diff options
Diffstat (limited to 'utils/atools.cc')
| -rw-r--r-- | utils/atools.cc | 8 |
1 files changed, 4 insertions, 4 deletions
diff --git a/utils/atools.cc b/utils/atools.cc index ba56dd6c..bce7822e 100644 --- a/utils/atools.cc +++ b/utils/atools.cc @@ -8,7 +8,7 @@ #include <boost/shared_ptr.hpp> #include "filelib.h" -#include "alignment_pharaoh.h" +#include "alignment_io.h" namespace po = boost::program_options; using namespace std; @@ -348,9 +348,9 @@ int main(int argc, char **argv) { } if (line1.empty() && !*in1) break; boost::shared_ptr<Array2D<bool> > out(new Array2D<bool>); - boost::shared_ptr<Array2D<bool> > a1 = AlignmentPharaoh::ReadPharaohAlignmentGrid(line1); + boost::shared_ptr<Array2D<bool> > a1 = AlignmentIO::ReadPharaohAlignmentGrid(line1); if (in2) { - boost::shared_ptr<Array2D<bool> > a2 = AlignmentPharaoh::ReadPharaohAlignmentGrid(line2); + boost::shared_ptr<Array2D<bool> > a2 = AlignmentIO::ReadPharaohAlignmentGrid(line2); cmd.Apply(*a1, *a2, out.get()); } else { Array2D<bool> dummy; @@ -358,7 +358,7 @@ int main(int argc, char **argv) { } if (cmd.Result() == 1) { - AlignmentPharaoh::SerializePharaohFormat(*out, &cout); + AlignmentIO::SerializePharaohFormat(*out, &cout); } } if (cmd.Result() == 2) |