merge with upstream

1 files changed, 0 insertions, 370 deletions

diff --git a/training/atools.cc b/training/atools.cc
deleted file mode 100644
index 42579627..00000000
--- a/training/atools.cc
+++ /dev/null
@@ -1,370 +0,0 @@
-#include <iostream>
-#include <sstream>
-#include <vector>
-
-#include <queue>
-#include <map>
-#include <boost/program_options.hpp>
-#include <boost/shared_ptr.hpp>
-
-#include "filelib.h"
-#include "aligner.h"
-#include "alignment_pharaoh.h"
-
-namespace po = boost::program_options;
-using namespace std;
-using boost::shared_ptr;
-
-struct Command {
-  virtual ~Command() {}
-  virtual string Name() const = 0;
-
-  // returns 1 for alignment grid output [default]
-  // returns 2 if Summary() should be called [for AER, etc]
-  virtual int Result() const { return 1; }
-
-  virtual bool RequiresTwoOperands() const { return true; }
-  virtual void Apply(const Array2D<bool>& a, const Array2D<bool>& b, Array2D<bool>* x) = 0;
-  void EnsureSize(const Array2D<bool>& a, const Array2D<bool>& b, Array2D<bool>* x) {
-    x->resize(max(a.width(), b.width()), max(a.height(), b.height()));
-  }
-  static bool Safe(const Array2D<bool>& a, int i, int j) {
-    if (i >= 0 && j >= 0 && i < a.width() && j < a.height())
-      return a(i,j);
-    else
-      return false;
-  }
-  virtual void Summary() { assert(!"Summary should have been overridden"); }
-};
-
-// compute fmeasure, second alignment is reference, first is hyp
-struct FMeasureCommand : public Command {
-  FMeasureCommand() : matches(), num_predicted(), num_in_ref() {}
-  int Result() const { return 2; }
-  string Name() const { return "fmeasure"; }
-  bool RequiresTwoOperands() const { return true; }
-  void Apply(const Array2D<bool>& hyp, const Array2D<bool>& ref, Array2D<bool>* x) {
-    (void) x;   // AER just computes statistics, not an alignment
-    int i_len = ref.width();
-    int j_len = ref.height();
-    for (int i = 0; i < i_len; ++i) {
-      for (int j = 0; j < j_len; ++j) {
-        if (ref(i,j)) {
-          ++num_in_ref;
-          if (Safe(hyp, i, j)) ++matches;
-        } 
-      }
-    }
-    for (int i = 0; i < hyp.width(); ++i)
-      for (int j = 0; j < hyp.height(); ++j)
-        if (hyp(i,j)) ++num_predicted;
-  }
-  void Summary() {
-    if (num_predicted == 0 || num_in_ref == 0) {
-      cerr << "Insufficient statistics to compute f-measure!\n";
-      abort();
-    }
-    const double prec = static_cast<double>(matches) / num_predicted;
-    const double rec = static_cast<double>(matches) / num_in_ref;
-    cout << "P: " << prec << endl;
-    cout << "R: " << rec << endl;
-    const double f = (2.0 * prec * rec) / (rec + prec);
-    cout << "F: " << f << endl;
-  }
-  int matches;
-  int num_predicted;
-  int num_in_ref;
-};
-
-struct DisplayCommand : public Command {
-  string Name() const { return "display"; }
-  bool RequiresTwoOperands() const { return false; }
-  void Apply(const Array2D<bool>& in, const Array2D<bool>&not_used, Array2D<bool>* x) {
-    *x = in;
-    cout << *x << endl;
-  }
-};
-
-struct ConvertCommand : public Command {
-  string Name() const { return "convert"; }
-  bool RequiresTwoOperands() const { return false; }
-  void Apply(const Array2D<bool>& in, const Array2D<bool>&not_used, Array2D<bool>* x) {
-    *x = in;
-  }
-};
-
-struct InvertCommand : public Command {
-  string Name() const { return "invert"; }
-  bool RequiresTwoOperands() const { return false; }
-  void Apply(const Array2D<bool>& in, const Array2D<bool>&not_used, Array2D<bool>* x) {
-    Array2D<bool>& res = *x;
-    res.resize(in.height(), in.width());
-    for (int i = 0; i < in.height(); ++i)
-      for (int j = 0; j < in.width(); ++j)
-        res(i, j) = in(j, i);
-  }
-};
-
-struct IntersectCommand : public Command {
-  string Name() const { return "intersect"; }
-  bool RequiresTwoOperands() const { return true; }
-  void Apply(const Array2D<bool>& a, const Array2D<bool>& b, Array2D<bool>* x) {
-    EnsureSize(a, b, x);
-    Array2D<bool>& res = *x;
-    for (int i = 0; i < a.width(); ++i)
-      for (int j = 0; j < a.height(); ++j)
-        res(i, j) = Safe(a, i, j) && Safe(b, i, j);
-  }
-};
-
-struct UnionCommand : public Command {
-  string Name() const { return "union"; }
-  bool RequiresTwoOperands() const { return true; }
-  void Apply(const Array2D<bool>& a, const Array2D<bool>& b, Array2D<bool>* x) {
-    EnsureSize(a, b, x);
-    Array2D<bool>& res = *x;
-    for (int i = 0; i < res.width(); ++i)
-      for (int j = 0; j < res.height(); ++j)
-        res(i, j) = Safe(a, i, j) || Safe(b, i, j);
-  }
-};
-
-struct RefineCommand : public Command {
-  RefineCommand() {
-    neighbors_.push_back(make_pair(1,0));
-    neighbors_.push_back(make_pair(-1,0));
-    neighbors_.push_back(make_pair(0,1));
-    neighbors_.push_back(make_pair(0,-1));
-  }
-  bool RequiresTwoOperands() const { return true; }
-
-  void Align(int i, int j) {
-    res_(i, j) = true;
-    is_i_aligned_[i] = true;
-    is_j_aligned_[j] = true;
-  }
-
-  bool IsNeighborAligned(int i, int j) const {
-    for (int k = 0; k < neighbors_.size(); ++k) {
-      const int di = neighbors_[k].first;
-      const int dj = neighbors_[k].second;
-      if (Safe(res_, i + di, j + dj))
-        return true;
-    }
-    return false;
-  }
-
-  bool IsNeitherAligned(int i, int j) const {
-    return !(is_i_aligned_[i] || is_j_aligned_[j]);
-  }
-
-  bool IsOneOrBothUnaligned(int i, int j) const {
-    return !(is_i_aligned_[i] && is_j_aligned_[j]);
-  }
-
-  bool KoehnAligned(int i, int j) const {
-    return IsOneOrBothUnaligned(i, j) && IsNeighborAligned(i, j);
-  }
-
-  typedef bool (RefineCommand::*Predicate)(int i, int j) const;
-
- protected:
-  void InitRefine(
-      const Array2D<bool>& a,
-      const Array2D<bool>& b) {
-    res_.clear();
-    EnsureSize(a, b, &res_);
-    in_.clear(); un_.clear(); is_i_aligned_.clear(); is_j_aligned_.clear();
-    EnsureSize(a, b, &in_);
-    EnsureSize(a, b, &un_);
-    is_i_aligned_.resize(res_.width(), false);
-    is_j_aligned_.resize(res_.height(), false);
-    for (int i = 0; i < in_.width(); ++i)
-      for (int j = 0; j < in_.height(); ++j) {
-        un_(i, j) = Safe(a, i, j) || Safe(b, i, j);
-        in_(i, j) = Safe(a, i, j) && Safe(b, i, j);
-        if (in_(i, j)) Align(i, j);
-    }
-  }
-  // "grow" the resulting alignment using the points in adds
-  // if they match the constraints determined by pred
-  void Grow(Predicate pred, bool idempotent, const Array2D<bool>& adds) {
-    if (idempotent) {
-      for (int i = 0; i < adds.width(); ++i)
-        for (int j = 0; j < adds.height(); ++j) {
-          if (adds(i, j) && !res_(i, j) &&
-              (this->*pred)(i, j)) Align(i, j);
-        }
-      return;
-    }
-    set<pair<int, int> > p;
-    for (int i = 0; i < adds.width(); ++i)
-      for (int j = 0; j < adds.height(); ++j)
-        if (adds(i, j) && !res_(i, j))
-          p.insert(make_pair(i, j));
-    bool keep_going = !p.empty();
-    while (keep_going) {
-      keep_going = false;
-      for (set<pair<int, int> >::iterator pi = p.begin();
-           pi != p.end(); ++pi) {
-        if ((this->*pred)(pi->first, pi->second)) {
-          Align(pi->first, pi->second);
-          p.erase(pi);
-          keep_going = true;
-        }
-      }
-    }
-  }
-  Array2D<bool> res_;  // refined alignment
-  Array2D<bool> in_;   // intersection alignment
-  Array2D<bool> un_;   // union alignment
-  vector<bool> is_i_aligned_;
-  vector<bool> is_j_aligned_;
-  vector<pair<int,int> > neighbors_;
-};
-
-struct DiagCommand : public RefineCommand {
-  DiagCommand() {
-    neighbors_.push_back(make_pair(1,1));
-    neighbors_.push_back(make_pair(-1,1));
-    neighbors_.push_back(make_pair(1,-1));
-    neighbors_.push_back(make_pair(-1,-1));
-  }
-};
-
-struct GDCommand : public DiagCommand {
-  string Name() const { return "grow-diag"; }
-  void Apply(const Array2D<bool>& a, const Array2D<bool>& b, Array2D<bool>* x) {
-    InitRefine(a, b);
-    Grow(&RefineCommand::KoehnAligned, false, un_);
-    *x = res_;
-  }
-};
-
-struct GDFCommand : public DiagCommand {
-  string Name() const { return "grow-diag-final"; }
-  void Apply(const Array2D<bool>& a, const Array2D<bool>& b, Array2D<bool>* x) {
-    InitRefine(a, b);
-    Grow(&RefineCommand::KoehnAligned, false, un_);
-    Grow(&RefineCommand::IsOneOrBothUnaligned, true, a);
-    Grow(&RefineCommand::IsOneOrBothUnaligned, true, b);
-    *x = res_;
-  }
-};
-
-struct GDFACommand : public DiagCommand {
-  string Name() const { return "grow-diag-final-and"; }
-  void Apply(const Array2D<bool>& a, const Array2D<bool>& b, Array2D<bool>* x) {
-    InitRefine(a, b);
-    Grow(&RefineCommand::KoehnAligned, false, un_);
-    Grow(&RefineCommand::IsNeitherAligned, true, a);
-    Grow(&RefineCommand::IsNeitherAligned, true, b);
-    *x = res_;
-  }
-};
-
-map<string, boost::shared_ptr<Command> > commands;
-
-void InitCommandLine(int argc, char** argv, po::variables_map* conf) {
-  po::options_description opts("Configuration options");
-  ostringstream os;
-  os << "[REQ] Operation to perform:";
-  for (map<string, boost::shared_ptr<Command> >::iterator it = commands.begin();
-       it != commands.end(); ++it) {
-    os << ' ' << it->first;
-  }
-  string cstr = os.str();
-  opts.add_options()
-        ("input_1,i", po::value<string>(), "[REQ] Alignment 1 file, - for STDIN")
-        ("input_2,j", po::value<string>(), "[OPT] Alignment 2 file, - for STDIN")
-	("command,c", po::value<string>()->default_value("convert"), cstr.c_str())
-        ("help,h", "Print this help message and exit");
-  po::options_description clo("Command line options");
-  po::options_description dcmdline_options;
-  dcmdline_options.add(opts);
-
-  po::store(parse_command_line(argc, argv, dcmdline_options), *conf);
-  po::notify(*conf);
-
-  if (conf->count("help") || conf->count("input_1") == 0 || conf->count("command") == 0) {
-    cerr << dcmdline_options << endl;
-    exit(1);
-  }
-  const string cmd = (*conf)["command"].as<string>();
-  if (commands.count(cmd) == 0) {
-    cerr << "Don't understand command: " << cmd << endl;
-    exit(1);
-  }
-  if (commands[cmd]->RequiresTwoOperands()) {
-    if (conf->count("input_2") == 0) {
-      cerr << "Command '" << cmd << "' requires two alignment files\n";
-      exit(1);
-    }
-    if ((*conf)["input_1"].as<string>() == "-" && (*conf)["input_2"].as<string>() == "-") {
-      cerr << "Both inputs cannot be STDIN\n";
-      exit(1);
-    }
-  } else {
-    if (conf->count("input_2") != 0) {
-      cerr << "Command '" << cmd << "' requires only one alignment file\n";
-      exit(1);
-    }
-  }
-}
-
-template<class C> static void AddCommand() {
-  C* c = new C;
-  commands[c->Name()].reset(c);
-}
-
-int main(int argc, char **argv) {
-  AddCommand<ConvertCommand>();
-  AddCommand<DisplayCommand>();
-  AddCommand<InvertCommand>();
-  AddCommand<IntersectCommand>();
-  AddCommand<UnionCommand>();
-  AddCommand<GDCommand>();
-  AddCommand<GDFCommand>();
-  AddCommand<GDFACommand>();
-  AddCommand<FMeasureCommand>();
-  po::variables_map conf;
-  InitCommandLine(argc, argv, &conf);
-  Command& cmd = *commands[conf["command"].as<string>()];
-  boost::shared_ptr<ReadFile> rf1(new ReadFile(conf["input_1"].as<string>()));
-  boost::shared_ptr<ReadFile> rf2;
-  if (cmd.RequiresTwoOperands())
-    rf2.reset(new ReadFile(conf["input_2"].as<string>()));
-  istream* in1 = rf1->stream();
-  istream* in2 = NULL;
-  if (rf2) in2 = rf2->stream();
-  while(*in1) {
-    string line1;
-    string line2;
-    getline(*in1, line1);
-    if (in2) {
-      getline(*in2, line2);
-      if ((*in1 && !*in2) || (*in2 && !*in1)) {
-        cerr << "Mismatched number of lines!\n";
-        exit(1);
-      }
-    }
-    if (line1.empty() && !*in1) break;
-    shared_ptr<Array2D<bool> > out(new Array2D<bool>);
-    shared_ptr<Array2D<bool> > a1 = AlignmentPharaoh::ReadPharaohAlignmentGrid(line1);
-    if (in2) {
-      shared_ptr<Array2D<bool> > a2 = AlignmentPharaoh::ReadPharaohAlignmentGrid(line2);
-      cmd.Apply(*a1, *a2, out.get());
-    } else {
-      Array2D<bool> dummy;
-      cmd.Apply(*a1, dummy, out.get());
-    }
-    
-    if (cmd.Result() == 1) {
-      AlignmentPharaoh::SerializePharaohFormat(*out, &cout);
-    }
-  }
-  if (cmd.Result() == 2)
-    cmd.Summary();
-  return 0;
-}
-