C++ TopSegmentIteratorConstPtr::getReversed方法代码示例

本文整理汇总了C++中TopSegmentIteratorConstPtr::getReversed方法的典型用法代码示例。如果您正苦于以下问题：C++ TopSegmentIteratorConstPtr::getReversed方法的具体用法？C++ TopSegmentIteratorConstPtr::getReversed怎么用？C++ TopSegmentIteratorConstPtr::getReversed使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类TopSegmentIteratorConstPtr的用法示例。

在下文中一共展示了TopSegmentIteratorConstPtr::getReversed方法的6个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的C++代码示例。

示例1: testTopSegment

void MappedSegmentMapAcrossTest::testTopSegment(AlignmentConstPtr alignment,
                                                TopSegmentIteratorConstPtr top)
{
  const Genome* parent = top->getGenome()->getParent();
  const Genome* other = top->getGenome()->getName() == "child1" ? 
     alignment->openGenome("child2") : alignment->openGenome("child1");
  set<MappedSegmentConstPtr> results;
  top->getMappedSegments(results, other, NULL, false);
  CuAssertTrue(_testCase, results.size() == 1);
  MappedSegmentConstPtr mseg = *results.begin();
  CuAssertTrue(_testCase, mseg->getSource()->getGenome() == top->getGenome());
  CuAssertTrue(_testCase, mseg->getSource()->getStartPosition() == 
               top->getStartPosition());
  CuAssertTrue(_testCase, 
               mseg->getSource()->getLength() == top->getLength());
  CuAssertTrue(_testCase, 
               mseg->getSource()->getReversed() == top->getReversed());
  BottomSegmentIteratorConstPtr bottom = parent->getBottomSegmentIterator();
  bottom->toParent(top);
  TopSegmentIteratorConstPtr sister = other->getTopSegmentIterator();
  sister->toChildG(bottom, other);
  CuAssertTrue(_testCase, mseg->getGenome() == sister->getGenome());
  CuAssertTrue(_testCase, 
               mseg->getStartPosition() == sister->getStartPosition());
  CuAssertTrue(_testCase, 
               mseg->getLength() == sister->getLength());
  CuAssertTrue(_testCase, 
               mseg->getReversed() == sister->getReversed());
}

开发者ID:dayin1989，项目名称:hal，代码行数:29，代码来源:halMappedSegmentTest.cpp

示例2: testBottomSegment

void MappedSegmentMapDownTest::testBottomSegment(
  AlignmentConstPtr alignment,
  BottomSegmentIteratorConstPtr bottom,
  hal_size_t childIndex)
{
  const Genome* child = bottom->getGenome()->getChild(childIndex);
  set<MappedSegmentConstPtr> results;
  bottom->getMappedSegments(results, child, NULL, false);
  CuAssertTrue(_testCase, results.size() == 1);
  MappedSegmentConstPtr mseg = *results.begin();
  CuAssertTrue(_testCase, mseg->getSource()->getGenome() == 
               bottom->getGenome());
  CuAssertTrue(_testCase, mseg->getSource()->getStartPosition() == 
               bottom->getStartPosition());
  CuAssertTrue(_testCase, 
               mseg->getSource()->getLength() == bottom->getLength());
  CuAssertTrue(_testCase, 
               mseg->getSource()->getReversed() == bottom->getReversed());
  TopSegmentIteratorConstPtr top = child->getTopSegmentIterator();
  top->toChild(bottom, childIndex);
  CuAssertTrue(_testCase, mseg->getGenome() == top->getGenome());
  CuAssertTrue(_testCase, 
               mseg->getStartPosition() == top->getStartPosition());
  CuAssertTrue(_testCase, 
               mseg->getLength() == top->getLength());
  CuAssertTrue(_testCase, 
               mseg->getReversed() == top->getReversed());
}

开发者ID:dayin1989，项目名称:hal，代码行数:28，代码来源:halMappedSegmentTest.cpp

示例3: identifyInsertionFromLeftBreakpoint

bool DefaultRearrangement::identifyInsertionFromLeftBreakpoint(
    TopSegmentIteratorConstPtr topSegment)
{
    assert(topSegment->getReversed() == false);
    if (scanInsertionCycle(topSegment) == true &&
            _cur->hasParent() == false)
    {
        _id = Insertion;
        return true;
    }
    _id = Invalid;
    return false;
}

开发者ID:ifiddes，项目名称:hal，代码行数:13，代码来源:defaultRearrangement.cpp

示例4: toRightNextUngapped

void DefaultGappedBottomSegmentIterator::toRightNextUngapped(
  TopSegmentIteratorConstPtr ts) const
{
  while (ts->hasParent() == false &&
         ts->getLength() <= _gapThreshold)
  {
    if ((!ts->getReversed() && ts->getTopSegment()->isLast()) ||
         (ts->getReversed() && ts->getTopSegment()->isFirst()))
    {
      break;
    }
    ts->toRight();
  }
}

开发者ID:BioinformaticsArchive，项目名称:hal，代码行数:14，代码来源:defaultGappedBottomSegmentIterator.cpp

示例5: checkCallBack

void TopSegmentSimpleIteratorTest::checkCallBack(AlignmentConstPtr alignment)
{
  const Genome* ancGenome = alignment->openGenome("Anc0");
  CuAssertTrue(_testCase, 
               ancGenome->getNumTopSegments() == _topSegments.size());
  TopSegmentIteratorConstPtr tsIt = ancGenome->getTopSegmentIterator(0);
  for (size_t i = 0; i < ancGenome->getNumTopSegments(); ++i)
  {
    CuAssertTrue(_testCase, 
                 (size_t)tsIt->getTopSegment()->getArrayIndex() == i);
    _topSegments[i].compareTo(tsIt, _testCase);
    tsIt->toRight();
  }
  tsIt = ancGenome->getTopSegmentIterator(
    ancGenome->getNumTopSegments() - 1);
  for (hal_index_t i = ancGenome->getNumTopSegments() - 1; i >= 0; --i)
  {
    CuAssertTrue(_testCase, tsIt->getTopSegment()->getArrayIndex() == i);
    _topSegments[i].compareTo(tsIt, _testCase);
    tsIt->toLeft();
  }

  tsIt = ancGenome->getTopSegmentIterator(0); 
  tsIt->slice(0, tsIt->getLength() - 1);
  for (hal_index_t i = 0; i < (hal_index_t)ancGenome->getSequenceLength(); ++i)
  {
    CuAssertTrue(_testCase, tsIt->getLength() == 1);
    CuAssertTrue(_testCase, tsIt->getStartPosition() == i);
    tsIt->toRight(tsIt->getStartPosition() + 1);
  }
  tsIt = ancGenome->getTopSegmentIterator(
    ancGenome->getNumTopSegments() - 1);
  tsIt->slice(tsIt->getLength() - 1, 0);
  for (hal_index_t i = ancGenome->getSequenceLength() - 1; i >= 0; --i)
  {
    CuAssertTrue(_testCase, tsIt->getLength() == 1);
    CuAssertTrue(_testCase, tsIt->getStartPosition() == i);
    tsIt->toLeft(tsIt->getStartPosition() - 1);
  }

  tsIt = ancGenome->getTopSegmentIterator(0); 
  tsIt->toReverse();
  CuAssertTrue(_testCase, tsIt->getReversed() == true);
  tsIt->slice(tsIt->getLength() - 1, 0);
  for (hal_index_t i = 0; i < (hal_index_t)ancGenome->getSequenceLength(); ++i)
  {
    CuAssertTrue(_testCase, tsIt->getLength() == 1);
    CuAssertTrue(_testCase, tsIt->getStartPosition() == i);
    tsIt->toLeft(tsIt->getStartPosition() + 1);
  }
  tsIt = ancGenome->getTopSegmentIterator(
    ancGenome->getNumTopSegments() - 1);
  tsIt->toReverse();
  tsIt->slice(0, tsIt->getLength() - 1);
  for (hal_index_t i = ancGenome->getSequenceLength() - 1; i >= 0; --i)
  {
    CuAssertTrue(_testCase, tsIt->getLength() == 1);
    CuAssertTrue(_testCase, tsIt->getStartPosition() == i);
    tsIt->toRight(tsIt->getStartPosition() - 1);
  }
}

开发者ID:BioinformaticsArchive，项目名称:hal，代码行数:61，代码来源:halTopSegmentTest.cpp

示例6: checkCallBack

void MappedSegmentMapExtraParalogsTest::checkCallBack(AlignmentConstPtr alignment)
{
  validateAlignment(alignment);

  const Genome *grandChild1 = alignment->openGenome("grandChild1");
  const Genome *grandChild2 = alignment->openGenome("grandChild2");
  const Genome *root = alignment->openGenome("root");

  TopSegmentIteratorConstPtr top = grandChild2->getTopSegmentIterator();
  set<MappedSegmentConstPtr> results;

  // First, check that by default we will only get the homologies in
  // or before the MRCA. (in this case, just seg 0 of grandChild1).
  top->getMappedSegments(results, grandChild1, NULL, true);
  CuAssertTrue(_testCase, results.size() == 1);
  MappedSegmentConstPtr mseg = *results.begin();
  // Source information should be preserved
  CuAssertTrue(_testCase, mseg->getSource()->getGenome() == top->getGenome());
  CuAssertTrue(_testCase, mseg->getSource()->getStartPosition() == 
               top->getStartPosition());
  CuAssertTrue(_testCase, 
               mseg->getSource()->getLength() == top->getLength());
  CuAssertTrue(_testCase, 
               mseg->getSource()->getReversed() == top->getReversed());

  // Check target information is correct
  CuAssertTrue(_testCase,
               mseg->getGenome() == grandChild1);
  CuAssertTrue(_testCase,
               mseg->getStartPosition() == 2);
  CuAssertTrue(_testCase,
               mseg->getLength() == 3);
  CuAssertTrue(_testCase,
               mseg->getReversed() == true);

  // Check that by using the grandparent as the coalescence limit we
  // will get all the paralogs.
  top->getMappedSegments(results, grandChild1, NULL, true, 0, root);
  CuAssertTrue(_testCase, results.size() == 3);
  set<MappedSegmentConstPtr>::iterator i = results.begin();
  bool found[3] = {false, false, false};
  for (; i != results.end(); ++i)
  {
      // Source information should be preserved
    CuAssertTrue(_testCase, mseg->getSource()->getGenome() == top->getGenome());
    CuAssertTrue(_testCase, mseg->getSource()->getStartPosition() == 
                 top->getStartPosition());
    CuAssertTrue(_testCase, 
                 mseg->getSource()->getLength() == top->getLength());
    CuAssertTrue(_testCase, 
                 mseg->getSource()->getReversed() == top->getReversed());
    
    // Check target information is correct
    CuAssertTrue(_testCase,
                 mseg->getGenome() == grandChild1);
    CuAssertTrue(_testCase,
                 mseg->getStartPosition() == 2
                 || mseg->getStartPosition() == 5
                 || mseg->getStartPosition() == 8);
    CuAssertTrue(_testCase,
                 mseg->getLength() == 3);
    CuAssertTrue(_testCase,
                 mseg->getReversed() == true);
    found[mseg->getArrayIndex()] = true;
  }
}

开发者ID:dayin1989，项目名称:hal，代码行数:66，代码来源:halMappedSegmentTest.cpp

注：本文中的TopSegmentIteratorConstPtr::getReversed方法示例由纯净天空整理自Github/MSDocs等开源代码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。