filterImperfectAln.cc File Reference

This takes two sets of alignments. 1 perfect and 1 imperfect. The output is the residues of the imperfect alignment that are correctly aligned. More...

#include <utility/exit.hh>
#include <utility/string_util.hh>
#include <utility/file/FileName.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/izstream.hh>
#include <core/types.hh>
#include <basic/Tracer.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/id/SequenceMapping.hh>
#include <core/sequence/util.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <core/sequence/Sequence.hh>
#include <devel/init.hh>
#include <utility/options/keys/FileOptionKey.fwd.hh>
#include <utility/options/keys/FileOptionKey.hh>
#include <utility/options/keys/FileVectorOptionKey.fwd.hh>
#include <utility/options/keys/FileVectorOptionKey.hh>
#include <basic/options/option.hh>
#include <basic/options/util.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/cm.OptionKeys.gen.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <map>

Namespaces
	filterImperfectAln

Functions
multimap< string, SequenceAlignment >	input_alignmentsMapped (vector1< std::string > align_fns)
void	output_alignments (vector1< SequenceAlignment > alns, std::ostream &out)
SequenceAlignment	filterAln (SequenceAlignment perfect_aln, SequenceAlignment orig_aln)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	tr ("filterImperfectAln")
	@usage: -in:file:alignent <imperfect_alignment> -in:file:perfect_alignment <perfect_alignment> -out:file:alignment <output_alignment> More...
basic::options::FileVectorOptionKey	filterImperfectAln::perfect_alignment ("filterImperfectAln:perfect_alignment")

Detailed Description

This takes two sets of alignments. 1 perfect and 1 imperfect. The output is the residues of the imperfect alignment that are correctly aligned.

Function Documentation

filterAln()

SequenceAlignment filterAln	(	SequenceAlignment	perfect_aln,
		SequenceAlignment	orig_aln
	)

References create_a3b_hbs::ii.

Referenced by main().

input_alignmentsMapped()

multimap<string,SequenceAlignment> input_alignmentsMapped

(

vector1< std::string >

align_fns

)

References cm::aln_format(), beta_nonlocal::jj, and option.

Referenced by main().

main()

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

References in::file::alignment(), out::file::alignment(), argv, test.T009_Exceptions::e, utility::file_basename(), filterAln(), basic::init(), input_alignmentsMapped(), subloop_histogram::iterator, option, output_alignments(), filterImperfectAln::perfect_alignment, and basic::options::OptionKeys::relax::sequence.

output_alignments()

void output_alignments	(	vector1< SequenceAlignment >	alns,
		std::ostream &	out
	)

References create_a3b_hbs::ii.

Referenced by main().

Variable Documentation

tr

basic::Tracer tr("filterImperfectAln") ( "filterImperfectAln"  )

static

@usage: -in:file:alignent <imperfect_alignment> -in:file:perfect_alignment <perfect_alignment> -out:file:alignment <output_alignment>

Author

TJ Brunette