static pathStep *get_first_step(pathStep * first_step, dBGraph * db_graph)
{
//printf("|");
WalkingFunctions wf;
pathStep tmp_step;
Nucleotide n;
path_step_assign(&tmp_step, first_step);
if(tmp_step.orientation == undefined){
tmp_step.orientation = reverse; //This will allow, when reversing the walk, to walk in the forward direction, which "naturally" appends the bases to the end of the path.
}else{
return first_step;
}
/* Check if forward node has one edge, if not that reverse node does.
While we're at it, assign label to n. */
if (db_node_has_precisely_one_edge_all_colours(tmp_step.node, tmp_step.orientation, &n)) {
} else if (db_node_has_precisely_one_edge_all_colours(tmp_step.node, opposite_orientation(tmp_step.orientation), &n)) {
tmp_step.orientation = opposite_orientation(tmp_step.orientation);
} else {
return NULL;
}
tmp_step.label = n;
/* If it's a blunt node in the opposite orientation, then we can't get a better starting step */
if (db_node_is_blunt_end_all_colours(first_step->node, opposite_orientation(tmp_step.orientation))) {
path_step_assign(first_step, &tmp_step);
return first_step;
}
//printf("#");
/* Otherwise, do a perfect path walk to try and get a better start step */
//Path * temp_path = path_new(limit, db_graph->kmer_size);
Path *temp_path = path_get_buffer_path();
temp_path->id = -2;
db_node_has_precisely_one_edge_all_colours(tmp_step.node, tmp_step.orientation, &tmp_step.label);
wf.get_starting_step = &get_first_step_identity;
wf.continue_backwards = &clean_path;
wf.post_step_action = &path_step_do_nothing;
wf.pre_step_action = &path_step_do_nothing;
wf.step_action = &path_step_do_nothing;
wf.continue_traversing = &continue_traversing;
wf.get_next_step = &get_next_step;
wf.output_callback = &path_do_nothing;
wf.node_callbacks.used = 0;
wf.step_actions.used = 0;
wf.path_callbacks.used = 0 ;
db_graph_add_path_callback_with_args(&wf, &store_last, (void *) first_step);
if (DEBUG) {
printf("[get_first_step]Orientation: %s\n", tmp_step.orientation == forward ? "forward" : "reverse");
printf("[get_first_step] (%d):", path_get_edges_count(temp_path));
path_step_print(first_step, db_graph->kmer_size, stdout);
printf("\n");
}
db_graph_generic_walk(&tmp_step, temp_path, &wf, db_graph);
path_free_buffer_path(temp_path);
return first_step;
}
/*----------------------------------------------------------------------*
* Function: *
* Purpose: *
* Params: *
* Returns: *
*----------------------------------------------------------------------*/
int grow_graph_from_node(dBNode* start_node, dBNode** best_node, dBGraph* graph)
{
Queue* nodes_to_walk;
dBNode* node;
int orientation;
int depth;
int current_graph_size = 0;
int best_coverage = 0;
int best_edges = 0;
*best_node = 0;
// Nucleotide iterator, used to walk all possible paths from a node
void walk_if_exists(Nucleotide n) {
//if (debug) printf("Trying nucleotide %i\n", n);
// If there is an edge in any colour for this nucleotide...
if (db_node_edge_exist_any_colour(node, n, orientation)) {
//if (debug) printf(" Edge exists\n");
// Get first node along this edge and check we've not already visited it...
Orientation next_orientation;
Nucleotide reverse_nucleotide;
dBNode * next_node;
next_node = db_graph_get_next_node(node, orientation, &next_orientation, n, &reverse_nucleotide, graph);
if (!next_node) {
log_and_screen_printf("Error: Something went wrong with db_graph_get_next_node\n");
exit(-1);
}
// If not already visited the first node, walk it...
if (!db_node_check_flag_visited(next_node)) {
pathStep first_step;
Path * new_path;
dBNode* end_node;
int i = 0;
// Get path
first_step.node = node;
first_step.orientation = orientation;
first_step.label = n;
new_path = path_new(MAX_EXPLORE_NODES, graph->kmer_size);
if (!new_path) {
log_and_screen_printf("ERROR: Not enough memory to allocate new path.\n");
exit(-1);
}
db_graph_get_perfect_path_with_first_edge_all_colours(&first_step, &db_node_action_do_nothing, new_path, graph);
// Add end node to list of nodes to visit
end_node = new_path->nodes[new_path->length-1];
if (!db_node_check_flag_visited(end_node)) {
if (!db_node_is_blunt_end_all_colours(end_node, new_path->orientations[new_path->length-1])) {
if (queue_push_node(nodes_to_walk, end_node, depth+1) == NULL) {
log_and_screen_printf("Queue too large. Ending.\n");
exit(1);
}
}
}
// Now go through all nodes, look for best and mark all as visited
for (i=0; i<new_path->length; i++) {
if (!db_node_check_flag_visited(new_path->nodes[i])) {
int this_coverage = element_get_coverage_all_colours(new_path->nodes[i]);
int this_edges = db_node_edges_count_all_colours(new_path->nodes[i], forward) + db_node_edges_count_all_colours(new_path->nodes[i], reverse);
if ((best_node == 0) ||
(this_coverage > best_coverage) ||
((this_coverage == best_coverage) && (this_edges < best_edges)))
{
best_coverage = this_coverage;
best_edges = this_edges;
*best_node = new_path->nodes[i];
}
db_node_action_set_flag_visited(new_path->nodes[i]);
current_graph_size++;
}
}
// Clean up
path_destroy(new_path);
}
}
}
// Start a queue of nodes to walk
//log_and_screen_printf("Allocating %d Mb to store queue information (max %d nodes, when full each node could be %d)...\n", ((METACORTEX_QUEUE_SIZE * sizeof(QueueItem*)) / 1024) / 1024, METACORTEX_QUEUE_SIZE, sizeof(QueueItem));
nodes_to_walk = queue_new(METACORTEX_QUEUE_SIZE);
if (!nodes_to_walk) {
log_and_screen_printf("Couldn't get memory for node queue.\n");
exit(-1);
}
// Add start node to list of nodes to visit
if (queue_push_node(nodes_to_walk, start_node, 0) == NULL) {
log_and_screen_printf("Queue too large. Ending.\n");
exit(-1);
}
if (!db_node_check_flag_visited(start_node)) {
db_node_action_set_flag_visited(start_node);
current_graph_size++;
}
// Now keep visiting nodes and walking paths
while (nodes_to_walk->number_of_items > 0) {
// Take top node from list
node = queue_pop_node(nodes_to_walk, &depth);
// Look at all paths out from here
orientation = forward;
nucleotide_iterator(&walk_if_exists);
orientation = reverse;
nucleotide_iterator(&walk_if_exists);
}
queue_free(nodes_to_walk);
// If we didn't find a start node, presumably this is a singleton?
if (*best_node == 0) {
printf("Note: didn't find a best node, setting to start node\n");
*best_node = start_node;
}
return current_graph_size;
}
