35 #ifndef OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTALGORITHMIDENTIFICATION_H 36 #define OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTALGORITHMIDENTIFICATION_H 86 if (data.empty())
return;
88 bool sorted = getRetentionTimes_(data, rt_data);
89 computeMedians_(rt_data, reference_, sorted);
90 if (reference_.empty())
92 throw Exception::MissingInformation(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
"Could not extract retention time information from the reference file");
103 template <
typename DataType>
104 void align(std::vector<DataType>& data,
105 std::vector<TransformationDescription>& transformations,
106 Int reference_index = -1)
108 checkParameters_(data.size());
109 startProgress(0, 3,
"aligning maps");
111 reference_index_ = reference_index;
113 bool use_internal_reference = (reference_index >= 0);
114 if (use_internal_reference)
116 if (reference_index >= data.size())
119 OPENMS_PRETTY_FUNCTION, reference_index,
122 setReference(data[reference_index]);
126 std::vector<SeqToList> rt_data(data.size() - use_internal_reference);
127 bool all_sorted =
true;
128 for (
Size i = 0, j = 0; i < data.size(); ++i)
130 if ((reference_index >= 0) && (i ==
Size(reference_index)))
134 all_sorted &= getRetentionTimes_(data[i], rt_data[j++]);
138 computeTransformations_(rt_data, transformations, all_sorted);
171 void computeMedians_(SeqToList& rt_data, SeqToValue& medians,
172 bool sorted =
false);
182 bool getRetentionTimes_(std::vector<PeptideIdentification>& peptides,
193 bool getRetentionTimes_(
PeakMap& experiment, SeqToList& rt_data);
207 template <
typename MapType>
210 bool use_feature_rt = param_.getValue(
"use_feature_rt").toBool();
212 feat_it != features.
end(); ++feat_it)
218 double rt_distance = std::numeric_limits<double>::max();
219 bool any_hit =
false;
220 for (std::vector<PeptideIdentification>::iterator pep_it =
221 feat_it->getPeptideIdentifications().begin(); pep_it !=
222 feat_it->getPeptideIdentifications().end(); ++pep_it)
224 if (!pep_it->getHits().empty())
227 double current_distance = fabs(pep_it->getRT() -
229 if (current_distance < rt_distance)
232 sequence = pep_it->getHits()[0].getSequence().toString();
233 rt_distance = current_distance;
238 if (any_hit) rt_data[sequence].push_back(feat_it->getRT());
242 getRetentionTimes_(feat_it->getPeptideIdentifications(), rt_data);
246 if (!use_feature_rt &&
247 param_.getValue(
"use_unassigned_peptides").toBool())
249 getRetentionTimes_(features.getUnassignedPeptideIdentifications(),
255 for (SeqToList::iterator rt_it = rt_data.begin(); rt_it != rt_data.end();
259 sort(rt_values.begin(), rt_values.end());
260 DoubleList::iterator it = unique(rt_values.begin(), rt_values.end());
261 rt_values.resize(it - rt_values.begin());
273 void computeTransformations_(std::vector<SeqToList>& rt_data,
274 std::vector<TransformationDescription>&
275 transforms,
bool sorted =
false);
284 void checkParameters_(
const Size runs);
292 void getReference_();
306 #endif // OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTALGORITHMIDENTIFICATION_H
A more convenient string class.
Definition: String.h:57
std::vector< double > DoubleList
Vector of double precision real types.
Definition: ListUtils.h:66
std::vector< SpectrumType >::iterator Iterator
Mutable iterator.
Definition: MSExperiment.h:116
Int overflow exception.
Definition: Exception.h:255
Iterator begin()
Definition: MSExperiment.h:162
bool getRetentionTimes_(MapType &features, SeqToList &rt_data)
Collect retention time data ("RT" MetaInfo) from peptide IDs contained in feature maps or consensus m...
Definition: MapAlignmentAlgorithmIdentification.h:208
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Int reference_index_
Index of input file to use as reference (if any)
Definition: MapAlignmentAlgorithmIdentification.h:154
Iterator end()
Definition: MSExperiment.h:172
A map alignment algorithm based on peptide identifications from MS2 spectra.
Definition: MapAlignmentAlgorithmIdentification.h:71
void align(std::vector< DataType > &data, std::vector< TransformationDescription > &transformations, Int reference_index=-1)
Align feature maps, consensus maps, peak maps, or peptide identifications.
Definition: MapAlignmentAlgorithmIdentification.h:104
std::map< String, DoubleList > SeqToList
Type to store retention times given for individual peptide sequences.
Definition: MapAlignmentAlgorithmIdentification.h:148
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:82
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:128
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:55
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
Size min_run_occur_
Minimum number of runs a peptide must occur in.
Definition: MapAlignmentAlgorithmIdentification.h:160
SeqToValue reference_
Reference retention times (per peptide sequence)
Definition: MapAlignmentAlgorithmIdentification.h:157
int Int
Signed integer type.
Definition: Types.h:103
void setReference(DataType &data)
Definition: MapAlignmentAlgorithmIdentification.h:83
std::map< String, double > SeqToValue
Type to store one representative retention time per peptide sequence.
Definition: MapAlignmentAlgorithmIdentification.h:151