C++ (Cpp) Genome::getParent Examples

Example #1

File: halReplaceGenome.cpp Project: dayin1989/hal

void copyFromTopAlignment(AlignmentConstPtr topAlignment,
                          AlignmentPtr mainAlignment, const string &genomeName)
{
  Genome *mainReplacedGenome = mainAlignment->openGenome(genomeName);
  const Genome *topReplacedGenome = topAlignment->openGenome(genomeName);
  topReplacedGenome->copyTopDimensions(mainReplacedGenome);
  topReplacedGenome->copyTopSegments(mainReplacedGenome);
  mainReplacedGenome->fixParseInfo();
  // Copy bot segments for the parent and top segments for the
  // siblings of the genome that's being replaced
  Genome *mainParent = mainReplacedGenome->getParent();
  const Genome *topParent = topReplacedGenome->getParent();
  topParent->copyBottomDimensions(mainParent);
  topParent->copyBottomSegments(mainParent);
  mainParent->fixParseInfo();
  vector<string> siblings = mainAlignment->getChildNames(mainParent->getName());
  for (size_t i = 0; i < siblings.size(); i++)
  {
    if (siblings[i] != genomeName)
    {
      Genome *mainChild = mainAlignment->openGenome(siblings[i]);
      const Genome *topChild  = topAlignment->openGenome(siblings[i]);
      topChild->copyTopDimensions(mainChild);
      topChild->copyTopSegments(mainChild);
      mainChild->fixParseInfo();
    }
  }
}