void DefaultGappedBottomSegmentIterator::toRightNextUngapped(
BottomSegmentIteratorConstPtr bs) const
{
while (bs->hasChild(_childIndex) == false &&
bs->getLength() <= _gapThreshold)
{
if ((!bs->getReversed() && bs->getBottomSegment()->isLast()) ||
(bs->getReversed() && bs->getBottomSegment()->isFirst()))
{
break;
}
bs->toRight();
}
}
DefaultGappedBottomSegmentIterator::DefaultGappedBottomSegmentIterator(
BottomSegmentIteratorConstPtr left,
hal_size_t childIndex,
hal_size_t gapThreshold,
bool atomic) :
_childIndex(childIndex),
_gapThreshold(gapThreshold),
_atomic(atomic)
{
if (left->getStartOffset() != 0 || left->getEndOffset() != 0)
{
throw hal_exception("offset not currently supported in gapped iterators");
}
const Genome* child =
left->getBottomSegment()->getGenome()->getChild(_childIndex);
if (child == NULL)
{
throw hal_exception("can't init GappedBottomIterator with no child genome");
}
assert(_atomic == false || _gapThreshold == 0);
_left = left->copy();
_right = left->copy();
_temp = left->copy();
_temp2 = left->copy();
_leftChild = child->getTopSegmentIterator();
_rightChild = _leftChild->copy();
_leftDup = _leftChild->copy();
_rightDup = _leftChild->copy();
extendRight();
}
void TopSegmentIteratorParseTest::checkCallBack(AlignmentConstPtr alignment)
{
BottomSegmentIteratorConstPtr bi;
TopSegmentIteratorConstPtr ti;
// case 1
const Genome* case1 = alignment->openGenome("case1");
ti = case1->getTopSegmentIterator();
bi = case1->getBottomSegmentIterator();
ti->toParseUp(bi);
CuAssertTrue(_testCase, bi->getStartPosition() == ti->getStartPosition());
CuAssertTrue(_testCase, bi->getLength() == ti->getLength());
bi->slice(3, 1);
ti->toParseUp(bi);
CuAssertTrue(_testCase, bi->getLength() ==
bi->getBottomSegment()->getLength() - 4);
CuAssertTrue(_testCase, bi->getStartPosition() == ti->getStartPosition());
CuAssertTrue(_testCase, bi->getLength() == ti->getLength());
// case 2
const Genome* case2 = alignment->openGenome("case2");
ti = case2->getTopSegmentIterator();
bi = case2->getBottomSegmentIterator(1);
ti->toParseUp(bi);
CuAssertTrue(_testCase, bi->getStartPosition() == ti->getStartPosition());
bi->slice(1, 1);
ti->toParseUp(bi);
CuAssertTrue(_testCase, bi->getStartPosition() == ti->getStartPosition());
// case 3
const Genome* case3 = alignment->openGenome("case3");
ti = case3->getTopSegmentIterator();
bi = case3->getBottomSegmentIterator();
ti->toParseUp(bi);
CuAssertTrue(_testCase, bi->getStartPosition() == ti->getStartPosition());
bi->slice(2, 1);
ti->toParseUp(bi);
CuAssertTrue(_testCase, bi->getStartPosition() == ti->getStartPosition());
// case 4
const Genome* case4 = alignment->openGenome("case4");
ti = case4->getTopSegmentIterator();
bi = case4->getBottomSegmentIterator(1);
ti->toParseUp(bi);
CuAssertTrue(_testCase, bi->getStartPosition() == ti->getStartPosition());
bi->slice(2, 2);
ti->toParseUp(bi);
CuAssertTrue(_testCase, bi->getStartPosition() == ti->getStartPosition());
}
//////////////////////////////////////////////////////////////////////////////
// INTERNAL METHODS
//////////////////////////////////////////////////////////////////////////////
bool DefaultGappedBottomSegmentIterator::compatible(
BottomSegmentIteratorConstPtr left,
BottomSegmentIteratorConstPtr right) const
{
assert(left->hasChild(_childIndex) && right->hasChild(_childIndex));
assert(left->equals(right) == false);
_leftChild->toChild(left, _childIndex);
_rightChild->toChild(right, _childIndex);
if (_leftChild->getTopSegment()->getParentReversed() !=
_rightChild->getTopSegment()->getParentReversed())
{
return false;
}
if (_leftChild->hasNextParalogy() != _rightChild->hasNextParalogy())
{
return false;
}
if ((!_leftChild->getReversed() &&
_leftChild->leftOf(_rightChild->getStartPosition()) == false) ||
(_leftChild->getReversed() &&
_leftChild->rightOf(_rightChild->getStartPosition()) == false))
{
return false;
}
if (left->getBottomSegment()->getSequence() !=
right->getBottomSegment()->getSequence() ||
_leftChild->getTopSegment()->getSequence() !=
_rightChild->getTopSegment()->getSequence())
{
return false;
}
while (true)
{
assert(_leftChild->isLast() == false);
_leftChild->toRight();
if (_leftChild->hasParent() == true ||
_leftChild->getLength() > _gapThreshold)
{
if (_leftChild->equals(_rightChild))
{
break;
}
else
{
return false;
}
}
}
_leftChild->toChild(left, _childIndex);
_rightChild->toChild(right, _childIndex);
if (_leftChild->hasNextParalogy() == true)
{
_leftDup->copy(_leftChild);
_leftDup->toNextParalogy();
_rightDup->copy(_rightChild);
_rightDup->toNextParalogy();
if ((_leftDup->getReversed() == false &&
_leftDup->leftOf(_rightDup->getStartPosition()) == false) ||
(_leftDup->getReversed() == true &&
_rightDup->leftOf(_leftDup->getStartPosition()) == false))
{
return false;
}
if (_leftDup->getTopSegment()->getSequence() !=
_rightDup->getTopSegment()->getSequence())
{
return false;
}
while (true)
{
assert(_leftDup->isLast() == false);
_leftDup->toRight();
if (_leftDup->hasParent() == true ||
_leftDup->getLength() > _gapThreshold)
{
if (_leftDup->equals(_rightDup))
{
break;
}
else
{
return false;
}
}
}
}
return true;
}
void hal::validateSequence(const Sequence* sequence)
{
// Verify that the DNA sequence doesn't contain funny characters
DNAIteratorConstPtr dnaIt = sequence->getDNAIterator();
hal_size_t length = sequence->getSequenceLength();
for (hal_size_t i = 0; i < length; ++i)
{
char c = dnaIt->getChar();
if (isNucleotide(c) == false)
{
stringstream ss;
ss << "Non-nucleotide character discoverd at position "
<< i << " of sequence " << sequence->getName() << ": " << c;
throw hal_exception(ss.str());
}
}
// Check the top segments
if (sequence->getGenome()->getParent() != NULL)
{
hal_size_t totalTopLength = 0;
TopSegmentIteratorConstPtr topIt = sequence->getTopSegmentIterator();
hal_size_t numTopSegments = sequence->getNumTopSegments();
for (hal_size_t i = 0; i < numTopSegments; ++i)
{
const TopSegment* topSegment = topIt->getTopSegment();
validateTopSegment(topSegment);
totalTopLength += topSegment->getLength();
topIt->toRight();
}
if (totalTopLength != length)
{
stringstream ss;
ss << "Sequence " << sequence->getName() << " has length " << length
<< " but its top segments add up to " << totalTopLength;
throw hal_exception(ss.str());
}
}
// Check the bottom segments
if (sequence->getGenome()->getNumChildren() > 0)
{
hal_size_t totalBottomLength = 0;
BottomSegmentIteratorConstPtr bottomIt =
sequence->getBottomSegmentIterator();
hal_size_t numBottomSegments = sequence->getNumBottomSegments();
for (hal_size_t i = 0; i < numBottomSegments; ++i)
{
const BottomSegment* bottomSegment = bottomIt->getBottomSegment();
validateBottomSegment(bottomSegment);
totalBottomLength += bottomSegment->getLength();
bottomIt->toRight();
}
if (totalBottomLength != length)
{
stringstream ss;
ss << "Sequence " << sequence->getName() << " has length " << length
<< " but its bottom segments add up to " << totalBottomLength;
throw hal_exception(ss.str());
}
}
}
void hal::validateTopSegment(const TopSegment* topSegment)
{
const Genome* genome = topSegment->getGenome();
hal_index_t index = topSegment->getArrayIndex();
if (index < 0 || index >= (hal_index_t)genome->getSequenceLength())
{
stringstream ss;
ss << "Segment out of range " << index << " in genome "
<< genome->getName();
throw hal_exception(ss.str());
}
if (topSegment->getLength() < 1)
{
stringstream ss;
ss << "Top segment " << index << " in genome " << genome->getName()
<< " has length 0 which is not currently supported";
throw hal_exception(ss.str());
}
const Genome* parentGenome = genome->getParent();
const hal_index_t parentIndex = topSegment->getParentIndex();
if (parentGenome != NULL && parentIndex != NULL_INDEX)
{
if (parentIndex >= (hal_index_t)parentGenome->getNumBottomSegments())
{
stringstream ss;
ss << "Parent index " << parentIndex << " of segment "
<< topSegment->getArrayIndex() << " out of range in genome "
<< parentGenome->getName();
throw hal_exception(ss.str());
}
BottomSegmentIteratorConstPtr bottomSegmentIterator =
parentGenome->getBottomSegmentIterator(parentIndex);
const BottomSegment* parentSegment =
bottomSegmentIterator->getBottomSegment();
if (topSegment->getLength() != parentSegment->getLength())
{
stringstream ss;
ss << "Parent length of segment " << topSegment->getArrayIndex()
<< " in genome " << genome->getName() << " has length "
<< parentSegment->getLength() << " which does not match "
<< topSegment->getLength();
throw hal_exception(ss.str());
}
}
const hal_index_t parseIndex = topSegment->getBottomParseIndex();
if (parseIndex == NULL_INDEX)
{
if (genome->getNumChildren() != 0)
{
stringstream ss;
ss << "Top Segment " << topSegment->getArrayIndex() << " in genome "
<< genome->getName() << " has null parse index";
throw hal_exception(ss.str());
}
}
else
{
if (parseIndex >= (hal_index_t)genome->getNumBottomSegments())
{
stringstream ss;
ss << "Top Segment " << topSegment->getArrayIndex() << " in genome "
<< genome->getName() << " has parse index out of range";
throw hal_exception(ss.str());
}
hal_offset_t parseOffset = topSegment->getBottomParseOffset();
BottomSegmentIteratorConstPtr bottomSegmentIterator =
genome->getBottomSegmentIterator(parseIndex);
const BottomSegment* parseSegment =
bottomSegmentIterator->getBottomSegment();
if (parseOffset >= parseSegment->getLength())
{
stringstream ss;
ss << "Top Segment " << topSegment->getArrayIndex() << " in genome "
<< genome->getName() << " has parse offset out of range";
throw hal_exception(ss.str());
}
if ((hal_index_t)parseOffset + parseSegment->getStartPosition() !=
topSegment->getStartPosition())
{
throw hal_exception("parse index broken in top segment in genome " +
genome->getName());
}
}
const hal_index_t paralogyIndex = topSegment->getNextParalogyIndex();
if (paralogyIndex != NULL_INDEX)
{
TopSegmentIteratorConstPtr pti =
genome->getTopSegmentIterator(paralogyIndex);
if (pti->getTopSegment()->getParentIndex() != topSegment->getParentIndex())
{
stringstream ss;
ss << "Top segment " << topSegment->getArrayIndex()
<< " has parent index "
<< topSegment->getParentIndex() << ", but next paraglog "
<< topSegment->getNextParalogyIndex() << " has parent Index "
<< pti->getTopSegment()->getParentIndex()
<< ". Paralogous top segments must share same parent.";
throw hal_exception(ss.str());
}
if (paralogyIndex == topSegment->getArrayIndex())
{
stringstream ss;
ss << "Top segment " << topSegment->getArrayIndex()
<< " has paralogy index " << topSegment->getNextParalogyIndex()
<< " which isn't allowed";
throw hal_exception(ss.str());
}
}
}
void
GappedSegmentSimpleIteratorTest::checkCallBack(AlignmentConstPtr alignment)
{
const Genome* child = alignment->openGenome("child");
const Genome* parent = alignment->openGenome("parent");
GappedTopSegmentIteratorConstPtr gtsIt =
child->getGappedTopSegmentIterator(0, 9999999);
GappedBottomSegmentIteratorConstPtr gbsIt =
parent->getGappedBottomSegmentIterator(0, 0, 9999999);
GappedTopSegmentIteratorConstPtr gtsItRev =
child->getGappedTopSegmentIterator(0, 9999999);
gtsItRev->toReverse();
GappedBottomSegmentIteratorConstPtr gbsItRev =
parent->getGappedBottomSegmentIterator(0, 0, 9999999);
gbsItRev->toReverse();
for (size_t i = 0; i < child->getNumTopSegments(); ++i)
{
TopSegmentIteratorConstPtr tsIt = gtsIt->getLeft();
CuAssertTrue(_testCase, tsIt->equals(gtsIt->getRight()));
CuAssertTrue(_testCase,
(size_t)tsIt->getTopSegment()->getArrayIndex() == i);
gtsIt->toRight();
BottomSegmentIteratorConstPtr bsIt = gbsIt->getLeft();
CuAssertTrue(_testCase, bsIt->equals(gbsIt->getRight()));
CuAssertTrue(_testCase,
(size_t)bsIt->getBottomSegment()->getArrayIndex() == i);
gbsIt->toRight();
TopSegmentIteratorConstPtr tsItRev = gtsItRev->getLeft();
CuAssertTrue(_testCase, tsItRev->equals(gtsItRev->getRight()));
CuAssertTrue(_testCase,
(size_t)tsItRev->getTopSegment()->getArrayIndex() == i);
gtsItRev->toLeft();
BottomSegmentIteratorConstPtr bsItRev = gbsItRev->getLeft();
CuAssertTrue(_testCase, bsItRev->equals(gbsItRev->getRight()));
CuAssertTrue(_testCase,
(size_t)bsItRev->getBottomSegment()->getArrayIndex() == i);
gbsItRev->toLeft();
}
gtsIt = child->getGappedTopSegmentIterator(
child->getNumTopSegments() - 1, 9999999);
gbsIt = parent->getGappedBottomSegmentIterator(
child->getNumTopSegments() - 1, 0, 9999999);
gtsItRev = child->getGappedTopSegmentIterator(
child->getNumTopSegments() - 1, 9999999);
gtsItRev->toReverse();
gbsItRev = parent->getGappedBottomSegmentIterator(
child->getNumTopSegments() - 1, 0, 9999999);
gbsItRev->toReverse();
for (hal_index_t i = child->getNumTopSegments() - 1; i >= 0; --i)
{
TopSegmentIteratorConstPtr tsIt = gtsIt->getLeft();
CuAssertTrue(_testCase, tsIt->equals(gtsIt->getRight()));
CuAssertTrue(_testCase, tsIt->getTopSegment()->getArrayIndex() == i);
CuAssertTrue(_testCase, gtsIt->getReversed() == false);
gtsIt->toLeft();
BottomSegmentIteratorConstPtr bsIt = gbsIt->getLeft();
CuAssertTrue(_testCase, bsIt->equals(gbsIt->getRight()));
CuAssertTrue(_testCase, bsIt->getBottomSegment()->getArrayIndex() == i);
CuAssertTrue(_testCase, gbsIt->getReversed() == false);
gbsIt->toLeft();
TopSegmentIteratorConstPtr tsItRev = gtsItRev->getLeft();
CuAssertTrue(_testCase, tsItRev->equals(gtsItRev->getRight()));
CuAssertTrue(_testCase, tsItRev->getTopSegment()->getArrayIndex() == i);
CuAssertTrue(_testCase, gtsItRev->getReversed() == true);
gtsItRev->toRight();
BottomSegmentIteratorConstPtr bsItRev = gbsItRev->getLeft();
CuAssertTrue(_testCase, bsItRev->equals(gbsItRev->getRight()));
CuAssertTrue(_testCase, bsItRev->getBottomSegment()->getArrayIndex() == i);
CuAssertTrue(_testCase, gbsItRev->getReversed() == true);
gbsItRev->toRight();
}
}
void
GappedSegmentIteratorIndelTest::checkCallBack(AlignmentConstPtr alignment)
{
const Genome* child = alignment->openGenome("child");
const Genome* parent = alignment->openGenome("parent");
GappedTopSegmentIteratorConstPtr gtsIt =
child->getGappedTopSegmentIterator(0, 9999999);
GappedBottomSegmentIteratorConstPtr gbsIt =
parent->getGappedBottomSegmentIterator(0, 0, 9999999);
GappedTopSegmentIteratorConstPtr gtsItRev =
child->getGappedTopSegmentIterator(0, 9999999);
gtsItRev->toReverse();
GappedBottomSegmentIteratorConstPtr gbsItRev =
parent->getGappedBottomSegmentIterator(0, 0, 9999999);
gbsItRev->toReverse();
for (size_t i = 0; i < child->getNumTopSegments(); i += 20)
{
TopSegmentIteratorConstPtr tsIt = gtsIt->getLeft();
CuAssertTrue(_testCase,
(size_t)tsIt->getTopSegment()->getArrayIndex() == i);
tsIt = gtsIt->getRight();
CuAssertTrue(_testCase,
(size_t)tsIt->getTopSegment()->getArrayIndex() == i + 19);
BottomSegmentIteratorConstPtr bsIt = gbsIt->getLeft();
CuAssertTrue(_testCase,
(size_t)bsIt->getBottomSegment()->getArrayIndex() == i);
bsIt = gbsIt->getRight();
CuAssertTrue(_testCase,
(size_t)bsIt->getBottomSegment()->getArrayIndex() == i + 19);
GappedBottomSegmentIteratorConstPtr gappedParent = gbsIt->copy();
gappedParent->toParent(gtsIt);
if (gappedParent->getReversed())
{
gappedParent->toReverse();
}
CuAssertTrue(_testCase,
gappedParent->equals(gbsIt));
GappedTopSegmentIteratorConstPtr gappedChild = gtsIt->copy();
gappedChild->toChild(gbsIt);
if (gappedChild->getReversed())
{
gappedChild->toReverse();
}
CuAssertTrue(_testCase, gappedChild->equals(gtsIt));
gtsIt->toRight();
gbsIt->toRight();
TopSegmentIteratorConstPtr tsItRev = gtsItRev->getLeft();
CuAssertTrue(_testCase,
(size_t)tsItRev->getTopSegment()->getArrayIndex() == i + 19);
tsItRev = gtsItRev->getRight();
CuAssertTrue(_testCase,
(size_t)tsItRev->getTopSegment()->getArrayIndex() == i);
gtsItRev->toLeft();
BottomSegmentIteratorConstPtr bsItRev = gbsItRev->getLeft();
CuAssertTrue(_testCase,
(size_t)bsItRev->getBottomSegment()->getArrayIndex() == i+19);
bsItRev = gbsItRev->getRight();
CuAssertTrue(_testCase,
(size_t)bsItRev->getBottomSegment()->getArrayIndex() == i);
gbsItRev->toLeft();
}
gtsIt = child->getGappedTopSegmentIterator(
child->getNumTopSegments() - 20, 9999999);
gbsIt = parent->getGappedBottomSegmentIterator(
child->getNumTopSegments() - 20, 0, 9999999);
gtsItRev = child->getGappedTopSegmentIterator(
child->getNumTopSegments() - 20, 9999999);
gtsItRev->toReverse();
gbsItRev = parent->getGappedBottomSegmentIterator(
child->getNumTopSegments() - 20, 0, 9999999);
gbsItRev->toReverse();
for (hal_index_t i = child->getNumTopSegments() - 1; i >= 0; i -= 20)
{
TopSegmentIteratorConstPtr tsIt = gtsIt->getLeft();
CuAssertTrue(_testCase, tsIt->getTopSegment()->getArrayIndex() == i - 19);
tsIt = gtsIt->getRight();
CuAssertTrue(_testCase, tsIt->getTopSegment()->getArrayIndex() == i);
CuAssertTrue(_testCase, gtsIt->getReversed() == false);
gtsIt->toLeft();
BottomSegmentIteratorConstPtr bsIt = gbsIt->getLeft();
CuAssertTrue(_testCase, bsIt->getBottomSegment()->getArrayIndex() == i-19);
bsIt = gbsIt->getRight();
CuAssertTrue(_testCase, bsIt->getBottomSegment()->getArrayIndex() == i);
CuAssertTrue(_testCase, gbsIt->getReversed() == false);
gbsIt->toLeft();
TopSegmentIteratorConstPtr tsItRev = gtsItRev->getLeft();
CuAssertTrue(_testCase, tsItRev->getTopSegment()->getArrayIndex() == i);
tsItRev = gtsItRev->getRight();
CuAssertTrue(_testCase, tsItRev->getTopSegment()->getArrayIndex() == i-19);
CuAssertTrue(_testCase, gtsItRev->getReversed() == true);
gtsItRev->toRight();
BottomSegmentIteratorConstPtr bsItRev = gbsItRev->getLeft();
CuAssertTrue(_testCase, bsItRev->getBottomSegment()->getArrayIndex() == i);
bsItRev = gbsItRev->getRight();
CuAssertTrue(_testCase, bsItRev->getBottomSegment()->getArrayIndex()==i-19);
CuAssertTrue(_testCase, gbsItRev->getReversed() == true);
gbsItRev->toRight();
}
}
