C++ (Cpp) TopSegmentIteratorConstPtr::slice示例

示例#1

文件： halMappedSegmentTest.cpp 项目： dayin1989/hal

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");
  }
}

示例#2

文件： halMappedSegmentTest.cpp 项目： dayin1989/hal

void MappedSegmentMapAcrossTest::checkCallBack(AlignmentConstPtr alignment)
{
  validateAlignment(alignment);
  const Genome* child1 = alignment->openGenome("child1");
  const Genome* child2 = alignment->openGenome("child2");
  TopSegmentIteratorConstPtr top = child2->getTopSegmentIterator();
  testTopSegment(alignment, top);
  top->slice(1,2);
  testTopSegment(alignment, top);
  top->toReverse();
  testTopSegment(alignment, top);
  top = child1->getTopSegmentIterator();
  testTopSegment(alignment, top);
  top->slice(1,2);
  testTopSegment(alignment, top);
  top->toReverse();
  testTopSegment(alignment, top);
}

示例#3

文件： halTopSegmentTest.cpp 项目： BioinformaticsArchive/hal

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);
  }
}