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C++ TopSegmentIteratorConstPtr类代码示例

本文整理汇总了C++中TopSegmentIteratorConstPtr类的典型用法代码示例。如果您正苦于以下问题：C++ TopSegmentIteratorConstPtr类的具体用法？C++ TopSegmentIteratorConstPtr怎么用？C++ TopSegmentIteratorConstPtr使用的例子？那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。


在下文中一共展示了TopSegmentIteratorConstPtr类的15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: resetStatus

void DefaultRearrangement::resetStatus(TopSegmentIteratorConstPtr topSegment)
{
    _id = Invalid;
    assert(topSegment.get());
    _genome = topSegment->getTopSegment()->getGenome();
    _parent = _genome->getParent();
    assert(_parent != NULL);

    _cur->setLeft(topSegment);
    _next->copy(_cur);
    _left->copy(_cur);
    _right->copy(_left);
    assert(_cur->getGapThreshold() == _gapThreshold);
    assert(_next->getGapThreshold() == _gapThreshold);
    assert(_left->getGapThreshold() == _gapThreshold);
    assert(_right->getGapThreshold() == _gapThreshold);
    assert(_leftParent->getGapThreshold() == _gapThreshold);
    assert(_rightParent->getGapThreshold() == _gapThreshold);
    assert(_curParent->getGapThreshold() == _gapThreshold);
    assert(_cur->getAtomic() == _atomic);
    assert(_next->getAtomic() == _atomic);
    assert(_left->getAtomic() == _atomic);
    assert(_right->getAtomic() == _atomic);
    assert(_leftParent->getAtomic() == _atomic);
    assert(_rightParent->getAtomic() == _atomic);
    assert(_curParent->getAtomic() == _atomic);
}
开发者ID:ifiddes，项目名称:hal，代码行数:27，代码来源:defaultRearrangement.cpp

示例2: validateAlignment

void MappedSegmentMapUpTest::checkCallBack(AlignmentConstPtr alignment)
{
  validateAlignment(alignment);
  const Genome* child1 = alignment->openGenome("child1");
  const Genome* child2 = alignment->openGenome("child2");
  TopSegmentIteratorConstPtr top = child2->getTopSegmentIterator();
  testTopSegment(alignment, top, "parent");
  top->slice(1,2);
  testTopSegment(alignment, top, "parent");
  top->toReverse();
  testTopSegment(alignment, top, "parent");
  top = child1->getTopSegmentIterator();
  testTopSegment(alignment, top, "parent");
  top->slice(1,2);
  testTopSegment(alignment, top, "parent");
  top->toReverse();
  testTopSegment(alignment, top, "parent");
  
  const Genome* g1 = alignment->openGenome("g1");
  for (hal_size_t i = 0; i < g1->getNumTopSegments(); ++i)
  {
    top = g1->getTopSegmentIterator(i);
    testTopSegment(alignment, top, "parent");
    top->slice(1,0);
    testTopSegment(alignment, top, "parent");
    top->toReverse();
    testTopSegment(alignment, top, "parent");
    top->slice(0,1);
    testTopSegment(alignment, top, "parent");
    top->toReverse();
    testTopSegment(alignment, top, "parent");
  }
}
开发者ID:dayin1989，项目名称:hal，代码行数:33，代码来源:halMappedSegmentTest.cpp

示例3: assert

void SummarizeMutations::subsAndGapInserts(
  GappedTopSegmentIteratorConstPtr gappedTop, MutationsStats& stats)
{
  assert(gappedTop->getReversed() == false);
  hal_size_t numGaps = gappedTop->getNumGaps();
  if (numGaps > 0)
  {
    stats._gapInsertionLength.add(gappedTop->getNumGapBases(), numGaps);
  }

  string parent, child;
  TopSegmentIteratorConstPtr l = gappedTop->getLeft();
  TopSegmentIteratorConstPtr r = gappedTop->getRight();
  BottomSegmentIteratorConstPtr p = 
     l->getTopSegment()->getGenome()->getParent()->getBottomSegmentIterator();

  for (TopSegmentIteratorConstPtr i = l->copy(); 
       i->getTopSegment()->getArrayIndex() <= 
          r->getTopSegment()->getArrayIndex();
       i->toRight())
  {
    if (i->hasParent())
    {
      p->toParent(i);
      i->getString(child);
      p->getString(parent);
      assert(child.length() == parent.length());
      for (size_t j = 0; j < child.length(); ++j)
      {
        if (isTransition(child[j], parent[j]))
        {
          ++stats._transitions;
          ++stats._subs;
        }
        else if (isTransversion(child[j], parent[j]))
        {
          ++stats._transversions;
          ++stats._subs;
        }
        else if (isSubstitution(child[j], parent[j]))
        {
          ++stats._subs;
        }
        else if (!isMissingData(child[j]) && !isMissingData(parent[j]))
        {
          ++stats._matches;
        }
      }
    }
  }
}
开发者ID:BioinformaticsArchive，项目名称:hal，代码行数:51，代码来源:halSummarizeMutations.cpp

示例4: scanTranslocationCycle

// If true, _leftParent will store the swapped segment (and _cur will store)
// the other half
// NEED TO REVISE WITH STRONGER CRITERIA -- right now any operation
// next to an endpoint can get confused with a translocation.
bool DefaultRearrangement::scanTranslocationCycle(
    TopSegmentIteratorConstPtr topSegment)
{
    assert(topSegment.get());
    resetStatus(topSegment);
    bool first = _cur->isFirst();
    bool last = _cur->isLast();
    if (_cur->hasParent() == false || (!first && !last))
    {
        return false;
    }

    _leftParent->toParent(_cur);
    bool pFirst = _leftParent->isFirst();
    //bool pLast = _leftParent->isLast();
    _rightParent->copy(_leftParent);

    first ? _right->toRight() : _right->toLeft();
    pFirst ? _rightParent->toRight() : _rightParent->toLeft();

    if (_right->hasParent() == false)
    {
        return true;
    }
    else
    {
        _curParent->toParent(_right);
        return _curParent->equals(_rightParent);
    }
    return false;
}
开发者ID:ifiddes，项目名称:hal，代码行数:35，代码来源:defaultRearrangement.cpp

示例5: checkGenome

void TopSegmentIteratorToSiteTest::checkGenome(const Genome* genome)
{
  TopSegmentIteratorConstPtr ti = genome->getTopSegmentIterator();
  for (hal_index_t pos = 0; 
       pos < (hal_index_t)genome->getSequenceLength(); ++pos)
  {
    ti->toSite(pos);
    CuAssertTrue(_testCase, ti->getStartPosition() == pos);
    CuAssertTrue(_testCase, ti->getLength() == 1);
    ti->toSite(pos, false);
    CuAssertTrue(_testCase, pos >= ti->getStartPosition() && 
                 pos < ti->getStartPosition() + (hal_index_t)ti->getLength());
    CuAssertTrue(_testCase, 
                 ti->getLength() == ti->getTopSegment()->getLength());
  }
}
开发者ID:BioinformaticsArchive，项目名称:hal，代码行数:16，代码来源:halTopSegmentTest.cpp

示例6: scanDuplicationCycle

// leaves duplication on _cur and _right
bool DefaultRearrangement::scanDuplicationCycle(
    TopSegmentIteratorConstPtr topSegment)
{
    assert(topSegment.get());
    resetStatus(topSegment);
    return _cur->hasNextParalogy() == true &&
           _cur->isCanonicalParalog() == false;
}
开发者ID:ifiddes，项目名称:hal，代码行数:9，代码来源:defaultRearrangement.cpp

示例7: testTopSegment

void MappedSegmentParseTest::testTopSegment(AlignmentConstPtr alignment,
                                            TopSegmentIteratorConstPtr top)
{
  const Genome* parent = alignment->openGenome("parent");
  set<MappedSegmentConstPtr> results;
  top->getMappedSegments(results, parent, NULL, false);

  vector<bool> covered(top->getLength(), false);
  
  CuAssertTrue(_testCase, results.size() >= 1);

  set<MappedSegmentConstPtr>::iterator i = results.begin();
  for (; i != results.end(); ++i)
  {
    MappedSegmentConstPtr mseg = *i;
    CuAssertTrue(_testCase, mseg->getSource()->getGenome() == top->getGenome());
    CuAssertTrue(_testCase, mseg->getGenome() == parent);
    for (hal_index_t j = mseg->getStartPosition(); j <= mseg->getEndPosition(); 
         ++j)
    {
      CuAssertTrue(_testCase, covered[j] == false);
      covered[j] = true;
    }
    CuAssertTrue(_testCase, mseg->getStartPosition() == 
                 mseg->getSource()->getStartPosition());
    CuAssertTrue(_testCase, mseg->getEndPosition() == 
                 mseg->getSource()->getEndPosition());

    set<MappedSegmentConstPtr> tResults;
    mseg->getMappedSegments(tResults, top->getGenome(), NULL, false);
    CuAssertTrue(_testCase, tResults.size() == 1);
    MappedSegmentConstPtr tmseg = *tResults.begin();
    CuAssertTrue(_testCase, tmseg->getGenome() == top->getGenome());
    CuAssertTrue(_testCase, tmseg->getSource()->getGenome() == 
                 mseg->getGenome());
    CuAssertTrue(_testCase, tmseg->getStartPosition() == 
                 mseg->getStartPosition());
    CuAssertTrue(_testCase, tmseg->getEndPosition() == 
                 mseg->getEndPosition());
    CuAssertTrue(_testCase, tmseg->getSource()->getStartPosition() == 
                 mseg->getStartPosition());
    CuAssertTrue(_testCase, tmseg->getSource()->getEndPosition() == 
                 mseg->getEndPosition());
  }
}
开发者ID:dayin1989，项目名称:hal，代码行数:45，代码来源:halMappedSegmentTest.cpp

示例8: CuAssertTrue

void MappedSegmentMapUpTest::testTopSegment(AlignmentConstPtr alignment,
                                            TopSegmentIteratorConstPtr top,
                                            const string& ancName)
{
  const Genome* parent = alignment->openGenome(ancName);
  set<MappedSegmentConstPtr> results;
  top->getMappedSegments(results, parent, 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);
  // extra hop for when top is in grand child
  if (bottom->getGenome() != parent)
  {
    TopSegmentIteratorConstPtr temp = 
       bottom->getGenome()->getTopSegmentIterator();
    temp->toParseUp(bottom);
    bottom->toParent(temp);
  }
  CuAssertTrue(_testCase, mseg->getGenome() == bottom->getGenome());
  CuAssertTrue(_testCase, 
               mseg->getStartPosition() == bottom->getStartPosition());
  CuAssertTrue(_testCase, 
               mseg->getLength() == bottom->getLength());
  CuAssertTrue(_testCase, 
               mseg->getReversed() == bottom->getReversed());
}
开发者ID:dayin1989，项目名称:hal，代码行数:34，代码来源:halMappedSegmentTest.cpp

示例9: compareTo

void TopSegmentStruct::compareTo(TopSegmentIteratorConstPtr it, 
                                 CuTest* testCase) const
{
  const TopSegment* seg = it->getTopSegment();
  CuAssertTrue(testCase, _length == seg->getLength());
  CuAssertTrue(testCase, _startPosition == seg->getStartPosition());
  CuAssertTrue(testCase, _nextParalogyIndex == seg->getNextParalogyIndex());
  CuAssertTrue(testCase, _parentIndex == seg->getParentIndex());
  CuAssertTrue(testCase, _bottomParseIndex == seg->getBottomParseIndex());
}
开发者ID:BioinformaticsArchive，项目名称:hal，代码行数:10，代码来源:halTopSegmentTest.cpp

示例10: 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11: checkCallBack

void TopSegmentSequenceTest::checkCallBack(AlignmentConstPtr alignment)
{
  const Genome* ancGenome = alignment->openGenome("Anc0");
  TopSegmentIteratorConstPtr tsIt = ancGenome->getTopSegmentIterator(100);
  CuAssertTrue(_testCase, tsIt->getTopSegment()->getStartPosition() == 500);
  CuAssertTrue(_testCase, tsIt->getTopSegment()->getLength() == 9);
  string seq;
  tsIt->getString(seq);
  CuAssertTrue(_testCase, seq == "CACACATTC");
  tsIt->toReverse();
  tsIt->getString(seq);
  CuAssertTrue(_testCase, seq == "GAATGTGTG");
}
开发者ID:BioinformaticsArchive，项目名称:hal，代码行数:13，代码来源:halTopSegmentTest.cpp

示例12: 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13: scanInversionCycle

// Segment is an inverted descendant of another Segment but
// otherwise no rearrangement.
bool DefaultRearrangement::scanInversionCycle(
    TopSegmentIteratorConstPtr topSegment)
{
    assert(topSegment.get());
    resetStatus(topSegment);
    bool first = _cur->isFirst();
    bool last = _cur->isLast();

    if (_cur->hasParent() == false)
    {
        return false;
    }
    _curParent->toParent(_cur);
    if (first == false)
    {
        _left->toLeft();
        if (_left->hasParent() == false)
        {
            return false;
        }
        _leftParent->toParent(_left);
        if (_leftParent->adjacentTo(_curParent) == false)
        {
            return false;
        }
    }
    if (last == false)
    {
        _right->toRight();
        if (_right->hasParent() == false)
        {
            return false;
        }
        _rightParent->toParent(_right);
        if (_rightParent->adjacentTo(_curParent) == false)
        {
            return false;
        }
    }
    return _cur->getParentReversed();
}
开发者ID:ifiddes，项目名称:hal，代码行数:43，代码来源:defaultRearrangement.cpp

示例14: scanNothingCycle

// Segment corresponds to no rearrangemnt.  This will happen when
// there is a rearrangement in the homolgous segment in its sibling
// genome.  In general, we can expect about half of segments to correspond
// to such cases.
bool DefaultRearrangement::scanNothingCycle(
    TopSegmentIteratorConstPtr topSegment)
{
    assert(topSegment.get());
    resetStatus(topSegment);
    bool first = _cur->isFirst();
    bool last = _cur->isLast();

    if (_cur->hasParent() == false)
    {
        return false;
    }
    _curParent->toParent(_cur);
    if (first == false)
    {
        _left->toLeft();
        if (_left->hasParent() == false)
        {
            return false;
        }
        _leftParent->toParent(_left);
        if (_leftParent->adjacentTo(_curParent) == false)
        {
            return false;
        }
        if (_left->getParentReversed() == true)
        {
            if (_cur->getParentReversed() == false ||
                    _leftParent->rightOf(_curParent->getStartPosition()) == false)
            {
                return false;
            }
        }
        else
        {
            if (_cur->getParentReversed() == true ||
                    _leftParent->leftOf(_curParent->getStartPosition()) == false)
            {
                return false;
            }
        }
    }
    if (last == false)
    {
        _right->toRight();
        if (_right->hasParent() == false)
        {
            return false;
        }
        _rightParent->toParent(_right);
        if (_rightParent->adjacentTo(_curParent) == false)
        {
            return false;
        }
        if (_right->getParentReversed() == true)
        {
            if (_cur->getParentReversed() == false ||
                    _rightParent->leftOf(_curParent->getStartPosition()) == false)
            {
                return false;
            }
        }
        else
        {
            if (_cur->getParentReversed() == true ||
                    _rightParent->rightOf(_curParent->getStartPosition()) == false)
            {
                return false;
            }
        }
    }
    return last && first ? _cur->getParentReversed() : true;
}
开发者ID:ifiddes，项目名称:hal，代码行数:77，代码来源:defaultRearrangement.cpp

示例15: validateDuplications

void hal::validateDuplications(const Genome* genome)
{
  const Genome* parent = genome->getParent();
  if (parent == NULL)
  {
    return;
  }
  TopSegmentIteratorConstPtr topIt = genome->getTopSegmentIterator();
  TopSegmentIteratorConstPtr endIt = genome->getTopSegmentEndIterator();
  vector<unsigned char> pcount(parent->getNumBottomSegments(), 0);
  for (; topIt != endIt; topIt->toRight())
  {
    if (topIt->hasParent())
    {
      if (pcount[topIt->getTopSegment()->getParentIndex()] < 250)
      {
        ++pcount[topIt->getTopSegment()->getParentIndex()];
      }
    }
  }
  for (topIt = genome->getTopSegmentIterator(); topIt != endIt; topIt->toRight())
  {
    if (topIt->hasParent())
    {
      size_t count = pcount[topIt->getTopSegment()->getParentIndex()];
      assert(count > 0);
      {
        if (topIt->hasNextParalogy() == false && count > 1)
        {
          stringstream ss;
          ss << "Top Segment " << topIt->getTopSegment()->getArrayIndex()
             << " in genome " << genome->getName() << " is not marked as a"
             << " duplication but it shares its parent " 
             << topIt->getTopSegment()->getArrayIndex() << " with at least " 
             << count - 1 << " other segments in the same genome";
          throw hal_exception(ss.str());
        }  
      }
    }
  }
}
开发者ID:BioinformaticsArchive，项目名称:hal，代码行数:41，代码来源:halValidate.cpp


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