Widget_Assembly Dynamic_Server::spawn_anonymous_assembly(
const std::string& alias_value
, const std::string& anon_tmpl
, const int& alias_type)
{
mApp;
Parsers::Node_Value_Parser& p = app->get_interpreter();
std::string resolvable {get_resolvable_string(anon_tmpl)};
std::string tmpl {get_template_name(anon_tmpl)};
Widget_Assembly a {};
Node_Value v {};
a.node = create_unique_node_name();
if (alias_type == Mogu_Syntax::user.integer)
{
p.set_user_id(atoi(alias_value.c_str()));
}
else if (alias_type == Mogu_Syntax::group.integer)
{
p.set_group_id(atoi(alias_value.c_str()));
}
p.give_input(resolvable, v);
Attribute_Tuple t {merge_node_attributes("",tmpl)};
a.children = std::get<0>(t);
a.trigger_map = std::get<1>(t);
a.attrdict = std::get<2>(t);
a.attrdict[Mogu_Syntax::text.integer] = v;
return a;
}
Widget_Assembly Dynamic_Server::spawn_anonymous_assembly
( const std::string& data_point
, const std::string& anon_tmpl
, const Source_Declaration_Type& type)
{
mApp;
Parsers::Node_Value_Parser& p = app->get_interpreter();
std::string resolvable {get_resolvable_string(anon_tmpl)};
std::string tmpl {get_template_name(anon_tmpl)};
Widget_Assembly a {};
Node_Value v{};
a.node = create_unique_node_name();
if (type == Source_Declaration_Type::group_members)
{
p.set_user_id(atoi(data_point.c_str()));
}
else if (type == Source_Declaration_Type::user_groups)
{
p.set_group_id(atoi(data_point.c_str()));
}
else
{
if (type==Source_Declaration_Type::user_list)
p.set_user_id(atoi(data_point.c_str()));
else if (type==Source_Declaration_Type::group_list)
p.set_group_id(atoi(data_point.c_str()));
resolvable = data_point;
}
p.give_input(resolvable,v);
Attribute_Tuple t {merge_node_attributes("",tmpl)};
a.children = std::get<0>(t);
a.trigger_map = std::get<1>(t);
a.attrdict = std::get<2>(t);
a.attrdict[Mogu_Syntax::text.integer] = v;
return a;
}
/**
* Builds a snp graph from the snps array
*/
graph *graph_from_snps(GapIO *io, snp_t *snp, int nsnps, double c_offset) {
graph *g = NULL;
int i, j;
int ntemplates, *templates = NULL;
node **tmpl_map = NULL;
int lookup[256];
if (verbosity)
puts("Building graph");
/* lookup table for fast base to index conversion */
for (i = 0; i < 256; i++)
lookup[i] = 0;
lookup['A'] = lookup['a'] = 1;
lookup['C'] = lookup['c'] = 2;
lookup['G'] = lookup['g'] = 3;
lookup['T'] = lookup['t'] = 4;
lookup['*'] = 5;
g = graph_create();
g->correlation_offset = c_offset;
/*
* Obtain a list of unique template numbers, by collecting and sorting.
* For each unique template we initialise the graph node.
*
* At the end of this we have ntemplates unique templates and
* tmpl_map[] indexed by Gap4 template number maps us to the
* node in the graph.
*/
for (ntemplates = i = 0; i < nsnps; i++) {
ntemplates += snp[i].nseqs;
}
templates = (int *)malloc(ntemplates * sizeof(int));
for (ntemplates = i = 0; i < nsnps; i++) {
for (j = 0; j < snp[i].nseqs; j++) {
templates[ntemplates++] = snp[i].seqs[j].tmplate;
}
}
tmpl_map = (node **)xcalloc(Ntemplates(io)+1, sizeof(*tmpl_map));
qsort(templates, ntemplates, sizeof(int), int_compare);
for (i = j = 0; i < ntemplates; j++) {
tmpl_map[templates[i]] = graph_add_node(g);
tmpl_map[templates[i]]->number = j;
tmpl_map[templates[i]]->tname =
strdup(get_template_name(io, templates[i]));
do {
i++;
} while (i < ntemplates && templates[i] == templates[i-1]);
}
xfree(templates);
ntemplates = j;
g->nsnps = nsnps;
g->ntemplates = ntemplates;
/*
* The matrix is of size nsnps by ntemplates. It initially will consist
* of entirely empty vectors.
*/
g->matrix = (int (*)[6])malloc(ntemplates * nsnps * sizeof(*g->matrix));
memset(&g->matrix[0][0], 0, ntemplates * nsnps * 6 * sizeof(int));
for (i = j = 0; j < ntemplates; i++) {
if (!tmpl_map[i])
continue;
tmpl_map[i]->matrix = &g->matrix[j * nsnps];
j++;
}
/* Create the snp_score array */
g->snp_scores = (double *)malloc(nsnps * sizeof(*g->snp_scores));
for (i = 0; i < nsnps; i++) {
g->snp_scores[i] = snp[i].score;
}
/* Now add basecalls to the matrix from snp info */
for (i = 0; i < nsnps; i++) {
for (j = 0; j < snp[i].nseqs; j++) {
node *n = tmpl_map[snp[i].seqs[j].tmplate];
n->matrix[i][lookup[snp[i].seqs[j].base]]++;
n->tscore = snp[i].seqs[j].tscore;
/* FIXME: confidence not yet used */
}
for (j = 0; j < ntemplates; j++) {
if (!g->nodes->node[j]->matrix[i][1] &&
!g->nodes->node[j]->matrix[i][2] &&
!g->nodes->node[j]->matrix[i][3] &&
!g->nodes->node[j]->matrix[i][4] &&
!g->nodes->node[j]->matrix[i][5])
g->nodes->node[j]->matrix[i][0]++;
}
}
return g;
}
virtual std::string get_template_full_name() { return get_template_base() + get_template_name(); }
