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OpenMS
2.5.0
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void store(const String &filename, const PeakMap &exp) const
Stores a map in a MSPFile file.
Int getCharge() const
returns the charge of the peptide
Base class for TOPP applications.
Definition: TOPPBase.h:144
const String & getModificationName() const
returns the name (ID) of the modification, or an empty string if none is set
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
Scales the intensity of peaks to the sqrt.
Definition: SqrtMower.h:51
MzData file (.mzData)
Definition: FileTypes.h:63
File adapter for MzData files.
Definition: MzDataFile.h:53
static FactoryProduct * create(const String &name)
return FactoryProduct according to unique identifier name
Definition: Factory.h:112
Normalizes the peak intensities spectrum-wise.
Definition: Normalizer.h:57
A method or algorithm argument contains illegal values.
Definition: Exception.h:648
void store(const 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.
void filterPeakMap(PeakMap &exp)
double compute_F(double dot_product, double delta_D, double dot_bias)
: computes the overall all score
Returns FactoryProduct* based on the name of the desired concrete FactoryProduct.
Definition: Factory.h:61
void insertHit(const PeptideHit &hit)
Appends a peptide hit.
PeakMassType
Peak mass type.
Definition: ProteinIdentification.h:211
This is a binned representation of a PeakSpectrum.
Definition: BinnedSpectrum.h:75
void setIdentifier(const String &id)
sets the identifier
WindowMower augments the highest peaks in a sliding or jumping window.
Definition: WindowMower.h:54
void filterPeakMap(PeakMap &exp)
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
double delta_D(double top_hit, double runner_up)
calculates the normalized distance between top_hit and runner_up.
void setMZ(CoordinateType mz)
Mutable access to m/z.
Definition: Peak1D.h:121
MzXML file (.mzXML)
Definition: FileTypes.h:64
void setSearchEngineVersion(const String &search_engine_version)
Sets the search engine version.
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:58
Iterator begin()
Definition: MSExperiment.h:157
const String & getOneLetterCode() const
returns the name as one letter code (String of size 1)
void setProteinAccession(const String &s)
set the protein accession the peptide matches to. If not available set to empty string.
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
const std::vector< Precursor > & getPrecursors() const
returns a const reference to the precursors
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Representation of a protein hit.
Definition: ProteinHit.h:57
Definition: ProteinIdentification.h:213
Base class for compare functors of spectra, that return a similarity value for two spectra.
Definition: PeakSpectrumCompareFunctor.h:52
void load(const String &filename, MapType &map)
Loads a map from a MzData file.
void setIntensity(IntensityType intensity)
Mutable access to the data point intensity (height)
Definition: Peak1D.h:112
database which holds all residue modifications from UniMod
Definition: ModificationsDB.h:74
File adapter for MzXML 3.1 files.
Definition: MzXMLFile.h:52
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
Base::const_iterator const_iterator
Definition: MSExperiment.h:125
const std::vector< PeptideIdentification > & getPeptideIdentifications() const
returns a const reference to the PeptideIdentification vector
bool clearMetaDataArrays()
Clears the meta data arrays of all contained spectra (float, integer and string arrays)
Unknown file extension.
Definition: FileTypes.h:60
Representation of a protein identification run.
Definition: ProteinIdentification.h:71
ParentPeakMower gets rid of high peaks that could stem from unfragmented precursor ions.
Definition: ParentPeakMower.h:54
Size size() const
Definition: MSExperiment.h:127
NLargest removes all but the n largest peaks.
Definition: NLargest.h:54
void setHits(const std::vector< PeptideHit > &hits)
Sets the peptide hits.
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
const StringDataArrays & getStringDataArrays() const
Returns a const reference to the string meta data arrays.
const std::vector< PeptideHit > & getHits() const
returns the peptide hits as const
static DateTime now()
Returns the current date and time.
static ModificationsDB * getInstance()
Returns a pointer to the modifications DB (singleton)
String charges
The allowed charges for the search.
Definition: ProteinIdentification.h:227
void setAccession(const String &accession)
sets the accession of the protein
const String & getAccession() const
returns the accession of the protein
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
std::vector< SpectrumType >::iterator Iterator
Mutable iterator.
Definition: MSExperiment.h:111
void addPeptideEvidence(const PeptideEvidence &peptide_evidence)
adds information on a peptide that is (potentially) identified by this PSM
void addSpectrum(const MSSpectrum &spectrum)
adds a spectrum to the list
void filterPeakMap(PeakMap &exp) const
std::vector< String > variable_modifications
Allowed variable modifications.
Definition: ProteinIdentification.h:230
PeakMassType mass_type
Mass type of the peaks.
Definition: ProteinIdentification.h:228
char getOrigin() const
Returns the origin (i.e. modified amino acid)
void sort()
Sorts the hits by score.
Representation of a residue.
Definition: Residue.h:61
Class to hold strings, numeric values, lists of strings and lists of numeric values.
Definition: DataValue.h:56
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...
void sortByIntensity(bool reverse=false)
Lexicographically sorts the peaks by their intensity.
void setScoreType(const String &type)
Sets the protein score type.
void store(const String &filename, const MapType &map) const
Stores a map in a MzXML file.
Class that stores the data for one layer.
Definition: LayerData.h:85
String db
The used database.
Definition: ProteinIdentification.h:224
Facilitates file handling by file type recognition.
Definition: FileHandler.h:62
const Residue & getResidue(Size index) const
returns a pointer to the residue at position index
Type
Actual file types enum.
Definition: FileTypes.h:58
Representation of a peptide evidence.
Definition: PeptideEvidence.h:50
MarkerMower uses PeakMarker to find peaks, those that are not marked get removed.
Definition: MarkerMower.h:54
Size size() const
returns the number of residues
void setHigherScoreBetter(bool value)
sets the peptide score orientation
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
void setPosition(PositionType const &position)
Mutable access to the position.
Definition: Peak1D.h:151
void setPrecursors(const std::vector< Precursor > &precursors)
sets the precursors
void setParameters(const Param ¶m)
Sets the parameters.
Similarity score of SpectraST.
Definition: SpectraSTSimilarityScore.h:62
void setMSLevel(UInt ms_level)
Sets the MS level.
static const String EMPTY
Empty string for comparisons.
Definition: String.h:64
void setCharge(Int charge)
sets the charge of the peptide
bool isModified() const
returns true if any of the residues or termini are modified
const Param & getParameters() const
Non-mutable access to the parameters.
void setSearchParameters(const SearchParameters &search_parameters)
Sets the search parameters.
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
void filterPeakMap(PeakMap &exp)
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
void sortByPosition()
Lexicographically sorts the peaks by their position.
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
void setSequence(const AASequence &sequence)
sets the peptide sequence
std::vector< String > fixed_modifications
Used fixed modifications.
Definition: ProteinIdentification.h:229
void filterPeakMap(PeakMap &exp)
This class handles csv files. Currently only loading is implemented.
Definition: CsvFile.h:49
void insertHit(const ProteinHit &input)
Appends a protein hit.
void filterPeakMap(PeakMap &exp)
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:234
A required parameter was not given.
Definition: TOPPBase.h:111
void load(const String &filename, std::vector< PeptideIdentification > &ids, PeakMap &exp)
Loads a map from a MSPFile file.
void filterPeakMap(PeakMap &exp)
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
void filterPeakMap(PeakMap &exp)
Iterator end()
Definition: MSExperiment.h:167
static void registerChildren()
registers all derived products
Scaler scales the peak by ranking the peaks and assigning intensity according to rank.
Definition: Scaler.h:51
void load(const String &filename, MapType &map)
Loads a map from a MzXML file.
double dot_bias(const BinnedSpectrum &bin1, const BinnedSpectrum &bin2, double dot_product=-1) const
Calculates how much of the dot product is dominated by a few peaks.
ThresholdMower removes all peaks below a threshold.
Definition: ThresholdMower.h:51
BinnedSpectrum transform(const PeakSpectrum &spec)
spectrum is transformed into a binned spectrum with bin size 1 and spread 1 and the intensities are n...
void filterPeakMap(PeakMap &exp)
void getAllSearchModifications(std::vector< String > &modifications) const
Collects all modifications that can be used for identification searches.
void store(const String &filename, const MapType &map) const
Stores a map in a MzData file.
void setDateTime(const DateTime &date)
Sets the date of the protein identification run.
bool precursor_mass_tolerance_ppm
Mass tolerance unit of precursor ions (true: ppm, false: Dalton)
Definition: ProteinIdentification.h:235
Management and storage of parameters / INI files.
Definition: Param.h:73
void setPos(CoordinateType pos)
Alias for setMZ()
Definition: Peak1D.h:133
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
BernNorm scales the peaks by ranking them and then scaling them according to rank.
Definition: BernNorm.h:56
static AASequence fromString(const String &s, bool permissive=true)
create AASequence object by parsing an OpenMS string
File adapter for MSP files (NIST spectra library)
Definition: MSPFile.h:53
void setPeptideIdentifications(const std::vector< PeptideIdentification > &identifications)
sets the PeptideIdentification vector
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
void setIdentifier(const String &id)
Sets the identifier.
const double C13C12_MASSDIFF_U
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
Search parameters of the DB search.
Definition: ProteinIdentification.h:221
Data filtering or extraction.
Definition: DataProcessing.h:71
void setMZ(double mz)
sets the MZ of the MS2 spectrum
void setRT(double rt)
Sets the absolute retention time (in seconds)
IntensityType getIntensity() const
Definition: Peak1D.h:110
const ResidueModification * getModification(Size index) const
Returns the modification with the given index. note: out-of-bounds check is only performed in debug m...
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
CoordinateType getMinRT() const
returns the minimal retention time value
bool empty() const
Returns if this PeptideIdentification result is empty.
void setScore(double score)
sets the PSM score
Representation of a peptide hit.
Definition: PeptideHit.h:54