Scaffolding  0.1
This program can assemble genome scaffolds using the pairing information in paired-end reads.
Classes | Typedefs | Functions
graph_parameters.hpp File Reference
#include <vector>
#include <queue>
#include <iostream>
#include <boost/graph/graph_traits.hpp>
#include <boost/graph/connected_components.hpp>
#include "graph_typedefs.hpp"
#include "graph_utils.hpp"
#include "low_priority_queue.hpp"

Go to the source code of this file.

Classes

struct  scaffold::graph_parameters::degree_less< Graph >
 comparator class, comparing two vertices u,v such that comp(u,v) = true <=> deg(u) < deg(v) More...
 
struct  scaffold::graph_parameters::degree_greater< Graph >
 comparator class, comparing two vertices u,v such that comp(u,v) = true <=> deg(u) > deg(v) More...
 
struct  scaffold::graph_parameters::interval
 an interval consists of a lower & an upper bound More...
 
struct  scaffold::graph_parameters::graph_parameters
 collection of graph parameters that can be computed More...
 

Typedefs

template<class Graph >
using scaffold::graph_parameters::vertex_ordering = std::vector< Vertex< Graph > >
 

Functions

std::ostream & scaffold::graph_parameters::operator<< (std::ostream &os, const interval &i)
 print intervals
 
std::ostream & scaffold::graph_parameters::operator<< (std::ostream &os, const graph_parameters &params)
 print all graph parameters
 
template<class Graph >
unsigned scaffold::graph_parameters::num_connected_components (const Graph &g, ComponentMap< Graph > &compMap, graph_parameters *const params=NULL)
 compute a component map and return the number of connected components More...
 
template<class Graph >
unsigned scaffold::graph_parameters::num_connected_components (const Graph &g, graph_parameters *const params=NULL)
 return the number of connected components (see num_connected_components() above)
 
template<class Graph >
std::pair< Vertex< Graph >, unsigned > scaffold::graph_parameters::get_max_degree (const Graph &g, graph_parameters *const params=NULL)
 compute the maximum degree of g and return a vertex that has this degree More...
 
template<class Graph >
unsigned scaffold::graph_parameters::h_index (const Graph &g, graph_parameters *const params=NULL)
 compute the h-index of the graph g More...
 
template<class Graph >
unsigned scaffold::graph_parameters::degeneracy (const Graph &g, vertex_ordering< Graph > *order=NULL, graph_parameters *const params=NULL)
 
template<class Graph >
unsigned scaffold::graph_parameters::feedback_vertex_set_greedy (const Graph &g, VertexSet< Graph > *FVS=NULL, graph_parameters *params=NULL)
 compute a greedy feedback vertex set and return the number of vertices therein More...
 
template<class Graph >
void scaffold::graph_parameters::compute_easy_parameters (const Graph &g, graph_parameters &params)
 compute the easy graph parameters More...
 

Detailed Description

compute simple graph parameters such as max degree, feedback edge set number, degeneracy, ...

many functions in this class take a pointer to a graph_parameters struct; if this is not NULL, they will store the respective value in the struct as well as returning it