void test(bool indexed)
{
if (os_) *os_ << "test(): indexed=\"" << boolalpha << indexed << "\"\n";
MSData tiny;
examples::initializeTiny(tiny);
Serializer_mzML::Config config;
config.indexed = indexed;
Serializer_mzML serializer(config);
ostringstream oss;
serializer.write(oss, tiny);
if (os_) *os_ << "oss:\n" << oss.str() << endl;
shared_ptr<istream> is(new istringstream(oss.str()));
// dummy would normally be read in from file
MSData dummy;
ParamGroupPtr pg1(new ParamGroup);
pg1->id = "CommonMS1SpectrumParams";
pg1->cvParams.push_back(MS_positive_scan);
pg1->cvParams.push_back(MS_full_scan);
dummy.paramGroupPtrs.push_back(pg1);
ParamGroupPtr pg2(new ParamGroup);
pg2->id = "CommonMS2SpectrumParams";
pg2->cvParams.push_back(MS_positive_scan);
pg2->cvParams.push_back(MS_full_scan);
dummy.paramGroupPtrs.push_back(pg2);
// so we don't have any dangling references
dummy.instrumentConfigurationPtrs.push_back(InstrumentConfigurationPtr(new InstrumentConfiguration("LCQDeca")));
dummy.dataProcessingPtrs.push_back(DataProcessingPtr(new DataProcessing("XcaliburProcessing")));
SpectrumListPtr sl = SpectrumList_mzML::create(is, dummy, indexed);
// check easy functions
unit_assert(sl.get());
unit_assert(sl->size() == 4);
unit_assert(sl->find ("S19") == 0);
unit_assert(sl->findNative("19") == 0);
unit_assert(sl->find("S20") == 1);
unit_assert(sl->findNative("20") == 1);
unit_assert(sl->find("S21") == 2);
unit_assert(sl->findNative("21") == 2);
unit_assert(sl->find("S22") == 3);
unit_assert(sl->findNative("22") == 3);
unit_assert(sl->findSpotID("A1").empty());
IndexList spotIndexList = sl->findSpotID("A1,42x42,4242x4242");
unit_assert(spotIndexList.size() == 1);
unit_assert(spotIndexList[0] == 3);
// check scan 19
SpectrumPtr s = sl->spectrum(0); // read without binary data
unit_assert(s.get());
unit_assert(s->id == "S19");
unit_assert(s->nativeID == "19");
unit_assert(s->spotID.empty());
unit_assert(s->cvParam(MS_ms_level).valueAs<int>() == 1);
unit_assert(s->binaryDataArrayPtrs.empty());
unit_assert(sl->spectrumIdentity(0).index == 0);
unit_assert(sl->spectrumIdentity(0).id == "S19");
unit_assert(sl->spectrumIdentity(0).nativeID == "19");
unit_assert(sl->spectrumIdentity(0).spotID.empty());
SpectrumPtr s_cache = sl->spectrum(0); // cache read
unit_assert(s_cache.get() == s.get());
s = sl->spectrum(0, true); // read with binary data
unit_assert(s_cache.get() != s.get());
vector<MZIntensityPair> pairs;
s->getMZIntensityPairs(pairs);
unit_assert(pairs.size() == 15);
for (int i=0; i<15; i++)
unit_assert(pairs[i].mz==i && pairs[i].intensity==15-i);
unit_assert(s->spectrumDescription.scan.paramGroupPtrs.size() == 1);
unit_assert(s->spectrumDescription.scan.paramGroupPtrs.back()->id == "CommonMS1SpectrumParams");
unit_assert(s->spectrumDescription.scan.paramGroupPtrs.back()->cvParams.size() == 2);
// check scan 20
s = sl->spectrum(1, true);
unit_assert(s.get());
unit_assert(s->id == "S20");
unit_assert(s->nativeID == "20");
unit_assert(s->spotID.empty());
unit_assert(s->cvParam(MS_ms_level).valueAs<int>() == 2);
unit_assert(sl->spectrumIdentity(1).index == 1);
unit_assert(sl->spectrumIdentity(1).id == "S20");
unit_assert(sl->spectrumIdentity(1).nativeID == "20");
unit_assert(sl->spectrumIdentity(1).spotID.empty());
pairs.clear();
s->getMZIntensityPairs(pairs);
unit_assert(pairs.size() == 10);
for (int i=0; i<10; i++)
unit_assert(pairs[i].mz==2*i && pairs[i].intensity==(10-i)*2);
unit_assert(s->spectrumDescription.scan.paramGroupPtrs.size() == 1);
unit_assert(s->spectrumDescription.scan.paramGroupPtrs.back()->id == "CommonMS2SpectrumParams");
unit_assert(s->spectrumDescription.scan.paramGroupPtrs.back()->cvParams.size() == 2);
// check scan 22 (MALDI)
s = sl->spectrum(3, true);
unit_assert(s.get());
unit_assert(s->id == "S22");
unit_assert(s->nativeID == "22");
unit_assert(s->spotID == "A1,42x42,4242x4242");
unit_assert(s->cvParam(MS_ms_level).valueAs<int>() == 1);
unit_assert(sl->spectrumIdentity(3).index == 3);
unit_assert(sl->spectrumIdentity(3).id == "S22");
unit_assert(sl->spectrumIdentity(3).nativeID == "22");
unit_assert(sl->spectrumIdentity(3).spotID == "A1,42x42,4242x4242");
}
