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#ifndef ASSEMBLY_DOTWRITER_H
#define ASSEMBLY_DOTWRITER_H 1
/** Written by Shaun Jackman <sjackman@bcgsc.ca>. */
#include "Common/UnorderedMap.h"
#include "Graph/ContigGraphAlgorithms.h"
#include <cassert>
#include <iostream>
#include <sstream>
class DotWriter
{
private:
typedef SequenceCollectionHash Graph;
typedef graph_traits<Graph>::vertex_descriptor V;
typedef graph_traits<Graph>::vertex_iterator Vit;
typedef graph_traits<Graph>::adjacency_iterator Ait;
typedef std::string VertexName;
DotWriter() : m_id(0) { }
/** Complement the specified name. */
static std::string
complementName(std::string s)
{
char c = *s.rbegin();
assert(c == '+' || c == '-');
*s.rbegin() = c == '+' ? '-' : '+';
return s;
}
/** Return the name of the specified vertex. */
const VertexName&
getName(const V& u) const
{
Names::const_iterator it = m_names.find(u);
if (it == m_names.end())
std::cerr << "error: cannot find vertex " << u << '\n';
assert(it != m_names.end());
return it->second;
}
/** Set the name of the specified vertex. */
void setName(const V& u, const VertexName& uname)
{
std::pair<Names::const_iterator, bool> inserted
= m_names.insert(Names::value_type(u, uname));
if (!inserted.second)
std::cerr << "error: duplicate vertex " << u << '\n';
assert(inserted.second);
(void)inserted;
}
/** Return whether this vertex is contiguous and not palindromic. */
bool contiguousOut(const Graph& g, const V& u)
{
return contiguous_out(g, u)
&& !u.isPalindrome()
&& !u.isPalindrome(SENSE)
&& !(*adjacent_vertices(u, g).first).isPalindrome();
}
/** Return the in-adjacent vertex. */
V adjacentVertexIn(const V& u, const Graph& g)
{
return source(*in_edges(u, g).first, g);
}
/** Return whether this vertex is contiguous and not palindromic. */
bool contiguousIn(const Graph& g, const V& u)
{
return contiguous_in(g, u)
&& !u.isPalindrome()
&& !u.isPalindrome(ANTISENSE)
&& !adjacentVertexIn(u, g).isPalindrome();
}
/** Write out the specified contig. */
void writeContig(std::ostream& out, const Graph& g, const V& u)
{
unsigned n = 0;
unsigned c = 0;
V v;
for (v = u; contiguousOut(g, v); v = *adjacent_vertices(v, g).first) {
++n;
c += get(vertex_coverage, g, v);
}
++n;
c += get(vertex_coverage, g, v);
// Output the canonical orientation of the contig.
V vrc = get(vertex_complement, g, v);
if (vrc < u)
return;
std::ostringstream ss;
ss << m_id << '+';
VertexName uname = ss.str();
VertexName vname(uname);
*vname.rbegin() = '-';
++m_id;
// Reorient the contig to agree with assembleContig.
bool rc;
Graph::const_iterator it = g.find(u, rc);
assert(it != g.end());
(void)it;
if (rc)
std::swap(uname, vname);
setName(u, uname);
if (u == vrc) {
// Palindrome
assert(n == 1);
} else
setName(vrc, vname);
unsigned l = n + V::length() - 1;
out << '"' << uname << "\" [l=" << l << " C=" << c << "]\n"
"\"" << vname << "\" [l=" << l << " C=" << c << "]\n";
}
/** Write out the contigs that split at the specified sequence. */
void
writeEdges(std::ostream& out, const Graph& g,
const V& u, const VertexName& uname) const
{
if (out_degree(u, g) == 0)
return;
out << '"' << uname << "\" -> {";
std::pair<Ait, Ait> adj = adjacent_vertices(u, g);
for (Ait vit = adj.first; vit != adj.second; ++vit) {
V v = *vit;
const VertexName& vname = getName(v);
out << " \"" << vname << '"';
if (v.isPalindrome())
out << " \"" << complementName(vname) << '"';
}
out << " }\n";
}
/** Output the edges of the specified vertex. */
void
writeEdges(std::ostream& out, const Graph& g, const V& u) const
{
std::string uname = complementName(getName(get(vertex_complement, g, u)));
writeEdges(out, g, u, uname);
if (u.isPalindrome()) {
uname = complementName(uname);
writeEdges(out, g, u, uname);
}
}
/** Write out a dot graph for the specified collection. */
void writeGraph(std::ostream& out, const Graph& g)
{
out << "digraph g {\n"
"graph [k=" << V::length() << "]\n"
"edge [d=" << -int(V::length() - 1) << "]\n";
std::pair<Vit, Vit> uits = vertices(g);
// Output the vertices.
for (Vit uit = uits.first; uit != uits.second; ++uit) {
V u = *uit;
if (get(vertex_removed, g, u))
continue;
if (!contiguousIn(g, u))
writeContig(out, g, u);
// Skip the second occurence of the palindrome.
if (u.isPalindrome()) {
assert(uit != uits.second);
++uit;
}
}
// Output the edges.
for (Vit uit = uits.first; uit != uits.second; ++uit) {
V u = *uit;
if (get(vertex_removed, g, u))
continue;
if (!contiguousOut(g, u))
writeEdges(out, g, u);
// Skip the second occurence of the palindrome.
if (u.isPalindrome()) {
assert(uit != uits.second);
++uit;
}
}
out << "}" << std::endl;
}
public:
/** Write out a dot graph for the specified collection. */
static
void write(std::ostream& out, const Graph& g)
{
DotWriter dotWriter;
dotWriter.writeGraph(out, g);
}
private:
typedef unordered_map<V, VertexName> Names;
/** A map of terminal k-mers to contig names. */
Names m_names;
/** The current contig name. */
unsigned m_id;
};
#endif
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