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OpenMS
2.4.0
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73 void preCheck(
Param& param)
const override;
90 void addModificationToPeptideHit_(
Feature& feature,
const String& modification)
const;
92 Feature mergeFeatures_(
Feature& labeled_channel_feature,
const AASequence& unmodified_sequence, std::map<AASequence, Feature>& unlabeled_features_index)
const;
Protease digestion_enzyme
The cleavage site information in details (from ProteaseDB)
Definition: ProteinIdentification.h:118
Base class for TOPP applications.
Definition: TOPPBase.h:150
static ProteaseDB * getInstance()
this member function serves as a replacement of the constructor
Definition: DigestionEnzymeDB.h:70
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...
String & substitute(char from, char to)
Replaces all occurrences of the character from by the character to.
static const int HEAVY_CHANNEL_ID_
Map ID for the heavy/bi-labeled channel.
Definition: O18Labeler.h:100
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:57
void setRT(double rt)
sets the RT of the MS2 spectrum where the identification occurred
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Definition: ProteinIdentification.h:95
const std::vector< PeptideHit > & getHits() const
returns the peptide hits as const
bool fragment_mass_tolerance_ppm
Mass tolerance unit of fragment ions (true: ppm, false: Dalton)
Definition: ProteinIdentification.h:115
static DateTime now()
Returns the current date and time.
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
const DigestionEnzymeType * getEnzyme(const String &name) const
Definition: DigestionEnzymeDB.h:99
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Simulate O-18 experiments.
Definition: O18Labeler.h:49
std::vector< String > variable_modifications
Allowed variable modifications.
Definition: ProteinIdentification.h:112
PeakMassType mass_type
Mass type of the peaks.
Definition: ProteinIdentification.h:110
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...
String db
The used database.
Definition: ProteinIdentification.h:106
static const String getProductName()
name of the model (needed by Factory)
Definition: O18Labeler.h:67
void setHigherScoreBetter(bool value)
sets the peptide score orientation
QString toQString() const
Conversion to Qt QString.
static String path(const String &file)
Returns the path of the file (without the file name).
void setCharge(Int charge)
sets the charge of the peptide
Read/write Mascot generic files (MGF).
Definition: MascotGenericFile.h:61
bool find(TFinder &finder, const Pattern< TNeedle, FuzzyAC > &me, PatternAuxData< TNeedle > &dh)
Definition: AhoCorasickAmbiguous.h:884
double fragment_mass_tolerance
Mass tolerance of fragment ions (Dalton or ppm)
Definition: ProteinIdentification.h:114
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:73
static BaseLabeler * create()
create new object (needed by Factory)
Definition: O18Labeler.h:61
void setSequence(const AASequence &sequence)
sets the peptide sequence
std::vector< String > fixed_modifications
Used fixed modifications.
Definition: ProteinIdentification.h:111
This class handles csv files. Currently only loading is implemented.
Definition: CsvFile.h:49
std::vector< FeatureMapSim > FeatureMapSimVector
Sim FeatureMap Vector.
Definition: SimTypes.h:99
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
double precursor_mass_tolerance
Mass tolerance of precursor ions (Dalton or ppm)
Definition: ProteinIdentification.h:116
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.
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
static const int LIGHT_CHANNEL_ID_
Map ID for the light/unlabeled channel.
Definition: O18Labeler.h:96
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...
An LC-MS feature.
Definition: Feature.h:70
Abstract base class for all kinds of labeling techniques.
Definition: BaseLabeler.h:49
ExitCodes
Exit codes.
Definition: TOPPBase.h:155
bool precursor_mass_tolerance_ppm
Mass tolerance unit of precursor ions (true: ppm, false: Dalton)
Definition: ProteinIdentification.h:117
Management and storage of parameters / INI files.
Definition: Param.h:74
Representation of a peptide/protein sequence.
Definition: AASequence.h:107
static AASequence fromString(const String &s, bool permissive=true)
create AASequence object by parsing an OpenMS string
void setMSLevels(const std::vector< Int > &levels)
sets the desired MS levels for peaks to load
Search parameters of the DB search.
Definition: ProteinIdentification.h:103
void setMZ(double mz)
sets the MZ of the MS2 spectrum
static const int MEDIUM_CHANNEL_ID_
Map ID for the medium/mono-labeled channel.
Definition: O18Labeler.h:98
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
void setScoreType(const String &type)
sets the peptide score type
Used to load and store idXML files.
Definition: IdXMLFile.h:63
void setScore(double score)
sets the PSM score
Representation of a peptide hit.
Definition: PeptideHit.h:54