C++ Genome::getNumBottomSegments方法代码示例

void GappedSegmentSimpleIteratorTest2::createCallBack(AlignmentPtr alignment)
{
  addIdenticalParentChild(alignment, 2, 100, 5);
  Genome* parent = alignment->openGenome(alignment->getRootName());
  Genome* child = parent->getChild(0);
  TopSegmentIteratorPtr ti = child->getTopSegmentIterator();
  BottomSegmentIteratorPtr bi = parent->getBottomSegmentIterator();
  hal_index_t i = 0;
  bool reversed = true;
  while (ti != child->getTopSegmentEndIterator())
  {
    if (i % 5 == 0)
    {
      reversed = !reversed;
      if (reversed && i < (hal_index_t)(parent->getNumBottomSegments() - 1))
      {
        makeInversion(ti, 5);
      }
    }

    ti->toRight();
    bi->toRight();
    ++i;
  }
}

void LodExtract::writeHomologies(const Genome* inParent,
                                 const vector<const Genome*>& inChildren)
{
  vector<const Genome*> inGenomes = inChildren;
  inGenomes.push_back(inParent);
  Genome* outParent = _outAlignment->openGenome(inParent->getName());
  assert(outParent != NULL && outParent->getNumBottomSegments() > 0);
  assert(inChildren.size() > 0);
  Genome* outChild = _outAlignment->openGenome(inChildren[0]->getName());
  BottomSegmentIteratorPtr bottom = outParent->getBottomSegmentIterator();
  TopSegmentIteratorPtr top = outChild->getTopSegmentIterator();

  // FOR EVERY BLOCK
  for (hal_size_t blockIdx = 0; blockIdx < _graph.getNumBlocks(); ++blockIdx)
  {
    SegmentMap segMap;
    const LodBlock* block = _graph.getBlock(blockIdx);

    for (hal_size_t segIdx = 0; segIdx < block->getNumSegments(); ++segIdx)
    {
      const LodSegment* segment = block->getSegment(segIdx);
      const Genome* genome = segment->getSequence()->getGenome();

      // ADD TO MAP
      pair<SegmentMap::iterator, bool> res = segMap.insert(
        pair<const Genome*, SegmentSet*>(genome, NULL));
      if (res.second == true)
      {
        assert(res.first->second == NULL);
        res.first->second = new SegmentSet();
      }
      res.first->second->insert(segment);    
    }      
    updateBlockEdges(inParent, segMap, block, bottom, top);
    
    // free the temporary sets! 
    for (SegmentMap::iterator mapIt = segMap.begin(); mapIt != segMap.end();
         ++mapIt)
    {
      delete mapIt->second;
    }
  }
}

void GenomeCopyTest::createCallBack(Alignment *alignment) {
    hal_size_t alignmentSize = alignment->getNumGenomes();
    CuAssertTrue(_testCase, alignmentSize == 0);

    // Hacky: Need a different alignment to test copying the bottom
    // segments correctly.  (the names of a node's children are used
    // when copying bottom segments, and two genomes can't have the same
    // name in the same alignment)
    _path = getTempFile();
    _secondAlignment =
        AlignmentPtr(getTestAlignmentInstances(alignment->getStorageFormat(), _path, WRITE_ACCESS | CREATE_ACCESS));

    Genome *ancGenome = alignment->addRootGenome("AncGenome", 0);
    Genome *leafGenome = alignment->addLeafGenome("LeafGenome1", "AncGenome", 0);
    // This genome will test copyDimensions, copyTopSegments,
    // copyBottomSegments, copySequence, copyMetadata
    Genome *copyRootGenome = _secondAlignment->addRootGenome("copyRootGenome", 0);
    Genome *copyLeafGenome = _secondAlignment->addLeafGenome("LeafGenome1", "copyRootGenome", 0);

    MetaData *ancMeta = ancGenome->getMetaData();
    ancMeta->set("Young", "Jeezy");

    vector<Sequence::Info> seqVec(1);
    seqVec[0] = Sequence::Info("Sequence", 1000000, 0, 700000);
    ancGenome->setDimensions(seqVec);
    seqVec[0] = Sequence::Info("Sequence", 1000000, 5000, 0);
    leafGenome->setDimensions(seqVec);
    string ancSeq = "CAT";
    hal_index_t n = ancGenome->getSequenceLength();
    DnaIteratorPtr dnaIt = ancGenome->getDnaIterator();
    for (; dnaIt->getArrayIndex() < n; dnaIt->toRight()) {
        size_t i = dnaIt->getArrayIndex() % ancSeq.size();
        dnaIt->setBase(ancSeq[i]);
    }
    dnaIt->flush();

    n = leafGenome->getSequenceLength();
    dnaIt = leafGenome->getDnaIterator();
    for (; dnaIt->getArrayIndex() < n; dnaIt->toRight()) {
        size_t i = dnaIt->getArrayIndex() % ancSeq.size();
        dnaIt->setBase(ancSeq[i]);
    }
    dnaIt->flush();

    TopSegmentIteratorPtr topIt = leafGenome->getTopSegmentIterator();
    n = leafGenome->getNumTopSegments();
    for (; topIt->getArrayIndex() < n; topIt->toRight()) {
        topIt->setCoordinates(topIt->getArrayIndex(), 1);
        topIt->tseg()->setParentIndex(3);
        topIt->tseg()->setParentReversed(true);
        topIt->tseg()->setBottomParseIndex(5);
        if (topIt->getArrayIndex() != 6) {
            topIt->tseg()->setNextParalogyIndex(6);
        } else {
            topIt->tseg()->setNextParalogyIndex(7);
        }
    }
    BottomSegmentIteratorPtr botIt = ancGenome->getBottomSegmentIterator();
    n = ancGenome->getNumBottomSegments();
    for (; botIt->getArrayIndex() < n; botIt->toRight()) {
        botIt->setCoordinates(botIt->getArrayIndex(), 1);
        botIt->bseg()->setChildIndex(0, 3);
        botIt->bseg()->setChildReversed(0, true);
        botIt->bseg()->setTopParseIndex(5);
    }

    seqVec[0] = Sequence::Info("Sequence", 3300, 0, 1100);
    copyRootGenome->setDimensions(seqVec);
    seqVec[0] = Sequence::Info("Sequence", 3300, 2200, 0);
    copyLeafGenome->setDimensions(seqVec);
    string copySeq = "TAG";
    dnaIt = copyRootGenome->getDnaIterator();
    n = copyRootGenome->getSequenceLength();
    for (; dnaIt->getArrayIndex() < n; dnaIt->toRight()) {
        size_t i = dnaIt->getArrayIndex() % copySeq.size();
        dnaIt->setBase(copySeq[i]);
    }
    dnaIt->flush();

    dnaIt = copyLeafGenome->getDnaIterator();
    n = copyLeafGenome->getSequenceLength();
    for (; dnaIt->getArrayIndex() < n; dnaIt->toRight()) {
        size_t i = dnaIt->getArrayIndex() % copySeq.size();
        dnaIt->setBase(copySeq[i]);
    }
    dnaIt->flush();

    topIt = copyLeafGenome->getTopSegmentIterator();
    n = copyLeafGenome->getNumTopSegments();
    for (; topIt->getArrayIndex() < n; topIt->toRight()) {
        topIt->setCoordinates(7, 8);
        topIt->tseg()->setParentIndex(9);
        topIt->tseg()->setParentReversed(false);
        topIt->tseg()->setBottomParseIndex(11);
        if (topIt->getArrayIndex() != 12) {
            topIt->tseg()->setNextParalogyIndex(12);
        } else {
            topIt->tseg()->setNextParalogyIndex(7);
        }
    }
//.........这里部分代码省略.........