C++ ConsensusMap::getMin方法代码示例

//.........这里部分代码省略.........
      }
      else if (in_type == FileTypes::CONSENSUSXML)       //consensus features
      {
        dp = cons.getDataProcessing();
      }
      int i = 0;
      for (vector<DataProcessing>::iterator it = dp.begin(); it != dp.end(); ++it)
      {
        os << "Data processing " << i << endl;
        os << "\tcompletion_time:   " << (*it).getCompletionTime().getDate() << 'T' << (*it).getCompletionTime().getTime() << endl;
        os << "\tsoftware name:     " << (*it).getSoftware().getName() << " version " << (*it).getSoftware().getVersion() << endl;
        for (set<DataProcessing::ProcessingAction>::const_iterator paIt = (*it).getProcessingActions().begin(); paIt != (*it).getProcessingActions().end(); ++paIt)
        {
          os << "\t\tprocessing action: " << DataProcessing::NamesOfProcessingAction[*paIt] << endl;
        }
      }
      ++i;
    }

    //-------------------------------------------------------------
    // statistics
    //-------------------------------------------------------------
    if (getFlag_("s"))
    {
      //-------------------------------------------------------------
      // Content statistics
      //-------------------------------------------------------------
      Map<String, int> meta_names;
      if (in_type == FileTypes::FEATUREXML) //features
      {
        os << "Number of features: " << feat.size() << endl
           << endl
           << "Ranges:" << endl
           << "  retention time:  " << String::number(feat.getMin()[Peak2D::RT], 2) << " : " << String::number(feat.getMax()[Peak2D::RT], 2) << endl
           << "  mass-to-charge:  " << String::number(feat.getMin()[Peak2D::MZ], 2) << " : " << String::number(feat.getMax()[Peak2D::MZ], 2) << endl
           << "  intensity:       " << String::number(feat.getMinInt(), 2) << " : " << String::number(feat.getMaxInt(), 2) << endl
           << endl;

        // Charge distribution
        Map<UInt, UInt> charges;
        for (Size i = 0; i < feat.size(); ++i)
        {
          charges[feat[i].getCharge()]++;
        }

        os << "Charge distribution" << endl;
        for (Map<UInt, UInt>::const_iterator it = charges.begin();
             it != charges.end(); ++it)
        {
          os << "charge " << it->first << ": " << it->second << endl;
        }
      }
      else if (in_type == FileTypes::CONSENSUSXML)       //consensus features
      {
        map<Size, UInt> num_consfeat_of_size;
        for (ConsensusMap::const_iterator cmit = cons.begin();
             cmit != cons.end(); ++cmit)
        {
          ++num_consfeat_of_size[cmit->size()];
        }

        os << endl << "Number of consensus features:" << endl;
        for (map<Size, UInt>::reverse_iterator i = num_consfeat_of_size.rbegin(); i != num_consfeat_of_size.rend(); ++i)
        {
          os << "  of size " << setw(2) << i->first << ": " << setw(6) << i->second << endl;
        }

  void PoseClusteringShiftSuperimposer::run(const ConsensusMap & map_model, const ConsensusMap & map_scene, TransformationDescription & transformation)
  {
    typedef ConstRefVector<ConsensusMap> PeakPointerArray_;
    typedef Math::LinearInterpolation<double, double> LinearInterpolationType_;

    LinearInterpolationType_ shift_hash_;

    // OLD STUFF
    //    LinearInterpolationType_ scaling_hash_1;
    //    LinearInterpolationType_ scaling_hash_2;
    //    LinearInterpolationType_ shift_hash_;
    //    LinearInterpolationType_ rt_high_hash_;

    /// Maximum deviation in mz of two partner points
    const double mz_pair_max_distance = param_.getValue("mz_pair_max_distance");

    /// Size of each shift bucket
    const double shift_bucket_size = param_.getValue("shift_bucket_size");

    const UInt struc_elem_length_datapoints = 21; // MAGIC ALERT: number of data points in structuring element for tophat filter, which removes baseline from histogram
    const double scaling_histogram_crossing_slope = 3.0; // MAGIC ALERT: used when distinguishing noise level and enriched histogram bins
    const double scaling_cutoff_stdev_multiplier = 1.5; // MAGIC ALERT: multiplier for stdev in cutoff for outliers
    const UInt loops_mean_stdev_cutoff = 3; // MAGIC ALERT: number of loops in stdev cutoff for outliers

    startProgress(0, 100, "shift pose clustering");
    UInt actual_progress = 0;
    setProgress(++actual_progress);

    // Optionally, we will write dumps of the hash table buckets.
    bool do_dump_buckets = false;
    String dump_buckets_basename;
    if (param_.getValue("dump_buckets") != "")
    {
      do_dump_buckets = true;
      dump_buckets_basename = param_.getValue("dump_buckets");
    }
    setProgress(++actual_progress);

    // Even more optionally, we will write dumps of the hashed pairs.
    bool do_dump_pairs = false;
    String dump_pairs_basename;
    if (param_.getValue("dump_pairs") != "")
    {
      do_dump_pairs = true;
      dump_pairs_basename = param_.getValue("dump_pairs");
    }
    setProgress(++actual_progress);

    //**************************************************************************
    // Select the most abundant data points only.  After that, disallow modifications
    // (we tend to have annoying issues with const_iterator versus iterator).
    PeakPointerArray_ model_map_ini(map_model.begin(), map_model.end());
    const PeakPointerArray_ & model_map(model_map_ini);
    PeakPointerArray_ scene_map_ini(map_scene.begin(), map_scene.end());
    const PeakPointerArray_ & scene_map(scene_map_ini);
    {
      // truncate the data as necessary
      // casting to SignedSize is done on PURPOSE here! (num_used_points will be maximal if -1 is used)
      const Size num_used_points = (SignedSize) param_.getValue("num_used_points");
      if (model_map_ini.size() > num_used_points)
      {
        model_map_ini.sortByIntensity(true);
        model_map_ini.resize(num_used_points);
      }
      model_map_ini.sortByComparator(Peak2D::MZLess());
      setProgress(++actual_progress);
      if (scene_map_ini.size() > num_used_points)
      {
        scene_map_ini.sortByIntensity(true);
        scene_map_ini.resize(num_used_points);
      }
      scene_map_ini.sortByComparator(Peak2D::MZLess());
      setProgress(++actual_progress);
      // Note: model_map_ini and scene_map_ini will not be used further below
    }
    setProgress((actual_progress = 10));

    //**************************************************************************
    // Preprocessing

    // get RT ranges (NOTE: we trust that min and max have been updated in the
    // ConsensusMap::convert() method !)

    const double model_low = map_model.getMin()[ConsensusFeature::RT];
    const double scene_low = map_scene.getMin()[ConsensusFeature::RT];
    const double model_high = map_model.getMax()[ConsensusFeature::RT];
    const double scene_high = map_scene.getMax()[ConsensusFeature::RT];

    // OLD STUFF
    //    const double rt_low = (maps[0].getMin()[ConsensusFeature::RT] + maps[1].getMin()[ConsensusFeature::RT]) / 2.;
    //    const double rt_high = (maps[0].getMax()[ConsensusFeature::RT] + maps[1].getMax()[ConsensusFeature::RT]) / 2.;

    // Initialize the hash tables: shift_hash_
    // OLD STUFF: was:  rt_scaling_hash_, rt_low_hash_, and rt_high_hash_
    {
      // (over)estimate the required number of buckets for shifting
      double max_shift = param_.getValue("max_shift");
      // actually the largest possible shift can be much smaller, depending on the data
      do
      {
//.........这里部分代码省略.........