void graph_add_edges(graph *g) {
node *n1, *n2;
int i, j;
for (i = 0; i < g->ntemplates; i++) {
n1 = g->nodes->node[i];
for (j = i+1; j < g->ntemplates; j++) {
int count;
double score;
n2 = g->nodes->node[j];
score = calc_edge_score(n1->matrix, n2->matrix,
g->snp_scores, g->nsnps, &count,
g->correlation_offset);
if (count) {
graph_add_edge(g, g->nodes->node[i], g->nodes->node[j], score);
}
}
}
/* Sort edges-out for each node by node number */
for (i = 0; i < g->ntemplates; i++) {
node_sort_edges(g->nodes->node[i]);
}
}
typename SubstEdgeScore<V,D>::value_type
SubstEdgeScore<V,D>::
edge_ext_score(const WorkArea& wa,
const Data& xx, const Data& yy,
const Edge& ix, const Edge& iy,
uint i, uint j) const
{
value_type s=0.0;
if (ix.p_pos().first==ix.c_pos().first ||
iy.p_pos().first==iy.c_pos().first) { // loop region
s = calc_edge_score(si_subst_, wa.gap, xx, yy,
ix.p_pos().first, ix.p_pos().second,
iy.p_pos().first, iy.p_pos().second);
} else { // buldge
s = calc_edge_score(si_subst_, wa.gap, xx, yy,
ix.p_pos().first, ix.c_pos().first-1,
iy.p_pos().first, iy.c_pos().first-1);
s += calc_edge_score(si_subst_, wa.gap, xx, yy,
ix.c_pos().second+1, ix.p_pos().second,
iy.c_pos().second+1, iy.p_pos().second);
}
return s;
}
/**
* Merges the nodes linked to by edge 'e' and sets any neighbouring
* edge / link scores to be invalid.
*/
void merge_node(graph *g, edge *e) {
node *n1, *n2;
node_array *na1, *na2, *na;
int i, j;
if (verbosity >= 2)
printf("Merging %d / %d (score %8.2f, link %8.2f) %s / %s\n",
e->n1->number, e->n2->number,
e->edge_score,
e->linkage_score,
e->n1->tname, e->n2->tname);
/*
print_matrix_node(g, e->n1);
print_matrix_node(g, e->n2);
*/
/* Find all the nodes linked to either n1 or n2 where n1 and n2
* are the nodes in this edge.
*/
n1 = e->n1;
n2 = e->n2;
na1 = node_neighbours(n1);
na2 = node_neighbours(n2);
na = node_array_union(na1, na2);
node_array_destroy(na1);
node_array_destroy(na2);
/* Attach n2 to the node_array in n1 - allows traceback */
if (!n1->merged) {
n1->merged = node_array_create();
}
node_array_add(n1->merged, n2);
/*
* Merge the matrix rows.
*/
for (i = 0; i < g->nsnps; i++) {
for (j = 0; j < 6; j++)
n1->matrix[i][j] += n2->matrix[i][j];
}
/*
* Forall nodes in our set, find the edges between that and n1
* and/or n2. If it links with both then set the edge score to be
* the average of the two values, otherwise use the single score.
* Set the linkage score to be undefined.
* Reset the edge to be between this node and n1 always (as n2
* will then be disconnected and considered to be merged with n1).
*/
for (i = 0; i < na->nnodes; i++) {
node *n = na->node[i];
edge *e1, *e2;
if (n == n1 || n == n2)
continue;
e1 = edge_find(n, n1);
e2 = edge_find(n, n2);
if (!e1 && !e2)
continue;
if (e1 && e2) {
/* links to both, so remove edge to n2 */
e1->edge_score = (e1->edge_score + e2->edge_score) / 2;
edge_unlink(e2);
} else if (e2) {
/* links only to n2, so relink edge to n1 */
if (e2->n1 == n)
e2->n2 = n1;
else
e2->n1 = n1;
edge_array_add(n1->edges, e2);
e1 = e2;
}
e1->linkage_score = UNDEF_SCORE;
e1->edge_score = UNDEF_SCORE;
}
node_array_destroy(na);
edge_unlink(e);
for (i = 0; i < g->nodes->nnodes; i++) {
if (g->nodes->node[i] == n2) {
g->nodes->node[i] = NULL;
break;
}
}
/* Recompute all undefined edge scores */
for (i = 0; i < g->edges->nedges; i++) {
edge *e;
if (!(e = g->edges->edge[i]))
continue;
if (!e->n1 || !e->n2)
continue;
e->edge_score =
calc_edge_score(e->n1->matrix, e->n2->matrix, g->snp_scores,
g->nsnps, NULL, g->correlation_offset);
}
}
