35 #ifndef OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTALGORITHMIDENTIFICATION_H 
   36 #define OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTALGORITHMIDENTIFICATION_H 
   78                                std::vector<TransformationDescription> &);
 
   81     virtual void alignFeatureMaps(std::vector<
FeatureMap<> > &,
 
   82                                   std::vector<TransformationDescription> &);
 
   85     virtual void alignConsensusMaps(std::vector<ConsensusMap> &,
 
   86                                     std::vector<TransformationDescription> &);
 
   89     virtual void alignPeptideIdentifications(
 
   90       std::vector<std::vector<PeptideIdentification> > &,
 
   91       std::vector<TransformationDescription> &);
 
   94     virtual void setReference(
Size reference_index = 0,
 
   95                               const String & reference_file = 
"");
 
  107     template <
typename MapType>
 
  109                    std::vector<TransformationDescription> & transformations)
 
  111       checkParameters_(maps.size());
 
  112       startProgress(0, 3, 
"aligning maps");
 
  114       if (reference_index_)     
 
  117         getRetentionTimes_(maps[reference_index_ - 1], rt_data);
 
  118         computeMedians_(rt_data, reference_, 
true);
 
  122       std::vector<SeqToList> rt_data(maps.size() - bool(reference_index_));
 
  123       for (
Size i = 0, j = 0; i < maps.size(); ++i)
 
  125         if (i == reference_index_ - 1) 
continue;  
 
  127         getRetentionTimes_(maps[i], rt_data[j++]);
 
  131       computeTransformations_(rt_data, transformations, 
true);
 
  146       return "identification";
 
  179                          bool sorted = 
false);
 
  190     void getRetentionTimes_(std::vector<PeptideIdentification> & peptides,
 
  211     template <
typename MapType>
 
  212     void getRetentionTimes_(MapType & features, 
SeqToList & rt_data);
 
  221     void computeTransformations_(std::vector<SeqToList> & rt_data,
 
  222                                  std::vector<TransformationDescription> &
 
  223                                  transforms, 
bool sorted = 
false);
 
  232     void checkParameters_(
const Size runs);
 
  240     void getReference_();
 
  254 #endif // OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTALGORITHMIDENTIFICATION_H 
void alignMaps(std::vector< MapType > &maps, std::vector< TransformationDescription > &transformations)
Align feature maps or consensus maps. 
Definition: MapAlignmentAlgorithmIdentification.h:108
DoubleReal score_threshold_
Score threshold for peptide hits. 
Definition: MapAlignmentAlgorithmIdentification.h:164
A more convenient string class. 
Definition: String.h:56
Base class for all map-alignment algorithms. 
Definition: MapAlignmentAlgorithm.h:58
Size reference_index_
Index of input file to use as reference (1-based!) 
Definition: MapAlignmentAlgorithmIdentification.h:158
std::map< String, DoubleReal > SeqToValue
Type to store one representative retention time per peptide sequence. 
Definition: MapAlignmentAlgorithmIdentification.h:155
static MapAlignmentAlgorithm * create()
Creates a new instance of this class (for Factory) 
Definition: MapAlignmentAlgorithmIdentification.h:138
A map alignment algorithm based on peptide identifications from MS2 spectra. 
Definition: MapAlignmentAlgorithmIdentification.h:66
std::map< String, DoubleList > SeqToList
Type to store retention times given for individual peptide sequences. 
Definition: MapAlignmentAlgorithmIdentification.h:152
Representation of a mass spectrometry experiment. 
Definition: MSExperiment.h:68
static String getProductName()
Returns the product name (for the Factory) 
Definition: MapAlignmentAlgorithmIdentification.h:144
size_t Size
Size type e.g. used as variable which can hold result of size() 
Definition: Types.h:144
Size min_run_occur_
Minimum number of runs a peptide must occur in. 
Definition: MapAlignmentAlgorithmIdentification.h:167
SeqToValue reference_
Reference retention times (per peptide sequence) 
Definition: MapAlignmentAlgorithmIdentification.h:161
Represents the peptide hits for a spectrum. 
Definition: PeptideIdentification.h:63