C++ BottomSegmentIteratorPtr::setChildReversed方法代码示例

void LodExtract::writeUnsampledSequence(const Sequence* outSequence,
                                        SegmentIteratorPtr outSegment)
{
  outSegment->setCoordinates(outSequence->getStartPosition(),
                             outSequence->getSequenceLength());
  if (outSegment->isTop())
  {
    assert(outSequence->getNumTopSegments() == 1);
    TopSegmentIteratorPtr top = outSegment.downCast<TopSegmentIteratorPtr>();
    top->setParentIndex(NULL_INDEX);
    top->setParentReversed(false);
    top->setNextParalogyIndex(NULL_INDEX);
    top->setBottomParseIndex(NULL_INDEX);
  }
  else
  {
    assert(outSequence->getNumBottomSegments() == 1);
    BottomSegmentIteratorPtr bottom = 
       outSegment.downCast<BottomSegmentIteratorPtr>();
    hal_size_t numChildren = bottom->getNumChildren();
    for (hal_size_t childNum = 0; childNum < numChildren; ++childNum)
    {
      bottom->setChildIndex(childNum, NULL_INDEX);
      bottom->setChildReversed(childNum, false);
    }
    bottom->setTopParseIndex(NULL_INDEX);
  }
}

void LodExtract::updateBlockEdges(const Genome* inParentGenome,
                                  SegmentMap& segMap,
                                  const LodBlock* block,
                                  BottomSegmentIteratorPtr bottom,
                                  TopSegmentIteratorPtr top)
{
  Genome* outParentGenome = bottom->getGenome();
  const LodSegment* rootSeg = NULL;
  SegmentSet* segSet;
  SegmentSet::iterator setIt;

  // Zap all segments in parent genome
  SegmentMap::iterator mapIt = segMap.find(inParentGenome);
  if (mapIt != segMap.end())
  {
    segSet = mapIt->second;
    assert(segSet != NULL);
    setIt = segSet->begin();
    for (; setIt != segSet->end(); ++setIt)
    {
      bottom->setArrayIndex(outParentGenome, (*setIt)->getArrayIndex());
      for (hal_size_t i = 0; i < bottom->getNumChildren(); ++i)
      {
        bottom->setChildIndex(i, NULL_INDEX);
        bottom->setTopParseIndex(NULL_INDEX);
      }
    }

    // Choose first segment as parent to all segments in the child genome
    setIt = segSet->begin();
    rootSeg = *(setIt);
    bottom->setArrayIndex(outParentGenome, (*setIt)->getArrayIndex());
  }

  // Do the child genomes
  const Genome* inGrandParentGenome = inParentGenome->getParent();
  SegmentSet::iterator nextIt;
  for (mapIt = segMap.begin(); mapIt != segMap.end(); ++mapIt)
  {
    if (mapIt->first != inParentGenome and mapIt->first != inGrandParentGenome)
    {
      Genome* outChildGenome = 
         _outAlignment->openGenome(mapIt->first->getName());
      hal_index_t childIndex = outParentGenome->getChildIndex(outChildGenome);
      assert(childIndex >= 0);
      segSet = mapIt->second;
      assert(segSet != NULL);
      for (setIt = segSet->begin(); setIt != segSet->end(); ++setIt)
      {
        top->setArrayIndex(outChildGenome, (*setIt)->getArrayIndex());
        top->setBottomParseIndex(NULL_INDEX);

        // Connect to parent
        if (rootSeg != NULL)
        {
          top->setParentIndex(bottom->getArrayIndex());
          bool reversed = (*setIt)->getFlipped() != rootSeg->getFlipped();
          top->setParentReversed(reversed);
          if (setIt == segSet->begin())
          {
            bottom->setChildIndex(childIndex, top->getArrayIndex());         
            bottom->setChildReversed(childIndex, reversed);      
          }
        }
        else
        {
          top->setParentIndex(NULL_INDEX);
        }

        // Connect to next paralogy
        SegmentSet::iterator setNext = setIt;
        ++setNext;
        if (setNext == segSet->end())
        {
          setNext = segSet->begin();
        }
        if (setNext == setIt)
        {
          top->setNextParalogyIndex(NULL_INDEX);
        }
        else
        {
          top->setNextParalogyIndex((*setNext)->getArrayIndex());
        }
      }
    }
  }
}

void Genome::copyBottomSegments(Genome *dest) const
{
  assert(getNumBottomSegments() == dest->getNumBottomSegments());
  hal_size_t inNc = getNumChildren();
  hal_size_t outNc = dest->getNumChildren();
  // The child indices aren't consistent across files--make sure each bottom
  // segment points to the correct children
  vector<string> inChildNames;
  vector<string> outChildNames;
  for (hal_size_t inChild = 0; inChild < inNc; ++inChild)
  {
    inChildNames.push_back(getChild(inChild)->getName());
  }
  for (hal_size_t outChild = 0; outChild < outNc; ++outChild)
  {
    outChildNames.push_back(dest->getChild(outChild)->getName());
  }
  map<hal_size_t, hal_size_t> inChildToOutChild;
  for (hal_size_t inChild = 0; inChild < inNc; inChild++)
  {
    hal_size_t outChild;
    for (outChild = 0; outChild < outNc; outChild++)
    {
      if (inChildNames[inChild] == outChildNames[outChild])
      {
        inChildToOutChild[inChild] = outChild;
        break;
      }
    }
    if (outChild == outNc)
    {
      inChildToOutChild[inChild] = outNc;
    }
  }

  // Go through each sequence in this genome, find the matching
  // sequence in the dest genome, then copy over the segments for each
  // sequence.
  SequenceIteratorConstPtr seqIt = getSequenceIterator();
  SequenceIteratorConstPtr seqEndIt = getSequenceEndIterator();

  for (; seqIt != seqEndIt; seqIt->toNext())
  {
    const Sequence *inSeq = seqIt->getSequence();
    const Sequence *outSeq = dest->getSequence(inSeq->getName());
    BottomSegmentIteratorPtr inBot = inSeq->getBottomSegmentIterator();
    BottomSegmentIteratorPtr outBot = outSeq->getBottomSegmentIterator();

    cout << "DEBUG: inSeq name: " << inSeq->getName() << ", outSeq name: " << outSeq->getName() << endl;

    if (inSeq->getName() != outSeq->getName()) {
      // This check is important enough that it can't be an assert.
      stringstream ss;
      ss << "When copying bottom segments: segment #" << inBot->getArrayIndex() << " of source genome is from sequence " << inBot->getSequence()->getName() << ", but segment #" << outBot->getArrayIndex() << " is from sequence " << outBot->getSequence()->getName();
      throw hal_exception(ss.str());
    }

    if (inSeq->getNumBottomSegments() != outSeq->getNumBottomSegments()) {
      stringstream ss;
      ss << "When copying bottom segments: sequence " << inSeq->getName() << " has " << inSeq->getNumBottomSegments() << " in genome " << getName() << ", while it has " << outSeq->getNumBottomSegments() << " in genome " << dest->getName();
      throw hal_exception(ss.str());      
    }

    hal_index_t inSegmentEnd = inSeq->getBottomSegmentArrayIndex() + inSeq->getNumBottomSegments();
    cout << "DEBUG: inSegmentStart: " << inSeq->getBottomSegmentArrayIndex() << " inSegmentEnd: " << inSegmentEnd << " num bottom segments: " << inSeq->getNumBottomSegments() << endl;
    for (; inBot->getArrayIndex() < inSegmentEnd; inBot->toRight(),
           outBot->toRight())
    {
      hal_index_t outStartPosition = inBot->getStartPosition() - inSeq->getStartPosition() + outSeq->getStartPosition();

      cout << "Decided on outStartPosition " << outStartPosition << " for seg index " << outBot->getArrayIndex() << " (src index " << inBot->getArrayIndex() << ")" << endl;

      if (dest->getSequenceBySite(outStartPosition) != outSeq) {
        stringstream ss;
        ss << "When copying bottom segments from " << getName() << " to " << dest->getName() << ": expected destination sequence " << outSeq->getName() << " for segment # " << inBot->getArrayIndex() << " but got " << dest->getSequenceBySite(outStartPosition)->getName();
        throw hal_exception(ss.str());
      }
      outBot->setCoordinates(outStartPosition, inBot->getLength());
      for(hal_size_t inChild = 0; inChild < inNc; inChild++) {
        hal_size_t outChild = inChildToOutChild[inChild];
        if (outChild != outNc) {
          outBot->setChildIndex(outChild, inBot->getChildIndex(inChild));
          cout << "genome " << getName() << ": Set child index " << inChild << " to " << inBot->getChildIndex(inChild) << endl;
          outBot->setChildReversed(outChild, inBot->getChildReversed(inChild));
        }
      }
      outBot->setTopParseIndex(inBot->getTopParseIndex());
    }
  }
}