static pathStep *get_next_step(pathStep * current_step, pathStep * next_step, pathStep * reverse_step, dBGraph * db_graph)
{
pathStep *step = db_graph_get_next_step(current_step, next_step, reverse_step, db_graph);
assert(step != NULL);
step->label = Undefined;
Nucleotide n;
// TODO: If this works, then there's possibly a bug to fix for the multi-colour situation
if (next_step->node == NULL) {
next_step->label = Undefined;
return next_step;
}
if (db_node_has_precisely_one_edge_all_colours(next_step->node, next_step->orientation, &n)) {
next_step->label = n;
}
if (!db_node_has_precisely_one_edge_all_colours(next_step->node, opposite_orientation(next_step->orientation), &n)) {
next_step->label = Undefined;
}
return next_step;
}
int perfect_path_get_path_with_callback_with_args(dBNode * node, Orientation orientation, void (*node_action) (dBNode * , void *), void * node_args, void (*path_action) (Path * , void *), void * path_args,dBGraph * db_graph)
{
WalkingFunctions wf;
perfect_path_get_funtions(&wf);
pathStep first;
first.node = node;
//first.orientation = orientation == undefined? reverse: orientation;
first.orientation = orientation;
first.label = Undefined;
if (orientation != undefined) {
db_node_has_precisely_one_edge_all_colours(node, orientation, &first.label);
wf.get_starting_step = &get_first_step_identity;
}
//wf.find_first_node = &find_first;
db_graph_add_node_action_with_args (&wf, node_action, node_args);
db_graph_add_path_callback_with_args (&wf, path_action, path_args);
Path *path = path_get_buffer_path();
int ret = db_graph_generic_walk(&first, path, &wf, db_graph);
path_free_buffer_path(path);
return ret;
}
static pathStep *get_next_step(pathStep * current_step, pathStep * next_step,
pathStep * reverse_step, dBGraph * db_graph)
{
pathStep *step = db_graph_get_next_step(current_step, next_step, reverse_step, db_graph);
assert(step != NULL);
if (step->node != NULL) {
step->label = Undefined;
Nucleotide n;
if (db_node_has_precisely_one_edge_all_colours
(next_step->node, next_step->orientation, &n)) {
next_step->label = n;
}else{
next_step->label = path_step_get_unvisited_edge_all_colours(next_step);
}
}
return next_step;
}
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;
}
