// SEQREADER.CC
// Read a sequence from a file.  The file is assumed to contain a single
// sequence, possibly split across multiple lines.  Case is not preserved.
//

#include <iostream>
#include <fstream>
#include <cstring>
#include <cctype>

using namespace std;

#include "SeqReader.h"
#include "vector.h"

const char *readSeq(const char *fileName, int *iseqLength)
{
  ifstream is(fileName);
  Vector<char> buffer;
  
  if (!is)
    {
      cout << "Error: could not open file " << fileName << endl;
      return NULL;
    }
  
  // Accumulate the sequence in a buffer (minus any whitespace).
  // Convert to lower case as we read.
  //
  while (!is.eof())
    {
      char c;
      
      is >> c;
      if (!is.eof() && !isspace(c))
	buffer.add(tolower(c));
    }
  
  char *seq = new char [buffer.length() + 1];
  memcpy(seq, buffer.elements(), buffer.length());
  seq[buffer.length()] = 0;
  *iseqLength = buffer.length();
  
  return seq;
}