OpenMS  2.4.0
O18Labeler.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Stephan Aiche$
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34 
35 #pragma once
36 
38 
39 namespace OpenMS
40 {
41 
49  class OPENMS_DLLAPI O18Labeler :
50  public BaseLabeler
51  {
52 public:
53 
55  O18Labeler();
56 
58  ~O18Labeler() override;
59 
61  static BaseLabeler* create()
62  {
63  return new O18Labeler();
64  }
65 
67  static const String getProductName()
68  {
69  return "o18";
70  }
71 
72  // redeclaration of virtual methods
73  void preCheck(Param& param) const override;
74 
75  void setUpHook(SimTypes::FeatureMapSimVector& /* channels */) override;
76 
77  void postDigestHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
78 
79  void postRTHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
80 
81  void postDetectabilityHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
82 
83  void postIonizationHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
84 
85  void postRawMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */) override;
86 
87  void postRawTandemMSHook(SimTypes::FeatureMapSimVector& /* features_to_simulate */, SimTypes::MSSimExperiment& /* simulated map */) override;
88 
89 protected:
90  void addModificationToPeptideHit_(Feature& feature, const String& modification) const;
91 
92  Feature mergeFeatures_(Feature& labeled_channel_feature, const AASequence& unmodified_sequence, std::map<AASequence, Feature>& unlabeled_features_index) const;
93 
94 private:
96  static const int LIGHT_CHANNEL_ID_;
98  static const int MEDIUM_CHANNEL_ID_;
100  static const int HEAVY_CHANNEL_ID_;
101  };
102 } // namespace OpenMS
103 
OpenMS::ProteinIdentification::SearchParameters::digestion_enzyme
Protease digestion_enzyme
The cleavage site information in details (from ProteaseDB)
Definition: ProteinIdentification.h:118
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:150
FileHandler.h
OpenMS::DigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >::getInstance
static ProteaseDB * getInstance()
this member function serves as a replacement of the constructor
Definition: DigestionEnzymeDB.h:70
OpenMS::MascotGenericFile::store
void store(const String &filename, const PeakMap &experiment, bool compact=false)
stores the experiment data in a MascotGenericFile that can be used as input for MASCOT shell executio...
OpenMS::String::substitute
String & substitute(char from, char to)
Replaces all occurrences of the character from by the character to.
OpenMS::O18Labeler::HEAVY_CHANNEL_ID_
static const int HEAVY_CHANNEL_ID_
Map ID for the heavy/bi-labeled channel.
Definition: O18Labeler.h:100
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:55
OpenMS::String
A more convenient string class.
Definition: String.h:57
JavaInfo.h
MzMLFile.h
OpenMS::PeptideIdentification::setRT
void setRT(double rt)
sets the RT of the MS2 spectrum where the identification occurred
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
IdXMLFile.h
OpenMS::ProteinIdentification::MONOISOTOPIC
Definition: ProteinIdentification.h:95
BaseLabeler.h
OpenMS::PeptideIdentification::getHits
const std::vector< PeptideHit > & getHits() const
returns the peptide hits as const
OpenMS::ProteinIdentification::SearchParameters::fragment_mass_tolerance_ppm
bool fragment_mass_tolerance_ppm
Mass tolerance unit of fragment ions (true: ppm, false: Dalton)
Definition: ProteinIdentification.h:115
OpenMS::DateTime::now
static DateTime now()
Returns the current date and time.
OpenMS::ListUtils::concatenate
static String concatenate(const std::vector< T > &container, const String &glue="")
Concatenates all elements of the container and puts the glue string between elements.
Definition: ListUtils.h:175
OpenMS::DigestionEnzymeDB::getEnzyme
const DigestionEnzymeType * getEnzyme(const String &name) const
Definition: DigestionEnzymeDB.h:99
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::O18Labeler
Simulate O-18 experiments.
Definition: O18Labeler.h:49
PeptideHit.h
OpenMS::ProteinIdentification::SearchParameters::variable_modifications
std::vector< String > variable_modifications
Allowed variable modifications.
Definition: ProteinIdentification.h:112
OpenMS::ProteinIdentification::SearchParameters::mass_type
PeakMassType mass_type
Mass type of the peaks.
Definition: ProteinIdentification.h:110
ProteaseDB.h
OpenMS::MetaInfoInterface::setMetaValue
void setMetaValue(const String &name, const DataValue &value)
Sets the DataValue corresponding to a name.
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::ProteinIdentification::SearchParameters::db
String db
The used database.
Definition: ProteinIdentification.h:106
OpenMS::O18Labeler::getProductName
static const String getProductName()
name of the model (needed by Factory)
Definition: O18Labeler.h:67
ProteinIdentification.h
OpenMS::PeptideIdentification::setHigherScoreBetter
void setHigherScoreBetter(bool value)
sets the peptide score orientation
OpenMS::String::toQString
QString toQString() const
Conversion to Qt QString.
OpenMS::File::path
static String path(const String &file)
Returns the path of the file (without the file name).
MascotGenericFile.h
OpenMS::PeptideHit::setCharge
void setCharge(Int charge)
sets the charge of the peptide
CsvFile.h
OpenMS::MascotGenericFile
Read/write Mascot generic files (MGF).
Definition: MascotGenericFile.h:61
seqan::find
bool find(TFinder &finder, const Pattern< TNeedle, FuzzyAC > &me, PatternAuxData< TNeedle > &dh)
Definition: AhoCorasickAmbiguous.h:884
OpenMS::ProteinIdentification::SearchParameters::fragment_mass_tolerance
double fragment_mass_tolerance
Mass tolerance of fragment ions (Dalton or ppm)
Definition: ProteinIdentification.h:114
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:73
OpenMS::O18Labeler::create
static BaseLabeler * create()
create new object (needed by Factory)
Definition: O18Labeler.h:61
OpenMS::PeptideHit::setSequence
void setSequence(const AASequence &sequence)
sets the peptide sequence
OpenMS::ProteinIdentification::SearchParameters::fixed_modifications
std::vector< String > fixed_modifications
Used fixed modifications.
Definition: ProteinIdentification.h:111
OpenMS::CsvFile
This class handles csv files. Currently only loading is implemented.
Definition: CsvFile.h:49
OpenMS::SimTypes::FeatureMapSimVector
std::vector< FeatureMapSim > FeatureMapSimVector
Sim FeatureMap Vector.
Definition: SimTypes.h:99
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
MSExperiment.h
OpenMS::ProteinIdentification::SearchParameters::precursor_mass_tolerance
double precursor_mass_tolerance
Mass tolerance of precursor ions (Dalton or ppm)
Definition: ProteinIdentification.h:116
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::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
OpenMS::O18Labeler::LIGHT_CHANNEL_ID_
static const int LIGHT_CHANNEL_ID_
Map ID for the light/unlabeled channel.
Definition: O18Labeler.h:96
OpenMS::String::substr
String substr(size_t pos=0, size_t n=npos) const
Wrapper for the STL substr() method. Returns a String object with its contents initialized to a subst...
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::BaseLabeler
Abstract base class for all kinds of labeling techniques.
Definition: BaseLabeler.h:49
OpenMS::TOPPBase::ExitCodes
ExitCodes
Exit codes.
Definition: TOPPBase.h:155
String.h
OpenMS::ProteinIdentification::SearchParameters::precursor_mass_tolerance_ppm
bool precursor_mass_tolerance_ppm
Mass tolerance unit of precursor ions (true: ppm, false: Dalton)
Definition: ProteinIdentification.h:117
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:74
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:107
OpenMS::AASequence::fromString
static AASequence fromString(const String &s, bool permissive=true)
create AASequence object by parsing an OpenMS string
OpenMS::PeakFileOptions::setMSLevels
void setMSLevels(const std::vector< Int > &levels)
sets the desired MS levels for peaks to load
PeptideIdentification.h
OpenMS::ProteinIdentification::SearchParameters
Search parameters of the DB search.
Definition: ProteinIdentification.h:103
OpenMS::PeptideIdentification::setMZ
void setMZ(double mz)
sets the MZ of the MS2 spectrum
OpenMS::O18Labeler::MEDIUM_CHANNEL_ID_
static const int MEDIUM_CHANNEL_ID_
Map ID for the medium/mono-labeled channel.
Definition: O18Labeler.h:98
File.h
OpenMS::MzMLFile::getOptions
PeakFileOptions & 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!
TOPPBase.h
OpenMS::PeptideIdentification::setScoreType
void setScoreType(const String &type)
sets the peptide score type
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:63
OpenMS::PeptideHit::setScore
void setScore(double score)
sets the PSM score
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:54