AAIndex1Entry.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1

#include <Bpp/Io/FileTools.h>
#include <Bpp/Text/StringTokenizer.h>
#include <Bpp/Text/TextTools.h>

#include "AAIndex1Entry.h"

using namespace bpp;
using namespace std;

AAIndex1Entry::AAIndex1Entry(std::istream& input) :
  ProteicAlphabetIndex1(),
  property_(20)
{
  // Parse entry:
  string line;
  bool ok = false;
  do
  {
    line = FileTools::getNextLine(input);
    if (line[0] == 'I')
    {
      string line1 = FileTools::getNextLine(input);
      string line2 = FileTools::getNextLine(input);
      StringTokenizer st1(line1, " ");
      StringTokenizer st2(line2, " ");
      if (st1.numberOfRemainingTokens() != 10 || st1.numberOfRemainingTokens() != 10)
        break;
      // Amino acids are in the same order in the AAIndex1 database than in the ProteicAlphabet class:
      for (unsigned int i = 0; i < 10; i++)
      {
        property_[i] = TextTools::toDouble(st1.nextToken());
      }
      for (unsigned int i = 10; i < 20; i++)
      {
        property_[i] = TextTools::toDouble(st2.nextToken());
      }
      // Jump to next entry...
      FileTools::getNextLine(input);
      ok = true;
    }
  }
  while (!ok);
  if (!ok)
    throw IOException("AAIndex1Entry: invalid AAIndex1 entry.");
}