OpenMS::Interfaces::ChromatogramPtr IndexedMzMLHandler::getChromatogramById(int id)
{
OpenMS::Interfaces::ChromatogramPtr cptr(new OpenMS::Interfaces::Chromatogram);
std::string text = IndexedMzMLHandler::getChromatogramById_helper_(id);
MzMLSpectrumDecoder(skip_xml_checks_).domParseChromatogram(text, cptr);
return cptr;
}
void createSet() {
FailoverQueue<Complex, ComplexPtr> ComplexFQ(TEST_PATH, 40);
assert(ComplexFQ.size() == 0);
for (int i = 0; i < 390; i++) {
ComplexPtr cptr(new Complex());
ComplexFQ.push(cptr);
}
assert(ComplexFQ.size() == 30);
}
// Check whether v is a scalar for purposes of inlining fused-broadcast
// arguments when lowering; should agree with broadcast.jl on what is a
// scalar. When in doubt, return false, since this is only an optimization.
value_t fl_julia_scalar(fl_context_t *fl_ctx, value_t *args, uint32_t nargs)
{
argcount(fl_ctx, "julia-scalar?", nargs, 1);
if (fl_isnumber(fl_ctx, args[0]) || fl_isstring(fl_ctx, args[0]))
return fl_ctx->T;
else if (iscvalue(args[0]) && fl_ctx->jl_sym == cv_type((cvalue_t*)ptr(args[0]))) {
jl_value_t *v = *(jl_value_t**)cptr(args[0]);
if (jl_isa(v,(jl_value_t*)jl_number_type) || jl_is_string(v))
return fl_ctx->T;
}
return fl_ctx->F;
}
void tst_QSharedPointer::constCorrectness()
{
{
QSharedPointer<Data> ptr = QSharedPointer<Data>(new Data);
QSharedPointer<const Data> cptr(ptr);
QSharedPointer<volatile Data> vptr(ptr);
cptr = ptr;
vptr = ptr;
ptr = qSharedPointerConstCast<Data>(cptr);
ptr = qSharedPointerConstCast<Data>(vptr);
ptr = cptr.constCast<Data>();
ptr = vptr.constCast<Data>();
#if !defined(Q_CC_HPACC) && !defined(QT_ARCH_PARISC)
// the aCC series 3 compiler we have on the PA-RISC
// machine crashes compiling this code
QSharedPointer<const volatile Data> cvptr(ptr);
QSharedPointer<const volatile Data> cvptr2(cptr);
QSharedPointer<const volatile Data> cvptr3(vptr);
cvptr = ptr;
cvptr2 = cptr;
cvptr3 = vptr;
ptr = qSharedPointerConstCast<Data>(cvptr);
ptr = cvptr.constCast<Data>();
#endif
}
{
Data *aData = new Data;
QSharedPointer<Data> ptr = QSharedPointer<Data>(aData);
const QSharedPointer<Data> cptr = ptr;
ptr = cptr;
QSharedPointer<Data> other = qSharedPointerCast<Data>(cptr);
other = qSharedPointerDynamicCast<Data>(cptr);
QCOMPARE(cptr.data(), aData);
QCOMPARE(cptr.operator->(), aData);
}
}
OpenSwath::ChromatogramPtr SpectrumAccessOpenMS::getChromatogramById(int id)
{
const MSChromatogramType& chromatogram = ms_experiment_->getChromatograms()[id];
OpenSwath::BinaryDataArrayPtr intensity_array(new OpenSwath::BinaryDataArray);
OpenSwath::BinaryDataArrayPtr rt_array(new OpenSwath::BinaryDataArray);
for (MSChromatogramType::const_iterator it = chromatogram.begin(); it != chromatogram.end(); it++)
{
rt_array->data.push_back(it->getRT());
intensity_array->data.push_back(it->getIntensity());
}
// push back rt first, then intensity.
// FEATURE (hroest) annotate which is which
std::vector<OpenSwath::BinaryDataArrayPtr> binaryDataArrayPtrs;
binaryDataArrayPtrs.push_back(rt_array);
binaryDataArrayPtrs.push_back(intensity_array);
OpenSwath::ChromatogramPtr cptr(new OpenSwath::Chromatogram);
cptr->binaryDataArrayPtrs = binaryDataArrayPtrs;
return cptr;
}
OpenSwath::ChromatogramPtr SpectrumAccessOpenMSCached::getChromatogramById(int id) const
{
if (cache_.getChromatogramIndex().empty())
{
// remove const from the cache since we need to recalculate the index
// and re-read the data.
(const_cast<CachedmzML*>(&cache_))->createMemdumpIndex(filename_cached_);
}
OpenSwath::BinaryDataArrayPtr rt_array(new OpenSwath::BinaryDataArray);
OpenSwath::BinaryDataArrayPtr intensity_array(new OpenSwath::BinaryDataArray);
std::ifstream ifs_((filename_cached_).c_str(), std::ios::binary);
ifs_.seekg(cache_.getChromatogramIndex()[id]);
cache_.readChromatogramFast(rt_array, intensity_array, ifs_);
// push back rt first, then intensity.
// FEATURE (hroest) annotate which is which
std::vector<OpenSwath::BinaryDataArrayPtr> binaryDataArrayPtrs;
binaryDataArrayPtrs.push_back(rt_array);
binaryDataArrayPtrs.push_back(intensity_array);
OpenSwath::ChromatogramPtr cptr(new OpenSwath::Chromatogram);
cptr->binaryDataArrayPtrs = binaryDataArrayPtrs;
return cptr;
}
/* This doesn't work once we start reallocating & copying the
* generated code on buffer fills, because the call is relative to the
* current pc.
*/
void x86_call( struct x86_function *p, void (*label)())
{
emit_1ub(p, 0xe8);
emit_1i(p, cptr(label) - x86_get_label(p) - 4);
}
