AAIndex2Entry.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include "../Alphabet/AlphabetTools.h"
#include "AAIndex2Entry.h"
 
using namespace bpp;
using namespace std;
 
#include <Bpp/Io/FileTools.h>
#include <Bpp/Text/TextTools.h>
#include <Bpp/Text/StringTokenizer.h>
 
AAIndex2Entry::AAIndex2Entry(std::istream& input, bool sym) :
  ProteicAlphabetIndex2(),
  property_(20, 20),
  sym_(sym)
{
  // Parse entry:
  string line;
  bool ok = false;
  bool diag = false;
  do
  {
    line = FileTools::getNextLine(input);
    if (line[0] == 'M')
    {
      for (size_t i = 0; i < 20; ++i)
      {
        line = FileTools::getNextLine(input);
        StringTokenizer st1(line, " ");
        if (i == 0 && st1.numberOfRemainingTokens() == 1)
        {
          // Lower triangle only:
          diag = true;
        }
        // Amino acids are in the same order in the AAIndex1 database than in the ProteicAlphabet class:
        if (diag)
        {
          if (st1.numberOfRemainingTokens() != i + 1)
            break;
          for (size_t j = 0; j <= i; ++j)
          {
            property_(i, j) = TextTools::toDouble(st1.nextToken());
          }
        }
        else
        {
          if (st1.numberOfRemainingTokens() != 20)
            break;
          for (size_t j = 0; j < 20; ++j)
          {
            property_(i, j) = TextTools::toDouble(st1.nextToken());
          }
        }
      }
      // Jump to next entry...
      FileTools::getNextLine(input);
      ok = true;
    }
  }
  while (!ok);
  if (!ok)
    throw IOException("AAIndex2Entry: invalid AAIndex2 entry.");
  if (!diag)
    sym_ = false;
}