cs_align.cc File Reference

#include <core/types.hh>
#include <devel/init.hh>
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <protocols/comparative_modeling/AlignmentSet.hh>
#include <core/sequence/util.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/NWAligner.hh>
#include <core/sequence/SWAligner.hh>
#include <core/sequence/CompositeScoringScheme.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <core/sequence/ChemicalShiftSequence.hh>
#include <core/sequence/ScoringScheme.hh>
#include <core/sequence/MatrixScoringScheme.hh>
#include <core/sequence/ScoringSchemeFactory.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/SilentStruct.hh>
#include <core/io/silent/SilentStructFactory.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/in.OptionKeys.gen.hh>
#include <basic/options/keys/cm.OptionKeys.gen.hh>
#include <utility/excn/Exceptions.hh>

Functions
void	print_matrix_to_file (std::string const &fn, core::sequence::SequenceOP seq1, core::sequence::SequenceOP seq2, core::sequence::ScoringSchemeOP ss)
int	main (int argc, char *argv[])

Detailed Description

Author

James Thompson

Function Documentation

main()

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

References out::file::alignment(), argv, utility::file::FileName::base(), utility::io::oc::cout, james::debug(), test.T009_Exceptions::e, end, utility::keys::AutoKey< O, S, C >::id(), basic::init(), beta_nonlocal::jj, cm::min_gap_extend(), cm::min_gap_open(), option, bin_torsions::output, print_matrix_to_file(), in::file::pssm(), basic::options::OptionKeys::recces::seq1, basic::options::OptionKeys::recces::seq2, cm::seq_score(), and challenge::ss.

print_matrix_to_file()

void print_matrix_to_file	(	std::string const &	fn,
		core::sequence::SequenceOP	seq1,
		core::sequence::SequenceOP	seq2,
		core::sequence::ScoringSchemeOP	ss
	)

References utility::io::oc::cout, ObjexxFCL::format::F(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, create_a3b_hbs::ii, beta_nonlocal::jj, erraser_single_res_analysis::out, basic::options::OptionKeys::recces::seq1, basic::options::OptionKeys::recces::seq2, and challenge::ss.

Referenced by main().