35 #ifndef OPENMS_FILTERING_DATAREDUCTION_SILACANALYZER_H 
   36 #define OPENMS_FILTERING_DATAREDUCTION_SILACANALYZER_H 
   39 #include <OpenMS/config.h> 
   62 #include <boost/algorithm/string/split.hpp> 
   63 #include <boost/algorithm/string/classification.hpp> 
  128       allow_missing_peaks(true)
 
  144       Int missed_cleavages_,
 
  145       UInt isotopes_per_peptide_min_,
 
  146       UInt isotopes_per_peptide_max_, 
 
  153       bool allow_missing_peaks_,
 
  155       std::map<String, DoubleReal> label_identifiers)
 
  157       selected_labels          = selected_labels_;
 
  158       charge_min               = charge_min_;
 
  159       charge_max               = charge_max_;
 
  160       missed_cleavages         = missed_cleavages_;
 
  161       isotopes_per_peptide_min = isotopes_per_peptide_min_;
 
  162       isotopes_per_peptide_max = isotopes_per_peptide_max_;
 
  164       rt_threshold           = rt_threshold_;
 
  166       intensity_cutoff       = intensity_cutoff_;
 
  167       intensity_correlation  = intensity_correlation_;
 
  168       model_deviation        = model_deviation_;
 
  169       allow_missing_peaks    = allow_missing_peaks_;
 
  171       calculateLabelsAndMassShifts(label_identifiers);
 
  183     void calculateLabelsAndMassShifts(std::map<String, DoubleReal> label_identifiers);
 
  188       std::vector<std::vector<SILACPattern> > data;
 
  190       std::vector<Clustering *> cluster_data;
 
  192       peak_width = estimatePeakWidth(exp);
 
  193       filterData(exp, peak_width, data); 
 
  194       clusterData(exp, peak_width, cluster_data, data);
 
  197       for (std::vector<Clustering *>::const_iterator it = cluster_data.begin(); it != cluster_data.end(); ++it)
 
  199         generateClusterConsensusByCluster(out_map, **it);
 
  241     void generateClusterConsensusByCluster(
ConsensusMap &, 
const Clustering &) 
const;
 
  246     void generateClusterConsensusByPattern(
ConsensusMap &, 
const Clustering &, 
UInt & cluster_id) 
const;
 
  251     void generateClusterDebug(std::ostream & out, 
const Clustering & clustering, 
UInt & cluster_id) 
const;
 
  257     void generateFilterConsensusByPattern(
ConsensusMap &, 
const std::vector<SILACPattern> &) 
const;
 
  272     void generateClusterFeatureByCluster(
FeatureMap<> &, 
const Clustering &) 
const;
 
  277     void readFilterConsensusByPattern(
ConsensusMap &, std::vector<std::vector<SILACPattern> > &);
 
  287       c_file.
load(filename, in);
 
  300       c_file.
store(filename, out);
 
  314       file.
store(filename, msq);
 
  326       f_file.
store(filename, out);
 
SILACClustering Clustering
Definition: SILACAnalyzer.h:122
A more convenient string class. 
Definition: String.h:56
DoubleReal model_deviation
Definition: SILACAnalyzer.h:115
void store(const String &filename, const FeatureMap<> &feature_map)
stores the map feature_map in file with name filename. 
String out
Definition: SILACAnalyzer.h:93
String selected_labels
Definition: SILACAnalyzer.h:103
void writeConsensus(const String &filename, ConsensusMap &out) const 
Write consensusXML from ConsensusMap to file. 
Definition: SILACAnalyzer.h:293
Algorithm to use for SILACAnalysis. 
Definition: SILACAnalyzer.h:86
String out_features
Definition: SILACAnalyzer.h:95
Size setUniqueId()
Assigns a new, valid unique id. Always returns 1. 
Definition: UniqueIdInterface.h:150
A container for consensus elements. 
Definition: ConsensusMap.h:60
Size applyMemberFunction(Size(Type::*member_function)())
Applies a member function of Type to the container itself and all consensus features. The returned values are accumulated. 
Definition: ConsensusMap.h:438
std::vector< std::vector< String > > & getSILAClabels()
Returns the list of SILAC labels, e.g. selected_labels="[Lys4,Arg6][Lys8,Arg10]" => SILAClabels[0][1]...
Definition: SILACAnalyzer.h:223
Size applyMemberFunction(Size(Type::*member_function)())
Applies a member function of Type to the container itself and all features (including subordinates)...
Definition: FeatureMap.h:496
void setExperimentType(const String &experiment_type)
Mutable access to the experiment type. 
Clustering implementation for SILAC stuff. 
Definition: SILACClustering.h:52
UInt isotopes_per_peptide_min
Definition: SILACAnalyzer.h:107
std::vector< std::vector< DoubleReal > > & getMassShifts()
Returns the list of mass shifts calcualted. 
Definition: SILACAnalyzer.h:231
void readConsensus(const String &filename, ConsensusMap &in) const 
Read consensusXML from file to ConsensusMap. 
Definition: SILACAnalyzer.h:284
void initialize(String selected_labels_, UInt charge_min_, UInt charge_max_, Int missed_cleavages_, UInt isotopes_per_peptide_min_, UInt isotopes_per_peptide_max_, DoubleReal rt_threshold_, DoubleReal rt_min_, DoubleReal intensity_cutoff_, DoubleReal intensity_correlation_, DoubleReal model_deviation_, bool allow_missing_peaks_, std::map< String, DoubleReal > label_identifiers)
Initializes the algorithm with parameters. 
Definition: SILACAnalyzer.h:139
File adapter for MzQuantML files. 
Definition: MzQuantMLFile.h:52
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:59
void run_all(MSExperiment< Peak1D > &exp, ConsensusMap &out_map)
Definition: SILACAnalyzer.h:185
MSQuantifications msq
Definition: SILACAnalyzer.h:124
Definition: MSQuantifications.h:51
void sortByPosition()
Sort features by position. Lexicographical comparison (first RT then m/z) is done. 
Definition: FeatureMap.h:310
Definition: PeakWidthEstimator.h:60
String out_filters
Definition: SILACAnalyzer.h:98
String out_debug
Definition: SILACAnalyzer.h:100
void writeMzQuantML(const String &filename, MSQuantifications &msq) const 
Write MzQuantML from ConsensusMap to file. 
Definition: SILACAnalyzer.h:306
DoubleReal rt_threshold
Definition: SILACAnalyzer.h:111
std::vector< std::vector< String > > SILAClabels
Definition: SILACAnalyzer.h:119
String out_mzq
Definition: SILACAnalyzer.h:96
void store(const String &filename, const MSQuantifications &cmsq) const 
Stores a map in a MzQuantML file. 
This class provides Input/Output functionality for feature maps. 
Definition: FeatureXMLFile.h:59
UInt charge_max
Definition: SILACAnalyzer.h:105
Int missed_cleavages
Definition: SILACAnalyzer.h:106
String in_filters
Definition: SILACAnalyzer.h:99
Base class for all classes that want to report their progess. 
Definition: ProgressLogger.h:56
bool allow_missing_peaks
Definition: SILACAnalyzer.h:116
std::vector< std::vector< DoubleReal > > massShifts
Definition: SILACAnalyzer.h:120
UInt isotopes_per_peptide_max
Definition: SILACAnalyzer.h:108
DoubleReal intensity_cutoff
Definition: SILACAnalyzer.h:113
String out_clusters
Definition: SILACAnalyzer.h:94
A single SILAC pattern containing multiple found points. 
Definition: SILACPattern.h:47
void sortByPosition()
Lexicographically sorts the peaks by their position (First RT then m/z). 
void store(const String &filename, const ConsensusMap &consensus_map)
Stores a consensus map to file. 
DoubleReal intensity_correlation
Definition: SILACAnalyzer.h:114
int Int
Signed integer type. 
Definition: Types.h:100
void load(const String &filename, ConsensusMap &map)
Loads a consensus map from file and calls updateRanges. 
DoubleReal rt_min
Definition: SILACAnalyzer.h:112
String in
Definition: SILACAnalyzer.h:92
SILACAnalyzer()
Definition: SILACAnalyzer.h:127
A 2-dimensional consensus feature. 
Definition: ConsensusFeature.h:59
void writeFeatures(const String &filename, FeatureMap<> &out) const 
Write featureXML from FeatureMap to file. 
Definition: SILACAnalyzer.h:320
UInt charge_min
Definition: SILACAnalyzer.h:104