RNY.cpp

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//
// File: RNY.cpp
// Created by: Laurent Gueguen
// Created on: Tue Jul 31 2007
//

/*
   Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)

   This software is a computer program whose purpose is to provide
   classes for sequences analysis.

   This software is governed by the CeCILL license under French law and
   abiding by the rules of distribution of free software. You can use,
   modify and/ or redistribute the software under the terms of the CeCILL
   license as circulated by CEA, CNRS and INRIA at the following URL
   "http://www.cecill.info".

   As a counterpart to the access to the source code and rights to copy,
   modify and redistribute granted by the license, users are provided
   only with a limited warranty and the software's author, the holder of
   the economic rights, and the successive licensors have only limited
   liability.

   In this respect, the user's attention is drawn to the risks associated
   with loading, using, modifying and/or developing or reproducing the
   software by the user in light of its specific status of free software,
   that may mean that it is complicated to manipulate, and that also
   therefore means that it is reserved for developers and experienced
   professionals having in-depth computer knowledge. Users are therefore
   encouraged to load and test the software's suitability as regards
   their requirements in conditions enabling the security of their
   systems and/or data to be ensured and, more generally, to use and
   operate it in the same conditions as regards security.

   The fact that you are presently reading this means that you have had
   knowledge of the CeCILL license and that you accept its terms.
 */

#include "RNY.h" // class's header file

// From Utils:
#include <Bpp/Text/TextTools.h>
#include "AlphabetTools.h"

#include <iostream>
using namespace std;
using namespace bpp;

/****************************************************************************************/

RNY::RNY(const NucleicAlphabet& na) : nuclalph_(na)
{
  // Initialization:
  vector<AlphabetState*> states;
  for (int i = 0; i < 351; ++i)
  {
    states.push_back(new AlphabetState(i, TextTools::toString(i), ""));
  }

  // Alphabet content definition:

  string s1;

  if (AlphabetTools::isDNAAlphabet(&na))
    s1 = "RCT-";
  else 
    s1 = "RCU-";
  
  string s2;
 
  if (AlphabetTools::isDNAAlphabet(&na))
    s2 = "AGCT-";
  else
    s2 = "AGCU-";
  
  string s3 = "AGY-";
  string s = "   ";


  // NNN (0->35)

  for (size_t i = 0; i < 3; ++i)
  {
    for (size_t j = 0; j < 4; ++j)
    {
      for (size_t k = 0; k < 3; ++k)
      {
        size_t l = i * 12 + j * 3 + k;
        s[0] = s1[i];
        s[1] = s2[j];
        s[2] = s3[k];
        states[l] = new AlphabetState(static_cast<int>(l), s, s);
      }
    }
  }

  // NN- (50->83)

  for (size_t i = 0; i < 3; ++i)
  {
    for (size_t j = 0; j < 4; ++j)
    {
      size_t l = 50 + 12 * i + j * 3;
      s[0] = s1[i];
      s[1] = s2[j];
      s[2] = s3[3];
      states[l] = new AlphabetState(static_cast<int>(l), s, s);
    }
  }

  // N-N (100->126)

  for (size_t i = 0; i < 3; ++i)
  {
    for (size_t k = 0; k < 3; ++k)
    {
      size_t l = 100 + 12 * i + k;
      s[0] = s1[i];
      s[1] = s2[4];
      s[2] = s3[k];
      states[l] = new AlphabetState(static_cast<int>(l), s, s);
    }
  }

  // N-- (150->152)

  for (size_t i = 0; i < 3; ++i)
  {
    size_t l = 150 + 12 * i;
    s[0] = s1[i];
    s[1] = s2[4];
    s[2] = s3[3];
    states[l] = new AlphabetState(static_cast<int>(l), s, s);
  }

  // -NN (200->211)

  for (size_t j = 0; j < 4; ++j)
  {
    for (size_t k = 0; k < 3; ++k)
    {
      size_t l = 200 + j * 3 + k;
      s[0] = s1[3];
      s[1] = s2[j];
      s[2] = s3[k];
      states[l] = new AlphabetState(static_cast<int>(l), s, s);
    }
  }


  // -N- (250->253)

  for (size_t j = 0; j < 4; ++j)
  {
    size_t l = 250 + 3 * j;
    s[0] = s1[3];
    s[1] = s2[j];
    s[2] = s3[3];
    states[l] = new AlphabetState(static_cast<int>(l), s, s);
  }

  // --N (300->302)

  for (size_t k = 0; k < 3; ++k)
  {
    size_t l = 300 + k;
    s[0] = s1[3];
    s[1] = s2[4];
    s[2] = s3[k];
    states[l] = new AlphabetState(static_cast<int>(l), s, s);
  }


  // --- (350)

  s[0] = s1[3];
  s[1] = s2[4];
  s[2] = s3[3];
  states[350] = new AlphabetState(350, s, s);

  // Register all states:
  for (size_t i = 0; i < states.size(); ++i)
    registerState(states[i]);
}

/****************************************************************************************/

vector<int> RNY::getAlias(int state) const throw (BadIntException)
{
  if (!isIntInAlphabet(state))
    throw BadIntException(state, "RNY::getAlias(int): Specified base unknown.");
  vector<int> v;

  int qs = state / 50;
  int rs = state % 50;
  int i, j, k;

  switch (qs)
  {
  case 0: // NNN
    v.resize(1);
    v[0] = rs;
    break;
  case 1: // NN-
    v.resize(3);
    for (k = 0; k < 3; ++k)
    {
      v[static_cast<size_t>(k)] = k + rs;
    }
    break;
  case 2: // N-N
    v.resize(4);
    for (j = 0; j < 4; ++j)
    {
      v[static_cast<size_t>(j)] = 3 * j + rs;
    }
    break;
  case 3: // N--
    v.resize(12);
    for (j = 0; j < 4; ++j)
    {
      for (k = 0; k < 3; ++k)
      {
        v[static_cast<size_t>(3 * j + k)] = rs + 3 * j + k;
      }
    }
    break;
  case 4: // -NN
    v.resize(3);
    for (i = 0; i < 3; ++i)
    {
      v[static_cast<size_t>(i)] = 12 * i + rs;
    }
    break;
  case 5: // -N-
    v.resize(9);
    for (i = 0; i < 3; ++i)
    {
      for (k = 0; k < 3; ++k)
      {
        v[static_cast<size_t>(3 * i + k)] = rs + 12 * i + k;
      }
    }
    break;
  case 6: // --N
    v.resize(12);
    for (i = 0; i < 3; ++i)
    {
      for (j = 0; j < 4; ++j)
      {
        v[static_cast<size_t>(4 * i + j)] = rs + 12 * i + 3 * j;
      }
    }
    break;
  case 7: // ---
    v.resize(36);
    for (i = 0; i < 3; ++i)
    {
      for (j = 0; j < 4; ++j)
      {
        for (k = 0; k < 3; ++k)
        {
          v[static_cast<size_t>(12 * i + 3 * j + k)] = 12 * i + 3 * j + k;
        }
      }
    }
    break;
  }
  return v;
}

const NucleicAlphabet& RNY::getLetterAlphabet() const
{
  return nuclalph_;
}

/****************************************************************************************/

vector<string> RNY::getAlias(const string& state) const throw (BadCharException)
{
  if (!isCharInAlphabet(state))
    throw BadCharException(state, "RNY::getAlias(int): Specified base unknown.");

  vector<int> v = getAlias(charToInt(state));
  vector<string> s;
  size_t size = v.size();
  s.resize(size);

  for (size_t i = 0; i < size; i++)
  {
    s[i] = AbstractAlphabet::intToChar(v[i]);
  }
  return s;
}

/****************************************************************************************/

string RNY::getRNY(const string& pos1, const string& pos2, const string& pos3) const throw (BadCharException)
{
  string tr;

  if (pos1 == "A" || pos1 == "G")
    tr = "R";
  else
    tr = pos1;

  tr += pos2;

  if (pos3 == "T" || pos3 == "U" || pos3 == "C")
    tr += "Y";
  else
    tr += pos3;

  // teste triplet;
  charToInt(tr);
  return tr;
}

/**************************************************************************************/
int RNY::getRNY(int i, int j, int k, const Alphabet& alph) const throw (BadCharException)
{
  if (! AlphabetTools::isNucleicAlphabet(&alph))
  {
    throw AlphabetException ("RNY::getRNY : Sequence must be Nucleic",
                             &alph);
  }

  char li = alph.intToChar(i)[0];
  char lj = alph.intToChar(j)[0];
  char lk = alph.intToChar(k)[0];

  int r = 0;
  int s = 0;

  switch (li)
  {
  case 'A':
  case 'G':
    r += 0;
    break;
  case 'C':
    r += 1;
    break;
  case 'T':
  case 'U':
    r += 2;
    break;
  case '-':
  case 'N':
    s += 1;
    break;
  default:
    throw BadCharException(&li, "RNY::getRNY(int,int;int,alph): Specified base unknown.");
  }

  r *= 4;
  s *= 2;

  switch (lj)
  {
  case 'A':
    r += 0;
    break;
  case 'G':
    r += 1;
    break;
  case 'C':
    r += 2;
    break;
  case 'T':
  case 'U':
    r += 3;
    break;
  case '-':
  case 'N':
    s += 1;
    break;
  default:
    throw BadCharException(&lj, "RNY::getRNY(int,int;int,alph): Specified base unknown.");
  }

  r *= 3;
  s *= 2;

  switch (lk)
  {
  case 'A':
    r += 0;
    break;
  case 'G':
    r += 1;
    break;
  case 'C':
  case 'T':
  case 'U':
    r += 2;
    break;
  case '-':
  case 'N':
    s += 1;
    break;
  default:
    throw BadCharException(&lk, "RNY::getRNY(int,int;int,alph): Specified base unknown.");
  }

  return 50 * s + r;
}

/****************************************************************************************/
bool RNY::isGap(int state) const
{
  return state == 350;
}

bool RNY::containsGap(const string& state) const throw (BadCharException)
{
  return state.find("-") != string::npos;
}

bool RNY::isUnresolved(const string& state) const
{
  return containsGap(state);
}

bool RNY::isUnresolved(int state) const
{
  return state >= 50 && state != 350;
}

/****************************************************************************************/

int RNY::charToInt(const string& state) const throw (BadCharException)
{
  if (state.size() != 3)
    throw BadCharException(state, "RNY::charToInt", this);
  else
    return AbstractAlphabet::charToInt(state);
}


/************************************************************/

string RNY::intToChar(int state) const throw (BadIntException)
{
  int i, j, k, l;
  for (i = 0; i < 3; ++i)
  {
    for (j = 0; j < 4; ++j)
    {
      for (k = 0; k < 3; ++k)
      {
        l = i * 12 + j * 3 + k;
        if (getState(l).getNum() == state)
          return getState(l).getLetter();
      }
    }
  }

  // NN- (50->83)

  for (i = 0; i < 3; ++i)
  {
    for (j = 0; j < 4; ++j)
    {
      l = 50 + 12 * i + j * 3;
      if (getState(l).getNum() == state)
        return getState(l).getLetter();
    }
  }

  // N-N (100->126)

  for (i = 0; i < 3; ++i)
  {
    for (k = 0; k < 3; ++k)
    {
      l = 100 + 12 * i + k;
      if (getState(l).getNum() == state)
        return getState(l).getLetter();
    }
  }

  // N-- (150->152)

  for (i = 0; i < 3; ++i)
  {
    l = 150 + 12 * i;
    if (getState(l).getNum() == state)
      return getState(l).getLetter();
  }

  // -NN (200->211)

  for (j = 0; j < 4; ++j)
  {
    for (k = 0; k < 3; ++k)
    {
      l = 200 + j * 3 + k;
      if (getState(l).getNum() == state)
        return getState(l).getLetter();
    }
  }


  // -N- (250->253)

  for (j = 0; j < 4; ++j)
  {
    l = 250 + 3 * j;
    if (getState(l).getNum() == state)
      return getState(l).getLetter();
  }

  // --N (300->302)

  for (k = 0; k < 3; ++k)
  {
    l = 300 + k;
    if (getState(l).getNum() == state)
      return getState(l).getLetter();
  }


  // --- (350)

  l = 350;
  if (getState(l).getNum() == state)
    return getState(l).getLetter();

  throw BadIntException(state, "RNY::intToChar: Specified base unknown", this);
  return "XXX";
}