C++ Genome::getNumTopSegments方法代码示例

void TopSegmentSimpleIteratorTest::createCallBack(Alignment *alignment) {
    Genome *ancGenome = alignment->addRootGenome("Anc0", 0);
    size_t numChildren = 9;
    for (size_t i = 0; i < numChildren; ++i) {
        alignment->addLeafGenome("Leaf" + std::to_string(i), "Anc0", 0.1);
    }
    vector<Sequence::Info> seqVec(1);
    seqVec[0] = Sequence::Info("Sequence", 1000000, 5000, 10000);
    ancGenome->setDimensions(seqVec);

    CuAssertTrue(_testCase, ancGenome->getNumChildren() == numChildren);

    _topSegments.clear();
    for (size_t i = 0; i < ancGenome->getNumTopSegments(); ++i) {
        TopSegmentStruct topSeg;
        topSeg.setRandom();
        topSeg._length = ancGenome->getSequenceLength() / ancGenome->getNumTopSegments();
        topSeg._startPosition = i * topSeg._length;
        _topSegments.push_back(topSeg);
    }

    TopSegmentIteratorPtr tsIt = ancGenome->getTopSegmentIterator(0);
    for (size_t i = 0; not tsIt->atEnd(); tsIt->toRight(), ++i) {
        CuAssertTrue(_testCase, (size_t)tsIt->getTopSegment()->getArrayIndex() == i);
        _topSegments[i].applyTo(tsIt);
    }
}

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.........

//.........这里部分代码省略.........

  ti = child2->getTopSegmentIterator();
  ts.set(0, 12, 0, false, 0);
  ts.applyTo(ti);
  
  for (size_t i = 0; i < 6; ++i)
  {
    bi = child2->getBottomSegmentIterator(i);
    bs.set(i * 2, 2, 0);
    bs._children.clear();
    bs._children.push_back(pair<hal_size_t, bool>(i, false));
    bs.applyTo(bi);

    ti = g1->getTopSegmentIterator(i);
    ts.set(i * 2, 2, i, false);
    ts.applyTo(ti);
  }

  for (size_t i = 0; i < 6; ++i)
  {
    bi = child1->getBottomSegmentIterator(i);
    bs.set(i * 2, 2, 0);
    bs._children.clear();
    bs._children.push_back(pair<hal_size_t, bool>(i, false));
    bs.applyTo(bi);

    ti = gi1->getTopSegmentIterator(i);
    ts.set(i * 2, 2, i, false);
    ts.applyTo(ti);
  }

  for (size_t i = 0; i < 5; ++i)
  {
    const Genome* g = gs[i];
    const Genome* parent = g->getParent();
    const Genome* child = i == 4 ? NULL : g->getChild(0);
    hal_size_t segLen = g->getSequenceLength() / g->getNumTopSegments();
    hal_size_t psegLen = parent->getSequenceLength() / 
       parent->getNumTopSegments();
    hal_size_t csegLen = 0;
    if (child)
    {
      csegLen =  child->getSequenceLength() / child->getNumTopSegments();
    }
    
    for (size_t j = 0; j < g->getNumTopSegments(); ++j)
    {
      bool inv = false;
      bi = parent->getBottomSegmentIterator(j);
      bs.set(j * segLen, segLen, (j * segLen) / psegLen);
      bs._children.clear();
      bs._children.push_back(pair<hal_size_t, bool>(j, inv));
      bs.applyTo(bi);

      hal_index_t bparse = NULL_INDEX;
      if (child != NULL)
      {
        bparse = (j * segLen) / csegLen;
      }
      ti = g->getTopSegmentIterator(j);
      ts.set(j * segLen, segLen, j, inv, bparse);
      ts.applyTo(ti);      
    }
  }
  
  for (size_t i = 0; i < 5; ++i)
  {
    const Genome* g = gis[i];
    const Genome* parent = g->getParent();
    const Genome* child = i == 4 ? NULL : g->getChild(0);
    hal_size_t segLen = g->getSequenceLength() / g->getNumTopSegments();
    hal_size_t psegLen = parent->getSequenceLength() / 
       parent->getNumTopSegments();
    hal_size_t csegLen = 0;
    if (child)
    {
      csegLen =  child->getSequenceLength() / child->getNumTopSegments();
    }
    
    for (size_t j = 0; j < g->getNumTopSegments(); ++j)
    {
      bool inv = rand() % 4 == 0;
      bi = parent->getBottomSegmentIterator(j);
      bs.set(j * segLen, segLen, (j * segLen) / psegLen);
      bs._children.clear();
      bs._children.push_back(pair<hal_size_t, bool>(j, inv));
      bs.applyTo(bi);

      hal_index_t bparse = NULL_INDEX;
      if (child != NULL)
      {
        bparse = (j * segLen) / csegLen;
      }
      ti = g->getTopSegmentIterator(j);
      ts.set(j * segLen, segLen, j, inv, bparse);
      ts.applyTo(ti);      
    }
  }

}