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debruijn_graph Struct Reference

Detailed description

Definition at line 35 of file assembly_graph.h.

#include <assembly_graph.h>


struct  view

Public Methods

 operator view ()
bool construct_graph (const D_SequenceSet &sequence_set, const D_VectorU32 &d_active_region_ids, const uint32 kmer_size, const bool allow_low_complexity)
void compute_edge_weights ()
void compute_in_degrees ()
void compute_in_adjacencies ()
void compute_subgraph_n_nodes ()
void compute_complexity ()
bool is_low_complexity (const uint32 subgraph_id)
bool has_cycles (const uint32 subgraph_id)
void topological_sort ()
void find_k_best_paths (const uint32 k)
void print_dot_graph (const D_SequenceSet &sequence_set)

Public Members

uint32 kmer_size
uint32 n_nodes
uint32 n_edges
uint32 n_subgraphs
D_VectorSetKmerCoord nodes
D_VectorU32 node_adjancency_map
D_VectorU32 node_adj_offests
D_VectorU32 node_out_degrees
D_VectorU32 node_in_degrees
D_VectorU32 edge_counts
D_VectorU32 edge_weights
D_VectorU8 edge_ref_flags
D_VectorU32 node_in_adjancency_map
D_VectorU32 node_in_adj_offests
D_VectorU32 subgraph_source_ids
D_VectorU32 subgraph_sink_ids
D_VectorU32 subgraph_n_nodes
D_VectorU32 topo_sorted_uids
D_VectorU32 topo_sorted_offsets
D_VectorU8 low_complexity
D_VectorU8 cycle_presence

Member Function Documentation

void debruijn_graph::compute_complexity ( )

Definition at line 576 of file assembly_graph_inl.h.

void debruijn_graph::compute_edge_weights ( )

Definition at line 480 of file assembly_graph_inl.h.

void debruijn_graph::compute_in_adjacencies ( )

Definition at line 525 of file assembly_graph_inl.h.

void debruijn_graph::compute_in_degrees ( )

Definition at line 492 of file assembly_graph_inl.h.

void debruijn_graph::compute_subgraph_n_nodes ( )

Definition at line 537 of file assembly_graph_inl.h.

bool debruijn_graph::construct_graph ( const D_SequenceSet sequence_set,
const D_VectorU32 d_active_region_ids,
const uint32  kmer_size,
const bool  allow_low_complexity 

Definition at line 280 of file assembly_graph_inl.h.

void debruijn_graph::find_k_best_paths ( const uint32  k)

Definition at line 596 of file assembly_graph_inl.h.

bool debruijn_graph::has_cycles ( const uint32  subgraph_id)

Definition at line 124 of file assembly_graph.h.

bool debruijn_graph::is_low_complexity ( const uint32  subgraph_id)

Definition at line 123 of file assembly_graph.h.

debruijn_graph::operator view ( )

Definition at line 92 of file assembly_graph.h.

void debruijn_graph::print_dot_graph ( const D_SequenceSet sequence_set)

Definition at line 610 of file assembly_graph_inl.h.

void debruijn_graph::topological_sort ( )

Definition at line 583 of file assembly_graph_inl.h.

Member Data Documentation

D_VectorU8 debruijn_graph::cycle_presence

Definition at line 66 of file assembly_graph.h.

D_VectorU32 debruijn_graph::edge_counts

Definition at line 48 of file assembly_graph.h.

D_VectorU8 debruijn_graph::edge_ref_flags

Definition at line 50 of file assembly_graph.h.

D_VectorU32 debruijn_graph::edge_weights

Definition at line 49 of file assembly_graph.h.

uint32 debruijn_graph::kmer_size

Definition at line 37 of file assembly_graph.h.

D_VectorU8 debruijn_graph::low_complexity

Definition at line 65 of file assembly_graph.h.

uint32 debruijn_graph::n_edges

Definition at line 39 of file assembly_graph.h.

uint32 debruijn_graph::n_nodes

Definition at line 38 of file assembly_graph.h.

uint32 debruijn_graph::n_subgraphs

Definition at line 40 of file assembly_graph.h.

D_VectorU32 debruijn_graph::node_adj_offests

Definition at line 45 of file assembly_graph.h.

D_VectorU32 debruijn_graph::node_adjancency_map

Definition at line 44 of file assembly_graph.h.

D_VectorU32 debruijn_graph::node_in_adj_offests

Definition at line 53 of file assembly_graph.h.

D_VectorU32 debruijn_graph::node_in_adjancency_map

Definition at line 52 of file assembly_graph.h.

D_VectorU32 debruijn_graph::node_in_degrees

Definition at line 47 of file assembly_graph.h.

D_VectorU32 debruijn_graph::node_out_degrees

Definition at line 46 of file assembly_graph.h.

D_VectorSetKmerCoord debruijn_graph::nodes

Definition at line 43 of file assembly_graph.h.

D_VectorU32 debruijn_graph::subgraph_n_nodes

Definition at line 58 of file assembly_graph.h.

D_VectorU32 debruijn_graph::subgraph_sink_ids

Definition at line 57 of file assembly_graph.h.

D_VectorU32 debruijn_graph::subgraph_source_ids

Definition at line 56 of file assembly_graph.h.

D_VectorU32 debruijn_graph::topo_sorted_offsets

Definition at line 62 of file assembly_graph.h.

D_VectorU32 debruijn_graph::topo_sorted_uids

Definition at line 61 of file assembly_graph.h.

The documentation for this struct was generated from the following files: