PWIZ_API_DECL void ChromatogramList_Thermo::createIndex() const
{
for (int controllerType = Controller_MS;
controllerType <= Controller_UV;
++controllerType)
{
long numControllers = rawfile_->getNumberOfControllersOfType((ControllerType) controllerType);
for (long n=1; n <= numControllers; ++n)
{
rawfile_->setCurrentController((ControllerType) controllerType, n);
// skip this controller if it has no spectra
if (rawfile_->value(NumSpectra) == 0)
continue;
switch ((ControllerType) controllerType)
{
case Controller_MS:
{
// support file-level TIC for all file types
index_.push_back(IndexEntry());
IndexEntry& ci = index_.back();
ci.controllerType = (ControllerType) controllerType;
ci.controllerNumber = n;
ci.filter = "";
ci.index = index_.size()-1;
ci.id = "TIC";
ci.chromatogramType = MS_TIC_chromatogram;
idMap_[ci.id] = ci.index;
// for certain filter types, support additional chromatograms
auto_ptr<StringArray> filterArray = rawfile_->getFilters();
ScanFilter filterParser;
for (size_t i=0, ic=filterArray->size(); i < ic; ++i)
{
string filterString = filterArray->item(i);
filterParser.initialize();
filterParser.parse(filterString);
switch (filterParser.scanType_)
{
case ScanType_SRM:
{
// produce spectra rather than a chromatogram
if (config_.srmAsSpectra)
break;
string precursorMZ = (format("%.10g") % filterParser.precursorMZs_[0]).str();
/*index_.push_back(IndexEntry());
IndexEntry& ci = index_.back();
ci.controllerType = (ControllerType) controllerType;
ci.controllerNumber = n;
ci.filter = filterString;
ci.index = index_.size()-1;
ci.id = "SRM TIC " + precursorMZ;
ci.q1 = filterParser.precursorMZs_[0];
idMap_[ci.id] = ci.index;*/
for (size_t j=0, jc=filterParser.scanRangeMin_.size(); j < jc; ++j)
{
index_.push_back(IndexEntry());
IndexEntry& ci = index_.back();
ci.chromatogramType = MS_SRM_chromatogram;
ci.controllerType = (ControllerType) controllerType;
ci.controllerNumber = n;
ci.filter = filterString;
ci.index = index_.size()-1;
ci.q1 = filterParser.precursorMZs_[0];
ci.q3 = (filterParser.scanRangeMin_[j] + filterParser.scanRangeMax_[j]) / 2.0;
ci.id = (format("SRM SIC %s,%.10g")
% precursorMZ
% ci.q3
).str();
ci.q3Offset = (filterParser.scanRangeMax_[j] - filterParser.scanRangeMin_[j]) / 2.0;
idMap_[ci.id] = ci.index;
}
}
break; // case ScanType_SRM
case ScanType_SIM:
{
// produce spectra rather than a chromatogram
if (config_.simAsSpectra)
break;
for (size_t j=0, jc=filterParser.scanRangeMin_.size(); j < jc; ++j)
{
index_.push_back(IndexEntry());
IndexEntry& ci = index_.back();
ci.chromatogramType = MS_SIM_chromatogram;
ci.controllerType = (ControllerType) controllerType;
ci.controllerNumber = n;
ci.filter = filterString;
ci.index = index_.size()-1;
ci.q1 = (filterParser.scanRangeMin_[j] + filterParser.scanRangeMax_[j]) / 2.0;
ci.id = (format("SIM SIC %.10g")
% ci.q1
).str();
// this should be q1Offset
ci.q3Offset = (filterParser.scanRangeMax_[j] - filterParser.scanRangeMin_[j]) / 2.0;
idMap_[ci.id] = ci.index;
}
}
break; // case ScanType_SIM
default:
case ScanType_Full:
/*{
string precursorMZ = lexical_cast<string>(filterParser.precursorMZs_[0]);
index_.push_back(make_pair(ChromatogramIdentity(), filterString));
ChromatogramIdentity& ci = index_.back().first;
ci.index = index_.size()-1;
ci.id = "SIC " + precursorMZ;
idMap_[ci.id] = ci.index;
}*/
break;
}
}
}
break; // case Controller_MS
case Controller_PDA:
{
// "Total Scan" appears to be the equivalent of the TIC
index_.push_back(IndexEntry());
IndexEntry& ci = index_.back();
ci.controllerType = (ControllerType) controllerType;
ci.controllerNumber = n;
ci.index = index_.size()-1;
ci.id = "Total Scan";
ci.chromatogramType = MS_absorption_chromatogram;
idMap_[ci.id] = ci.index;
}
break; // case Controller_PDA
case Controller_Analog:
{
// "ECD" appears to be the equivalent of the TIC
index_.push_back(IndexEntry());
IndexEntry& ci = index_.back();
ci.controllerType = (ControllerType) controllerType;
ci.controllerNumber = n;
ci.index = index_.size()-1;
ci.id = "ECD";
ci.chromatogramType = MS_emission_chromatogram;
idMap_[ci.id] = ci.index;
}
default:
// TODO: are there sensible default chromatograms for other controller types?
break;
}
}
}
/*ostringstream imStream;
std::auto_ptr<LabelValueArray> imArray = rawfile_->getInstrumentMethods();
for(size_t i=0, end=imArray->size(); i < end; ++i)
imStream << imArray->label(i) << imArray->value(i) << endl;
string im = imStream.str();
// Parent Center Width Time CE Q1PW Q3PW TubeLens
boost::regex scanEventRegex("^\S+\s+\S+\s+\S+\s+\S+\s+\S+\s+\S+\s+\S+\s+\S+\s+$");*/
}
PWIZ_API_DECL ChromatogramPtr ChromatogramList_Thermo::chromatogram(size_t index, bool getBinaryData) const
{
boost::call_once(indexInitialized_.flag, boost::bind(&ChromatogramList_Thermo::createIndex, this));
if (index>size())
throw runtime_error(("[ChromatogramList_Thermo::chromatogram()] Bad index: "
+ lexical_cast<string>(index)).c_str());
const IndexEntry& ci = index_[index];
ChromatogramPtr result(new Chromatogram);
result->index = ci.index;
result->id = ci.id;
result->set(ci.chromatogramType);
rawfile_->setCurrentController(ci.controllerType, ci.controllerNumber);
switch (ci.chromatogramType)
{
default:
break;
case MS_TIC_chromatogram:
{
ChromatogramDataPtr cd = rawfile_->getChromatogramData(
Type_TIC, Operator_None, Type_MassRange,
"", "", "", 0,
0, rawfile_->rt(rawfile_->value(NumSpectra)),
Smoothing_None, 0);
pwiz::msdata::TimeIntensityPair* data = reinterpret_cast<pwiz::msdata::TimeIntensityPair*>(cd->data());
if (getBinaryData) result->setTimeIntensityPairs(data, cd->size(), UO_minute, MS_number_of_counts);
else result->defaultArrayLength = cd->size();
}
break;
case MS_SIC_chromatogram: // generate SIC for <precursor>
{
ChromatogramDataPtr cd = rawfile_->getChromatogramData(
Type_BasePeak, Operator_None, Type_MassRange,
index_[index].filter, "", "", 0,
0, rawfile_->rt(rawfile_->value(NumSpectra)),
Smoothing_None, 0);
pwiz::msdata::TimeIntensityPair* data = reinterpret_cast<pwiz::msdata::TimeIntensityPair*>(cd->data());
if (getBinaryData) result->setTimeIntensityPairs(data, cd->size(), UO_minute, MS_number_of_counts);
else result->defaultArrayLength = cd->size();
}
break;
/*case 3: // generate SRM TIC for <precursor>
{
vector<string> tokens;
bal::split(tokens, ci.id, bal::is_any_of(" "));
ChromatogramDataPtr cd = rawfile_->getChromatogramData(
Type_TIC, Operator_None, Type_MassRange,
"ms2 " + tokens[2], "", "", 0,
0, rawfile_->rt(rawfile_->value(NumSpectra)),
Smoothing_None, 0);
pwiz::msdata::TimeIntensityPair* data = reinterpret_cast<pwiz::msdata::TimeIntensityPair*>(cd->data());
if (getBinaryData) result->setTimeIntensityPairs(data, cd->size(), UO_minute, MS_number_of_counts);
else result->defaultArrayLength = cd->size();
}
break;*/
case MS_SRM_chromatogram:
{
result->precursor.isolationWindow.set(MS_isolation_window_target_m_z, ci.q1, MS_m_z);
ScanFilter filterParser;
filterParser.parse(ci.filter);
ActivationType activationType = filterParser.activationType_;
if (activationType == ActivationType_Unknown)
activationType = ActivationType_CID; // assume CID
SetActivationType(activationType, result->precursor.activation);
if (filterParser.activationType_ == ActivationType_CID)
result->precursor.activation.set(MS_collision_energy, filterParser.precursorEnergies_[0]);
result->product.isolationWindow.set(MS_isolation_window_target_m_z, ci.q3, MS_m_z);
result->product.isolationWindow.set(MS_isolation_window_lower_offset, ci.q3Offset, MS_m_z);
result->product.isolationWindow.set(MS_isolation_window_upper_offset, ci.q3Offset, MS_m_z);
string q1 = (format("%.10g") % ci.q1).str();
string q3Range = (format("%.10g-%.10g")
% (ci.q3 - ci.q3Offset)
% (ci.q3 + ci.q3Offset)
).str();
ChromatogramDataPtr cd = rawfile_->getChromatogramData(
Type_MassRange, Operator_None, Type_MassRange,
"SRM ms2 " + q1, q3Range, "", 0,
0, rawfile_->rt(rawfile_->value(NumSpectra)),
Smoothing_None, 0);
pwiz::msdata::TimeIntensityPair* data = reinterpret_cast<pwiz::msdata::TimeIntensityPair*>(cd->data());
if (getBinaryData) result->setTimeIntensityPairs(data, cd->size(), UO_minute, MS_number_of_counts);
else result->defaultArrayLength = cd->size();
}
break;
case MS_SIM_chromatogram:
{
result->precursor.isolationWindow.set(MS_isolation_window_target_m_z, ci.q1, MS_m_z);
result->precursor.isolationWindow.set(MS_isolation_window_lower_offset, ci.q3Offset, MS_m_z);
result->precursor.isolationWindow.set(MS_isolation_window_upper_offset, ci.q3Offset, MS_m_z);
string q1Range = (format("%.10g-%.10g")
% (ci.q1 - ci.q3Offset)
% (ci.q1 + ci.q3Offset)
).str();
ChromatogramDataPtr cd = rawfile_->getChromatogramData(
Type_MassRange, Operator_None, Type_MassRange,
"SIM ms [" + q1Range + "]", q1Range, "", 0,
0, rawfile_->rt(rawfile_->value(NumSpectra)),
Smoothing_None, 0);
pwiz::msdata::TimeIntensityPair* data = reinterpret_cast<pwiz::msdata::TimeIntensityPair*>(cd->data());
if (getBinaryData) result->setTimeIntensityPairs(data, cd->size(), UO_minute, MS_number_of_counts);
else result->defaultArrayLength = cd->size();
}
break;
case MS_absorption_chromatogram: // generate "Total Scan" chromatogram for entire run
{
ChromatogramDataPtr cd = rawfile_->getChromatogramData(
Type_TotalScan, Operator_None, Type_MassRange,
"", "", "", 0,
0, rawfile_->rt(rawfile_->value(NumSpectra)),
Smoothing_None, 0);
pwiz::msdata::TimeIntensityPair* data = reinterpret_cast<pwiz::msdata::TimeIntensityPair*>(cd->data());
if (getBinaryData) result->setTimeIntensityPairs(data, cd->size(), UO_minute, MS_number_of_counts);
else result->defaultArrayLength = cd->size();
}
break;
case MS_mass_chromatogram: // generate "ECD" chromatogram for entire run
{
ChromatogramDataPtr cd = rawfile_->getChromatogramData(
Type_ECD, Operator_None, Type_MassRange,
"", "", "", 0,
0, std::numeric_limits<double>::max(),
Smoothing_None, 0);
pwiz::msdata::TimeIntensityPair* data = reinterpret_cast<pwiz::msdata::TimeIntensityPair*>(cd->data());
if (getBinaryData) result->setTimeIntensityPairs(data, cd->size(), UO_minute, MS_number_of_counts);
else result->defaultArrayLength = cd->size();
}
break;
}
return result;
}
int main(int argc, char* argv[])
{
try
{
if (argc > 2)
throw runtime_error("Usage: ScanFilterTest [Thermo RAW filename]");
else if (argc == 1)
{
// unit test static strings
for (size_t i=0; i < testScanFiltersSize; ++i)
{
const TestScanFilter& f = testScanFilters[i];
try
{
vector<double> cidParentMass = parseDoubleArray(f.cidParentMassArray);
vector<double> cidParentEnergy = parseDoubleArray(f.cidEnergyArray);
vector<double> scanRangeMin = parseDoubleArray(f.scanRangeMinArray);
vector<double> scanRangeMax = parseDoubleArray(f.scanRangeMaxArray);
double compensationVoltage = 0.0;
if (string(f.compensationVoltage) != "")
compensationVoltage = lexical_cast<double> (f.compensationVoltage);
ScanFilter scanFilter;
scanFilter.parse(f.filter);
testFilter(scanFilter,
f.scanSegment,
f.scanEvent,
f.accurateMassType,
f.coronaOn,
f.detectorSet,
f.photoIonizationOn,
f.sourceCIDOn,
f.turboScanOn,
f.supplementalCIDOn,
f.widebandOn,
f.enhancedOn,
f.dependentActive,
f.lockMassOn,
f.faimsOn,
compensationVoltage,
f.massAnalyzerType,
f.polarityType,
f.dataPointType,
f.ionizationType,
f.scanType,
f.msLevel,
cidParentMass,
cidParentEnergy,
scanRangeMin,
scanRangeMax);
}
catch (exception& e)
{
cout << "Unit test on filter \"" << f.filter << "\" failed:\n" << e.what() << endl;
}
}
}
return 0;
}
catch (exception& e)
{
cout << "Caught exception: " << e.what() << endl;
}
catch (...)
{
cout << "Caught unknown exception.\n";
}
return 1;
}