/**
* Write the read if it matches and then pass it down the chain if
* appropriate.
*/
void readMatch(bool matches,
std::shared_ptr<bam_hdr_t> &header,
std::shared_ptr<bam1_t> &read) {
if (matches) {
count++;
if (output_file) {
sam_write1(output_file.get(), header.get(), read.get());
}
}
if (next && checkChain(chain, matches)) {
next->processRead(header, read);
}
}
/**
* We want this chromosome if our query is interested or the next link can
* make use of it _if_ it will see it upon failure (otherwise, its behaviour
* is determined by ours.
*/
bool wantChromosome(std::shared_ptr<bam_hdr_t> &header, uint32_t tid) {
return CheckIterator::wantChromosome(header, tid) ||
next && checkChain(chain, false) &&
next->wantChromosome(header, tid);
}
/* makeGraphs:
* Generate dags modeling the row and column constraints.
* If the table has cc columns, we create the graph
* 0 -> 1 -> 2 -> ... -> cc
* and if a cell starts in column c with span cspan, with
* width w, we add the edge c -> c+cspan [minlen = w].
*
* We might simplify the graph by removing multiedges,
* using the max minlen, but will affect the balancing?
*/
void makeGraphs(htmltbl_t * tbl, graph_t * rowg, graph_t * colg)
{
htmlcell_t *cp;
htmlcell_t **cells;
node_t *t;
node_t *lastn;
node_t *h;
edge_t *e;
int i;
int* minc;
int* minr;
lastn = NULL;
for (i = 0; i <= tbl->cc; i++) {
t = agnode(colg, nToName(i));
alloc_elist(tbl->rc, ND_in(t));
alloc_elist(tbl->rc, ND_out(t));
if (lastn) {
ND_next(lastn) = t;
lastn = t;
} else {
lastn = GD_nlist(colg) = t;
}
}
lastn = NULL;
for (i = 0; i <= tbl->rc; i++) {
t = agnode(rowg, nToName(i));
alloc_elist(tbl->cc, ND_in(t));
alloc_elist(tbl->cc, ND_out(t));
if (lastn) {
ND_next(lastn) = t;
lastn = t;
} else {
lastn = GD_nlist(rowg) = t;
}
}
minr = N_NEW(tbl->rc, int);
minc = N_NEW(tbl->cc, int);
for (cells = tbl->u.n.cells; *cells; cells++) {
int x, y, c, r;
cp = *cells;
x = (cp->data.box.UR.x + (cp->cspan-1))/cp->cspan;
for (c = 0; c < cp->cspan; c++)
minc[cp->col + c] = MAX(minc[cp->col + c],x);
y = (cp->data.box.UR.y + (cp->rspan-1))/cp->rspan;
for (r = 0; r < cp->rspan; r++)
minr[cp->row + r] = MAX(minr[cp->row + r],y);
}
for (cells = tbl->u.n.cells; *cells; cells++) {
int x, y, c, r;
cp = *cells;
t = agfindnode(colg, nToName(cp->col));
h = agfindnode(colg, nToName(cp->col + cp->cspan));
e = agedge(colg, t, h);
x = 0;
for (c = 0; c < cp->cspan; c++)
x += minc[cp->col + c];
ED_minlen(e) = x;
/* ED_minlen(e) = cp->data.box.UR.x; */
#ifdef DEBUG
fprintf(stderr, "col edge %s -> %s %d\n", t->name, h->name,
ED_minlen(e));
#endif
elist_append(e, ND_out(t));
elist_append(e, ND_in(h));
t = agfindnode(rowg, nToName(cp->row));
h = agfindnode(rowg, nToName(cp->row + cp->rspan));
e = agedge(rowg, t, h);
y = 0;
for (r = 0; r < cp->rspan; r++)
y += minr[cp->row + r];
ED_minlen(e) = y;
/* ED_minlen(e) = cp->data.box.UR.y; */
#ifdef DEBUG
fprintf(stderr, "row edge %s -> %s %d\n", t->name, h->name,
ED_minlen(e));
#endif
elist_append(e, ND_out(t));
elist_append(e, ND_in(h));
}
/* Make sure that 0 <= 1 <= 2 ...k. This implies graph connected. */
checkChain(colg);
checkChain(rowg);
free (minc);
free (minr);
}