IGraph * Sequencer::buildGraph(std::vector<std::string>& reads){
IGraph * graph = new Graph();
graph->insertVertex(reads.at(0));
for(int i = int(reads.size() - 1);i>0 ; i-- ){
for(int j = i-1; j>=0; j--){
if( reads.at(i).compare(reads.at(j)) == 0){
break;
}
if(j == 0){
graph->insertVertex(reads.at(i));
}
}
}
std::vector<IVertex *> graph_vertices = graph->getVertices();
int size_graph_vertices = graph_vertices.size();
int max_overlap = 0;
for(int i=0; i< size_graph_vertices; i++){
for(int j=0; j< size_graph_vertices; j++){
//find overlap
if(i != j){
int overlap = 0;
for(int k = 0; k< graph_vertices.at(i)->getName().size(); k++){
int l = 0;
int count = 0;
int m = k;
while( graph_vertices.at(i)->getName()[m] == graph_vertices.at(j)->getName()[l] ){
m++;
l++;
count++;
}
if(count > overlap){
overlap = count;
}
}
if(max_overlap < overlap){
max_overlap = overlap;
}
if(overlap>0){
IEdge *edge = new Edge();
edge->setTarget(graph_vertices.at(j));
edge->setWeight(overlap);
graph_vertices.at(i)->addEdge(edge);
}
}
}
}
for(int i=0; i< size_graph_vertices; i++){
IVertex* vert = graph_vertices.at(i);
for(int j =0; j < vert->getEdges().size(); j++){
IEdge * edg = vert->getEdges()[j];
int wt = max_overlap - edg->getWeight();
edg->setWeight(max_overlap - edg->getWeight());
}
}
return graph;
}
/**
* O(V + Vlog(V) + Elog(V))
* @param G [description]
* @param s [description]
*/
void MST_prim(IGraph &G, IGraph::vertex &s, double inf = 1e100){
int n = G.numVertices();
bool *isQ = new bool[n];
IGraph::vertex ** pi = new IGraph::vertex *[n];
typedef pair<double, int> vi;
vector<vi> vertices;
IndexedPriorityQueue<double, less<double> > Q(n);
for (int i = 0; i < n; ++i)
{
vertices.push_back(make_pair(inf, i));
Q.insert(i, inf);
pi[i] = NULL;
isQ[i] = true;
}
vertices[s.id].first = 0;
Q.changeKey(s.id, 0);
int it = 0;
while(!Q.isEmpty()){
int id = Q.minIndex(); // O(1)
Q.deleteMin(); // O(lg(v))
cout << id << endl;
isQ[id] = false;
IGraph::vertex *u = G.getVertex(id);
for (IGraph::vertex::iterator v = u->begin(); v != u->end(); ++v)
{
double w = G.getEdge(id, v->second->id);
if(isQ[v->second->id] && w < vertices[v->second->id].first){// O(1)
pi[v->second->id] = u;
Q.changeKey(v->second->id, w); // O(log(v))
vertices[v->second->id].first = w;
}
}
}
cout << "PRIMs : ";
for (int i = 0; i < n; ++i)
{
if(pi[i] != NULL)
cout << pi[i]->id << " ";
else
cout << "nil ";
}
cout << endl;
delete [] isQ;
}
/**
* O(V + E)
* @param G Graph
* @param s source vertex
*/
void BFS(IGraph &G, IGraph::vertex &s){
int n = G.numVertices();
int *color = new int[n];
int *d = new int[n];
IGraph::vertex **pi = new IGraph::vertex*[n];
for (IGraph::vertex_iterator v = G.begin(); v != G.end(); ++v)
{
color[v->id] = WHITE;
pi[v->id] = NULL;
d[v->id] = 1000000;
}
color[s.id] = GRAY;
d[s.id] = 0;
queue<IGraph::vertex * > Q;
Q.push(&s);
while(!Q.empty()){
IGraph::vertex * u = Q.front();
for (IGraph::vertex::iterator e = u->begin(); e != u->end(); e++)
{
IGraph::vertex * v = e->second;
if(color[v->id] == WHITE){
color[v->id] = GRAY;
d[v->id] = d[u->id] + 1;
pi[v->id] = u;
Q.push(&(*v));
}
}
color[u->id] = BLACK;
Q.pop();
}
cout << "S : " << s.id << endl;
for (int i = 0; i < n; ++i)
{
if(pi[i] != NULL)
cout << pi[i]->id << " ";
else
cout << "nil ";
}
cout << endl;
delete [] color;
delete [] d;
delete [] pi;
}
void complete2Tournament(IGraph &comp, IGraph &tour, bool unweighted = true){
//if(comp.isComplete()){
// cout << "complete2Tournament" << endl;
for (IGraph::vertex_iterator v = comp.begin(); v != comp.end(); v++){
IGraph::vertex::iterator end = v->end();
for (IGraph::vertex::iterator u = v->begin(); u != end; u++){
if(!(tour.edgeExists(v->id,u->second->id) || tour.edgeExists(u->second->id, v->id))){
double w1 = comp.getEdge(v->id, u->second->id);
double w2 = comp.getEdge(u->second->id, v->id);
double wVal = (unweighted)? 1 : abs(w1 - w2);
if(w1 > w2)
tour.addEdge(v->id, u->second->id, (unweighted)? 1 : w1);
else if(w1 < w2)
tour.addEdge(u->second->id, v->id, (unweighted)? 1 : w2);
else{
tour.addEdge(u->second->id, v->id, (unweighted)? 1 : w2);
tour.addEdge(v->id, u->second->id, (unweighted)? 1 : w1);
}
}
}
}
//}
}
void assertValidCover(IGraph *graph, vector<Node*> cover) {
IGraph *g = new Graph(graph);
for (Node *node : cover) {
g->removeNode(node);
}
if (g->nbEdges() == 0) {
rlutil::setColor(2);
cout << "OK" << endl;
rlutil::setColor(7);
} else {
rlutil::setColor(12);
cout << "FAILED : The provided cover is not a valid solution." << endl;
rlutil::setColor(7);
}
delete g;
}
int tour_ham_merge_and_count(IGraph &tour, int *A, int *buffer, int ini, int fim, int meio){
memset(buffer, 0, sizeof(int)*(fim-ini+1));
int count = 0;
int i = ini;
int j = meio + 1;
int k = 0;
while(i < meio + 1 && j <= fim){
if(tour.edgeExists(A[i], A[j])){
buffer[k] = A[i];
i++;
}else{
buffer[k] = A[j];
count += meio - i + 1;
j++;
}
k++;
}
if(i < meio + 1){
memcpy(buffer + k, A + i, sizeof(int)*(meio-i+1));
}else{
memcpy(buffer + k, A + j, sizeof(int)*(fim-j+1));
}
memcpy(A + ini, buffer, sizeof(int)*(fim-ini+1));
return count;
}
void DFSImplementation (const IGraph& graph, Visitor& visitor, std::vector<bool>& visited, int vertex_start) {
std::stack <int> vertices_stack;
vertices_stack.push(vertex_start);
while (!vertices_stack.empty()) {
int current_vertex = vertices_stack.top();
if (!visited[current_vertex]) {
visited[current_vertex] = true;
visitor.StartProcessingVertex(current_vertex);
std::vector<int> current_vertex_incidences = graph.GetIncidenceList(current_vertex);
for (int i = 0; i < current_vertex_incidences.size(); ++i) {
int next_incident_vertex = current_vertex_incidences[i];
visitor.ProcessingEdge(current_vertex, next_incident_vertex);
if (!visited[next_incident_vertex]) vertices_stack.push(next_incident_vertex);
}
}
else {
visitor.LeaveVertex(current_vertex);
vertices_stack.pop();
}
}
} if (!visited[vertex]) DFSImplementation(graph, visitor, visited, vertex);
/**
* complexity : O(V + E)
* @param G Graph
* @param s source vertex
*/
void DFS(IGraph &G, IGraph::vertex &s){
int n = G.numVertices();
int *color = new int[n];
int *d = new int[n];
int *f = new int[n];
IGraph::vertex **pi = new IGraph::vertex*[n];
for (IGraph::vertex_iterator v = G.begin(); v != G.end(); ++v)
{
color[v->id] = WHITE;
pi[v->id] = NULL;
d[v->id] = 0;
f[v->id] = 0;
}
int dtime = 0;
DFS_visit(G, s, color, d, f, pi, dtime);
for (IGraph::vertex_iterator v = G.begin(); v != G.end(); ++v)
{
if(color[v->id] == WHITE){
DFS_visit(G, *v, color, d, f, pi, dtime);
}
}
cout << "S : " << s.id << endl;
for (int i = 0; i < n; ++i)
{
if(pi[i] != NULL)
cout << pi[i]->id << "(" << d[i] << "/" << f[i] << ") ";
else
cout << "nil" << "(" << d[i] << "/" << f[i] << ") ";
}
cout << endl;
delete [] color;
delete [] d;
delete [] f;
delete [] pi;
}
void FAS_pivot(IGraph &graph, std::vector<int> &vertices){
if(vertices.size() <= 1) return;
// pick random pivot
int i = vertices[rand()%(vertices.size())];
std::vector<int> vL;
std::vector<int> vR;
for (int j = 0; j < vertices.size(); ++j)
{
if(i == vertices[j]) continue;
if(graph.edgeExists(vertices[j], i)){
vL.push_back(vertices[j]);
}else if(graph.edgeExists(i, vertices[j])){
vR.push_back(vertices[j]);
}
}
FAS_pivot(graph, vL);
FAS_pivot(graph, vR);
vertices.clear();
for (int k = 0; k < vL.size(); ++k)
{
vertices.push_back(vL[k]);
}
vertices.push_back(i);
for (int k = 0; k < vR.size(); ++k)
{
vertices.push_back(vR[k]);
}
}
inline void TestIGraphHasEdge(const IGraph& graph, const std::vector<Edge> &list_of_edges,
int vertex_a, int vertex_b) {
bool has_edge_between_a_and_b = graph.HasEdge(vertex_a, vertex_b);
bool right_has_edge_between_a_and_b = false;
for (int edge_index = 0; edge_index < list_of_edges.size(); ++edge_index) {
if (list_of_edges[edge_index].begin_ == vertex_a && list_of_edges[edge_index].end_ == vertex_b) {
right_has_edge_between_a_and_b = true;
break;
}
}
if (right_has_edge_between_a_and_b != has_edge_between_a_and_b) {
throw std::logic_error("TestIGraphHasEdge: FAIL");
}
}
inline void TestIGraphGetIncidenceList(const IGraph& graph, const std::vector<Edge> &list_of_edges, int vertex) {
std::unordered_set<int> right_insidence_vertices_set;
std::vector<int> incidence_list = graph.GetIncidenceList(vertex);
std::unordered_set<int> incidence_vertices_set(incidence_list.begin(), incidence_list.end());
for (int edge_index = 0; edge_index < list_of_edges.size(); ++edge_index) {
if (list_of_edges[edge_index].begin_ == vertex) {
right_insidence_vertices_set.insert(list_of_edges[edge_index].end_);
}
}
if (incidence_vertices_set != right_insidence_vertices_set) {
throw std::logic_error("IGraph::GetIncidenceList : FAIL");
}
}
void DVhamiltonPathForTournament(IGraph &tour, int * path){
int * buffer = new int[tour.numVertices()];
tour_ham_sort_and_count(tour, path, buffer, 0, tour.numVertices() - 1);
}
inline void TestIGraphGetNumberOfVertices (const IGraph& graph, int vertices_amount) {
if (graph.GetNumberOfVertices() != vertices_amount) {
throw std::logic_error("IGraph::GetNumberOfVertices: FAIL");
}
}
/*!
* \brief Calback function invoking layout algorithms from Dia's menu
* \ingroup LayoutPlugin
*/
static ObjectChange *
layout_callback (DiagramData *data,
const gchar *filename,
guint flags, /* further additions */
void *user_data,
GraphCreateFunc func)
{
ObjectChange *changes = NULL;
GList *nodes = NULL, *edges = NULL, *list;
const char *algorithm = (const char*)user_data;
/* from the selection create two lists */
list = data_get_sorted_selected (data);
while (list) {
DiaObject *o = (DiaObject *)list->data;
if (!maybe_edge (o))
nodes = g_list_append (nodes, o);
//FIXME: neither 1 nor num_handles-1 is guaranteed to be the second connection
// it entirely depends on the objects implementation
else if ( o->num_handles > 1 && o->handles[0]->connected_to
&& (o->handles[1]->connected_to || o->handles[o->num_handles-1]->connected_to))
edges = g_list_append (edges, o);
list = g_list_next(list);
}
if (g_list_length (edges) < 1 || g_list_length (nodes) < 2) {
message_warning (_("Please select edges and nodes to layout."));
} else {
IGraph *g = func ? func () : NULL;
if (!g)
message_error (_("Graph creation failed"));
else {
std::vector<double> coords;
/* transfer nodes and edges */
for (list = nodes; list != NULL; list = g_list_next(list)) {
DiaObject *o = (DiaObject *)list->data;
const Rectangle *bbox = dia_object_get_bounding_box (o);
g->AddNode (bbox->left, bbox->top, bbox->right, bbox->bottom);
}
for (list = edges; list != NULL; list = g_list_next(list)) {
DiaObject *o = (DiaObject *)list->data;
DiaObject *src = o->handles[0]->connected_to->object;
// see above: there is no guarantee ...
DiaObject *dst = o->handles[1]->connected_to ?
o->handles[1]->connected_to->object : o->handles[o->num_handles-1]->connected_to->object;
if (_obj_get_bends (o, coords))
g->AddEdge (g_list_index (nodes, src), g_list_index (nodes, dst), &coords[0], coords.size());
else
g->AddEdge (g_list_index (nodes, src), g_list_index (nodes, dst), NULL, 0);
}
IGraph::eResult res;
if ((res = g->Layout (algorithm)) != IGraph::SUCCESS) {
const char *sErr;
switch (res) {
case IGraph::NO_MODULE : sErr = _("No such module."); break;
case IGraph::OUT_OF_MEMORY : sErr = _("Out of memory."); break;
case IGraph::NO_TREE: sErr = _("Not a tree."); break;
case IGraph::NO_FOREST: sErr = _("Not a forest."); break;
case IGraph::FAILED_ALGORITHM: sErr = _("Failed algorithm."); break;
case IGraph::FAILED_PRECONDITION: sErr = _("Failed precondition."); break;
case IGraph::CRASHED : sErr = _("OGDF crashed."); break;
default : sErr = _("Unknown reason"); break;
}
message_warning (_("Layout '%s' failed.\n%s"), (const char*)user_data, sErr);
} else {
changes = change_list_create ();
/* transfer back information */
int n;
for (n = 0, list = nodes; list != NULL; list = g_list_next (list), ++n) {
Point pt;
if (g->GetNodePosition (n, &pt.x, &pt.y)) {
DiaObject *o = (DiaObject *)list->data;
GPtrArray *props = g_ptr_array_new ();
//FIXME: can't use "obj_pos", it is not read in usual update_data impementations
// "elem_corner" will only work for Element derived classes, but that covers most
// of the cases here ...
prop_list_add_point (props, "elem_corner", &pt);
change_list_add (changes, object_apply_props (o, props));
}
}
// first update to reuse the connected points
diagram_update_connections_selection(DIA_DIAGRAM (data));
/* use edge bends, if any */
int e;
for (e = 0, list = edges; list != NULL; list = g_list_next (list), ++e) {
DiaObject *o = (DiaObject *)list->data;
// number of bends / 2 is the number of points
int n = g->GetEdgeBends (e, NULL, 0);
if (n >= 0) { // with 0 it is just a reset of the exisiting line
try {
coords.resize (n);
} catch (std::bad_alloc& ex) {
g_warning ("%s", ex.what());
continue;
}
g->GetEdgeBends (e, &coords[0], n);
change_list_add (changes, _obj_set_bends (o, coords));
}
}
/* update view */
diagram_update_connections_selection(DIA_DIAGRAM (data));
}
g->Release ();
}
}
g_list_free (nodes);
g_list_free (edges);
return changes;
}
void DFS (const IGraph& graph, Visitor& visitor) {
std::vector<bool> visited(graph.GetNumberOfVertices(), false);
for (int vertex = 0; vertex < graph.GetNumberOfVertices(); ++vertex)
if (!visited[vertex]) DFSImplementation(graph, visitor, visited, vertex);
}
