2 files changed, 16 insertions, 16 deletions
diff --git a/training/Makefile.am b/training/Makefile.am
index 490de774..48b19932 100644
--- a/training/Makefile.am
+++ b/training/Makefile.am
@@ -14,37 +14,36 @@ noinst_PROGRAMS = \
   optimize_test
 
 atools_SOURCES = atools.cc
-atools_LDADD = $(top_srcdir)/decoder/libcdec.a -lz
+atools_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/utils/libutils.a -lz
 
 model1_SOURCES = model1.cc
-model1_LDADD = $(top_srcdir)/decoder/libcdec.a -lz
+model1_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/utils/libutils.a -lz
 
 grammar_convert_SOURCES = grammar_convert.cc
-grammar_convert_LDADD = $(top_srcdir)/decoder/libcdec.a -lz
+grammar_convert_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/utils/libutils.a -lz
 
 optimize_test_SOURCES = optimize_test.cc optimize.cc
-optimize_test_LDADD = $(top_srcdir)/decoder/libcdec.a -lz
+optimize_test_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/utils/libutils.a -lz
 
 collapse_weights_SOURCES = collapse_weights.cc
-collapse_weights_LDADD = $(top_srcdir)/decoder/libcdec.a -lz
+collapse_weights_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/utils/libutils.a -lz
 
 lbfgs_test_SOURCES = lbfgs_test.cc
-lbfgs_test_LDADD = $(top_srcdir)/decoder/libcdec.a -lz
+lbfgs_test_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/utils/libutils.a -lz
 
 mr_optimize_reduce_SOURCES = mr_optimize_reduce.cc optimize.cc
-mr_optimize_reduce_LDADD = $(top_srcdir)/decoder/libcdec.a -lz
+mr_optimize_reduce_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/utils/libutils.a -lz
 
 mr_em_map_adapter_SOURCES = mr_em_map_adapter.cc
-mr_em_map_adapter_LDADD = $(top_srcdir)/decoder/libcdec.a -lz
+mr_em_map_adapter_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/utils/libutils.a -lz
 
 mr_reduce_to_weights_SOURCES = mr_reduce_to_weights.cc
-mr_reduce_to_weights_LDADD = $(top_srcdir)/decoder/libcdec.a -lz
+mr_reduce_to_weights_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/utils/libutils.a -lz
 
 mr_em_adapted_reduce_SOURCES = mr_em_adapted_reduce.cc
-mr_em_adapted_reduce_LDADD = $(top_srcdir)/decoder/libcdec.a -lz
+mr_em_adapted_reduce_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/utils/libutils.a -lz
 
 plftools_SOURCES = plftools.cc
-plftools_LDADD = $(top_srcdir)/decoder/libcdec.a -lz
-
-AM_CPPFLAGS = -W -Wall -Wno-sign-compare $(GTEST_CPPFLAGS) -I$(top_srcdir)/decoder
+plftools_LDADD = $(top_srcdir)/decoder/libcdec.a $(top_srcdir)/utils/libutils.a -lz
 
+AM_CPPFLAGS = -W -Wall -Wno-sign-compare $(GTEST_CPPFLAGS) -I$(top_srcdir)/decoder -I$(top_srcdir)/utils -I$(top_srcdir)/mteval
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)