bool DefaultGappedBottomSegmentIterator::isMissingData(double nThreshold) const
{
if (nThreshold >= 1.0)
{
return false;
}
hal_index_t start = min(_left->getStartPosition(), _right->getEndPosition());
DNAIteratorConstPtr di = _left->getGenome()->getDNAIterator(start);
hal_size_t length = getLength();
size_t maxNs = nThreshold * (double)length;
size_t Ns = 0;
char c;
for (size_t i = 0; i < length; ++i, di->toRight())
{
c = di->getChar();
if (c == 'N' || c == 'n')
{
++Ns;
}
if (Ns > maxNs)
{
return true;
}
if ((length - i) < (maxNs - Ns))
{
break;
}
}
return false;
}
void MappedSegmentColCompareTest::createColArray()
{
hal_size_t N = _ref->getSequenceLength();
_colArray.clear();
_colArray.resize(N);
set<const Genome*> tgtSet;
tgtSet.insert(_tgt);
ColumnIteratorConstPtr colIt = _ref->getColumnIterator(&tgtSet, 0, 0,
NULL_INDEX, false,
false, false, true);
while (true)
{
const ColumnIterator::ColumnMap* colMap = colIt->getColumnMap();
ColumnIterator::ColumnMap::const_iterator colMapIt = colMap->begin();
vector<pair<hal_index_t, bool> > insertList;
// Pass 1 find all homologies in target
for (; colMapIt != colMap->end(); colMapIt++)
{
if (colMapIt->first->getGenome() == _tgt)
{
ColumnIterator::DNASet* dnaSet = colMapIt->second;
ColumnIterator::DNASet::const_iterator dnaIt = dnaSet->begin();
for (; dnaIt != dnaSet->end(); ++dnaIt)
{
DNAIteratorConstPtr dna = *dnaIt;
insertList.push_back(
pair<hal_index_t, bool>(dna->getArrayIndex(), dna->getReversed()));
}
}
else
{
CuAssertTrue(_testCase, colMapIt->first->getGenome() == _ref);
}
}
// Pass 2 update each reference position with all homologies found
// in Pass 1
for (colMapIt = colMap->begin(); colMapIt != colMap->end(); colMapIt++)
{
if (colMapIt->first->getGenome() == _ref)
{
ColumnIterator::DNASet* dnaSet = colMapIt->second;
ColumnIterator::DNASet::const_iterator dnaIt = dnaSet->begin();
for (; dnaIt != dnaSet->end(); ++dnaIt)
{
DNAIteratorConstPtr dna = *dnaIt;
for (size_t insIdx = 0; insIdx < insertList.size(); ++insIdx)
{
_colArray[dna->getArrayIndex()].insert(insertList[insIdx]);
}
}
}
}
if (colIt->lastColumn())
{
break;
}
colIt->toRight();
}
}
void Genome::copySequence(Genome *dest) const
{
DNAIteratorConstPtr inDna = getDNAIterator();
DNAIteratorPtr outDna = dest->getDNAIterator();
hal_size_t n = getSequenceLength();
assert(n == dest->getSequenceLength());
for (; (hal_size_t)inDna->getArrayIndex() < n; inDna->toRight(),
outDna->toRight())
{
outDna->setChar(inDna->getChar());
}
}
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());
}
}
}