BppOAlphabetIndex1Format.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/AAChargeIndex.h"
#include "../AlphabetIndex/AAChenGuHuangHydrophobicityIndex.h"
#include "../AlphabetIndex/AAChouFasmanAHelixIndex.h"
#include "../AlphabetIndex/AAChouFasmanBSheetIndex.h"
#include "../AlphabetIndex/AAChouFasmanTurnIndex.h"
#include "../AlphabetIndex/AAIndex1Entry.h"
#include "../AlphabetIndex/AAMassIndex.h"
#include "../AlphabetIndex/AASEA1030Index.h"
#include "../AlphabetIndex/AASEAInf10Index.h"
#include "../AlphabetIndex/AASEASup30Index.h"
#include "../AlphabetIndex/AASurfaceIndex.h"
#include "../AlphabetIndex/AAVolumeIndex.h"
#include "../AlphabetIndex/CodonFromProteicAlphabetIndex1.h"
#include "../AlphabetIndex/GranthamAAPolarityIndex.h"
#include "../AlphabetIndex/GranthamAAVolumeIndex.h"
#include "../AlphabetIndex/KD_AAHydropathyIndex.h"
#include "../AlphabetIndex/KleinAANetChargeIndex.h"
#include "BppOAlphabetIndex1Format.h"
 
using namespace bpp;
using namespace std;
 
unique_ptr<AlphabetIndex1> BppOAlphabetIndex1Format::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();
      BppOAlphabetIndex1Format reader1(alphaPtr, message_, false);
 
      shared_ptr<AlphabetIndex1> ai2(reader1.read(description));
      if (!AlphabetTools::isProteicAlphabet(ai2->alphabet()))
        throw Exception("BppOAlphabetIndex2Format::read. Not a Proteic Alphabet for CodonAlphabetIndex1.");
 
      return make_unique<CodonFromProteicAlphabetIndex1>(gencode_, ai2);
    }
 
    // Currently, only protein indices are supported:
    if (!AlphabetTools::isProteicAlphabet(*alphabet_))
      throw Exception("BppOAlphabetIndex1Format::read. This index is only supported with a protein alphabet.");
    if (name == "GranthamPolarity")
    {
      return make_unique<GranthamAAPolarityIndex>();
    }
    else if (name == "GranthamVolume")
    {
      return make_unique<GranthamAAVolumeIndex>();
    }
    else if (name == "KleinCharge")
    {
      return make_unique<KleinAANetChargeIndex>();
    }
    else if (name == "KDHydropathy")
    {
      return make_unique<KD_AAHydropathyIndex>();
    }
    else if (name == "ChouFasmanAHelix")
    {
      return make_unique<AAChouFasmanAHelixIndex>();
    }
    else if (name == "ChouFasmanBSheet")
    {
      return make_unique<AAChouFasmanBSheetIndex>();
    }
    else if (name == "ChouFasmanTurn")
    {
      return make_unique<AAChouFasmanTurnIndex>();
    }
    else if (name == "ChenGuHuangHydrophobicity")
    {
      return make_unique<AAChenGuHuangHydrophobicityIndex>();
    }
    else if (name == "Surface")
    {
      return make_unique<AASurfaceIndex>();
    }
    else if (name == "Mass")
    {
      return make_unique<AAMassIndex>();
    }
    else if (name == "Volume")
    {
      return make_unique<AAVolumeIndex>();
    }
    else if (name == "Charge")
    {
      return make_unique<AAChargeIndex>();
    }
    else if (name == "SEAMedium")
    {
      return make_unique<AASEA1030Index>();
    }
    else if (name == "SEAHigh")
    {
      return make_unique<AASEASup30Index>();
    }
    else if (name == "SEALow")
    {
      return make_unique<AASEAInf10Index>();
    }
    else if (name == "User")
    {
      string aax1FilePath = ApplicationTools::getAFilePath("file", args, true, true, "", false);
      ifstream aax1File(aax1FilePath.c_str(), ios::in);
      auto I = make_unique<AAIndex1Entry>(aax1File);
      aax1File.close();
      return I;
    }
    else
    {
      throw Exception("Invalid index1 '" + name + "'.");
    }
  }
  else
  {
    return nullptr;
  }
}