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 InternalCalibration::calibrateMapGlobally(const FeatureMap<> & feature_map, FeatureMap<> & calibrated_feature_map, std::vector<PeptideIdentification> & ref_ids, String trafo_file_name)
{
checkReferenceIds_(ref_ids);
calibrated_feature_map = feature_map;
// clear the ids
for (Size f = 0; f < calibrated_feature_map.size(); ++f)
{
calibrated_feature_map[f].getPeptideIdentifications().clear();
}
// map the reference ids onto the features
IDMapper mapper;
Param param;
param.setValue("rt_tolerance", (DoubleReal)param_.getValue("rt_tolerance"));
param.setValue("mz_tolerance", param_.getValue("mz_tolerance"));
param.setValue("mz_measure", param_.getValue("mz_tolerance_unit"));
mapper.setParameters(param);
std::vector<ProteinIdentification> vec;
mapper.annotate(calibrated_feature_map, ref_ids, vec);
// calibrate
calibrateMapGlobally(calibrated_feature_map, calibrated_feature_map, trafo_file_name);
// copy the old ids
calibrated_feature_map.setUnassignedPeptideIdentifications(feature_map.getUnassignedPeptideIdentifications());
for (Size f = 0; f < feature_map.size(); ++f)
{
calibrated_feature_map[f].getPeptideIdentifications().clear();
if (!feature_map[f].getPeptideIdentifications().empty())
{
calibrated_feature_map[f].setPeptideIdentifications(feature_map[f].getPeptideIdentifications());
}
}
}
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);
}
}
START_SECTION((std::vector<ProteinIdentification>& getProteinIdentifications())) FeatureMap<> tmp; tmp.getProteinIdentifications().resize(1); TEST_EQUAL(tmp.getProteinIdentifications().size(),1) END_SECTION START_SECTION((void setProteinIdentifications(const std::vector<ProteinIdentification>& protein_identifications))) FeatureMap<> tmp; tmp.setProteinIdentifications(std::vector<ProteinIdentification>(2)); TEST_EQUAL(tmp.getProteinIdentifications().size(),2) END_SECTION START_SECTION((const std::vector<PeptideIdentification>& getUnassignedPeptideIdentifications() const)) FeatureMap<> tmp; TEST_EQUAL(tmp.getUnassignedPeptideIdentifications().size(),0) END_SECTION START_SECTION((std::vector<PeptideIdentification>& getUnassignedPeptideIdentifications())) FeatureMap<> tmp; tmp.getUnassignedPeptideIdentifications().resize(1); TEST_EQUAL(tmp.getUnassignedPeptideIdentifications().size(),1) END_SECTION START_SECTION((void setUnassignedPeptideIdentifications(const std::vector<PeptideIdentification>& unassigned_peptide_identifications))) FeatureMap<> tmp; tmp.setUnassignedPeptideIdentifications(std::vector<PeptideIdentification>(2)); TEST_EQUAL(tmp.getUnassignedPeptideIdentifications().size(),2) END_SECTION START_SECTION((const std::vector<DataProcessing>& getDataProcessing() const))
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 main_(int, const char **)
{
String in = getStringOption_("in");
StringList out = getStringList_("out");
SeedListGenerator seed_gen;
// results (actually just one result, except for consensusXML input):
Map<UInt64, SeedListGenerator::SeedList> seed_lists;
Size num_maps = 0;
FileTypes::Type in_type = FileHandler::getType(in);
if (in_type == FileTypes::CONSENSUSXML)
{
ConsensusMap consensus;
ConsensusXMLFile().load(in, consensus);
num_maps = consensus.getFileDescriptions().size();
if (out.size() != num_maps)
{
writeLog_("Error: expected " + String(num_maps) +
" output filenames");
return ILLEGAL_PARAMETERS;
}
seed_gen.generateSeedLists(consensus, seed_lists);
}
else if (out.size() > 1)
{
writeLog_("Error: expected only one output filename");
return ILLEGAL_PARAMETERS;
}
else if (in_type == FileTypes::MZML)
{
MSExperiment<> experiment;
MzMLFile().load(in, experiment);
seed_gen.generateSeedList(experiment, seed_lists[0]);
}
else if (in_type == FileTypes::IDXML)
{
vector<ProteinIdentification> proteins;
vector<PeptideIdentification> peptides;
IdXMLFile().load(in, proteins, peptides);
seed_gen.generateSeedList(peptides, seed_lists[0],
getFlag_("use_peptide_mass"));
}
else if (in_type == FileTypes::FEATUREXML)
{
FeatureMap features;
FeatureXMLFile().load(in, features);
seed_gen.generateSeedList(
features.getUnassignedPeptideIdentifications(), seed_lists[0]);
}
// output:
num_maps = 0;
for (Map<UInt64, SeedListGenerator::SeedList>::Iterator it =
seed_lists.begin(); it != seed_lists.end(); ++it, ++num_maps)
{
FeatureMap features;
seed_gen.convertSeedList(it->second, features);
//annotate output with data processing info:
addDataProcessing_(features, getProcessingInfo_(
DataProcessing::DATA_PROCESSING));
FeatureXMLFile().store(out[num_maps], features);
}
return EXECUTION_OK;
}