BppOBranchModelFormat.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include <Bpp/Io/BppODiscreteDistributionFormat.h>
#include <Bpp/Io/BppOParametrizableFormat.h>
#include <Bpp/Io/FileTools.h>
#include <Bpp/Io/OutputStream.h>
#include <Bpp/Seq/Alphabet/AlphabetTools.h>
#include <Bpp/Seq/App/SequenceApplicationTools.h>
#include <Bpp/Text/KeyvalTools.h>
#include <Bpp/Text/StringTokenizer.h>
#include <Bpp/Text/TextTools.h>
 
#include "../App/PhylogeneticsApplicationTools.h"
#include "../Model/MultinomialFromTransitionModel.h"
#include "../Model/TransitionFromTransitionModel.h"
#include "BppOBranchModelFormat.h"
#include "BppOFrequencySetFormat.h"
 
// From Numeric
 
#include <Bpp/Numeric/Prob/ConstantDistribution.h>
#include <Bpp/Numeric/AutoParameter.h>
 
 
#include <Bpp/Text/StringTokenizer.h>
 
using namespace bpp;
 
// From the STL:
#include <iomanip>
#include <set>
 
using namespace std;
 
std::unique_ptr<BranchModelInterface> BppOBranchModelFormat::readBranchModel(
    shared_ptr<const Alphabet> alphabet,
    const string& modelDescription,
    const std::map<size_t, std::shared_ptr<const AlignmentDataInterface>>& mData,
    size_t nData,
    bool parseArguments)
{
  unparsedArguments_.clear();
  unique_ptr<BranchModelInterface> model;
  string modelName = "";
  map<string, string> args;
  KeyvalTools::parseProcedure(modelDescription, modelName, args);
 
  // get data number
 
  if (args.find("data") != args.end())
    nData = TextTools::to<size_t>(args["data"]);
 
 
  // //////////////////////////////////
  // / MIXED MODELS
  // ////////////////////////////////
 
  if (modelName == "Multinomial")
  {
    // We have to parse the nested model first:
    if (args.find("model") == args.end())
      throw Exception("BppOBranchModelFormat::read. Missing argument 'model' for model " + modelName);
    string nestedModelDescription = args["model"];
    BppOTransitionModelFormat nestedReader(ALL, false, allowMixed_, allowGaps_, verbose_, warningLevel_);
    if (geneticCode_)
      nestedReader.setGeneticCode(geneticCode_);
 
    std::shared_ptr<TransitionModelInterface> nestedModel = nestedReader.readTransitionModel(alphabet, nestedModelDescription, mData, nData, false);
    map<string, string> unparsedParameterValuesNested(nestedReader.getUnparsedArguments());
 
    model.reset(new MultinomialFromTransitionModel(nestedModel));
  }
 
  if (!model)
    model = readTransitionModel(alphabet, modelDescription, mData, nData, parseArguments);
  else
  {
    if (verbose_)
      ApplicationTools::displayResult("Branch model", modelName);
 
    updateParameters_(*model, args);
 
    if (parseArguments)
    {
      if (nData)
        initialize_(*model, mData.at(nData));
      else
        initialize_(*model, 0);
    }
  }
 
  if (verbose_)
  {
    if (nData != 0)
      ApplicationTools::displayResult("Data used ", TextTools::toString(nData));
  }
 
 
  return model;
}