diff options
Diffstat (limited to 'utils/atools.cc')
| -rw-r--r-- | utils/atools.cc | 11 |
1 files changed, 5 insertions, 6 deletions
diff --git a/utils/atools.cc b/utils/atools.cc index c0a91731..bce7822e 100644 --- a/utils/atools.cc +++ b/utils/atools.cc @@ -8,11 +8,10 @@ #include <boost/shared_ptr.hpp> #include "filelib.h" -#include "alignment_pharaoh.h" +#include "alignment_io.h" namespace po = boost::program_options; using namespace std; -using boost::shared_ptr; struct Command { virtual ~Command() {} @@ -348,10 +347,10 @@ int main(int argc, char **argv) { } } if (line1.empty() && !*in1) break; - shared_ptr<Array2D<bool> > out(new Array2D<bool>); - shared_ptr<Array2D<bool> > a1 = AlignmentPharaoh::ReadPharaohAlignmentGrid(line1); + boost::shared_ptr<Array2D<bool> > out(new Array2D<bool>); + boost::shared_ptr<Array2D<bool> > a1 = AlignmentIO::ReadPharaohAlignmentGrid(line1); if (in2) { - 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; @@ -359,7 +358,7 @@ int main(int argc, char **argv) { } if (cmd.Result() == 1) { - AlignmentPharaoh::SerializePharaohFormat(*out, &cout); + AlignmentIO::SerializePharaohFormat(*out, &cout); } } if (cmd.Result() == 2) |