get_cbust_pssm.hpp

#include "matrix.hpp"
#include <iosfwd> // "forward declaration" of istream
#include <string>

namespace cb {
// Like get_weighted_pssm, but if a line beginning #GAP is present,
// reads a numeric gap value from this line.
std::istream &get_cbust_pssm(
    std::istream &strm,      // stream to read from
    mcf::matrix<float> &mat, // store the matrix here
    std::string &title,      // store title line minus leading '>'
    float &weight,           // = 1 by default if not specified
    float &gap,              // = -1 by default if not specified
    unsigned alphsize = 4);  // perhaps it should guess alphsize from the input
}