30 template <
typename MapType>
31 concept
IsFCMap = std::same_as<MapType, OpenMS::FeatureMap> || std::same_as<MapType, OpenMS::ConsensusMap>;
65 template <
typename DataType>
void setReference(
const DataType& data)
68 if (data.empty())
return;
71 use_feature_rt_ = param_.getValue(
"use_feature_rt").toBool();
72 score_cutoff_ = param_.getValue(
"score_cutoff").toBool();
73 score_type_ = (std::string)param_.getValue(
"score_type");
74 bool sorted = getRetentionTimes_(data, rt_data);
75 computeMedians_(rt_data, reference_, sorted);
77 if (reference_.empty())
79 throw Exception::MissingInformation(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
"Could not extract retention time information from the reference file");
92 template <
typename DataType>
93 void align(
const std::vector<DataType>& data,
94 std::vector<TransformationDescription>& transformations,
95 Int reference_index = -1)
97 checkParameters_(data.size());
98 startProgress(0, 3,
"aligning maps");
100 reference_index_ = reference_index;
102 bool use_internal_reference = (reference_index >= 0);
103 if (use_internal_reference)
105 if (reference_index >=
Int(data.size()))
108 OPENMS_PRETTY_FUNCTION,
109 reference_index, data.size());
111 setReference(data[reference_index]);
115 std::vector<SeqToList> rt_data(data.size() - use_internal_reference);
116 bool all_sorted =
true;
117 for (
Size i = 0, j = 0; i < data.size(); ++i)
119 if ((reference_index >= 0) && (i ==
Size(reference_index)))
123 all_sorted &= getRetentionTimes_(data[i], rt_data[j++]);
127 computeTransformations_(rt_data, transformations, all_sorted);
152 bool use_feature_rt_{};
161 bool score_cutoff_{};
167 bool (*better_) (double, double) = [](
double,
double) {
return true;};
179 bool sorted =
false);
222 better_ = [](double, double)
225 else if (features[0].getPeptideIdentifications()[0].isHigherScoreBetter())
227 better_ = [](
double a,
double b)
232 better_ = [](
double a,
double b)
236 for (
auto feat_it = features.cbegin(); feat_it != features.cend(); ++feat_it)
242 double rt_distance = std::numeric_limits<double>::max();
243 bool any_hit =
false;
245 feat_it->getPeptideIdentifications().begin(); pep_it !=
246 feat_it->getPeptideIdentifications().end(); ++pep_it)
248 if (!pep_it->getHits().empty())
251 double current_distance = fabs(pep_it->getRT() -
253 if (current_distance < rt_distance)
255 const PeptideHit* best_hit = getBestScoringHit(pep_it->getHits(), pep_it->isHigherScoreBetter());
256 if (best_hit && better_(best_hit->
getScore(), min_score_))
259 rt_distance = current_distance;
265 if (any_hit) rt_data[sequence].push_back(feat_it->getRT());
269 getRetentionTimes_(feat_it->getPeptideIdentifications(), rt_data);
273 if (!use_feature_rt_ &&
274 param_.getValue(
"use_unassigned_peptides").toBool())
276 getRetentionTimes_(features.getUnassignedPeptideIdentifications(),
282 for (SeqToList::iterator rt_it = rt_data.begin(); rt_it != rt_data.end();
286 sort(rt_values.begin(), rt_values.end());
287 DoubleList::iterator it = unique(rt_values.begin(), rt_values.end());
288 rt_values.resize(it - rt_values.begin());
301 std::vector<TransformationDescription>&
302 transforms,
bool sorted =
false);
String toString() const
returns the peptide as string with modifications embedded in brackets
Class for storing MS run data with peptide and protein identifications.
Definition: AnnotatedMSRun.h:36
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:66
Int overflow exception.
Definition: Exception.h:211
typename VecMember::const_iterator const_iterator
Definition: ExposedVector.h:69
Definition: IdentificationData.h:87
A map alignment algorithm based on peptide identifications from MS2 spectra.
Definition: MapAlignmentAlgorithmIdentification.h:56
void computeTransformations_(std::vector< SeqToList > &rt_data, std::vector< TransformationDescription > &transforms, bool sorted=false)
Compute retention time transformations from RT data grouped by peptide sequence.
bool getRetentionTimes_(const PeptideIdentificationList &peptides, SeqToList &rt_data)
Collect retention time data from peptide IDs.
void setReference(const DataType &data)
Definition: MapAlignmentAlgorithmIdentification.h:65
bool getRetentionTimes_(const IdentificationData &id_data, SeqToList &rt_data)
Collect retention time data from spectrum matches.
~MapAlignmentAlgorithmIdentification() override
Destructor.
std::map< String, double > SeqToValue
Type to store one representative retention time per peptide sequence.
Definition: MapAlignmentAlgorithmIdentification.h:140
void checkParameters_(const Size runs)
Check that parameter values are valid.
void getReference_()
Get reference retention times.
bool getRetentionTimes_(const IsFCMap auto &features, SeqToList &rt_data)
Collect retention time data from peptide IDs contained in feature maps or consensus maps.
Definition: MapAlignmentAlgorithmIdentification.h:218
String score_type_
Score type to use for filtering.
Definition: MapAlignmentAlgorithmIdentification.h:164
Int reference_index_
Index of input file to use as reference (if any)
Definition: MapAlignmentAlgorithmIdentification.h:143
const PeptideHit * getBestScoringHit(const std::vector< PeptideHit > &hits, const bool is_higher_score_better)
Get the best-scoring PeptideHit from a list of hits.
SeqToValue reference_
Reference retention times (per peptide sequence)
Definition: MapAlignmentAlgorithmIdentification.h:146
double min_score_
Minimum score to reach for a peptide to be considered.
Definition: MapAlignmentAlgorithmIdentification.h:158
Size min_run_occur_
Minimum number of runs a peptide must occur in.
Definition: MapAlignmentAlgorithmIdentification.h:149
std::map< String, DoubleList > SeqToList
Type to store retention times given for individual peptide sequences.
Definition: MapAlignmentAlgorithmIdentification.h:137
MapAlignmentAlgorithmIdentification & operator=(const MapAlignmentAlgorithmIdentification &)
Assignment operator intentionally not implemented -> private.
MapAlignmentAlgorithmIdentification()
Default constructor.
IdentificationData::ScoreTypeRef handleIdDataScoreType_(const IdentificationData &id_data)
Helper function to find/define the score type for processing IdentificationData.
void align(const std::vector< DataType > &data, std::vector< TransformationDescription > &transformations, Int reference_index=-1)
Align feature maps, consensus maps, or peptide identifications.
Definition: MapAlignmentAlgorithmIdentification.h:93
void computeMedians_(SeqToList &rt_data, SeqToValue &medians, bool sorted=false)
Compute the median retention time for each peptide sequence.
MapAlignmentAlgorithmIdentification(const MapAlignmentAlgorithmIdentification &)
Copy constructor intentionally not implemented -> private.
Represents a single spectrum match (candidate) for a specific tandem mass spectrum (MS/MS).
Definition: PeptideHit.h:50
double getScore() const
returns the PSM score
const AASequence & getSequence() const
returns the peptide sequence
Container for peptide identifications from multiple spectra.
Definition: PeptideIdentificationList.h:66
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:27
A more convenient string class.
Definition: String.h:34
int Int
Signed integer type.
Definition: Types.h:72
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:97
std::vector< double > DoubleList
Vector of double precision real types.
Definition: ListUtils.h:36
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19
concept IsFCMap
Definition: MapAlignmentAlgorithmIdentification.h:31
Wrapper that adds operator< to iterators, so they can be used as (part of) keys in maps/sets or multi...
Definition: MetaData.h:20