BppOAlphabetIndex2Format.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include <Bpp/App/ApplicationTools.h>
#include <Bpp/Text/KeyvalTools.h>
#include <memory>
#include <string>
 
#include "../Alphabet/AlphabetTools.h"
#include "../AlphabetIndex/AAIndex2Entry.h"
#include "../AlphabetIndex/AlphabetIndex1.h"
#include "../AlphabetIndex/BLOSUM50.h"
#include "../AlphabetIndex/CodonFromProteicAlphabetIndex2.h"
#include "../AlphabetIndex/GranthamAAChemicalDistance.h"
#include "../AlphabetIndex/MiyataAAChemicalDistance.h"
#include "../AlphabetIndex/SimpleIndexDistance.h"
#include "BppOAlphabetIndex1Format.h"
#include "BppOAlphabetIndex2Format.h"
 
using namespace bpp;
using namespace std;
 
unique_ptr<AlphabetIndex2> BppOAlphabetIndex2Format::read(const std::string& description)
{
  if (description != "None")
  {
    string name;
    map<string, string> args;
    KeyvalTools::parseProcedure(description, name, args);
    if (verbose_)
      ApplicationTools::displayResult(message_, description);
 
    if (AlphabetTools::isCodonAlphabet(*alphabet_))
    {
      if (!gencode_)
        throw Exception("BppOAlphabetIndex2Format::read. Missing genetic code for codon alphabet.");
 
      auto alphaPtr = gencode_->getTargetAlphabet();
      BppOAlphabetIndex2Format reader2(alphaPtr, message_, false);
 
      shared_ptr<AlphabetIndex2> ai2(reader2.read(description));
      if (!AlphabetTools::isProteicAlphabet(ai2->alphabet()))
        throw Exception("BppOAlphabetIndex2Format::read. Not a Proteic Alphabet for CodonAlphabetIndex2.");
 
      return make_unique<CodonFromProteicAlphabetIndex2>(gencode_, ai2);
    }
 
    // Currently, only protein indices are supported:
    if (!AlphabetTools::isProteicAlphabet(*alphabet_))
      throw Exception("BppOAlphabetIndex2Format::read. This index is only supported with a protein alphabet.");
 
    if (name == "Blosum50")
    {
      return make_unique<BLOSUM50>();
    }
    else if (name == "Grantham")
    {
      bool sym = ApplicationTools::getBooleanParameter("symmetrical", args, true, "", true, 1);
      auto M = make_unique<GranthamAAChemicalDistance>();
      M->setSymmetric(sym);
      if (!sym)
        M->setPC1Sign(true);
      return M;
    }
    else if (name == "Miyata")
    {
      bool sym = ApplicationTools::getBooleanParameter("symmetrical", args, true, "", true, 1);
      auto M = make_unique<MiyataAAChemicalDistance>();
      M->setSymmetric(sym);
      return M;
    }
    else if (name == "Diff")
    {
      string index1Desc = ApplicationTools::getStringParameter("index1", args, "None", "", true, 1);
      bool sym = ApplicationTools::getBooleanParameter("symmetrical", args, true, "", true);
      BppOAlphabetIndex1Format index1Reader(alphabet_, "", false);
      auto index1 = index1Reader.read(index1Desc);
      if (index1)
      {
        auto M = make_unique<SimpleIndexDistance>(std::move(index1));
        M->setSymmetric(sym);
        return M;
      }
      else
      {
        throw Exception("BppOAlphabetIndex2Format::read. Diff: index1 should be provided.");
      }
    }
    else if (name == "User")
    {
      bool sym = ApplicationTools::getBooleanParameter("symmetrical", args, true, "", true, 1);
      string aax2FilePath = ApplicationTools::getAFilePath("file", args, true, true, "", false);
      ifstream aax2File(aax2FilePath.c_str(), ios::in);
      auto M = make_unique<AAIndex2Entry>(aax2File, sym);
      aax2File.close();
      return M;
    }
    else
    {
      throw Exception("Invalid index2 '" + name + "'.");
    }
  }
  else
  {
    return 0;
  }
}