void
build_svg(
const fs::path & file,
const string & title,
const seq_t & seq,
float_t min_threshold,
match_result_vec_t & results,
size_t max_num_factors,
bool show_labels,
bool open,
match_result_vec_t * max_chain,
const std::string & notes,
float max_threshold )
{
XMLPlatformUtils::Initialize();
//find the maximum score
for (match_result_vec_t::const_iterator i = results.begin();
results.end() != i;
++i)
{
max_threshold = std::max( max_threshold, i->result.score );
}
SvgDomDocument doc(seq.size(), min_threshold, max_threshold, title, seq, show_labels);
//for each hit result
size_t idx = 0;
unsigned num_added = 0;
for (match_result_vec_t::iterator i = results.begin();
results.end() != i;
++i, ++idx)
{
i->number = idx;
BiobaseTablePssmEntry * pssm_entry = BiobaseDb::singleton().get_pssm_entry(i->link);
assert((size_t) i->result.position < seq.size());
if (min_threshold <= i->result.score)
{
const bool is_in_max_chain =
0 != max_chain
&&
max_chain->end() != std::find_if( max_chain->begin(), max_chain->end(), std::bind1st( detail::hit_is_same(), *i ) );
doc.add_result(
i->result,
*pssm_entry,
idx,
is_in_max_chain );
++num_added;
}
}
if (0 == num_added)
{
throw std::logic_error( "No hits above threshold" );
}
factor_scores_map_t factors;
find_factors_for_matches(results, factors);
//cout << factors.size() << " factors associated with these matches" << std::endl;
//for each factor - in score order
while (! factors.empty() && 0 != max_num_factors--)
{
//find the factor with the highest score
factor_scores_map_t::iterator best = factors.end();
for (factor_scores_map_t::iterator f = factors.begin();
factors.end() != f;
++f)
{
if (factors.end() == best || f->second.score > best->second.score)
{
best = f;
}
}
assert(best != factors.end());
Factor * factor = BiobaseDb::singleton().get_entry<FACTOR_DATA>(best->first);
if (0 != factor)
{
doc.add_factor(factor, best->second.hits);
}
factors.erase(best);
}
if( notes.size() )
{
doc.add_notes( notes );
}
add_tooltip_support(doc.doc, doc.doc_root);
dom_print(doc.doc, file._BOOST_FS_NATIVE().c_str());
//copy the script to the same directory
try
{
fs::path script(BioEnvironment::singleton().get_svg_script_file());
fs::path script_dest(file.branch_path());
script_dest /= script.leaf();
//only copy if destination older
if (! fs::exists(script_dest) || fs::last_write_time(script) > fs::last_write_time(script_dest))
{
//remove first if exists
if (fs::exists(script_dest))
{
fs::remove(script_dest);
}
fs::copy_file(script, script_dest);
}
}
catch (const std::exception & ex)
{
cerr << ex.what() << endl;
}
XMLPlatformUtils::Terminate();
if (open)
{
open_file(file);
}
}
