void GappedBottomSegmentIterator::toRightNextUngapped(TopSegmentIteratorPtr topSeqIt) const {
    while (topSeqIt->tseg()->hasParent() == false && topSeqIt->getLength() <= _gapThreshold) {
        if ((!topSeqIt->getReversed() && topSeqIt->getTopSegment()->isLast()) ||
            (topSeqIt->getReversed() && topSeqIt->getTopSegment()->isFirst())) {
            break;
        }
        topSeqIt->toRight();
    }
}
Exemplo n.º 2
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void TopSegmentSimpleIteratorTest::checkCallBack(const Alignment *alignment) {
    const Genome *ancGenome = alignment->openGenome("Anc0");
    CuAssertTrue(_testCase, ancGenome->getNumTopSegments() == _topSegments.size());
    TopSegmentIteratorPtr 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);
    }
}