From 80686d4e567bae579ea39e009826a2de92cd4ace Mon Sep 17 00:00:00 2001
From: redpony <redpony@ec762483-ff6d-05da-a07a-a48fb63a330f>
Date: Wed, 11 Aug 2010 02:37:10 +0000
Subject: major refactor, break bad circular deps

git-svn-id: https://ws10smt.googlecode.com/svn/trunk@509 ec762483-ff6d-05da-a07a-a48fb63a330f
---
 training/atools.cc | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

(limited to 'training/atools.cc')

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)
-- 
cgit v1.2.3