diff options
Diffstat (limited to 'training')
| -rw-r--r-- | training/atools.cc | 11 |
1 files changed, 5 insertions, 6 deletions
diff --git a/training/atools.cc b/training/atools.cc index 42579627..82e30c38 100644 --- a/training/atools.cc +++ b/training/atools.cc @@ -8,7 +8,6 @@ #include <boost/shared_ptr.hpp> #include "filelib.h" -#include "aligner.h" #include "alignment_pharaoh.h" namespace po = boost::program_options; @@ -79,7 +78,7 @@ struct FMeasureCommand : public Command { struct DisplayCommand : public Command { string Name() const { return "display"; } bool RequiresTwoOperands() const { return false; } - void Apply(const Array2D<bool>& in, const Array2D<bool>¬_used, Array2D<bool>* x) { + void Apply(const Array2D<bool>& in, const Array2D<bool>&, Array2D<bool>* x) { *x = in; cout << *x << endl; } @@ -88,7 +87,7 @@ struct DisplayCommand : public Command { struct ConvertCommand : public Command { string Name() const { return "convert"; } bool RequiresTwoOperands() const { return false; } - void Apply(const Array2D<bool>& in, const Array2D<bool>¬_used, Array2D<bool>* x) { + void Apply(const Array2D<bool>& in, const Array2D<bool>&, Array2D<bool>* x) { *x = in; } }; @@ -96,7 +95,7 @@ struct ConvertCommand : public Command { struct InvertCommand : public Command { string Name() const { return "invert"; } bool RequiresTwoOperands() const { return false; } - void Apply(const Array2D<bool>& in, const Array2D<bool>¬_used, Array2D<bool>* x) { + void Apply(const Array2D<bool>& in, const Array2D<bool>&, Array2D<bool>* x) { Array2D<bool>& res = *x; res.resize(in.height(), in.width()); for (int i = 0; i < in.height(); ++i) @@ -275,8 +274,8 @@ void InitCommandLine(int argc, char** argv, po::variables_map* conf) { } string cstr = os.str(); opts.add_options() - ("input_1,i", po::value<string>(), "[REQ] Alignment 1 file, - for STDIN") - ("input_2,j", po::value<string>(), "[OPT] Alignment 2 file, - for STDIN") + ("input_1,i", po::value<string>(), "[REQUIRED] Alignment 1 file, - for STDIN") + ("input_2,j", po::value<string>(), "Alignment 2 file, - for STDIN") ("command,c", po::value<string>()->default_value("convert"), cstr.c_str()) ("help,h", "Print this help message and exit"); po::options_description clo("Command line options"); |