Sequence.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include <Bpp/Text/TextTools.h>
 
#include "Alphabet/AlphabetTools.h"
#include "Sequence.h" // class's header file
#include "StringSequenceTools.h"
 
using namespace bpp;
 
// From the STL:
#include <iostream>
 
using namespace std;
 
/******************************************************************************/
 
void Sequence::setContent(const std::string& sequence)
{
  // Remove blanks in sequence
  auto alphaPtr = getAlphabet();
  content_ = StringSequenceTools::codeSequence(TextTools::removeWhiteSpaces(sequence), alphaPtr);
  // Warning, an exception may be thrown here!
}
 
/******************************************************************************/
 
void Sequence::setToSizeR(size_t newSize)
{
  // Size verification
  size_t seqSize = content_.size();
  if (newSize == seqSize)
    return;
 
  if (newSize < seqSize)
  {
    content_.resize(newSize);
    return;
  }
 
  // Add gaps up to specified size
  int gap = getAlphabet()->getGapCharacterCode();
  while (content_.size() < newSize)
    content_.push_back(gap);
}
 
/******************************************************************************/
 
void Sequence::setToSizeL(size_t newSize)
{
  // Size verification
  size_t seqSize = content_.size();
  if (newSize == seqSize)
    return;
 
  if (newSize < seqSize)
  {
    // We must truncate sequence from the left.
    // This is a very unefficient method!
    content_.erase(content_.begin(), content_.begin() + static_cast<ptrdiff_t>(seqSize - newSize));
    return;
  }
 
  // Add gaps up to specified size
  int gap = getAlphabet()->getGapCharacterCode();
  content_.insert(content_.begin(), newSize - seqSize, gap);
}
 
/******************************************************************************/
 
void Sequence::append(const SequenceInterface& seq)
{
  if (seq.getAlphabet()->getAlphabetType() != getAlphabet()->getAlphabetType())
    throw AlphabetMismatchException("Sequence::append", getAlphabet(), seq.getAlphabet());
  // Check list for incorrect characters
  for (auto i : seq.getContent())
  {
    content_.push_back(i);
  }
}
 
void Sequence::append(const std::vector<int>& content)
{
  // Check list for incorrect characters
  for (auto i : content)
  {
    if (!getAlphabet()->isIntInAlphabet(i))
      throw BadIntException(i, "Sequence::append", getAlphabet());
  }
  // Sequence is valid:
  for (auto i : content)
  {
    content_.push_back(i);
  }
}
 
void Sequence::append(const std::vector<std::string>& content)
{
  // Check list for incorrect characters
  for (auto i : content)
  {
    if (!getAlphabet()->isCharInAlphabet(i))
      throw BadCharException(i, "Sequence::append", getAlphabet());
  }
 
  // BasicSequence is valid:
  for (auto i : content)
  {
    content_.push_back(getAlphabet()->charToInt(i));
  }
}
 
void Sequence::append(const std::string& content)
{
  auto alphaPtr = getAlphabet();
  append(StringSequenceTools::codeSequence(content, alphaPtr));
}
 
/******************************************************************************/