int main()
{
// Insert of two features into a map and iterate over the features.
FeatureMap map;
Feature feature;
feature.setRT(15.0);
feature.setMZ(571.3);
map.push_back(feature); //append feature 1
feature.setRT(23.3);
feature.setMZ(1311.3);
map.push_back(feature); //append feature 2
// Iteration over FeatureMap
for (auto it = map.begin(); it != map.end(); ++it)
{
cout << it->getRT() << " - " << it->getMZ() << endl;
}
// Calculate and output the ranges
map.updateRanges();
cout << "Int: " << map.getMinInt() << " - " << map.getMaxInt() << endl;
cout << "RT: " << map.getMin()[0] << " - " << map.getMax()[0] << endl;
cout << "m/z: " << map.getMin()[1] << " - " << map.getMax()[1] << endl;
// ... and many more
return 0;
} //end of main
ExitCodes main_(int, const char **)
{
String in = getStringOption_("in"), out = getStringOption_("out");
FileTypes::Type in_type = FileHandler::getType(in);
if (in_type == FileTypes::FEATUREXML)
{
FeatureMap<> features;
FeatureXMLFile().load(in, features);
for (FeatureMap<>::Iterator feat_it = features.begin();
feat_it != features.end(); ++feat_it)
{
resolveConflict_(feat_it->getPeptideIdentifications());
}
addDataProcessing_(features,
getProcessingInfo_(DataProcessing::FILTERING));
FeatureXMLFile().store(out, features);
}
else // consensusXML
{
ConsensusMap consensus;
ConsensusXMLFile().load(in, consensus);
for (ConsensusMap::Iterator cons_it = consensus.begin();
cons_it != consensus.end(); ++cons_it)
{
resolveConflict_(cons_it->getPeptideIdentifications());
}
addDataProcessing_(consensus,
getProcessingInfo_(DataProcessing::FILTERING));
ConsensusXMLFile().store(out, consensus);
}
return EXECUTION_OK;
}
CAddonButtonMap::DriverMap CAddonButtonMap::CreateLookupTable(const FeatureMap& features)
{
using namespace JOYSTICK;
DriverMap driverMap;
for (FeatureMap::const_iterator it = features.begin(); it != features.end(); ++it)
{
const ADDON::JoystickFeature& feature = it->second;
switch (feature.Type())
{
case JOYSTICK_FEATURE_TYPE_SCALAR:
{
driverMap[CPeripheralAddonTranslator::TranslatePrimitive(feature.Primitive(JOYSTICK_SCALAR_PRIMITIVE))] = it->first;
break;
}
case JOYSTICK_FEATURE_TYPE_ANALOG_STICK:
{
std::vector<JOYSTICK_FEATURE_PRIMITIVE> primitives = {
JOYSTICK_ANALOG_STICK_UP,
JOYSTICK_ANALOG_STICK_DOWN,
JOYSTICK_ANALOG_STICK_RIGHT,
JOYSTICK_ANALOG_STICK_LEFT,
};
for (auto primitive : primitives)
driverMap[CPeripheralAddonTranslator::TranslatePrimitive(feature.Primitive(primitive))] = it->first;
break;
}
case JOYSTICK_FEATURE_TYPE_ACCELEROMETER:
{
std::vector<JOYSTICK_FEATURE_PRIMITIVE> primitives = {
JOYSTICK_ACCELEROMETER_POSITIVE_X,
JOYSTICK_ACCELEROMETER_POSITIVE_Y,
JOYSTICK_ACCELEROMETER_POSITIVE_Z,
};
for (auto primitive : primitives)
{
CDriverPrimitive translatedPrimitive = CPeripheralAddonTranslator::TranslatePrimitive(feature.Primitive(primitive));
driverMap[translatedPrimitive] = it->first;
// Map opposite semiaxis
CDriverPrimitive oppositePrimitive = CDriverPrimitive(translatedPrimitive.Index(), 0, translatedPrimitive.SemiAxisDirection() * -1, 1);
driverMap[oppositePrimitive] = it->first;
}
break;
}
default:
break;
}
}
return driverMap;
}
double length_sq() {
double l = 0.0;
FeatureIterator fit;
for (fit = feat_map.begin(); fit != feat_map.end(); fit++) {
Feature &f = fit->second;
l += f.value * f.value;
}
return l;
}
void SeedListGenerator::convertSeedList(const FeatureMap& features,
SeedList& seeds)
{
seeds.clear();
for (FeatureMap::ConstIterator feat_it = features.begin();
feat_it != features.end(); ++feat_it)
{
DPosition<2> point(feat_it->getRT(), feat_it->getMZ());
seeds.push_back(point);
}
}
CAddonButtonMap::DriverMap CAddonButtonMap::CreateLookupTable(const FeatureMap& features)
{
DriverMap driverMap;
for (FeatureMap::const_iterator it = features.begin(); it != features.end(); ++it)
{
const ADDON::JoystickFeature& feature = it->second;
switch (feature.Type())
{
case JOYSTICK_FEATURE_TYPE_SCALAR:
{
driverMap[CPeripheralAddonTranslator::TranslatePrimitive(feature.Primitive())] = it->first;
break;
}
case JOYSTICK_FEATURE_TYPE_ANALOG_STICK:
{
driverMap[CPeripheralAddonTranslator::TranslatePrimitive(feature.Up())] = it->first;
driverMap[CPeripheralAddonTranslator::TranslatePrimitive(feature.Down())] = it->first;
driverMap[CPeripheralAddonTranslator::TranslatePrimitive(feature.Right())] = it->first;
driverMap[CPeripheralAddonTranslator::TranslatePrimitive(feature.Left())] = it->first;
break;
}
case JOYSTICK_FEATURE_TYPE_ACCELEROMETER:
{
CDriverPrimitive x_axis(CPeripheralAddonTranslator::TranslatePrimitive(feature.PositiveX()));
CDriverPrimitive y_axis(CPeripheralAddonTranslator::TranslatePrimitive(feature.PositiveY()));
CDriverPrimitive z_axis(CPeripheralAddonTranslator::TranslatePrimitive(feature.PositiveZ()));
driverMap[x_axis] = it->first;
driverMap[y_axis] = it->first;
driverMap[z_axis] = it->first;
CDriverPrimitive x_axis_opposite(x_axis.Index(), x_axis.SemiAxisDirection() * -1);
CDriverPrimitive y_axis_opposite(y_axis.Index(), y_axis.SemiAxisDirection() * -1);
CDriverPrimitive z_axis_opposite(z_axis.Index(), z_axis.SemiAxisDirection() * -1);
driverMap[x_axis_opposite] = it->first;
driverMap[y_axis_opposite] = it->first;
driverMap[z_axis_opposite] = it->first;
break;
}
default:
break;
}
}
return driverMap;
}
void markFeatureLocations_(FeatureMap & feature_map, MSExperiment<> & exp, QImage & image, bool transpose, QColor color)
{
double xcoef = image.width(), ycoef = image.height();
if (transpose)
{
xcoef /= exp.getMaxRT() - exp.getMinRT();
ycoef /= exp.getMaxMZ() - exp.getMinMZ();
}
else
{
xcoef /= exp.getMaxMZ() - exp.getMinMZ();
ycoef /= exp.getMaxRT() - exp.getMinRT();
}
for (FeatureMap::Iterator feat_iter = feature_map.begin();
feat_iter != feature_map.end(); ++feat_iter)
{
const ConvexHull2D convex_hull = feat_iter->getConvexHull();
DBoundingBox<2> box = convex_hull.getBoundingBox();
double rt = feat_iter->getRT();
double mz = feat_iter->getMZ();
double lower_mz = box.minY();
double lower_rt = box.minX();
double upper_mz = box.maxY();
double upper_rt = box.maxX();
int lx, ly, ux, uy, cx, cy;
if (transpose)
{
lx = int(xcoef * (lower_rt - exp.getMinRT()));
ly = int(ycoef * (exp.getMaxMZ() - lower_mz));
ux = int(xcoef * (upper_rt - exp.getMinRT()));
uy = int(ycoef * (exp.getMaxMZ() - upper_mz));
cx = int(xcoef * (rt - exp.getMinRT()));
cy = int(ycoef * (mz - lower_mz));
}
else
{
lx = int(xcoef * (lower_mz - exp.getMinMZ()));
ly = int(ycoef * (exp.getMaxRT() - lower_rt));
ux = int(xcoef * (upper_mz - exp.getMinMZ()));
uy = int(ycoef * (exp.getMaxRT() - upper_rt));
cx = int(xcoef * (mz - exp.getMinMZ()));
cy = int(ycoef * (exp.getMaxRT() - rt));
}
addFeatureBox_(ly, lx, uy, ux, image, color);
addPoint_(cx, cy, image, Qt::black); // mark center
}
}
void MapAlignmentTransformer::transformSingleFeatureMap(FeatureMap<> & fmap,
const TransformationDescription & trafo)
{
for (vector<Feature>::iterator fmit = fmap.begin(); fmit != fmap.end(); ++fmit)
{
applyToFeature_(*fmit, trafo);
}
// adapt RT values of unassigned peptides:
if (!fmap.getUnassignedPeptideIdentifications().empty())
{
transformSinglePeptideIdentification(
fmap.getUnassignedPeptideIdentifications(), trafo);
}
}
void QuantitativeExperimentalDesign::mergeFeatureMaps_(FeatureMap<> & out, const String & experiment, StringList & file_paths)
{
FeatureMap<> map;
LOG_INFO << "Merge feature maps: " << endl;
UInt counter = 1;
for (StringList::Iterator file_it = file_paths.begin(); file_it != file_paths.end(); ++file_it, ++counter)
{
//load should clear the map
FeatureXMLFile().load(*file_it, map);
for (FeatureMap<>::iterator it = map.begin(); it != map.end(); ++it)
{
it->setMetaValue("experiment", DataValue(experiment));
}
out += map;
}
}
void MapAlignmentTransformer::transformRetentionTimes(
FeatureMap& fmap, const TransformationDescription& trafo,
bool store_original_rt)
{
for (vector<Feature>::iterator fmit = fmap.begin(); fmit != fmap.end();
++fmit)
{
applyToFeature_(*fmit, trafo, store_original_rt);
}
// adapt RT values of unassigned peptides:
if (!fmap.getUnassignedPeptideIdentifications().empty())
{
transformRetentionTimes(fmap.getUnassignedPeptideIdentifications(), trafo,
store_original_rt);
}
}
Int main()
{
FeatureMap map;
Feature feature;
feature.setRT(15.0);
feature.setMZ(571.3);
map.push_back(feature); //append feature 1
feature.setRT(23.3);
feature.setMZ(1311.3);
map.push_back(feature); //append feature 2
for (FeatureMap::Iterator it = map.begin(); it != map.end(); ++it)
{
cout << it->getRT() << " - " << it->getMZ() << endl;
}
return 0;
} //end of main
ExitCodes main_(int, const char**)
{
//input file names
String in = getStringOption_("in");
String out = getStringOption_("out");
String out_mzq = getStringOption_("out_mzq");
//prevent loading of fragment spectra
PeakFileOptions options;
options.setMSLevels(vector<Int>(1, 1));
//reading input data
MzMLFile f;
f.getOptions() = options;
f.setLogType(log_type_);
PeakMap exp;
f.load(in, exp);
exp.updateRanges();
if (exp.getSpectra().empty())
{
throw OpenMS::Exception::FileEmpty(__FILE__, __LINE__, __FUNCTION__, "Error: No MS1 spectra in input file.");
}
// determine type of spectral data (profile or centroided)
SpectrumSettings::SpectrumType spectrum_type = exp[0].getType();
if (spectrum_type == SpectrumSettings::RAWDATA)
{
if (!getFlag_("force"))
{
throw OpenMS::Exception::IllegalArgument(__FILE__, __LINE__, __FUNCTION__, "Error: Profile data provided but centroided spectra expected. To enforce processing of the data set the -force flag.");
}
}
//load seeds
FeatureMap seeds;
if (getStringOption_("seeds") != "")
{
FeatureXMLFile().load(getStringOption_("seeds"), seeds);
}
//setup of FeatureFinder
FeatureFinder ff;
ff.setLogType(log_type_);
// A map for the resulting features
FeatureMap features;
// get parameters specific for the feature finder
Param feafi_param = getParam_().copy("algorithm:", true);
writeDebug_("Parameters passed to FeatureFinder", feafi_param, 3);
// Apply the feature finder
ff.run(FeatureFinderAlgorithmPicked::getProductName(), exp, features, feafi_param, seeds);
features.applyMemberFunction(&UniqueIdInterface::setUniqueId);
// DEBUG
if (debug_level_ > 10)
{
FeatureMap::Iterator it;
for (it = features.begin(); it != features.end(); ++it)
{
if (!it->isMetaEmpty())
{
vector<String> keys;
it->getKeys(keys);
LOG_INFO << "Feature " << it->getUniqueId() << endl;
for (Size i = 0; i < keys.size(); i++)
{
LOG_INFO << " " << keys[i] << " = " << it->getMetaValue(keys[i]) << endl;
}
}
}
}
//-------------------------------------------------------------
// writing files
//-------------------------------------------------------------
//annotate output with data processing info
addDataProcessing_(features, getProcessingInfo_(DataProcessing::QUANTITATION));
// write features to user specified output file
FeatureXMLFile map_file;
// Remove detailed convex hull information and subordinate features
// (unless requested otherwise) to reduce file size of feature files
// unless debugging is turned on.
if (debug_level_ < 5)
{
FeatureMap::Iterator it;
for (it = features.begin(); it != features.end(); ++it)
{
it->getConvexHull().expandToBoundingBox();
for (Size i = 0; i < it->getConvexHulls().size(); ++i)
{
it->getConvexHulls()[i].expandToBoundingBox();
}
it->getSubordinates().clear();
}
}
map_file.store(out, features);
if (!out_mzq.trim().empty())
{
MSQuantifications msq(features, exp.getExperimentalSettings(), exp[0].getDataProcessing());
msq.assignUIDs();
MzQuantMLFile file;
file.store(out_mzq, msq);
}
return EXECUTION_OK;
}
ExitCodes main_(int, const char**)
{
//-------------------------------------------------------------
// parameter handling
//-------------------------------------------------------------
// file list
StringList file_list = getStringList_("in");
// file type
FileHandler file_handler;
FileTypes::Type force_type;
if (getStringOption_("in_type").size() > 0)
{
force_type = FileTypes::nameToType(getStringOption_("in_type"));
}
else
{
force_type = file_handler.getType(file_list[0]);
}
// output file names and types
String out_file = getStringOption_("out");
bool annotate_file_origin = getFlag_("annotate_file_origin");
rt_gap_ = getDoubleOption_("rt_concat:gap");
vector<String> trafo_out = getStringList_("rt_concat:trafo_out");
if (trafo_out.empty())
{
// resize now so we don't have to worry about indexing out of bounds:
trafo_out.resize(file_list.size());
}
else if (trafo_out.size() != file_list.size())
{
writeLog_("Error: Number of transformation output files must equal the number of input files (parameters 'rt_concat:trafo_out'/'in')!");
return ILLEGAL_PARAMETERS;
}
//-------------------------------------------------------------
// calculations
//-------------------------------------------------------------
if (force_type == FileTypes::FEATUREXML)
{
FeatureMap out;
FeatureXMLFile fh;
for (Size i = 0; i < file_list.size(); ++i)
{
FeatureMap map;
fh.load(file_list[i], map);
if (annotate_file_origin)
{
for (FeatureMap::iterator it = map.begin(); it != map.end(); ++it)
{
it->setMetaValue("file_origin", DataValue(file_list[i]));
}
}
if (rt_gap_ > 0.0) // concatenate in RT
{
adjustRetentionTimes_(map, trafo_out[i], i == 0);
}
out += map;
}
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
// annotate output with data processing info
addDataProcessing_(out, getProcessingInfo_(DataProcessing::FORMAT_CONVERSION));
fh.store(out_file, out);
}
else if (force_type == FileTypes::CONSENSUSXML)
{
ConsensusMap out;
ConsensusXMLFile fh;
fh.load(file_list[0], out);
// skip first file
for (Size i = 1; i < file_list.size(); ++i)
{
ConsensusMap map;
fh.load(file_list[i], map);
if (annotate_file_origin)
{
for (ConsensusMap::iterator it = map.begin(); it != map.end(); ++it)
{
it->setMetaValue("file_origin", DataValue(file_list[i]));
}
}
if (rt_gap_ > 0.0) // concatenate in RT
{
adjustRetentionTimes_(map, trafo_out[i], i == 0);
}
out += map;
}
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
// annotate output with data processing info
addDataProcessing_(out, getProcessingInfo_(DataProcessing::FORMAT_CONVERSION));
fh.store(out_file, out);
}
else if (force_type == FileTypes::TRAML)
{
TargetedExperiment out;
TraMLFile fh;
for (Size i = 0; i < file_list.size(); ++i)
{
TargetedExperiment map;
fh.load(file_list[i], map);
out += map;
}
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
// annotate output with data processing info
Software software;
software.setName("FileMerger");
software.setVersion(VersionInfo::getVersion());
out.addSoftware(software);
fh.store(out_file, out);
}
else // raw data input (e.g. mzML)
{
// RT
bool rt_auto_number = getFlag_("raw:rt_auto");
bool rt_filename = getFlag_("raw:rt_filename");
bool rt_custom = false;
DoubleList custom_rts = getDoubleList_("raw:rt_custom");
if (!custom_rts.empty())
{
rt_custom = true;
if (custom_rts.size() != file_list.size())
{
writeLog_("Custom retention time list (parameter 'raw:rt_custom') must have as many elements as there are input files (parameter 'in')!");
return ILLEGAL_PARAMETERS;
}
}
// MS level
Int ms_level = getIntOption_("raw:ms_level");
MSExperiment<> out;
UInt rt_auto = 0;
UInt native_id = 0;
for (Size i = 0; i < file_list.size(); ++i)
{
String filename = file_list[i];
// load file
force_type = file_handler.getType(file_list[i]);
MSExperiment<> in;
file_handler.loadExperiment(filename, in, force_type, log_type_);
if (in.empty() && in.getChromatograms().empty())
{
writeLog_(String("Warning: Empty file '") + filename + "'!");
continue;
}
out.reserve(out.size() + in.size());
// warn if custom RT and more than one scan in input file
if (rt_custom && in.size() > 1)
{
writeLog_(String("Warning: More than one scan in file '") + filename + "'! All scans will have the same retention time!");
}
// handle special raw data options:
for (MSExperiment<>::iterator spec_it = in.begin();
spec_it != in.end(); ++spec_it)
{
float rt_final = spec_it->getRT();
if (rt_auto_number)
{
rt_final = ++rt_auto;
}
else if (rt_custom)
{
rt_final = custom_rts[i];
}
else if (rt_filename)
{
static const boost::regex re("rt(\\d+(\\.\\d+)?)");
boost::smatch match;
bool found = boost::regex_search(filename, match, re);
if (found)
{
rt_final = String(match[1]).toFloat();
}
else
{
writeLog_("Warning: could not extract retention time from filename '" + filename + "'");
}
}
// none of the rt methods were successful
if (rt_final < 0)
{
writeLog_(String("Warning: No valid retention time for output scan '") + rt_auto + "' from file '" + filename + "'");
}
spec_it->setRT(rt_final);
spec_it->setNativeID("spectrum=" + String(native_id));
if (ms_level > 0)
{
spec_it->setMSLevel(ms_level);
}
++native_id;
}
// if we have only one spectrum, we can annotate it directly, for more spectra, we just name the source file leaving the spectra unannotated (to avoid a long and redundant list of sourceFiles)
if (in.size() == 1)
{
in[0].setSourceFile(in.getSourceFiles()[0]);
in.getSourceFiles().clear(); // delete source file annotated from source file (it's in the spectrum anyways)
}
if (rt_gap_ > 0.0) // concatenate in RT
{
adjustRetentionTimes_(in, trafo_out[i], i == 0);
}
// add spectra to output
for (MSExperiment<>::const_iterator spec_it = in.begin();
spec_it != in.end(); ++spec_it)
{
out.addSpectrum(*spec_it);
}
// also add the chromatograms
for (vector<MSChromatogram<ChromatogramPeak> >::const_iterator
chrom_it = in.getChromatograms().begin(); chrom_it !=
in.getChromatograms().end(); ++chrom_it)
{
out.addChromatogram(*chrom_it);
}
// copy experimental settings from first file
if (i == 0)
{
out.ExperimentalSettings::operator=(in);
}
else // otherwise append
{
out.getSourceFiles().insert(out.getSourceFiles().end(), in.getSourceFiles().begin(), in.getSourceFiles().end()); // could be emtpty if spectrum was annotated above, but that's ok then
}
}
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
// annotate output with data processing info
addDataProcessing_(out, getProcessingInfo_(DataProcessing::FORMAT_CONVERSION));
MzMLFile f;
f.setLogType(log_type_);
f.store(out_file, out);
}
return EXECUTION_OK;
}
ExitCodes main_(int, const char **)
{
String in = getStringOption_("in"), out = getStringOption_("out"),
id_out = getStringOption_("id_out");
if (out.empty() && id_out.empty())
{
throw Exception::RequiredParameterNotGiven(__FILE__, __LINE__,
__PRETTY_FUNCTION__,
"out/id_out");
}
vector<ProteinIdentification> proteins;
vector<PeptideIdentification> peptides;
FileTypes::Type in_type = FileHandler::getType(in);
if (in_type == FileTypes::MZML)
{
MSExperiment<> experiment;
MzMLFile().load(in, experiment);
// what about unassigned peptide IDs?
for (MSExperiment<>::Iterator exp_it = experiment.begin();
exp_it != experiment.end(); ++exp_it)
{
peptides.insert(peptides.end(),
exp_it->getPeptideIdentifications().begin(),
exp_it->getPeptideIdentifications().end());
exp_it->getPeptideIdentifications().clear();
}
experiment.getProteinIdentifications().swap(proteins);
if (!out.empty())
{
addDataProcessing_(experiment,
getProcessingInfo_(DataProcessing::FILTERING));
MzMLFile().store(out, experiment);
}
}
else if (in_type == FileTypes::FEATUREXML)
{
FeatureMap features;
FeatureXMLFile().load(in, features);
features.getUnassignedPeptideIdentifications().swap(peptides);
for (FeatureMap::Iterator feat_it = features.begin();
feat_it != features.end(); ++feat_it)
{
peptides.insert(peptides.end(),
feat_it->getPeptideIdentifications().begin(),
feat_it->getPeptideIdentifications().end());
feat_it->getPeptideIdentifications().clear();
}
features.getProteinIdentifications().swap(proteins);
if (!out.empty())
{
addDataProcessing_(features,
getProcessingInfo_(DataProcessing::FILTERING));
FeatureXMLFile().store(out, features);
}
}
else // consensusXML
{
ConsensusMap consensus;
ConsensusXMLFile().load(in, consensus);
consensus.getUnassignedPeptideIdentifications().swap(peptides);
for (ConsensusMap::Iterator cons_it = consensus.begin();
cons_it != consensus.end(); ++cons_it)
{
peptides.insert(peptides.end(),
cons_it->getPeptideIdentifications().begin(),
cons_it->getPeptideIdentifications().end());
cons_it->getPeptideIdentifications().clear();
}
consensus.getProteinIdentifications().swap(proteins);
if (!out.empty())
{
addDataProcessing_(consensus,
getProcessingInfo_(DataProcessing::FILTERING));
ConsensusXMLFile().store(out, consensus);
}
}
if (!id_out.empty())
{
// IDMapper can match a peptide ID to several overlapping features,
// resulting in duplicates; this shouldn't be the case for peak data
if (in_type != FileTypes::MZML) removeDuplicates_(peptides);
IdXMLFile().store(id_out, proteins, peptides);
}
return EXECUTION_OK;
}
ExitCodes common_main_(FeatureGroupingAlgorithm * algorithm,
bool labeled = false)
{
//-------------------------------------------------------------
// parameter handling
//-------------------------------------------------------------
StringList ins;
if (labeled) ins.push_back(getStringOption_("in"));
else ins = getStringList_("in");
String out = getStringOption_("out");
//-------------------------------------------------------------
// check for valid input
//-------------------------------------------------------------
// check if all input files have the correct type
FileTypes::Type file_type = FileHandler::getType(ins[0]);
for (Size i = 0; i < ins.size(); ++i)
{
if (FileHandler::getType(ins[i]) != file_type)
{
writeLog_("Error: All input files must be of the same type!");
return ILLEGAL_PARAMETERS;
}
}
//-------------------------------------------------------------
// set up algorithm
//-------------------------------------------------------------
Param algorithm_param = getParam_().copy("algorithm:", true);
writeDebug_("Used algorithm parameters", algorithm_param, 3);
algorithm->setParameters(algorithm_param);
//-------------------------------------------------------------
// perform grouping
//-------------------------------------------------------------
// load input
ConsensusMap out_map;
StringList ms_run_locations;
if (file_type == FileTypes::FEATUREXML)
{
vector<ConsensusMap > maps(ins.size());
FeatureXMLFile f;
FeatureFileOptions param = f.getOptions();
// to save memory don't load convex hulls and subordinates
param.setLoadSubordinates(false);
param.setLoadConvexHull(false);
f.setOptions(param);
Size progress = 0;
setLogType(ProgressLogger::CMD);
startProgress(0, ins.size(), "reading input");
for (Size i = 0; i < ins.size(); ++i)
{
FeatureMap tmp;
f.load(ins[i], tmp);
out_map.getFileDescriptions()[i].filename = ins[i];
out_map.getFileDescriptions()[i].size = tmp.size();
out_map.getFileDescriptions()[i].unique_id = tmp.getUniqueId();
// copy over information on the primary MS run
const StringList& ms_runs = tmp.getPrimaryMSRunPath();
ms_run_locations.insert(ms_run_locations.end(), ms_runs.begin(), ms_runs.end());
// to save memory, remove convex hulls, subordinates:
for (FeatureMap::Iterator it = tmp.begin(); it != tmp.end();
++it)
{
it->getSubordinates().clear();
it->getConvexHulls().clear();
it->clearMetaInfo();
}
MapConversion::convert(i, tmp, maps[i]);
maps[i].updateRanges();
setProgress(progress++);
}
endProgress();
// exception for "labeled" algorithms: copy file descriptions
if (labeled)
{
out_map.getFileDescriptions()[1] = out_map.getFileDescriptions()[0];
out_map.getFileDescriptions()[0].label = "light";
out_map.getFileDescriptions()[1].label = "heavy";
}
// group
algorithm->group(maps, out_map);
}
else
{
vector<ConsensusMap> maps(ins.size());
ConsensusXMLFile f;
for (Size i = 0; i < ins.size(); ++i)
{
f.load(ins[i], maps[i]);
maps[i].updateRanges();
// copy over information on the primary MS run
const StringList& ms_runs = maps[i].getPrimaryMSRunPath();
ms_run_locations.insert(ms_run_locations.end(), ms_runs.begin(), ms_runs.end());
}
// group
algorithm->group(maps, out_map);
// set file descriptions:
bool keep_subelements = getFlag_("keep_subelements");
if (!keep_subelements)
{
for (Size i = 0; i < ins.size(); ++i)
{
out_map.getFileDescriptions()[i].filename = ins[i];
out_map.getFileDescriptions()[i].size = maps[i].size();
out_map.getFileDescriptions()[i].unique_id = maps[i].getUniqueId();
}
}
else
{
// components of the output map are not the input maps themselves, but
// the components of the input maps:
algorithm->transferSubelements(maps, out_map);
}
}
// assign unique ids
out_map.applyMemberFunction(&UniqueIdInterface::setUniqueId);
// annotate output with data processing info
addDataProcessing_(out_map,
getProcessingInfo_(DataProcessing::FEATURE_GROUPING));
// set primary MS runs
out_map.setPrimaryMSRunPath(ms_run_locations);
// write output
ConsensusXMLFile().store(out, out_map);
// some statistics
map<Size, UInt> num_consfeat_of_size;
for (ConsensusMap::const_iterator cmit = out_map.begin();
cmit != out_map.end(); ++cmit)
{
++num_consfeat_of_size[cmit->size()];
}
LOG_INFO << "Number of consensus features:" << endl;
for (map<Size, UInt>::reverse_iterator i = num_consfeat_of_size.rbegin();
i != num_consfeat_of_size.rend(); ++i)
{
LOG_INFO << " of size " << setw(2) << i->first << ": " << setw(6)
<< i->second << endl;
}
LOG_INFO << " total: " << setw(6) << out_map.size() << endl;
return EXECUTION_OK;
}
ExitCodes main_(int, const char **)
{
//input and output file names ..
String in = getStringOption_("in");
String out = getStringOption_("out");
//prevent loading of fragment spectra
PeakFileOptions options;
options.setMSLevels(vector<Int>(1, 1));
//reading input data
MzMLFile f;
f.getOptions() = options;
f.setLogType(log_type_);
PeakMap exp;
f.load(in, exp);
exp.updateRanges();
//no seeds supported
FeatureMap<> seeds;
//setup of FeatureFinder
FeatureFinder ff;
ff.setLogType(log_type_);
// A map for the resulting features
FeatureMap<> features;
// get parameters specific for the feature finder
Param feafi_param = getParam_().copy("algorithm:", true);
writeDebug_("Parameters passed to FeatureFinder", feafi_param, 3);
// Apply the feature finder
ff.run(FeatureFinderAlgorithmIsotopeWavelet<Peak1D, Feature>::getProductName(), exp, features, feafi_param, seeds);
features.applyMemberFunction(&UniqueIdInterface::setUniqueId);
// DEBUG
if (debug_level_ > 10)
{
FeatureMap<>::Iterator it;
for (it = features.begin(); it != features.end(); ++it)
{
if (!it->isMetaEmpty())
{
vector<String> keys;
it->getKeys(keys);
LOG_INFO << "Feature " << it->getUniqueId() << endl;
for (Size i = 0; i < keys.size(); i++)
{
LOG_INFO << " " << keys[i] << " = " << it->getMetaValue(keys[i]) << endl;
}
}
}
}
//-------------------------------------------------------------
// writing files
//-------------------------------------------------------------
//annotate output with data processing info
addDataProcessing_(features, getProcessingInfo_(DataProcessing::QUANTITATION));
// write features to user specified output file
FeatureXMLFile map_file;
map_file.store(out, features);
return EXECUTION_OK;
}
FeatureIterator begin() {
return feat_map.begin();
}
ExitCodes main_(int, const char**)
{
//-------------------------------------------------------------
// parameter handling
//-------------------------------------------------------------
//file list
StringList file_list = getStringList_("in");
//file type
FileHandler fh;
FileTypes::Type force_type;
if (getStringOption_("in_type").size() > 0)
{
force_type = FileTypes::nameToType(getStringOption_("in_type"));
}
else
{
force_type = fh.getType(file_list[0]);
}
//output file names and types
String out_file = getStringOption_("out");
//-------------------------------------------------------------
// calculations
//-------------------------------------------------------------
bool annotate_file_origin = getFlag_("annotate_file_origin");
if (force_type == FileTypes::FEATUREXML)
{
FeatureMap<> out;
for (Size i = 0; i < file_list.size(); ++i)
{
FeatureMap<> map;
FeatureXMLFile fh;
fh.load(file_list[i], map);
if (annotate_file_origin)
{
for (FeatureMap<>::iterator it = map.begin(); it != map.end(); ++it)
{
it->setMetaValue("file_origin", DataValue(file_list[i]));
}
}
out += map;
}
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
//annotate output with data processing info
addDataProcessing_(out, getProcessingInfo_(DataProcessing::FORMAT_CONVERSION));
FeatureXMLFile f;
f.store(out_file, out);
}
else if (force_type == FileTypes::CONSENSUSXML)
{
ConsensusMap out;
ConsensusXMLFile fh;
fh.load(file_list[0], out);
//skip first file
for (Size i = 1; i < file_list.size(); ++i)
{
ConsensusMap map;
ConsensusXMLFile fh;
fh.load(file_list[i], map);
if (annotate_file_origin)
{
for (ConsensusMap::iterator it = map.begin(); it != map.end(); ++it)
{
it->setMetaValue("file_origin", DataValue(file_list[i]));
}
}
out += map;
}
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
//annotate output with data processing info
addDataProcessing_(out, getProcessingInfo_(DataProcessing::FORMAT_CONVERSION));
ConsensusXMLFile f;
f.store(out_file, out);
}
else if (force_type == FileTypes::TRAML)
{
TargetedExperiment out;
for (Size i = 0; i < file_list.size(); ++i)
{
TargetedExperiment map;
TraMLFile fh;
fh.load(file_list[i], map);
out += map;
}
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
//annotate output with data processing info
Software software;
software.setName("FileMerger");
software.setVersion(VersionInfo::getVersion());
out.addSoftware(software);
TraMLFile f;
f.store(out_file, out);
}
else
{
// we might want to combine different types, thus we only
// query in_type (which applies to all files)
// and not the suffix or content of a single file
force_type = FileTypes::nameToType(getStringOption_("in_type"));
//rt
bool rt_auto_number = getFlag_("raw:rt_auto");
bool rt_filename = getFlag_("raw:rt_filename");
bool rt_custom = false;
DoubleList custom_rts = getDoubleList_("raw:rt_custom");
if (custom_rts.size() != 0)
{
rt_custom = true;
if (custom_rts.size() != file_list.size())
{
writeLog_("Custom retention time list must have as many elements as there are input files!");
printUsage_();
return ILLEGAL_PARAMETERS;
}
}
//ms level
bool user_ms_level = getFlag_("raw:user_ms_level");
MSExperiment<> out;
out.reserve(file_list.size());
UInt rt_auto = 0;
UInt native_id = 0;
std::vector<MSChromatogram<ChromatogramPeak> > all_chromatograms;
for (Size i = 0; i < file_list.size(); ++i)
{
String filename = file_list[i];
//load file
MSExperiment<> in;
fh.loadExperiment(filename, in, force_type, log_type_);
if (in.empty() && in.getChromatograms().empty())
{
writeLog_(String("Warning: Empty file '") + filename + "'!");
continue;
}
out.reserve(out.size() + in.size());
//warn if custom RT and more than one scan in input file
if (rt_custom && in.size() > 1)
{
writeLog_(String("Warning: More than one scan in file '") + filename + "'! All scans will have the same retention time!");
}
for (MSExperiment<>::const_iterator it2 = in.begin(); it2 != in.end(); ++it2)
{
//handle rt
Real rt_final = it2->getRT();
if (rt_auto_number)
{
rt_final = ++rt_auto;
}
else if (rt_custom)
{
rt_final = custom_rts[i];
}
else if (rt_filename)
{
if (!filename.hasSubstring("rt"))
{
writeLog_(String("Warning: cannot guess retention time from filename as it does not contain 'rt'"));
}
for (Size i = 0; i < filename.size(); ++i)
{
if (filename[i] == 'r' && ++i != filename.size() && filename[i] == 't' && ++i != filename.size() && isdigit(filename[i]))
{
String rt;
while (i != filename.size() && (filename[i] == '.' || isdigit(filename[i])))
{
rt += filename[i++];
}
if (rt.size() > 0)
{
// remove dot from rt3892.98.dta
// ^
if (rt[rt.size() - 1] == '.')
{
// remove last character
rt.erase(rt.end() - 1);
}
}
try
{
float tmp = rt.toFloat();
rt_final = tmp;
}
catch (Exception::ConversionError)
{
writeLog_(String("Warning: cannot convert the found retention time in a value '" + rt + "'."));
}
}
}
}
// none of the rt methods were successful
if (rt_final == -1)
{
writeLog_(String("Warning: No valid retention time for output scan '") + rt_auto + "' from file '" + filename + "'");
}
out.addSpectrum(*it2);
out.getSpectra().back().setRT(rt_final);
out.getSpectra().back().setNativeID(native_id);
if (user_ms_level)
{
out.getSpectra().back().setMSLevel((int)getIntOption_("raw:ms_level"));
}
++native_id;
}
// if we had only one spectrum, we can annotate it directly, for more spectra, we just name the source file leaving the spectra unannotated (to avoid a long and redundant list of sourceFiles)
if (in.size() == 1)
{
out.getSpectra().back().setSourceFile(in.getSourceFiles()[0]);
in.getSourceFiles().clear(); // delete source file annotated from source file (its in the spectrum anyways)
}
// copy experimental settings from first file
if (i == 0)
{
out.ExperimentalSettings::operator=(in);
}
else // otherwise append
{
out.getSourceFiles().insert(out.getSourceFiles().end(), in.getSourceFiles().begin(), in.getSourceFiles().end()); // could be emtpty if spectrum was annotated above, but that's ok then
}
// also add the chromatograms
for (std::vector<MSChromatogram<ChromatogramPeak> >::const_iterator it2 = in.getChromatograms().begin(); it2 != in.getChromatograms().end(); ++it2)
{
all_chromatograms.push_back(*it2);
}
}
// set the chromatograms
out.setChromatograms(all_chromatograms);
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
//annotate output with data processing info
addDataProcessing_(out, getProcessingInfo_(DataProcessing::FORMAT_CONVERSION));
MzMLFile f;
f.setLogType(log_type_);
f.store(out_file, out);
}
return EXECUTION_OK;
}
// searches for a features with coordinates within the tolerance in this map
// NOTE: It might happen that there are several features at similar coordinates.
// In this case, the program cannot be sure which one is the correct. So we decided
// to use the one with the strongest intensity.
bool readMapFile_(String filename, vector<double> & intensities,
CoordinateType tol_mz, CoordinateType tol_rt,
DPosition<2> fpos1, DPosition<2> fpos2)
{
if (!File::exists(filename))
{
cout << "File " << filename << " not found. " << endl;
return false;
}
cout << "Reading from " << filename << endl;
FeatureXMLFile map_file;
FeatureMap map;
map_file.load(filename, map);
Feature * feat1 = 0;
Feature * feat2 = 0;
FeatureMap::iterator iter = map.begin();
while (iter != map.end())
{
// cout << "Read: " << *iter << endl;
if ((iter->getRT() < fpos1[Feature::RT] + tol_rt) &&
(iter->getRT() > fpos1[Feature::RT] - tol_rt) &&
(iter->getMZ() < fpos1[Feature::MZ] + tol_mz) &&
(iter->getMZ() > fpos1[Feature::MZ] - tol_mz))
{
// cout << "Found feature1 at " << endl;
// cout << iter->getRT() << " " << iter->getMZ() << " " << iter->getIntensity() << endl;
// feature at correct position found, save intensity
if (!feat1)
{
feat1 = &(*iter);
}
else if (feat1->getIntensity() < iter->getIntensity())
{
feat1 = &(*iter);
}
// f1_sum += iter->getIntensity();
}
if ((iter->getRT() < fpos2[Feature::RT] + tol_rt) &&
(iter->getRT() > fpos2[Feature::RT] - tol_rt) &&
(iter->getMZ() < fpos2[Feature::MZ] + tol_mz) &&
(iter->getMZ() > fpos2[Feature::MZ] - tol_mz))
{
// cout << "Found feature2 at " << endl;
// cout << iter->getRT() << " " << iter->getMZ() << " " << iter->getIntensity() << endl;
// same as above
if (!feat2)
{
feat2 = &(*iter);
}
else if (feat2->getIntensity() < iter->getIntensity())
{
feat2 = &(*iter);
}
// f2_sum += iter->getIntensity();
}
++iter;
} // end of while
if (feat1 != 0 && feat2 != 0) //(f1_sum != 0 && f2_sum != 0)
{
cout << "Feature 1: " << *feat1 << endl;
cout << "Feature 2: " << *feat2 << endl;
cout << "Intensity ratio : " << (feat1->getIntensity() / feat2->getIntensity()) << endl;
intensities.push_back(feat1->getIntensity() / feat2->getIntensity());
return true;
}
if (!feat1)
writeDebug_(String("Feature 1 was not found. "), 1);
if (!feat2)
writeDebug_(String("Feature 2 was not found. "), 1);
return false;
}