
          val = -1.0;
        }
        else {
          istringstream is2(tmp);
          if ( !(is2>>val) ) {
            cerr<<"TcParser::parse_line(), input error"<<endl;
            cerr<<"line "<<line_num<<": "<<line<<"\nis ill formated"<<endl;
            cleanup();
            return false;
          }
        }
        tc.push_back(val);
        num_parsed++;
//         if ( num_parsed == 14 ) {
//           break;
//         }
      }

      return true;
    }
    //Nothing more to do
    cleanup();
  }
  else {
    cerr<<"No file handle in TcParser::parse_line()"<<endl;
  }
  return false;
}

void TcParser::cleanup()
{
  if  (pInFile) {
    
    pInFile->close();
    delete pInFile;
    pInFile = 0;

  }
  
}

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