File: fasta.cpp

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#include "fasta.hpp"

#include <boost/algorithm/string/trim.hpp>
using boost::algorithm::trim;

#include <algorithm>
using std::min;

#include <ostream>
using std::endl;

#include <stdexcept>
using std::runtime_error;


namespace sequence{

  FastaRecord::FastaRecord(const string &h)
    : header(h)
  {
  }
  
  FastaRecord::FastaRecord()
  {
  }

  istream &operator>>(istream &inputStream, FastaRecord &fr)
  {
    fr.header.clear();
    fr.sequence.clear();

    if('>' != inputStream.get())
      throw runtime_error("Error in FASTA file format.");
    getline(inputStream, fr.header);
    while(inputStream.good() && '>' != inputStream.peek()){
      string line;
      getline(inputStream, line);
      fr.sequence += line;
    }
    return inputStream;
  }

  ostream &operator<<(ostream &outputStream, const FastaRecord &fr)
  {
    outputStream << '>' << fr.header;
    
    for(string::size_type i = 0; i < fr.sequence.length(); ++i){
      if(0 == i % CHARS_PER_LINE)
	outputStream << '\n';
      outputStream << fr.sequence[i];
    }

    outputStream << endl;

    return outputStream;
  }
  
  istream &operator>>(istream &inputStream, Fasta &fa)
  {
    fa.clear();
    string line;
    while(getline(inputStream, line))
      if(not line.empty() and '>' == line[0])
	fa.push_back(FastaRecord(line.substr(1)));
      else{
       	trim(line);
	if(not line.empty())
	  fa.rbegin()->sequence += line;
      }
    return inputStream;
  }

  ostream &operator<<(ostream &outputStream, const Fasta &fa)
  {
    for(Fasta::const_iterator i = fa.begin(); i != fa.end(); ++i)
      outputStream << *i;
    return outputStream;
  }
  
}