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