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#ifndef FASTAIO_H
#define FASTAIO_H 1
#include "Graph/Properties.h"
#include <boost/graph/graph_traits.hpp>
#include <cassert>
#include <istream>
#include <sstream>
#include <string>
using boost::graph_traits;
/** Read the vertices from a FASTA file. */
template <typename Graph>
std::istream& read_fasta(std::istream& in, Graph& g)
{
assert(in);
typedef typename graph_traits<Graph>::vertex_descriptor V;
typedef typename vertex_property<Graph>::type VP;
for (std::string uname;
in.peek() != EOF && in >> expect(">") >> uname;) {
std::string comment;
getline(in, comment);
assert(in);
std::istringstream ss(comment);
VP vp;
ss >> vp;
size_t n = 0;
while (in >> std::ws && in.peek() != '>' && in) {
in >> Ignore('\n');
assert(in);
assert(in.gcount() > 1);
n += in.gcount() - 1;
}
put(vertex_length, vp, n);
V u = add_vertex(vp, g);
put(vertex_name, g, u, uname);
}
assert(in.eof());
return in;
}
#endif
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