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/* ***************************************************************************
*
* KisSplice
* de-novo calling alternative splicing events from RNA-seq data.
*
* ***************************************************************************
*
* Copyright INRIA
* contributors : Vincent Lacroix
* Pierre Peterlongo
* Gustavo Sacomoto
* Vincent Miele
* Alice Julien-Laferriere
* David Parsons
*
* pierre.peterlongo@inria.fr
* vincent.lacroix@univ-lyon1.fr
*
* This software is a computer program whose purpose is to detect alternative
* splicing events from RNA-seq data.
*
* This software is governed by the CeCILL license under French law and
* abiding by the rules of distribution of free software. You can use,
* modify and/ or redistribute the software under the terms of the CeCILL
* license as circulated by CEA, CNRS and INRIA at the following URL
* "http://www.cecill.info".
* As a counterpart to the access to the source code and rights to copy,
* modify and redistribute granted by the license, users are provided only
* with a limited warranty and the software's author, the holder of the
* economic rights, and the successive licensors have only limited
* liability.
* In this respect, the user's attention is drawn to the risks associated
* with loading, using, modifying and/or developing or reproducing the
* software by the user in light of its specific status of free software,
* that may mean that it is complicated to manipulate, and that also
* therefore means that it is reserved for developers and experienced
* professionals having in-depth computer knowledge. Users are therefore
* encouraged to load and test the software's suitability as regards their
* requirements in conditions enabling the security of their systems and/or
* data to be ensured and, more generally, to use and operate it in the
* same conditions as regards security.
*
* The fact that you are presently reading this means that you have had
* knowledge of the CeCILL license and that you accept its terms.
*/
// ===========================================================================
// Include Libraries
// ===========================================================================
#include <stdio.h>
#include <list>
#include <vector>
#include <stack>
// ===========================================================================
// Include Project Files
// ===========================================================================
#include "CGraph.h"
#include "CEdge.h"
#include "SplitBcc.h"
// ===========================================================================
// Declare Used Namespaces
// ===========================================================================
using namespace std;
//================================ Methods for finding all the BCCs of the graph
/*!
\brief Extract the new bcc founded.
\param g the graph we are working on
\param edge: the edge where to stop the bcc extraction
\param backtrace_lifo: the stack of the already visited edges(last-in first-out)
\param g_bcc: a vector of the current bccs founded in the object
At the end of output_component, g_bcc will have a new bcc.
edge is the reference edge, as it was encounter twice, it defines the bcc.
output_component will extract all the edges of the stack backtrace_lifo:
from the top to the edge edge.
*/
void output_component( CGraph &g, CEdge edge, stack<CEdge>& backtrace_lifo,
vector< vector<CEdge> >& g_bcc )
{
// Components with only 2 nodes cannot contain a bubble,
// nothing to do for those
if ( edge == backtrace_lifo.top() || edge.swap_ends() == backtrace_lifo.top() )
{
backtrace_lifo.pop();
return;
}
vector<CEdge> new_bcc;
CEdge top;
// extract the whole bcc: all the edges from top to edge
do
{
top = backtrace_lifo.top();
int u = top.getFirst();
int v = top.getSecond();
new_bcc.push_back( CEdge( u ,v ) );
backtrace_lifo.pop();
}
while ( edge != top && edge.swap_ends() != top );
g_bcc.push_back( new_bcc );
}
/*!
\brief Depth first search algorithm (dfs) on the cgraph object from a node: node_id
\param g The graph (compressed) we are working on
\param node_id The index of the node we are visiting
\param backtrace_lifo: the already visited edges
\param g_bcc: a vector of the current bcc founded in the object
\param visited: a vector of boolean, defines if a node was already visited in the
depth_first search algorithm (default FALSE)
\param parent: a vector, the node from where the dfs algorithm arrived to the
current node, default -1.
\param dfs_tree_node_id: the order in which the nodes are reached during the
dfs (depth of the node)
\param low_point: a vector, the low point value for each node
\param node_id_counter: the number of nodes visited during the dfs algorithm.
The depth-first search algorithm visits all nodes accessible from
node_id (i.e: all its successors) recursively.
The nodes are numbered in the order they are reached during the search
with dfs_tree_node_id (depth).
The low_point value is the lowest depth of the neighbors of all descendants of the node
in the depth-first-search tree.
*/
void dfs_visit(CGraph &g, int node_id, stack<CEdge>& backtrace_lifo, vector<vector<CEdge> >& g_bcc, bool* &visited, int* &parent, int* &dfs_tree_node_id, int* &low_point, int node_id_counter)
{
// update the visited state of the node, its depth and low-point
visited[node_id] = true;
low_point[node_id] = dfs_tree_node_id[node_id] = ++node_id_counter;
int *p = g.get_adj_list(node_id);
for ( int i = 0; i < g.get_adj_list_sz(node_id) ; i++, p++ )
{
int v = *p;
if ( !visited[v] )
{
backtrace_lifo.push( CEdge( node_id, v ) );
parent[v] = node_id;
dfs_visit( g, v, backtrace_lifo, g_bcc, visited, parent, dfs_tree_node_id, low_point, node_id_counter);
if (low_point[v] >= dfs_tree_node_id[node_id])
{
//if ... then node_id is an articulation point.
// the bcc founded is extract with output_component
output_component(g, CEdge( node_id, v ), backtrace_lifo, g_bcc );
}
low_point[node_id] = min(low_point[node_id],low_point[v]);
}
else if ( parent[node_id] != v && dfs_tree_node_id[v] < dfs_tree_node_id[node_id])
// TODO: Can the second condition not be satisfied ?
{
// update low_point if v was already visited
backtrace_lifo.push( CEdge( node_id, v ) );
low_point[node_id] = min(low_point[node_id],dfs_tree_node_id[v]);
}
// else do nothing (we would be following the previous edge backwards)
}
}
/*!
\brief Extracts the bi-connected components of the CGraph object.
Calls the dfs method on all the unvisited nodes of the CGraph object.
\param g the graph we are working on
*/
vector<vector<CEdge> > find_bcc(CGraph &g)
{
int nb_nodes = g.get_n_nodes();
// Used by the recursive algorithm: dfs_visit
stack<CEdge> backtrace_lifo;
vector<vector<CEdge> > g_bcc;
bool *visited = new bool[nb_nodes];
int *parent = new int[nb_nodes];
int *dfs_tree_node_id = new int[nb_nodes];
int *low_point = new int[nb_nodes];
int node_id_counter = 0;
for ( int i = 0 ; i < nb_nodes ; i++ )
{
visited[i] = false;
parent[i] = -1;
}
for ( int i = 0; i < nb_nodes ; i++ )
{
if (!visited[i])
{
dfs_visit(g, i, backtrace_lifo, g_bcc, visited, parent, dfs_tree_node_id, low_point, node_id_counter);
}
}
delete[] visited;
delete[] parent;
delete[] dfs_tree_node_id;
delete[] low_point;
return g_bcc;
}
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