/*
* Removes a single match object and replots.
*/
void obj_remove(Tcl_Interp *interp, char *cs_plot, obj_match *obj,
mobj_repeat *r, HTablePtr T[]) {
DeleteRepeats(interp, r, cs_plot, T);
/* Sorry about the arithmetic! I'm feeling terse today */
memmove(obj, obj+1, (--r->num_match - (obj - r->match)) * sizeof(*obj));
if (r->num_match > 0) {
PlotRepeats(r->io, r);
} else {
csmatch_remove(r->io, cs_plot, r, T);
}
}
/*
* Handle a REG_JOIN_TO request for match objects
* 'r' isn't always a mobj_repeat, but sometimes a mobj_template or
* mobj_fij. For the time being though these are all equivalent.
*/
void csmatch_join_to(GapIO *io, int contig, reg_join *j, mobj_repeat *r,
HTablePtr T[], char *cs_plot) {
int i;
/*
printf("Joining %d to %d at offset %d\n",
contig, j->contig, j->offset);
*/
for (i = 0; i < r->num_match; i++) {
if (abs(r->match[i].c1) == contig) {
r->match[i].pos1 += j->offset;
r->match[i].c1 = r->match[i].c1 > 0
? j->contig : -j->contig;
}
if (abs(r->match[i].c2) == contig) {
r->match[i].pos2 += j->offset;
r->match[i].c2 = r->match[i].c2 > 0
? j->contig : -j->contig;
}
/* For FIJ: remove match if moved onto diagonal */
if (r->match_type == REG_TYPE_FIJ &&
r->match[i].c1 == r->match[i].c2) {
obj_match *o = &r->match[i];
if (i <= r->current) r->current--;
i--;
memmove(o, o+1, (--r->num_match - (o - r->match)) * sizeof(*o));
}
}
if (r->num_match > 0) {
DeleteRepeats(GetInterp(), r, cs_plot, T);
PlotRepeats(io, r);
} else {
csmatch_remove(io, cs_plot, r, T);
}
return;
}
void check_assembly_callback(GapIO *io, tg_rec contig, void *fdata,
reg_data *jdata) {
mobj_checkass *r = (mobj_checkass *)fdata;
obj_cs *cs;
int cs_id;
cs_id = type_to_result(io, REG_TYPE_CONTIGSEL, 0);
cs = result_data(io, cs_id);
switch (jdata->job) {
case REG_QUERY_NAME:
sprintf(jdata->name.line, "Check Assembly");
break;
case REG_JOIN_TO:
csmatch_join_to(io, contig, &jdata->join, (mobj_repeat *)r,
csplot_hash, cs->window);
break;
case REG_COMPLEMENT:
csmatch_complement(io, contig, (mobj_repeat *)r, csplot_hash,
cs->window);
break;
case REG_GET_OPS:
if (r->all_hidden)
jdata->get_ops.ops = "PLACEHOLDER\0PLACEHOLDER\0Information\0"
"PLACEHOLDER\0Hide all\0Reveal all\0Sort Matches\0"
"SEPARATOR\0Remove\0";
else
jdata->get_ops.ops = "Use for 'Next'\0Reset 'Next'\0Information\0"
"Configure\0Hide all\0Reveal all\0Sort Matches\0"
"SEPARATOR\0Remove\0";
break;
case REG_INVOKE_OP:
switch (jdata->invoke_op.op) {
case 0: /* Next */
Tcl_VarEval(GetInterp(), "CSLastUsed ", CPtr2Tcl(r), NULL);
break;
case 1: /* Reset Next */
csmatch_reset_next((mobj_repeat *)r);
break;
case 2: /* Information */
csmatch_info((mobj_repeat *)r, "Check Assembly");
break;
case 3: /* Configure */
csmatch_configure(io, cs->window, (mobj_repeat *)r);
break;
case 4: /* Hide all */
csmatch_hide(GetInterp(), cs->window, (mobj_repeat *)r,
csplot_hash);
break;
case 5: /* Reveal all */
csmatch_reveal(GetInterp(), cs->window, (mobj_repeat *)r,
csplot_hash);
break;
case 6: /* Sort */
qsort(r->match, r->num_match, sizeof(obj_checkass), sort_func);
csmatch_reset_hash(csplot_hash, (mobj_repeat *)r);
r->current = -1;
break;
case 7: /* Remove */
csmatch_remove(io, cs->window, (mobj_repeat *)r,
csplot_hash);
break;
}
break;
case REG_PARAMS:
jdata->params.string = r->params;
break;
case REG_NUMBER_CHANGE:
csmatch_renumber(io, contig, jdata->number.number,
(mobj_repeat *)r, csplot_hash, cs->window);
break;
case REG_ORDER:
csmatch_replot(io, (mobj_repeat *)r, csplot_hash, cs->window);
break;
case REG_QUIT:
csmatch_remove(io, cs->window, (mobj_repeat *)r, csplot_hash);
break;
case REG_DELETE:
csmatch_contig_delete(io, (mobj_repeat *)r, contig,
cs->window, csplot_hash);
break;
case REG_LENGTH:
csmatch_replot(io, (mobj_repeat *)r, csplot_hash, cs->window);
break;
}
}
