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#ifndef ADJIO_H
#define ADJIO_H 1
#include "ContigID.h"
#include "ContigGraph.h"
#include "IOUtil.h"
#include <boost/graph/graph_traits.hpp>
#include <algorithm> // for count
#include <cassert>
#include <cstdlib>
#include <istream>
#include <ostream>
#include <utility>
using namespace std::rel_ops;
using boost::graph_traits;
template <typename EdgeProp>
void write_edge_prop(std::ostream& out, const EdgeProp& ep)
{
if (ep != EdgeProp())
out << " [" << ep << ']';
}
static inline void write_edge_prop(std::ostream&, const no_property&)
{
}
/** Output a contig adjacency graph. */
template <typename Graph>
std::ostream& write_adj(std::ostream& out, const Graph& g)
{
typedef typename graph_traits<Graph>::vertex_descriptor
vertex_descriptor;
typedef typename graph_traits<Graph>::vertex_iterator
vertex_iterator;
typedef typename graph_traits<Graph>::out_edge_iterator
out_edge_iterator;
std::pair<vertex_iterator, vertex_iterator> vit = vertices(g);
bool sense = false;
for (vertex_iterator u = vit.first; u != vit.second; ++u,
sense = !sense) {
if (get(vertex_removed, g, *u))
continue;
if (!sense)
out << get(vertex_contig_name, g, *u)
<< get(vertex_bundle, g, *u);
out << "\t;";
std::pair<out_edge_iterator, out_edge_iterator>
adj = out_edges(*u, g);
for (out_edge_iterator e = adj.first; e != adj.second; ++e) {
vertex_descriptor v = target(*e, g);
assert(!get(vertex_removed, g, v));
out << ' ' << get(vertex_name, g, v ^ sense);
write_edge_prop(out, get(edge_bundle, g, e));
}
if (sense)
out << '\n';
}
return out;
}
/** Read the edges of a graph in dist format. */
template <typename Graph, typename BetterEP>
std::istream& readDistEdges(std::istream& in, ContigGraph<Graph>& g,
typename graph_traits<Graph>::vertex_descriptor u,
BetterEP betterEP)
{
typedef typename graph_traits<Graph>::vertex_descriptor V;
typedef typename graph_traits<Graph>::edge_descriptor E;
typedef typename Graph::edge_property_type EP;
for (std::string vname; getline(in >> std::ws, vname, ',');) {
assert(!vname.empty());
V v = find_vertex(vname, g);
v = v ^ get(vertex_sense, g, u);
EP ep;
in >> ep;
assert(in);
if (in.peek() != ' ')
in >> Ignore(' ');
E e;
bool found;
boost::tie(e, found) = edge(u, v, g);
if (found) {
// Parallel edge
EP& ref = g[e];
ref = betterEP(ref, ep);
} else
g.Graph::add_edge(u, v, ep);
}
assert(in.eof());
return in;
}
/** Read a contig adjacency graph.
* @param betterEP handle parallel edges
*/
template <typename Graph, typename BetterEP>
std::istream& read_adj(std::istream& in, ContigGraph<Graph>& g,
BetterEP betterEP)
{
if (in.eof()) {
// Allow reading an empty file if the graph is not empty.
assert(num_vertices(g) > 0);
return in;
}
assert(in);
typedef typename Graph::vertex_descriptor vertex_descriptor;
typedef typename Graph::vertex_property_type vertex_property_type;
typedef typename Graph::edge_property_type edge_property_type;
// Check for ADJ or DIST format.
std::string line;
getline(in, line);
assert(in);
unsigned numSemicolons
= std::count(line.begin(), line.end(), ';');
if (numSemicolons > 2) {
std::cerr << "error: expected 0, 1 or 2 semicolons and saw "
<< numSemicolons << '\n';
exit(EXIT_FAILURE);
}
bool faiFormat = numSemicolons == 0;
bool adjFormat = numSemicolons == 2;
// Read the vertex properties.
if (adjFormat || faiFormat) {
assert(num_vertices(g) == 0);
in.clear();
in.seekg(0, std::ios::beg);
assert(in);
for (std::string uname; in >> uname;) {
vertex_property_type vp;
if (faiFormat) {
unsigned length;
in >> length;
put(vertex_length, vp, length);
} else
in >> vp;
in >> Ignore('\n');
assert(in);
vertex_descriptor u = add_vertex(vp, g);
put(vertex_name, g, u, uname);
}
assert(in.eof());
}
assert(num_vertices(g) > 0);
g_contigNames.lock();
if (faiFormat)
return in;
// Read the edges.
in.clear();
in.seekg(0, std::ios::beg);
assert(in);
for (std::string name; in >> name;) {
if (adjFormat)
in >> Ignore(';');
vertex_descriptor u = find_vertex(name, false, g);
for (int sense = false; sense <= true; ++sense) {
std::string s;
getline(in, s, !sense ? ';' : '\n');
assert(in.good());
std::istringstream ss(s);
if (!adjFormat) {
readDistEdges(ss, g, u ^ sense, betterEP);
} else
for (std::string vname; ss >> vname;) {
ss >> std::ws;
vertex_descriptor v = find_vertex(vname, g);
assert(!edge(u ^ sense, v ^ sense, g).second);
if (ss.peek() == '[') {
ss.get();
edge_property_type ep;
ss >> ep >> Ignore(']');
g.Graph::add_edge(u ^ sense, v ^ sense, ep);
} else
g.Graph::add_edge(u ^ sense, v ^ sense);
}
assert(ss.eof());
}
}
assert(in.eof());
return in;
}
template <typename Graph>
class AdjWriter
{
const Graph& m_g;
public:
AdjWriter(const Graph& g) : m_g(g) { }
friend std::ostream& operator<<(std::ostream& out,
const AdjWriter& o)
{
return write_adj<Graph>(out, o.m_g);
}
};
template <typename Graph>
AdjWriter<Graph> adj_writer(const Graph& g)
{
return AdjWriter<Graph>(g);
}
#endif
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