C++ (Cpp) Genome::getSequenceBySite Examples

Example #1

File: halGenomeTest.cpp Project: glennhickey/hal

void GenomeCopySegmentsWhenSequencesOutOfOrderTest::checkCallBack(const Alignment *alignment) {
    // FIXME: halAlignment->open() fails miserably but
    // openHalAlignmentReadOnly works? Probably some state isn't cleared
    // on close.
    AlignmentPtr tmp(getTestAlignmentInstances(alignment->getStorageFormat(), _path, WRITE_ACCESS));
    _secondAlignment = tmp;

    Genome *copyRootGenome = _secondAlignment->openGenome("root");
    Sequence *sequence2 = copyRootGenome->getSequenceBySite(0);
    CuAssertStrEquals(_testCase, sequence2->getName().c_str(), "Sequence1");
    Sequence *sequence1 = copyRootGenome->getSequenceBySite(170);
    CuAssertStrEquals(_testCase, sequence1->getName().c_str(), "Sequence2");

    Genome *copyInternalGenome = _secondAlignment->openGenome("internal");
    sequence2 = copyInternalGenome->getSequenceBySite(0);
    CuAssertStrEquals(_testCase, sequence2->getName().c_str(), "Sequence2");
    sequence1 = copyInternalGenome->getSequenceBySite(170);
    CuAssertStrEquals(_testCase, sequence1->getName().c_str(), "Sequence1");

    checkBottomSegments(copyInternalGenome, 10, _testCase);

    validateAlignment(_secondAlignment.get());

    _secondAlignment->close();
    remove(_path.c_str());
}