void initializeAnalyzers(MSDataAnalyzerContainer& analyzers,
const vector<string>& commands)
{
shared_ptr<MSDataCache> cache(new MSDataCache);
analyzers.push_back(cache);
for (vector<string>::const_iterator it=commands.begin(); it!=commands.end(); ++it)
{
string name, args;
istringstream iss(*it);
iss >> name;
getline(iss, args);
if (supportedAnalyzer(name, analyzer_strings<MetadataReporter>::id()))
{
MSDataAnalyzerPtr anal(new MetadataReporter);
analyzers.push_back(anal);
}
else if (supportedAnalyzer(name, analyzer_strings<RunSummary>::id()))
{
MSDataAnalyzerPtr anal(new RunSummary(*cache, args));
analyzers.push_back(anal);
}
else if (supportedAnalyzer(name, analyzer_strings<SpectrumTable>::id()))
{
MSDataAnalyzerPtr anal(new SpectrumTable(*cache, args));
analyzers.push_back(anal);
}
else if (supportedAnalyzer(name, analyzer_strings<SpectrumBinaryData>::id()))
{
MSDataAnalyzerPtr anal(new SpectrumBinaryData(*cache, args));
analyzers.push_back(anal);
}
else if (supportedAnalyzer(name, analyzer_strings<RegionSlice>::id()))
{
MSDataAnalyzerPtr anal(new RegionSlice(*cache, args));
analyzers.push_back(anal);
}
else if (supportedAnalyzer(name, analyzer_strings<RegionTIC>::id()))
{
MSDataAnalyzerPtr anal(new RegionTIC(*cache, args));
analyzers.push_back(anal);
}
else if (supportedAnalyzer(name, analyzer_strings<RegionSIC>::id()))
{
MSDataAnalyzerPtr anal(new RegionSIC(*cache, args));
analyzers.push_back(anal);
}
else if (supportedAnalyzer(name, analyzer_strings<Pseudo2DGel>::id()))
{
MSDataAnalyzerPtr anal(new Pseudo2DGel(*cache, args));
analyzers.push_back(anal);
}
else
{
cerr << "Unknown analysis command \"" << name << "\". Expected one of:" << supportedAnalyzers << "." << endl;
}
}
}
void testUpdateRequest()
{
if (os_) *os_ << "testUpdateRequest()\n";
vector<MZIntensityPair> pairs(100);
SpectrumListSimplePtr sl(new SpectrumListSimple);
for (size_t i=0; i<10; i++)
{
SpectrumPtr spectrum(new Spectrum);
spectrum->setMZIntensityPairs(pairs, MS_number_of_detector_counts);
spectrum->index = i;
spectrum->id = "scan=" + lexical_cast<string>(i);
sl->spectra.push_back(spectrum);
}
MSData msd;
msd.run.spectrumListPtr = sl;
MSDataAnalyzerContainer analyzers;
shared_ptr<MSDataCache> cache(new MSDataCache);
analyzers.push_back(cache);
analyzers.push_back(MSDataAnalyzerPtr(new EvenRequester));
MSDataAnalyzerDriver driver(analyzers);
driver.analyze(msd);
for (size_t i=0, end=cache->size(); i<end; i++)
{
const SpectrumInfo& info = cache->at(i);
if (os_) *os_ << info.index << " " << info.id << endl;
// cache has only been updated with the spectra requested by EvenRequester
unit_assert(i%2==0 && info.index==i && info.id=="scan="+lexical_cast<string>(i) ||
i%2==1 && info.index==(size_t)-1&& info.id.empty());
}
if (os_) *os_ << endl;
}
void testConfig(const RegionAnalyzer::Config& config)
{
MSData msd;
initialize(msd);
shared_ptr<MSDataCache> cache(new MSDataCache);
shared_ptr<RegionAnalyzer> regionAnalyzer(new RegionAnalyzer(config, *cache));
MSDataAnalyzerContainer analyzers;
analyzers.push_back(cache);
analyzers.push_back(regionAnalyzer);
MSDataAnalyzerDriver driver(analyzers);
driver.analyze(msd);
unit_assert(regionAnalyzer->spectrumStats().size() == 5);
if (os_) *os_ << "sumIntensity (max) (peak):\n";
vector<RegionAnalyzer::SpectrumStats>::const_iterator it =
regionAnalyzer->spectrumStats().begin();
if (os_) *os_ << *it << endl;
unit_assert(it->sumIntensity == 0);
unit_assert_equal(it->max.mz, 0, epsilon_);
unit_assert_equal(it->max.intensity, 0, epsilon_);
unit_assert_equal(it->peak.mz, 0, epsilon_);
unit_assert_equal(it->peak.intensity, 0, epsilon_);
++it;
if (os_) *os_ << *it << endl;
unit_assert(it->sumIntensity == 5);
unit_assert_equal(it->max.mz, 3.1, epsilon_);
unit_assert_equal(it->max.intensity, 2, epsilon_);
unit_assert_equal(it->peak.mz, 3.1, epsilon_);
unit_assert_equal(it->peak.intensity, 2, epsilon_);
++it;
if (os_) *os_ << *it << endl;
unit_assert(it->sumIntensity == 6); // with omitted sample intensity 4
unit_assert_equal(it->max.mz, 1.9, epsilon_);
unit_assert_equal(it->max.intensity, 3, epsilon_);
unit_assert_equal(it->peak.mz, 2.9, epsilon_); // found the peak by interpolation
unit_assert_equal(it->peak.intensity, 4, epsilon_);
++it;
if (os_) *os_ << *it << endl;
unit_assert(it->sumIntensity == 5);
unit_assert_equal(it->max.mz, 3.1, epsilon_);
unit_assert_equal(it->max.intensity, 2, epsilon_);
unit_assert_equal(it->peak.mz, 3.1, epsilon_);
unit_assert_equal(it->peak.intensity, 2, epsilon_);
++it;
if (os_) *os_ << *it << endl;
unit_assert(it->sumIntensity == 0);
unit_assert_equal(it->max.mz, 0, epsilon_);
unit_assert_equal(it->max.intensity, 0, epsilon_);
unit_assert_equal(it->peak.mz, 0, epsilon_);
unit_assert_equal(it->peak.intensity, 0, epsilon_);
// Stats
const RegionAnalyzer::Stats& stats = regionAnalyzer->stats();
if (os_) *os_ << stats << endl;
unit_assert(stats.nonzeroCount == 3);
unit_assert_equal(stats.sum_sumIntensity, 16, epsilon_);
unit_assert_equal(stats.sum_peak_intensity, 8, epsilon_);
unit_assert_equal(stats.mean_peak_mz, 3, epsilon_);
unit_assert_equal(stats.variance_peak_mz, .01, epsilon_);
unit_assert_equal(stats.sd_peak_mz, .1, epsilon_);
unit_assert(stats.indexApex == 2);
}