Cleanup.

moses/TranslationModel/BilingualDynSuffixArray.h

@@ -13,7 +13,6 @@
 #include "moses/TargetPhraseCollection.h"
 #include <map>
 
-using namespace std;
 namespace Moses
 {
 class PhraseDictionaryDynSuffixArray;

moses/TranslationModel/DynSuffixArray.h

@@ -11,7 +11,7 @@
 
 namespace Moses
 {
-using namespace std;
+
 typedef std::vector<unsigned> vuint_t;
 
 
@@ -25,8 +25,8 @@ class ComparePosition
 
 public:
   ComparePosition(vuint_t const& crp, vuint_t const& sfa);
-  bool operator()(unsigned const& i, vector<wordID_t> const& phrase) const;
-  bool operator()(vector<wordID_t> const& phrase, unsigned const& i) const;
+  bool operator()(unsigned const& i, std::vector<wordID_t> const& phrase) const;
+  bool operator()(std::vector<wordID_t> const& phrase, unsigned const& i) const;
 };
 
 

moses/TranslationModel/UG/generic/file_io/ug_stream.h

@@ -18,20 +18,22 @@
 
 namespace ugdiss
 {
-using namespace std;
-using namespace boost::iostreams;
 
-/** open input file that is possibly compressed
- *  decompression filters are automatically added based on the file name
- *  gzip for .gz; bzip2 for bz2.
- */
-filtering_istream* open_input_stream(string fname);
-void open_input_stream(string fname, filtering_istream& in);
-// filtering_streambuf<input>* open_input_stream(string fname);
+  /** open input file that is possibly compressed
+   *  decompression filters are automatically added based on the file name
+   *  gzip for .gz; bzip2 for bz2.
+   */
+  boost::iostreams::filtering_istream* 
+  open_input_stream(std::string fname);
 
-filtering_ostream* open_output_stream(string fname);
-void open_output_stream(string fname, filtering_ostream& in);
+  void open_input_stream(std::string fname, 
+			 boost::iostreams::filtering_istream& in);
 
+  boost::iostreams::filtering_ostream* 
+  open_output_stream(std::string fname);
+
+  void open_output_stream(std::string fname, 
+			  boost::iostreams::filtering_ostream& in);
 
 }
 #endif

moses/TranslationModel/UG/generic/program_options/ug_splice_arglist.h

@@ -3,7 +3,6 @@
 #include <vector>
 #include <string>
 namespace Moses {
-  using namespace std;
 
   // Function to splice the argument list (e.g. before handing it over to
   // Moses LoadParam() function. /filter/ is a vector of argument names
@@ -12,7 +11,7 @@ namespace Moses {
   filter_arguments(int const argc_in, char const* const* const argv_in,
 		   int & argc_moses, char*** argv_moses,
 		   int & argc_other, char*** argv_other,
-		   vector<pair<string,int> > const& filter);
+		   std::vector<std::pair<std::string, int> > const& filter);
 
 
 } // namespace Moses

moses/TranslationModel/UG/generic/sampling/Sampling.h

@@ -11,24 +11,23 @@
 
 namespace Moses
 {
-using namespace std;
 
-// select a random sample of size /s/ without restitution from the range of
-// integers [0,N);
+// select a random sample of size /s/ without restitution from the
+// range of integers [0,N);
 template<typename idx_t>
 void
-randomSample(vector<idx_t>& v, size_t s, size_t N)
+randomSample(std::vector<idx_t>& v, size_t s, size_t N)
 {
   // see also Knuth: Art of Computer Programming Vol. 2, p. 142
 
-  s = min(s,N);
+  s = std::min(s,N);
   v.resize(s);
 
-  // the first option tries to be a bit more efficient than O(N) in picking
-  // the samples. The threshold is an ad-hoc, off-the-cuff guess. I still
-  // need to figure out the optimal break-even point between a linear sweep
-  // and repeatedly picking random numbers with the risk of hitting the same
-  // number many times.
+  // the first option tries to be a bit more efficient than O(N) in
+  // picking the samples. The threshold is an ad-hoc, off-the-cuff
+  // guess. I still need to figure out the optimal break-even point
+  // between a linear sweep and repeatedly picking random numbers with
+  // the risk of hitting the same number many times.
   if (s*10<N) {
     boost::dynamic_bitset<uint64_t> check(N,0);
     for (size_t i = 0; i < v.size(); i++) {

moses/TranslationModel/UG/generic/sorting/VectorIndexSorter.h

@@ -1,3 +1,4 @@
+// -*- mode: c++; indent-tabs-mode: nil; tab-width: 2 -*-
 #ifndef __vector_index_sorter_h
 #define __vector_index_sorter_h
 #include <boost/shared_ptr.hpp>
@@ -5,8 +6,8 @@
 #include <vector>
 // VectorIndexSorter; (c) 2007-2012 Ulrich Germann
 
-// A VectorIndexSorter is a function object for sorting indices into a vector
-// of objects (instead of sorting the vector itself).
+// A VectorIndexSorter is a function object for sorting indices into a
+// vector of objects (instead of sorting the vector itself).
 //
 // typcial use:
 // vector<thingy> my_vector;
@@ -16,13 +17,9 @@
 
 namespace Moses
 {
-  // using namespace std;
-
-
-  using std::greater;
 
   template<typename VAL,
-	   typename COMP = greater<VAL>,
+	   typename COMP = std::greater<VAL>,
 	   typename IDX_T=size_t>
   class
   VectorIndexSorter

moses/TranslationModel/UG/generic/stringdist/ug_stringdist.h

@@ -17,10 +17,6 @@
 #include "moses/TranslationModel/UG/mm/tpt_typedefs.h"
 
 
-using namespace std;
-//using namespace boost;
-using namespace ugdiss;
-
 namespace stringdist
 {
   float
@@ -32,7 +28,7 @@ namespace stringdist
   float
   fillAlignmentMatrix(UChar const* a, size_t const lenA,
 		      UChar const* b, size_t const lenB,
-		      vector<vector<float> > & M);
+		      std::vector<std::vector<float> > & M);
 
   class StringDiff
   {
@@ -67,21 +63,21 @@ namespace stringdist
     };
   private:
     UnicodeString a,b;
-    vector<Segment> difflist;
-    vector<int> diffcnt;
+    std::vector<Segment> difflist;
+    std::vector<int> diffcnt;
   public:
-    UnicodeString const& set_a(string const& a);
-    UnicodeString const& set_b(string const& b);
+    UnicodeString const& set_a(std::string const& a);
+    UnicodeString const& set_b(std::string const& b);
     UnicodeString const& get_a() const;
     UnicodeString const& get_b() const;
-    StringDiff(string const& a, string const& b);
+    StringDiff(std::string const& a, std::string const& b);
     StringDiff();
     size_t size();
     size_t align(bool force=false); // returns the levenshtein distance
     void showDiff(std::ostream& out);
     float levenshtein();
     Segment const& operator[](uint32_t i) const;
-    void fillAlignmentMatrix(vector<vector<float> > & M) const;
+    void fillAlignmentMatrix(std::vector<std::vector<float> > & M) const;
     vector<int> const& getFeatures() const;
   };
 }

moses/TranslationModel/UG/mm/obsolete/ug_bitext_base.h

@@ -24,8 +24,6 @@
 #include "ug_corpus_token.h"
 #include "tpt_pickler.h"
 
-using namespace ugdiss;
-using namespace std;
 namespace Moses {
 
   typedef L2R_Token<SimpleWordId>      Token;
@@ -44,7 +42,7 @@ namespace Moses {
       class job;
       class worker;
       list<job> joblist;
-      vector<sptr<boost::thread> > workers;
+      std::vector<SPTR<boost::thread> > workers;
       bool shutdown;
       size_t doomed;
     public:
@@ -52,10 +50,10 @@ namespace Moses {
       agenda(bitext_base const& bitext);
       ~agenda();
       void add_workers(int n);
-      sptr<pstats> add_job(mmbitext::iter const& phrase,
+      SPTR<pstats> add_job(mmbitext::iter const& phrase,
 			   size_t const max_samples);
       bool get_task(uint64_t & sid, uint64_t & offset, uint64_t & len,
-		    bool & fwd, sptr<bitext_base::pstats> & stats);
+		    bool & fwd, SPTR<bitext_base::pstats> & stats);
     };
 
     // stores the list of unfinished jobs;
@@ -76,19 +74,19 @@ namespace Moses {
     find_trg_phr_bounds
     (size_t const sid, size_t const start, size_t const stop,
      size_t & s1, size_t & s2, size_t & e1, size_t & e2,
-     vector<uchar> * core_alignment, bool const flip) const;
+     std::vector<uchar> * core_alignment, bool const flip) const;
 
-    boost::unordered_map<uint64_t,sptr<pstats> > cache1,cache2;
+    boost::unordered_map<uint64_t,SPTR<pstats> > cache1,cache2;
   private:
-    sptr<pstats>
+    SPTR<pstats>
     prep2(iter const& phrase);
   public:
     mmbitext();
     ~mmbitext();
 
-    void open(string const base, string const L1, string const L2);
+    void open(std::string const base, std::string const L1, std::string const L2);
 
-    sptr<pstats> lookup(iter const& phrase);
+    SPTR<pstats> lookup(iter const& phrase);
     void prep(iter const& phrase);
   };
 
@@ -99,15 +97,15 @@ namespace Moses {
   {
     uint32_t my_rcnt; // unweighted count
     float    my_wcnt; // weighted count
-    vector<pair<size_t, vector<uchar> > > my_aln;
+    std::vector<pair<size_t, std::vector<uchar> > > my_aln;
     boost::mutex lock;
   public:
     jstats();
     jstats(jstats const& other);
     uint32_t rcnt() const;
     float    wcnt() const;
-    vector<pair<size_t, vector<uchar> > > const & aln() const;
-    void add(float w, vector<uchar> const& a);
+    std::vector<pair<size_t, std::vector<uchar> > > const & aln() const;
+    void add(float w, std::vector<uchar> const& a);
   };
 
   struct
@@ -126,11 +124,12 @@ namespace Moses {
     size_t in_progress; // keeps track of how many threads are currently working on this
     boost::unordered_map<uint64_t, jstats> trg;
     pstats();
-    // vector<phrase> nbest;
+    // std::vector<phrase> nbest;
     // void select_nbest(size_t const N=10);
     void release();
     void register_worker();
-    void add(mmbitext::iter const& trg_phrase, float const w, vector<uchar> const& a);
+    void add(mmbitext::iter const& trg_phrase, float const w, 
+	     std::vector<uchar> const& a);
   };
 
   class
@@ -157,7 +156,7 @@ namespace Moses {
     size_t         ctr;
     size_t         len;
     bool           fwd;
-    sptr<mmbitext::pstats> stats;
+    SPTR<mmbitext::pstats> stats;
     bool step(uint64_t & sid, uint64_t & offset);
   };
 

moses/TranslationModel/UG/mm/tpt_tightindex.h

@@ -10,9 +10,7 @@
 #include <iostream>
 #include <sstream>
 #include "tpt_typedefs.h"
-// #include <stdint.h>
 #include <cassert>
-// // using namespace std;
 
 #ifndef uchar
 #endif

moses/TranslationModel/UG/mm/tpt_tokenindex.h

@@ -21,7 +21,6 @@
 #include <vector>
 #include <map>
 
-// // using namespace std;
 namespace bio=boost::iostreams;
 
 namespace sapt

moses/TranslationModel/UG/mm/ug_bitext.h

@@ -77,7 +77,7 @@ namespace sapt
   using Moses::ttaskwptr;
   using tpt::binread;
   using tpt::binwrite;
-  // using namespace ugdiss;
+
   float lbop(size_t const tries, size_t const succ, float const confidence);
   void write_bitvector(bitvector const& v, std::ostream& out);
 

moses/TranslationModel/UG/mm/ug_bitext_agenda_job.h

@@ -130,7 +130,6 @@ int Bitext<Token>::agenda::job
 
   if (!m_bias) return 1;
 
-  // // using namespace boost::math;
   typedef boost::math::binomial_distribution<> binomial;
 
   std::ostream* log = m_bias->loglevel > 1 ? m_bias->log : NULL;
@@ -138,7 +137,6 @@ int Bitext<Token>::agenda::job
   float p = (*m_bias)[sid];
   id_type docid = m_bias->GetClass(sid);
   
-  // uint32_t k = docid < stats->indoc.size() ? stats->indoc[docid] : 0;
   typedef pstats::indoc_map_t::const_iterator id_iter;
   id_iter m = stats->indoc.find(docid);
   uint32_t k = m != stats->indoc.end() ? m->second : 0 ;

moses/TranslationModel/UG/mm/ug_conll_bottom_up_token.h

@@ -7,7 +7,6 @@
 #include "ug_typedefs.h"
 namespace sapt
 {
-  // using namespace std;
 
   template<typename T>
   class ConllBottomUpToken : public T

moses/TranslationModel/UG/mm/ug_conll_record.h

@@ -7,7 +7,6 @@
 
 namespace sapt
 {
-  // using namespace std;
   
   using tpt::id_type;
   using tpt::uchar;

moses/TranslationModel/UG/mm/ug_deptree.h

@@ -15,7 +15,6 @@
 #include "ug_conll_bottom_up_token.h"
 #include "ug_typedefs.h"
 
-// using namespace std;
 namespace sapt
 {
 

moses/TranslationModel/UG/mm/ug_im_tsa.h

@@ -24,13 +24,8 @@
 
 namespace sapt
 {
-  // using namespace std;
-  // using namespace boost;
   namespace bio=boost::iostreams;
 
-  // template<typename TOKEN> class imBitext<TOKEN>;
-
-
   template<typename TOKEN, typename SORTER>
   class TsaSorter
   {
@@ -44,8 +39,8 @@ namespace sapt
   public:
     TsaSorter(SORTER sorter, iter& begin, iter& end)
       : m_sorter(sorter),
-	m_begin(begin),
-	m_end(end) { }
+        m_begin(begin),
+        m_end(end) { }
     
     bool 
     operator()()
@@ -62,7 +57,7 @@ namespace sapt
   class imTSA : public TSA<TOKEN>
   {
     typedef typename Ttrack<TOKEN>::Position cpos;
-    // friend class imBitext<TOKEN>;
+
   public:
     class tree_iterator;
     friend class tree_iterator;

moses/TranslationModel/UG/mm/ug_im_ttrack.h

@@ -19,8 +19,6 @@
 #include "util/exception.hh"
 #include "moses/Util.h"
 
-// #include "ug_vocab.h"
-
 // define the corpus buffer size (in sentences) and the
 // for adding additional sentences:
 #define IMTTRACK_INCREMENT_SIZE 100000

moses/TranslationModel/UG/mm/ug_lexical_phrase_scorer1.h

@@ -11,7 +11,6 @@
 #include <boost/unordered_map.hpp>
 #include "tpt_pickler.h"
 
-// using namespace std;
 namespace ugdiss
 {
 

moses/TranslationModel/UG/mm/ug_lexical_phrase_scorer2.h

@@ -14,7 +14,7 @@
 #include "tpt_pickler.h"
 #include "ug_mm_2d_table.h"
 #include "util/exception.hh"
-// using namespace std;
+
 namespace sapt
 {
 

moses/TranslationModel/UG/mm/ug_lru_cache.h

@@ -14,8 +14,6 @@
 
 namespace lru_cache
 {
-  // using namespace std;
-  // using namespace boost;
 
   template<typename KEY, typename VAL>
   class LRU_Cache

moses/TranslationModel/UG/mm/ug_mm_2d_table.h

@@ -13,7 +13,6 @@
 namespace bio=boost::iostreams;
 namespace sapt
 {
-  // using namespace std;
   template<typename OFFSET, typename ID, typename VAL, typename INIT>
   class
   mm2dTable

moses/TranslationModel/UG/mm/ug_mm_tsa.h

@@ -19,7 +19,6 @@
 
 namespace sapt
 {
-  // using namespace std;
   namespace bio=boost::iostreams;
 
   template<typename TOKEN>

moses/TranslationModel/UG/mm/ug_mm_ttrack.h

@@ -26,7 +26,6 @@
 
 namespace sapt
 {
-  // using namespace std;
   namespace bio=boost::iostreams;
 
   template<typename TKN=id_type>

moses/TranslationModel/UG/mm/ug_tsa_base.h

@@ -21,8 +21,6 @@
 namespace sapt
 {
 
-  // using namespace std;
-  // using namespace boost;
   namespace bio=boost::iostreams;
 
   template<typename TKN>

moses/TranslationModel/UG/mm/ug_tsa_bitset_cache.h

@@ -18,7 +18,7 @@
 
 namespace sapt
 {
-  // using namespace std;
+
   template<typename TSA>
   class
   BitSetCache

moses/TranslationModel/UG/mm/ug_ttrack_base.h

@@ -20,11 +20,9 @@
 #include "tpt_typedefs.h"
 #include "tpt_tokenindex.h"
 #include "moses/Util.h"
-// #include "ug_vocab.h"
 
 namespace sapt
 {
-  // using namespace std;
 
   typedef boost::dynamic_bitset<uint64_t> bdBitset;
   using tpt::count_type;

moses/TranslationModel/UG/mm/ug_typedefs.h

@@ -10,7 +10,6 @@
 #include "tpt_typedefs.h"
 namespace sapt
 {
-  // using namespace std;
   typedef boost::dynamic_bitset<uint64_t> bitvector;
 
   typedef std::vector<std::vector<float> > flt_2d_table;

moses/TranslationModel/UG/sapt_phrase_key.h

@@ -1,13 +0,0 @@
-//-*- c++ -*-
-#pragma once
-#include <stdint.h>
-
-using namespace std;
-namespace sapt
-{
-  using namespace Moses;
-  using namespace std;
-
-
-
-}

moses/TranslationModel/WordCoocTable.h

@@ -13,8 +13,6 @@
 namespace Moses
 {
 
-using namespace std;
-
 #ifndef bitvector
 typedef boost::dynamic_bitset<uint64_t> bitvector;
 #endif
@@ -27,9 +25,9 @@ typedef boost::dynamic_bitset<uint64_t> bitvector;
 class WordCoocTable
 {
   typedef map<wordID_t,uint32_t> my_map_t;
-  vector<my_map_t> m_cooc;
-  vector<uint32_t> m_marg1;
-  vector<uint32_t> m_marg2;
+  std::vector<my_map_t> m_cooc;
+  std::vector<uint32_t> m_marg1;
+  std::vector<uint32_t> m_marg2;
 public:
   WordCoocTable();
   WordCoocTable(wordID_t const VocabSize1, wordID_t const VocabSize2);