void test()
{
MSData msd;
examples::initializeTiny(msd);
SpectrumListPtr originalList = msd.run.spectrumListPtr;
SpectrumListPtr defaultArrayLengthSortedList(
new SpectrumList_Sorter(originalList, DefaultArrayLengthSorter()));
SpectrumListPtr msLevelUnstableSortedList(
new SpectrumList_Sorter(originalList, MSLevelSorter()));
SpectrumListPtr msLevelStableSortedList(
new SpectrumList_Sorter(originalList, MSLevelSorter(), true));
SpectrumListPtr sillySortedList(
new SpectrumList_Sorter(msLevelStableSortedList, DefaultArrayLengthSorter()));
if (os_)
{
*os_ << "Original spectrum list (" << originalList->size() << "):\n";
TextWriter write(*os_);
write(*originalList);
*os_ << endl;
}
if (os_)
{
*os_ << "Default array length sorted spectrum list (" << defaultArrayLengthSortedList->size() << "):\n";
TextWriter write(*os_);
write(*defaultArrayLengthSortedList);
*os_ << endl;
}
if (os_)
{
*os_ << "MS level unstable sorted spectrum list (" << msLevelUnstableSortedList->size() << "):\n";
TextWriter write(*os_);
write(*msLevelUnstableSortedList);
*os_ << endl;
}
if (os_)
{
*os_ << "MS level stable sorted spectrum list (" << msLevelStableSortedList->size() << "):\n";
TextWriter write(*os_);
write(*msLevelStableSortedList);
*os_ << endl;
}
if (os_)
{
*os_ << "Silly (nested) sorted spectrum list (" << sillySortedList->size() << "):\n";
TextWriter write(*os_);
write(*sillySortedList);
*os_ << endl;
}
unit_assert_operator_equal(originalList->size(), defaultArrayLengthSortedList->size());
unit_assert_operator_equal(originalList->size(), msLevelUnstableSortedList->size());
unit_assert_operator_equal(originalList->size(), msLevelStableSortedList->size());
unit_assert_operator_equal(originalList->size(), sillySortedList->size());
SpectrumPtr s;
// assert that the original list is unmodified
unit_assert_operator_equal("scan=19", originalList->spectrumIdentity(0).id);
unit_assert_operator_equal(0, originalList->spectrumIdentity(0).index);
unit_assert_operator_equal("scan=20", originalList->spectrumIdentity(1).id);
unit_assert_operator_equal(1, originalList->spectrumIdentity(1).index);
unit_assert_operator_equal("scan=21", originalList->spectrumIdentity(2).id);
unit_assert_operator_equal(2, originalList->spectrumIdentity(2).index);
unit_assert_operator_equal("scan=22", originalList->spectrumIdentity(3).id);
unit_assert_operator_equal(3, originalList->spectrumIdentity(3).index);
s = originalList->spectrum(0);
unit_assert_operator_equal("scan=19", s->id);
unit_assert_operator_equal(0, s->index);
// validate the default array length sorted list (ascending order, scan=19 and scan=22 are interchangeable)
unit_assert_operator_equal("scan=21", defaultArrayLengthSortedList->spectrumIdentity(0).id);
unit_assert_operator_equal(0, defaultArrayLengthSortedList->spectrumIdentity(0).index);
unit_assert_operator_equal("scan=20", defaultArrayLengthSortedList->spectrumIdentity(1).id);
unit_assert_operator_equal(1, defaultArrayLengthSortedList->spectrumIdentity(1).index);
unit_assert_operator_equal(2, defaultArrayLengthSortedList->spectrumIdentity(2).index);
unit_assert_operator_equal(3, defaultArrayLengthSortedList->spectrumIdentity(3).index);
s = defaultArrayLengthSortedList->spectrum(0);
unit_assert_operator_equal("scan=21", s->id);
unit_assert_operator_equal(0, s->index);
s = defaultArrayLengthSortedList->spectrum(1);
unit_assert_operator_equal("scan=20", s->id);
unit_assert_operator_equal(1, s->index);
s = defaultArrayLengthSortedList->spectrum(2);
unit_assert_operator_equal(2, s->index);
s = defaultArrayLengthSortedList->spectrum(3);
unit_assert_operator_equal(3, s->index);
for (size_t i=1, end=defaultArrayLengthSortedList->size(); i < end; ++i)
unit_assert(defaultArrayLengthSortedList->spectrum(i)->defaultArrayLength >=
defaultArrayLengthSortedList->spectrum(i-1)->defaultArrayLength);
// validate the MS level unstable sorted list (scan=19, scan=21, and scan=22 are interchangeable)
unit_assert_operator_equal(0, msLevelUnstableSortedList->spectrumIdentity(0).index);
unit_assert_operator_equal(1, msLevelUnstableSortedList->spectrumIdentity(1).index);
unit_assert_operator_equal(2, msLevelUnstableSortedList->spectrumIdentity(2).index);
unit_assert_operator_equal("scan=20", msLevelUnstableSortedList->spectrumIdentity(3).id);
unit_assert_operator_equal(3, msLevelUnstableSortedList->spectrumIdentity(3).index);
s = msLevelUnstableSortedList->spectrum(0);
unit_assert_operator_equal(0, s->index);
s = msLevelUnstableSortedList->spectrum(1);
unit_assert_operator_equal(1, s->index);
s = msLevelUnstableSortedList->spectrum(2);
unit_assert_operator_equal(2, s->index);
s = msLevelUnstableSortedList->spectrum(3);
unit_assert_operator_equal("scan=20", s->id);
unit_assert_operator_equal(3, s->index);
// validate the MS level stable sorted list (scan=19, scan=21, and scan=22 should stay in order)
unit_assert_operator_equal("scan=19", msLevelStableSortedList->spectrumIdentity(0).id);
unit_assert_operator_equal(0, msLevelStableSortedList->spectrumIdentity(0).index);
unit_assert_operator_equal("scan=21", msLevelStableSortedList->spectrumIdentity(1).id);
unit_assert_operator_equal(1, msLevelStableSortedList->spectrumIdentity(1).index);
unit_assert_operator_equal("sample=1 period=1 cycle=23 experiment=1", msLevelStableSortedList->spectrumIdentity(2).id);
unit_assert_operator_equal(2, msLevelStableSortedList->spectrumIdentity(2).index);
unit_assert_operator_equal("scan=20", msLevelStableSortedList->spectrumIdentity(3).id);
unit_assert_operator_equal(3, msLevelStableSortedList->spectrumIdentity(3).index);
s = msLevelStableSortedList->spectrum(0);
unit_assert_operator_equal("scan=19", s->id);
unit_assert_operator_equal(0, s->index);
s = msLevelStableSortedList->spectrum(1);
unit_assert_operator_equal("scan=21", s->id);
unit_assert_operator_equal(1, s->index);
s = msLevelStableSortedList->spectrum(2);
unit_assert_operator_equal("sample=1 period=1 cycle=23 experiment=1", s->id);
unit_assert_operator_equal(2, s->index);
s = msLevelStableSortedList->spectrum(3);
unit_assert_operator_equal("scan=20", s->id);
unit_assert_operator_equal(3, s->index);
// validate the silly (nested) sorted list
unit_assert_operator_equal("scan=21", sillySortedList->spectrumIdentity(0).id);
unit_assert_operator_equal(0, sillySortedList->spectrumIdentity(0).index);
unit_assert_operator_equal("scan=20", sillySortedList->spectrumIdentity(1).id);
unit_assert_operator_equal(1, sillySortedList->spectrumIdentity(1).index);
unit_assert_operator_equal(2, sillySortedList->spectrumIdentity(2).index);
unit_assert_operator_equal(3, sillySortedList->spectrumIdentity(3).index);
s = sillySortedList->spectrum(0);
unit_assert_operator_equal("scan=21", s->id);
unit_assert_operator_equal(0, s->index);
s = sillySortedList->spectrum(1);
unit_assert_operator_equal("scan=20", s->id);
unit_assert_operator_equal(1, s->index);
s = sillySortedList->spectrum(2);
unit_assert_operator_equal(2, s->index);
s = sillySortedList->spectrum(3);
unit_assert_operator_equal(3, s->index);
for (size_t i=1, end=sillySortedList->size(); i < end; ++i)
unit_assert(sillySortedList->spectrum(i)->defaultArrayLength >=
sillySortedList->spectrum(i-1)->defaultArrayLength);
}
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");
}
