pick_frags.cc File Reference

#include <core/types.hh>
#include <devel/init.hh>
#include <basic/prof.hh>
#include <basic/Tracer.hh>
#include <core/chemical/AA.hh>
#include <basic/options/option.hh>
#include <core/sequence/util.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/SequenceProfile.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <core/sequence/NWAligner.hh>
#include <core/sequence/SWAligner.hh>
#include <core/sequence/L1ScoringScheme.hh>
#include <core/sequence/MatrixScoringScheme.hh>
#include <core/sequence/SimpleScoringScheme.hh>
#include <core/sequence/ScoringScheme.fwd.hh>
#include <core/sequence/ScoringSchemeFactory.hh>
#include <utility/vector1.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <utility/file/FileName.hh>
#include <utility/file/file_sys_util.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/char.functions.hh>
#include <ObjexxFCL/string.functions.hh>
#include <numeric/random/random.hh>
#include <fstream>
#include <iostream>
#include <string>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/james.OptionKeys.gen.hh>
#include <basic/options/keys/frags.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <utility/excn/Exceptions.hh>

Classes
class	VallReader
class	VallIndex
struct	compare_VallIndex_lt
struct	compare_VallIndex_gt
class	HeapContainer< T, Comparator >

Functions
int	main (int argc, char *argv[])

Detailed Description

Author

James Thompson

Function Documentation

main()

int main	(	int	argc,
		char *	argv[]
	)

References argv, utility::io::oc::cerr, utility::io::oc::cout, basic::options::OptionKeys::james::debug, test.T009_Exceptions::e, end, ObjexxFCL::format::F(), basic::options::OptionKeys::in::file::fasta, kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, basic::options::OptionKeys::out::file::frag_prefix, usec::frag_size, basic::options::OptionKeys::frags::frag_sizes, create_a3b_hbs::i, test.T110_numeric::I, kmeans_adaptive_kernel_density_bb_dependent_rotlib::idx, utility::vector1< T, A >::index(), basic::init(), create_a3b_hbs::j, solution_counts::lines, basic::options::OptionKeys::frags::n_frags, basic::options::option, bin_torsions::output, PROF_START, PROF_STOP, basic::options::OptionKeys::frags::scoring::profile_score, create_a3b_hbs::score, basic::SEQUENCE_COMPARISON, challenge::ss, ObjexxFCL::string_of(), and basic::options::OptionKeys::in::file::vall.