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");
}
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;
}
}
}
}
}
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();
}
}
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);
}
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());
}
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());
}
}
}
}
}
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());
}
}
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::validateBottomSegment(const BottomSegment* bottomSegment)
{
const Genome* genome = bottomSegment->getGenome();
hal_index_t index = bottomSegment->getArrayIndex();
if (index < 0 || index >= (hal_index_t)genome->getSequenceLength())
{
stringstream ss;
ss << "Bottom segment out of range " << index << " in genome "
<< genome->getName();
throw hal_exception(ss.str());
}
if (bottomSegment->getLength() < 1)
{
stringstream ss;
ss << "Bottom segment " << index << " in genome " << genome->getName()
<< " has length 0 which is not currently supported";
throw hal_exception(ss.str());
}
hal_size_t numChildren = bottomSegment->getNumChildren();
for (hal_size_t child = 0; child < numChildren; ++child)
{
const Genome* childGenome = genome->getChild(child);
const hal_index_t childIndex = bottomSegment->getChildIndex(child);
if (childGenome != NULL && childIndex != NULL_INDEX)
{
if (childIndex >= (hal_index_t)childGenome->getNumTopSegments())
{
stringstream ss;
ss << "Child " << child << " index " <<childIndex << " of segment "
<< bottomSegment->getArrayIndex() << " out of range in genome "
<< childGenome->getName();
throw hal_exception(ss.str());
}
TopSegmentIteratorConstPtr topSegmentIteratr =
childGenome->getTopSegmentIterator(childIndex);
const TopSegment* childSegment = topSegmentIteratr->getTopSegment();
if (childSegment->getLength() != bottomSegment->getLength())
{
stringstream ss;
ss << "Child " << child << " with index "
<< childSegment->getArrayIndex()
<< " and start position " << childSegment->getStartPosition()
<< " and sequence " << childSegment->getSequence()->getName()
<< " has length " << childSegment->getLength()
<< " but parent with index " << bottomSegment->getArrayIndex()
<< " and start position " << bottomSegment->getStartPosition()
<< " in sequence " << bottomSegment->getSequence()->getName()
<< " has length " << bottomSegment->getLength();
throw hal_exception(ss.str());
}
if (childSegment->getNextParalogyIndex() == NULL_INDEX &&
childSegment->getParentIndex() != bottomSegment->getArrayIndex())
{
throw hal_exception("parent / child index mismatch (parent=" +
genome->getName() + " child=" +
childGenome->getName());
}
if (childSegment->getParentReversed() !=
bottomSegment->getChildReversed(child))
{
throw hal_exception("parent / child reversal mismatch (parent=" +
genome->getName() + " child=" +
childGenome->getName());
}
}
}
const hal_index_t parseIndex = bottomSegment->getTopParseIndex();
if (parseIndex == NULL_INDEX)
{
if (genome->getParent() != NULL)
{
stringstream ss;
ss << "Bottom segment " << bottomSegment->getArrayIndex() << " in genome "
<< genome->getName() << " has null parse index";
throw hal_exception(ss.str());
}
}
else
{
if (parseIndex >= (hal_index_t)genome->getNumTopSegments())
{
stringstream ss;
ss << "BottomSegment " << bottomSegment->getArrayIndex() << " in genome "
<< genome->getName() << " has parse index " << parseIndex
<< " greater than the number of top segments, "
<< (hal_index_t)genome->getNumTopSegments();
throw hal_exception(ss.str());
}
TopSegmentIteratorConstPtr parseIterator =
genome->getTopSegmentIterator(parseIndex);
const TopSegment* parseSegment = parseIterator->getTopSegment();
hal_offset_t parseOffset = bottomSegment->getTopParseOffset();
if (parseOffset >= parseSegment->getLength())
{
stringstream ss;
ss << "BottomSegment " << bottomSegment->getArrayIndex() << " in genome "
<< genome->getName() << " has parse offset, " << parseOffset
<< ", greater than the length of the segment, "
<< parseSegment->getLength();
throw hal_exception(ss.str());
}
if ((hal_index_t)parseOffset + parseSegment->getStartPosition() !=
bottomSegment->getStartPosition())
{
throw hal_exception("parse index broken in bottom segment in genome " +
genome->getName());
}
}
}
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();
}
}
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);
}
}
