// This is the main search algorithm for the (D)ERPA.
std::vector< double >
solve_region( const MatrixFactory &mf, const interval_t ®ion,
const std::vector< double > lower_vals,
const std::vector< double > upper_vals,
double epsilon ) {
// Determine # solutions
int num_solutions = get_num_solutions( lower_vals, region.lower(),
upper_vals, region.upper() );
// If no solutions, return empty.
if ( 0 == num_solutions ) {
return std::vector< double >(); }
// If the interval has no width, but has solutions, return the value.
if ( std::abs( region.upper() - region.lower() ) < epsilon ) {
return std::vector< double >( 1, region.lower() ); }
// If 1 solution, root_find.
if ( 1 == num_solutions ) {
std::vector< double > temp( 1,
root_find_solution( mf, region, lower_vals, upper_vals,
epsilon ) );
return temp; }
// If > 1 solution, sub-divide region.
double center = boost::numeric::median( region );
std::vector< double > center_vals
= util::sorted_eigenvalues( mf.build( center ) );
std::vector< double > solutions
= solve_region( mf, interval_t( region.lower(), center ),
lower_vals, center_vals, epsilon );
{ std::vector< double > upper_solutions
= solve_region( mf, interval_t( center, region.upper() ),
center_vals, upper_vals, epsilon );
solutions.insert( solutions.end(), upper_solutions.begin(),
upper_solutions.end() ); }
return solutions; }
interval_map_t makeIntervalMap (DataFrame incl) {
CharacterVector incl_chroms = incl["chrom"] ;
IntegerVector incl_starts = incl["start"] ;
IntegerVector incl_ends = incl["end"] ;
int nr = incl.nrows() ;
interval_map_t interval_map ;
for(int i=0; i<nr; ++i) {
std::string chrom = as<std::string>(incl_chroms[i]) ;
if (!interval_map.count(chrom))
interval_map[chrom] = intervalVector() ;
interval_map[chrom].push_back(interval_t(incl_starts[i], incl_ends[i], i)) ;
}
return interval_map ;
}
