Defines main function of locarna. More...

#include <iostream>
#include <iomanip>
#include <fstream>
#include <vector>
#include <memory>
#include "LocARNA/scoring.hh"
#include "LocARNA/sequence.hh"
#include "LocARNA/basepairs.hh"
#include "LocARNA/alignment.hh"
#include "LocARNA/aligner.hh"
#include "LocARNA/rna_data.hh"
#include "LocARNA/arc_matches.hh"
#include "LocARNA/edge_probs.hh"
#include "LocARNA/ribosum.hh"
#include "LocARNA/ribofit.hh"
#include "LocARNA/anchor_constraints.hh"
#include "LocARNA/trace_controller.hh"
#include "LocARNA/global_stopwatch.hh"
#include "LocARNA/pfold_params.hh"
#include "LocARNA/rna_ensemble.hh"
#include "LocARNA/main_helper.icc"
#include "LocARNA/options.hh"

Include dependency graph for locarna.cc:

Functions
template<typename pf_score_t >
int	run_and_report ()
	Helper of main() of executable locarna_p. More...

int	main (int argc, char **argv)
	Main method of executable locarna. More...

Variables
const std::string	VERSION_STRING = (std::string)PACKAGE_STRING
	Version string (from configure.ac via autoconf system)

const bool	DO_TRACE = true
	Switch on/off trace back. More...

command_line_parameters	clp
	holds command line parameters of locarna

option_def	my_options []
	defines command line parameters

Detailed Description

Defines main function of locarna.

LocARNA: global and LOCal Alignment of RNA

Copyright (C) Sebastian Will <will(@)informatik.uni-freiburg.de>

Function Documentation

◆ main()

int main	(	int	argc,
		char **	argv
	)

Main method of executable locarna.

Parameters

argc	argument counter
argv	argument vector

Returns: success

◆ run_and_report()

template<typename pf_score_t >

int run_and_report ( )

Helper of main() of executable locarna_p.

Returns: success

Variable Documentation

◆ DO_TRACE

const bool DO_TRACE = true

Switch on/off trace back.

Note: never made it into command line (since no one asked me kindly)