OpenMS  2.4.0
MapAlignmentAlgorithmIdentification.h
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31 // $Maintainer: Hendrik Weisser $
32 // $Authors: Eva Lange, Clemens Groepl, Hendrik Weisser $
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34 
35 #pragma once
36 
46 
47 #include <cmath> // for "abs"
48 #include <limits> // for "max"
49 #include <map>
50 
51 namespace OpenMS
52 {
71  public DefaultParamHandler,
72  public ProgressLogger
73  {
74 public:
77 
80 
81  // Set a reference for the alignment
82  template <typename DataType> void setReference(DataType& data)
83  {
84  reference_.clear();
85  if (data.empty()) return; // empty input resets the reference
86  SeqToList rt_data;
87  bool sorted = getRetentionTimes_(data, rt_data);
88  computeMedians_(rt_data, reference_, sorted);
89  if (reference_.empty())
90  {
91  throw Exception::MissingInformation(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Could not extract retention time information from the reference file");
92  }
93  }
94 
102  template <typename DataType>
103  void align(std::vector<DataType>& data,
104  std::vector<TransformationDescription>& transformations,
105  Int reference_index = -1)
106  {
107  checkParameters_(data.size());
108  startProgress(0, 3, "aligning maps");
109 
110  reference_index_ = reference_index;
111  // is reference one of the input files?
112  bool use_internal_reference = (reference_index >= 0);
113  if (use_internal_reference)
114  {
115  if (reference_index >= data.size())
116  {
117  throw Exception::IndexOverflow(__FILE__, __LINE__,
118  OPENMS_PRETTY_FUNCTION, reference_index,
119  data.size());
120  }
121  setReference(data[reference_index]);
122  }
123 
124  // one set of RT data for each input map, except reference (if any):
125  std::vector<SeqToList> rt_data(data.size() - use_internal_reference);
126  bool all_sorted = true;
127  for (Size i = 0, j = 0; i < data.size(); ++i)
128  {
129  if ((reference_index >= 0) && (i == Size(reference_index)))
130  {
131  continue; // skip reference map, if any
132  }
133  all_sorted &= getRetentionTimes_(data[i], rt_data[j++]);
134  }
135  setProgress(1);
136 
137  computeTransformations_(rt_data, transformations, all_sorted);
138  setProgress(2);
139 
140  setProgress(3);
141  endProgress();
142  }
143 
144 protected:
145 
147  typedef std::map<String, DoubleList> SeqToList;
148 
150  typedef std::map<String, double> SeqToValue;
151 
154 
157 
160 
170  void computeMedians_(SeqToList& rt_data, SeqToValue& medians,
171  bool sorted = false);
172 
181  bool getRetentionTimes_(std::vector<PeptideIdentification>& peptides,
182  SeqToList& rt_data);
183 
192  bool getRetentionTimes_(PeakMap& experiment, SeqToList& rt_data);
193 
206  template <typename MapType>
207  bool getRetentionTimes_(MapType& features, SeqToList& rt_data)
208  {
209  bool use_feature_rt = param_.getValue("use_feature_rt").toBool();
210  for (typename MapType::Iterator feat_it = features.begin();
211  feat_it != features.end(); ++feat_it)
212  {
213  if (use_feature_rt)
214  {
215  // find the peptide ID closest in RT to the feature centroid:
216  String sequence;
217  double rt_distance = std::numeric_limits<double>::max();
218  bool any_hit = false;
219  for (std::vector<PeptideIdentification>::iterator pep_it =
220  feat_it->getPeptideIdentifications().begin(); pep_it !=
221  feat_it->getPeptideIdentifications().end(); ++pep_it)
222  {
223  if (!pep_it->getHits().empty())
224  {
225  any_hit = true;
226  double current_distance = fabs(pep_it->getRT() -
227  feat_it->getRT());
228  if (current_distance < rt_distance)
229  {
230  pep_it->sort();
231  sequence = pep_it->getHits()[0].getSequence().toString();
232  rt_distance = current_distance;
233  }
234  }
235  }
236 
237  if (any_hit) rt_data[sequence].push_back(feat_it->getRT());
238  }
239  else
240  {
241  getRetentionTimes_(feat_it->getPeptideIdentifications(), rt_data);
242  }
243  }
244 
245  if (!use_feature_rt &&
246  param_.getValue("use_unassigned_peptides").toBool())
247  {
248  getRetentionTimes_(features.getUnassignedPeptideIdentifications(),
249  rt_data);
250  }
251 
252  // remove duplicates (can occur if a peptide ID was assigned to several
253  // features due to overlap or annotation tolerance):
254  for (SeqToList::iterator rt_it = rt_data.begin(); rt_it != rt_data.end();
255  ++rt_it)
256  {
257  DoubleList& rt_values = rt_it->second;
258  sort(rt_values.begin(), rt_values.end());
259  DoubleList::iterator it = unique(rt_values.begin(), rt_values.end());
260  rt_values.resize(it - rt_values.begin());
261  }
262  return true; // RTs were already sorted for duplicate detection
263  }
264 
272  void computeTransformations_(std::vector<SeqToList>& rt_data,
273  std::vector<TransformationDescription>&
274  transforms, bool sorted = false);
275 
283  void checkParameters_(const Size runs);
284 
291  void getReference_();
292 
293 private:
294 
297 
300 
301  };
302 
303 } // namespace OpenMS
304 
DefaultParamHandler.h
OpenMS::FileTypes::IDXML
@ IDXML
OpenMS identification format (.idXML)
Definition: FileTypes.h:66
OpenMS::ProgressLogger::setProgress
void setProgress(SignedSize value) const
Sets the current progress.
OpenMS::ExperimentalDesign
Representation of the Experimental Design in OpenMS. Instances can be loaded via the ExperimentalDesi...
Definition: ExperimentalDesign.h:85
OpenMS::Param::copy
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
OpenMS::ExperimentalDesignFile::load
static ExperimentalDesign load(const String &tsv_file, bool require_spectra_files)
Loads an experimental design from a tabular separated file.
OpenMS::MapAlignmentTransformer::transformRetentionTimes
static void transformRetentionTimes(PeakMap &msexp, const TransformationDescription &trafo, bool store_original_rt=false)
Applies the given transformation to a peak map.
OpenMS::MapAlignmentAlgorithmIdentification::SeqToValue
std::map< String, double > SeqToValue
Type to store one representative retention time per peptide sequence.
Definition: MapAlignmentAlgorithmIdentification.h:150
OpenMS::MapAlignmentAlgorithmIdentification::min_run_occur_
Size min_run_occur_
Minimum number of runs a peptide must occur in.
Definition: MapAlignmentAlgorithmIdentification.h:159
ExperimentalDesignFile.h
Int
OpenMS::DataProcessing::ALIGNMENT
@ ALIGNMENT
Retention time alignment of different maps.
Definition: DataProcessing.h:68
OpenMS::ExperimentalDesign::getFractionToMSFilesMapping
std::map< unsigned int, std::vector< String > > getFractionToMSFilesMapping() const
return fraction index to file paths (ordered by fraction_group)
OpenMS::MzMLFile::store
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
OpenMS::FileTypes::MZML
@ MZML
MzML file (.mzML)
Definition: FileTypes.h:72
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:55
OpenMS::String
A more convenient string class.
Definition: String.h:57
OpenMS::MSExperiment::begin
Iterator begin()
Definition: MSExperiment.h:157
OpenMS::DoubleList
std::vector< double > DoubleList
Vector of double precision real types.
Definition: ListUtils.h:65
ConsensusMap.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::FileTypes::CONSENSUSXML
@ CONSENSUSXML
OpenMS consensus map format (.consensusXML)
Definition: FileTypes.h:67
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
LOG_INFO
#define LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:454
OpenMS::Param::getValue
const DataValue & getValue(const String &key) const
Returns a value of a parameter.
OpenMS::ProgressLogger::startProgress
void startProgress(SignedSize begin, SignedSize end, const String &label) const
Initializes the progress display.
OpenMS::MapAlignmentAlgorithmIdentification::setReference
void setReference(DataType &data)
Definition: MapAlignmentAlgorithmIdentification.h:82
TransformationDescription.h
OpenMS::MapAlignmentAlgorithmIdentification::getRetentionTimes_
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:207
MapAlignmentAlgorithmSpectrumAlignment.h
OpenMS::ProgressLogger::endProgress
void endProgress() const
Ends the progress display.
ListUtils.h
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::TransformationDescription::fitModel
void fitModel(const String &model_type, const Param &params=Param())
Fits a model to the data.
OpenMS::IdXMLFile::load
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::MSExperiment::Iterator
std::vector< SpectrumType >::iterator Iterator
Mutable iterator.
Definition: MSExperiment.h:111
OpenMS::MSExperiment::getSize
UInt64 getSize() const
returns the total number of peaks
OpenMS::MapAlignmentAlgorithmSpectrumAlignment::align
virtual void align(std::vector< PeakMap > &, std::vector< TransformationDescription > &)
Align peak maps.
OpenMS::FileTypes::FEATUREXML
@ FEATUREXML
OpenMS feature file (.featureXML)
Definition: FileTypes.h:65
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
ProgressLogger.h
OpenMS::MzMLFile::load
void load(const String &filename, PeakMap &map)
Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled u...
OpenMS::FeatureXMLFile::loadSize
Size loadSize(const String &filename)
OpenMS::FeatureXMLFile::load
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
FeatureMap.h
OpenMS::FileTypes::Type
Type
Actual file types enum.
Definition: FileTypes.h:58
OpenMS::MapAlignmentAlgorithmPoseClustering::align
void align(const FeatureMap &map, TransformationDescription &trafo)
MapAlignmentAlgorithmIdentification.h
OpenMS::MapAlignmentAlgorithmIdentification::align
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:103
OpenMS::FileHandler::getType
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
OpenMS::MapAlignmentAlgorithmPoseClustering
A map alignment algorithm based on pose clustering.
Definition: MapAlignmentAlgorithmPoseClustering.h:70
OpenMS::DefaultParamHandler::setParameters
void setParameters(const Param &param)
Sets the parameters.
OpenMS::DefaultParamHandler::getParameters
const Param & getParameters() const
Non-mutable access to the parameters.
OpenMS::MapAlignmentAlgorithmSpectrumAlignment
A map alignment algorithm based on spectrum similarity (dynamic programming).
Definition: MapAlignmentAlgorithmSpectrumAlignment.h:54
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:75
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:73
OpenMS::FeatureXMLFile::store
void store(const String &filename, const FeatureMap &feature_map)
stores the map feature_map in file with name filename.
OpenMS::ConsensusXMLFile::load
void load(const String &filename, ConsensusMap &map)
Loads a consensus map from file and calls updateRanges.
OpenMS::MapAlignmentAlgorithmIdentification::SeqToList
std::map< String, DoubleList > SeqToList
Type to store retention times given for individual peptide sequences.
Definition: MapAlignmentAlgorithmIdentification.h:147
OpenMS::MapAlignmentAlgorithmIdentification
A map alignment algorithm based on peptide identifications from MS2 spectra.
Definition: MapAlignmentAlgorithmIdentification.h:70
OpenMS::Exception::IndexOverflow
Int overflow exception.
Definition: Exception.h:254
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
ExperimentalDesign.h
OpenMS::MapAlignmentAlgorithmIdentification::reference_index_
Int reference_index_
Index of input file to use as reference (if any)
Definition: MapAlignmentAlgorithmIdentification.h:153
MSExperiment.h
OpenMS::IdXMLFile::store
void store(String filename, const std::vector< ProteinIdentification > &protein_ids, const std::vector< PeptideIdentification > &peptide_ids, const String &document_id="")
Stores the data in an idXML file.
OpenMS::MapAlignmentAlgorithmIdentification::reference_
SeqToValue reference_
Reference retention times (per peptide sequence)
Definition: MapAlignmentAlgorithmIdentification.h:156
OpenMS::FeatureFileOptions::setLoadSubordinates
void setLoadSubordinates(bool sub)
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:93
OpenMS::TransformationXMLFile
Used to load and store TransformationXML files.
Definition: TransformationXMLFile.h:56
OpenMS::MSExperiment::end
Iterator end()
Definition: MSExperiment.h:167
MapAlignmentAlgorithmPoseClustering.h
OpenMS::FeatureXMLFile
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
OpenMS::MSExperiment::updateRanges
void updateRanges() override
Updates minimum and maximum position/intensity.
MapAlignerBase.h
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:74
OpenMS::TransformationXMLFile::store
void store(String filename, const TransformationDescription &transformation)
Stores the data in an TransformationXML file.
OpenMS::Exception::MissingInformation
Not all required information provided.
Definition: Exception.h:195
OpenMS::FeatureFileOptions::setLoadConvexHull
void setLoadConvexHull(bool convex)
PeptideIdentification.h
OpenMS::TransformationDescription
Generic description of a coordinate transformation.
Definition: TransformationDescription.h:60
OpenMS::MapAlignmentAlgorithmPoseClustering::setReference
void setReference(const MapType &map)
Sets the reference for the alignment.
Definition: MapAlignmentAlgorithmPoseClustering.h:87
StandardTypes.h
OpenMS::FeatureXMLFile::getOptions
FeatureFileOptions & getOptions()
Mutable access to the options for loading/storing.
OpenMS::ProgressLogger::setLogType
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
OpenMS::ExperimentalDesign::sameNrOfMSFilesPerFraction
bool sameNrOfMSFilesPerFraction() const
OpenMS::ConsensusXMLFile
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:61
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:63