Minimize using #include headers in headers.

Should use it in .cpp files.

35 files changed, 93 insertions, 146 deletions

diff --git a/mert/BleuScorer.cpp b/mert/BleuScorer.cpp
index 7844d4a51..c7bd0e90f 100644
--- a/mert/BleuScorer.cpp
+++ b/mert/BleuScorer.cpp
@@ -1,4 +1,9 @@
 #include "BleuScorer.h"
+#include <cmath>
+#include <fstream>
+#include <iterator>
+#include <stdexcept>
+#include "Util.h"
 
 BleuScorer::BleuScorer(const string& config)
     : StatisticsBasedScorer("BLEU",config),
diff --git a/mert/BleuScorer.h b/mert/BleuScorer.h
index c5681ad55..7e0e18b53 100644
--- a/mert/BleuScorer.h
+++ b/mert/BleuScorer.h
@@ -1,16 +1,10 @@
 #ifndef __BLEUSCORER_H__
 #define __BLEUSCORER_H__
 
-#include <algorithm>
-#include <cmath>
 #include <iostream>
-#include <iterator>
-#include <set>
-#include <sstream>
-#include <stdexcept>
 #include <string>
 #include <vector>
-#include <limits.h>
+
 #include "Types.h"
 #include "ScoreData.h"
 #include "Scorer.h"
diff --git a/mert/CderScorer.cpp b/mert/CderScorer.cpp
index e503eb7e5..fc8d69f5f 100644
--- a/mert/CderScorer.cpp
+++ b/mert/CderScorer.cpp
@@ -1,8 +1,6 @@
 #include "CderScorer.h"
-
+#include <fstream>
 #include <stdexcept>
-#include <iostream>
-#include <algorithm>
 
 CderScorer::CderScorer(const string& config)
     : StatisticsBasedScorer("CDER",config) {}
diff --git a/mert/CderScorer.h b/mert/CderScorer.h
index 802690a99..359ac31e9 100644
--- a/mert/CderScorer.h
+++ b/mert/CderScorer.h
@@ -3,10 +3,10 @@
 
 #include <algorithm>
 #include <iostream>
+#include <iterator>
 #include <string>
 #include <vector>
 #include "Types.h"
-#include "ScoreData.h"
 #include "Scorer.h"
 
 using namespace std;
diff --git a/mert/Data.cpp b/mert/Data.cpp
index 2d3318753..a9b09357a 100644
--- a/mert/Data.cpp
+++ b/mert/Data.cpp
@@ -7,6 +7,7 @@
  */
 
 #include <cassert>
+#include <cmath>
 #include <fstream>
 
 #include "Data.h"
diff --git a/mert/FeatureArray.cpp b/mert/FeatureArray.cpp
index 3b3dd8c38..cffafa82a 100644
--- a/mert/FeatureArray.cpp
+++ b/mert/FeatureArray.cpp
@@ -6,10 +6,9 @@
  *
  */
 
-#include <fstream>
 #include "FeatureArray.h"
-#include "Util.h"
 #include "FileStream.h"
+#include "Util.h"
 
 namespace {
 const char FEATURES_TXT_BEGIN[] = "FEATURES_TXT_BEGIN_0";
diff --git a/mert/FeatureArray.h b/mert/FeatureArray.h
index c1c12fc47..9012e0830 100644
--- a/mert/FeatureArray.h
+++ b/mert/FeatureArray.h
@@ -9,16 +9,13 @@
 #ifndef FEATURE_ARRAY_H
 #define FEATURE_ARRAY_H
 
-using namespace std;
-
-#include <limits>
 #include <vector>
 #include <iostream>
 #include <fstream>
-
-#include "Util.h"
 #include "FeatureStats.h"
 
+using namespace std;
+
 class FeatureArray
 {
 private:
diff --git a/mert/FeatureData.cpp b/mert/FeatureData.cpp
index 07bfa6a02..ed76bca3b 100644
--- a/mert/FeatureData.cpp
+++ b/mert/FeatureData.cpp
@@ -6,8 +6,9 @@
  *
  */
 
-#include <fstream>
 #include "FeatureData.h"
+
+#include <limits>
 #include "FileStream.h"
 #include "Util.h"
 
diff --git a/mert/FeatureData.h b/mert/FeatureData.h
index 3a96e74f1..6934cdcba 100644
--- a/mert/FeatureData.h
+++ b/mert/FeatureData.h
@@ -11,11 +11,9 @@
 
 using namespace std;
 
-#include <limits>
 #include <vector>
 #include <iostream>
-
-#include "Util.h"
+#include <stdexcept>
 #include "FeatureArray.h"
 
 class FeatureData
diff --git a/mert/FeatureStats.cpp b/mert/FeatureStats.cpp
index 86778e770..e7682518c 100644
--- a/mert/FeatureStats.cpp
+++ b/mert/FeatureStats.cpp
@@ -6,10 +6,11 @@
  *
  */
 
-#include <cmath>
-#include <fstream>
 #include "FeatureStats.h"
 
+#include <cmath>
+#include "Util.h"
+
 namespace {
 const int kAvailableSize = 8;
 } // namespace
diff --git a/mert/FeatureStats.h b/mert/FeatureStats.h
index fb7d46350..2ba17aed8 100644
--- a/mert/FeatureStats.h
+++ b/mert/FeatureStats.h
@@ -11,11 +11,12 @@
 
 using namespace std;
 
-#include <limits>
-#include <vector>
+#include <fstream>
 #include <iostream>
-
-#include "Util.h"
+#include <map>
+#include <string>
+#include <vector>
+#include "Types.h"
 
 // Minimal sparse vector
 class SparseVector {
diff --git a/mert/Makefile.am b/mert/Makefile.am
index fe2909e1a..a93be4b81 100644
--- a/mert/Makefile.am
+++ b/mert/Makefile.am
@@ -13,6 +13,7 @@ BleuScorer.cpp \
 Point.cpp \
 PerScorer.cpp \
 Scorer.cpp \
+ScorerFactory.cpp \
 Optimizer.cpp \
 TERsrc/alignmentStruct.cpp \
 TERsrc/hashMap.cpp \
diff --git a/mert/MergeScorer.cpp b/mert/MergeScorer.cpp
index 2e3fb5de4..0b9de73f1 100644
--- a/mert/MergeScorer.cpp
+++ b/mert/MergeScorer.cpp
@@ -1,9 +1,17 @@
 #include "MergeScorer.h"
+
+#include <cmath>
+#include <stdexcept>
+#include "ScoreStats.h"
+#include "TerScorer.h"
+#include "BleuScorer.h"
+#include "PerScorer.h"
+#include "CderScorer.h"
+
 #include "TERsrc/tercalc.h"
 #include "TERsrc/terAlignment.h"
 
 using namespace TERCpp;
-using namespace std;
 
 MergeScorer::MergeScorer(const string& config)
     : StatisticsBasedScorer("MERGE",config), kLENGTH(4) {}
diff --git a/mert/MergeScorer.h b/mert/MergeScorer.h
index 67b4b5e48..10e034ac6 100644
--- a/mert/MergeScorer.h
+++ b/mert/MergeScorer.h
@@ -1,31 +1,19 @@
 #ifndef __MERGESCORER_H__
 #define __MERGESCORER_H__
 
-#include <algorithm>
-#include <cmath>
 #include <iostream>
-#include <iterator>
 #include <set>
-#include <sstream>
-#include <stdexcept>
 #include <string>
 #include <vector>
-#include <limits.h>
-#include "Types.h"
-#include "ScoreData.h"
+
 #include "Scorer.h"
-#include "TerScorer.h"
-#include "BleuScorer.h"
-#include "PerScorer.h"
-#include "CderScorer.h"
-//#include "TERsrc/tercalc.h"
-//#include "TERsrc/terAlignment.h"
 
 using namespace std;
-using namespace TERCpp;
 
 // enum MergeReferenceLengthStrategy { MERGE_AVERAGE, MERGE_SHORTEST, MERGE_CLOSEST };
 
+class PerScorer;
+class ScoreStats;
 
 /**
  * Merge scoring.
diff --git a/mert/Optimizer.cpp b/mert/Optimizer.cpp
index 13067ea1d..cd9703ddd 100644
--- a/mert/Optimizer.cpp
+++ b/mert/Optimizer.cpp
@@ -1,11 +1,15 @@
+#include "Optimizer.h"
+
+#include <cmath>
 #include <cassert>
 #include <vector>
 #include <limits>
-#include <list>
+#include <map>
 #include <cfloat>
 #include <iostream>
 
-#include "Optimizer.h"
+#include "Point.h"
+#include "Util.h"
 
 using namespace std;
 
diff --git a/mert/Optimizer.h b/mert/Optimizer.h
index 8ca804926..aa588994d 100644
--- a/mert/Optimizer.h
+++ b/mert/Optimizer.h
@@ -2,16 +2,16 @@
 #define OPTIMIZER_H
 
 #include <vector>
-#include "FeatureStats.h"
+#include <string>
 #include "FeatureData.h"
-#include "FeatureArray.h"
 #include "Scorer.h"
-#include "Point.h"
 #include "Types.h"
 
+using namespace std;
+
 typedef float featurescore;
 
-using namespace std;
+class Point;
 
 /**
  * Abstract optimizer class.
diff --git a/mert/PerScorer.cpp b/mert/PerScorer.cpp
index 6564a7f22..765cb0876 100644
--- a/mert/PerScorer.cpp
+++ b/mert/PerScorer.cpp
@@ -1,5 +1,13 @@
 #include "PerScorer.h"
 
+#include <fstream>
+#include <stdexcept>
+
+#include "ScoreStats.h"
+#include "Util.h"
+
+using namespace std;
+
 PerScorer::PerScorer(const string& config)
   : StatisticsBasedScorer("PER",config) {}
 
diff --git a/mert/PerScorer.h b/mert/PerScorer.h
index f8d0fa59c..800a3caf1 100644
--- a/mert/PerScorer.h
+++ b/mert/PerScorer.h
@@ -1,22 +1,18 @@
 #ifndef __PERSCORER_H__
 #define __PERSCORER_H__
 
-#include <algorithm>
-#include <cmath>
 #include <iostream>
-#include <iterator>
 #include <set>
 #include <sstream>
-#include <stdexcept>
 #include <string>
 #include <vector>
 #include "Types.h"
-#include "ScoreData.h"
 #include "Scorer.h"
 
-
 using namespace std;
 
+class ScoreStats;
+
 /**
  * An implementation of position-independent word error rate.
  * This is defined as
diff --git a/mert/Point.cpp b/mert/Point.cpp
index a21c754fb..9b4899dc5 100644
--- a/mert/Point.cpp
+++ b/mert/Point.cpp
@@ -1,7 +1,9 @@
 #include "Point.h"
+
 #include <cmath>
 #include <cstdlib>
 #include <cassert>
+#include "FeatureStats.h"
 
 using namespace std;
 
diff --git a/mert/Point.h b/mert/Point.h
index 0aa649b1a..55d173215 100644
--- a/mert/Point.h
+++ b/mert/Point.h
@@ -1,10 +1,12 @@
 #ifndef POINT_H
 #define POINT_H
 
+#include <fstream>
+#include <map>
 #include <vector>
 #include "Types.h"
-#include "FeatureStats.h"
 
+class FeatureStats;
 class Optimizer;
 
 /**
diff --git a/mert/ScoreArray.cpp b/mert/ScoreArray.cpp
index c7e4daaf6..7c2bfc423 100644
--- a/mert/ScoreArray.cpp
+++ b/mert/ScoreArray.cpp
@@ -6,7 +6,6 @@
  *
  */
 
-#include <fstream>
 #include "ScoreArray.h"
 #include "Util.h"
 #include "FileStream.h"
diff --git a/mert/ScoreArray.h b/mert/ScoreArray.h
index a25943a19..83c786c3e 100644
--- a/mert/ScoreArray.h
+++ b/mert/ScoreArray.h
@@ -11,12 +11,10 @@
 
 using namespace std;
 
-#include <limits>
 #include <vector>
 #include <iostream>
-#include <fstream>
+#include <string>
 
-#include "Util.h"
 #include "ScoreStats.h"
 
 class ScoreArray
diff --git a/mert/ScoreData.cpp b/mert/ScoreData.cpp
index 875d75fe9..e79595d06 100644
--- a/mert/ScoreData.cpp
+++ b/mert/ScoreData.cpp
@@ -6,7 +6,6 @@
  *
  */
 
-#include <fstream>
 #include "ScoreData.h"
 #include "Scorer.h"
 #include "Util.h"
diff --git a/mert/ScoreData.h b/mert/ScoreData.h
index 295344ed0..cb4fb30f9 100644
--- a/mert/ScoreData.h
+++ b/mert/ScoreData.h
@@ -9,14 +9,15 @@
 #ifndef SCORE_DATA_H
 #define SCORE_DATA_H
 
-using namespace std;
-
-#include <limits>
+#include <fstream>
 #include <vector>
 #include <iostream>
-
-#include "Util.h"
+#include <stdexcept>
+#include <string>
 #include "ScoreArray.h"
+#include "ScoreStats.h"
+
+using namespace std;
 
 class Scorer;
 
diff --git a/mert/ScoreStats.cpp b/mert/ScoreStats.cpp
index 3d7ac42a1..eb1750983 100644
--- a/mert/ScoreStats.cpp
+++ b/mert/ScoreStats.cpp
@@ -6,7 +6,7 @@
  *
  */
 
-#include <fstream>
+#include "Util.h"
 #include "ScoreStats.h"
 
 namespace {
diff --git a/mert/ScoreStats.h b/mert/ScoreStats.h
index 3a609120d..43a6f1f23 100644
--- a/mert/ScoreStats.h
+++ b/mert/ScoreStats.h
@@ -9,14 +9,15 @@
 #ifndef SCORE_STATS_H
 #define SCORE_STATS_H
 
-using namespace std;
-
-#include <limits>
 #include <vector>
 #include <iostream>
+#include <fstream>
 #include <cstdlib>
+#include <cstring>
 
-#include "Util.h"
+#include "Types.h"
+
+using namespace std;
 
 class ScoreStats
 {
diff --git a/mert/Scorer.h b/mert/Scorer.h
index 801f40d98..c36f2e03a 100644
--- a/mert/Scorer.h
+++ b/mert/Scorer.h
@@ -1,12 +1,7 @@
 #ifndef __SCORER_H__
 #define __SCORER_H__
 
-#include <algorithm>
-#include <cmath>
 #include <iostream>
-#include <iterator>
-#include <limits>
-#include <set>
 #include <sstream>
 #include <stdexcept>
 #include <string>
diff --git a/mert/ScorerFactory.h b/mert/ScorerFactory.h
index 3a1da4783..f6054c770 100644
--- a/mert/ScorerFactory.h
+++ b/mert/ScorerFactory.h
@@ -1,53 +1,17 @@
 #ifndef __SCORER_FACTORY_H
 #define __SCORER_FACTORY_H
 
-#include <algorithm>
-#include <cmath>
-#include <iostream>
-#include <iterator>
-#include <set>
-#include <sstream>
-#include <stdexcept>
-#include <string>
 #include <vector>
-#include "Types.h"
-#include "Scorer.h"
-#include "BleuScorer.h"
-#include "PerScorer.h"
-#include "TerScorer.h"
-#include "CderScorer.h"
-#include "MergeScorer.h"
+#include <string>
 
-using namespace std;
+class Scorer;
 
 class ScorerFactory
 {
 public:
-  static vector<string> getTypes() {
-    vector<string> types;
-    types.push_back(string("BLEU"));
-    types.push_back(string("PER"));
-    types.push_back(string("TER"));
-    types.push_back(string("CDER"));
-    types.push_back(string("MERGE"));
-    return types;
-  }
+  static std::vector<std::string> getTypes();
 
-  static Scorer* getScorer(const string& type, const string& config = "") {
-    if (type == "BLEU") {
-      return (BleuScorer*) new BleuScorer(config);
-    } else if (type == "PER") {
-      return (PerScorer*) new PerScorer(config);
-    } else if (type == "TER") {
-      return (TerScorer*) new TerScorer(config);
-    } else if (type == "CDER") {
-      return (CderScorer*) new CderScorer(config);
-    } else if (type == "MERGE") {
-      return (MergeScorer*) new MergeScorer(config);
-    } else {
-      throw runtime_error("Unknown scorer type: " + type);
-    }
-  }
+  static Scorer* getScorer(const std::string& type, const std::string& config = "");
 
 private:
   ScorerFactory() {}
diff --git a/mert/TerScorer.cpp b/mert/TerScorer.cpp
index 3efedafa0..3f4ca65e8 100644
--- a/mert/TerScorer.cpp
+++ b/mert/TerScorer.cpp
@@ -1,9 +1,15 @@
 #include "TerScorer.h"
+
+#include <cmath>
+#include <sstream>
+#include <stdexcept>
+
+#include "ScoreStats.h"
 #include "TERsrc/tercalc.h"
 #include "TERsrc/terAlignment.h"
+#include "Util.h"
 
 using namespace TERCpp;
-using namespace std;
 
 TerScorer::TerScorer(const string& config)
     : StatisticsBasedScorer("TER",config), kLENGTH(2) {}
diff --git a/mert/TerScorer.h b/mert/TerScorer.h
index 411d942bf..0e9996a99 100644
--- a/mert/TerScorer.h
+++ b/mert/TerScorer.h
@@ -1,27 +1,19 @@
 #ifndef __TERSCORER_H__
 #define __TERSCORER_H__
 
-#include <algorithm>
-#include <cmath>
 #include <iostream>
-#include <iterator>
 #include <set>
-#include <sstream>
-#include <stdexcept>
 #include <string>
 #include <vector>
-#include <limits.h>
+
 #include "Types.h"
-#include "ScoreData.h"
 #include "Scorer.h"
-#include "TERsrc/tercalc.h"
-#include "TERsrc/terAlignment.h"
 
 using namespace std;
-using namespace TERCpp;
 
 // enum TerReferenceLengthStrategy { TER_AVERAGE, TER_SHORTEST, TER_CLOSEST };
 
+class ScoreStats;
 
 /**
  * TER scoring
diff --git a/mert/Timer.cpp b/mert/Timer.cpp
index 9c917408a..373eb4a2e 100644
--- a/mert/Timer.cpp
+++ b/mert/Timer.cpp
@@ -1,8 +1,5 @@
-#include <ctime>
-#include <iostream>
-#include <iomanip>
-#include "Util.h"
 #include "Timer.h"
+#include "Util.h"
 
 double Timer::elapsed_time()
 {
diff --git a/mert/Timer.h b/mert/Timer.h
index 71cc00cd8..403547620 100644
--- a/mert/Timer.h
+++ b/mert/Timer.h
@@ -4,7 +4,6 @@
 #include <ctime>
 #include <iostream>
 #include <iomanip>
-#include "Util.h"
 
 class Timer
 {
diff --git a/mert/Util.cpp b/mert/Util.cpp
index a5d68713e..3769c71e7 100644
--- a/mert/Util.cpp
+++ b/mert/Util.cpp
@@ -6,9 +6,7 @@
  *
  */
 
-#include <stdexcept>
 #include "Util.h"
-
 #include "Timer.h"
 
 using namespace std;
diff --git a/mert/Util.h b/mert/Util.h
index 0880a7d3d..e59a9288d 100644
--- a/mert/Util.h
+++ b/mert/Util.h
@@ -9,15 +9,8 @@
 #ifndef UTIL_H
 #define UTIL_H
 
-using namespace std;
-
 #include <stdexcept>
 #include <limits>
-
-#define US_NOSET (numeric_limits<unsigned short>::max())
-
-#define MAX_LINE  1024
-
 #include <vector>
 #include <map>
 #include <iostream>
@@ -26,11 +19,11 @@ using namespace std;
 #include <cstring>
 
 #include "Types.h"
-#include "ScoreStats.h"
-#include "FeatureStats.h"
 
-class ScoreStats;
-class FeatureStats;
+using namespace std;
+
+#define US_NOSET (numeric_limits<unsigned short>::max())
+#define MAX_LINE  1024
 
 #ifdef TRACE_ENABLE
 #define TRACE_ERR(str) { std::cerr << str; }
diff --git a/mert/evaluator.cpp b/mert/evaluator.cpp
index 8545f086a..c1d6039da 100644
--- a/mert/evaluator.cpp
+++ b/mert/evaluator.cpp
@@ -1,3 +1,4 @@
+#include <fstream>
 #include <iostream>
 #include <string>
 #include <vector>