diff options
Diffstat (limited to 'training/atools.cc')
| -rw-r--r-- | training/atools.cc | 7 |
1 files changed, 4 insertions, 3 deletions
diff --git a/training/atools.cc b/training/atools.cc index af62804d..805e3c1d 100644 --- a/training/atools.cc +++ b/training/atools.cc @@ -9,6 +9,7 @@ #include "filelib.h" #include "aligner.h" +#include "alignment_pharaoh.h" namespace po = boost::program_options; using namespace std; @@ -349,9 +350,9 @@ int main(int argc, char **argv) { } if (line1.empty() && !*in1) break; shared_ptr<Array2D<bool> > out(new Array2D<bool>); - shared_ptr<Array2D<bool> > a1 = AlignerTools::ReadPharaohAlignmentGrid(line1); + shared_ptr<Array2D<bool> > a1 = AlignmentPharaoh::ReadPharaohAlignmentGrid(line1); if (in2) { - shared_ptr<Array2D<bool> > a2 = AlignerTools::ReadPharaohAlignmentGrid(line2); + shared_ptr<Array2D<bool> > a2 = AlignmentPharaoh::ReadPharaohAlignmentGrid(line2); cmd.Apply(*a1, *a2, out.get()); } else { Array2D<bool> dummy; @@ -359,7 +360,7 @@ int main(int argc, char **argv) { } if (cmd.Result() == 1) { - AlignerTools::SerializePharaohFormat(*out, &cout); + AlignmentPharaoh::SerializePharaohFormat(*out, &cout); } } if (cmd.Result() == 2) |