OpenMS  2.6.0
MzCalibration.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
27 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Chris Bielow $
32 // $Authors: Juliane Schmachtenberg $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
37 #include <OpenMS/QC/QCBase.h>
38 
40 
41 namespace OpenMS
42 {
43  class FeatureMap;
44  class MSExperiment;
45  class PeptideIdentification;
46 
58  class OPENMS_DLLAPI MzCalibration : public QCBase
59  {
60  public:
62  MzCalibration();
63 
65  virtual ~MzCalibration() = default;
66 
76  void compute(FeatureMap& features, const MSExperiment& exp, const QCBase::SpectraMap& map_to_spectrum);
77 
80  Status requires() const override;
81 
83  const String& getName() const override;
84 
85  private:
87  void addMzMetaValues_(PeptideIdentification& peptide_ID, const MSExperiment& exp, const QCBase::SpectraMap& map_to_spectrum);
88 
89  double mz_raw_;
90  double mz_ref_;
91  bool no_mzml_;
92  };
93 }
94 
95 
DefaultParamHandler.h
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:144
FileHandler.h
TextFile.h
OpenMS::MzCalibration::no_mzml_
bool no_mzml_
Definition: MzCalibration.h:91
ListUtilsIO.h
OpenMS::QCBase::Status
Storing a status of available/needed inputs (i.e. a set of Requires) as UInt64.
Definition: QCBase.h:120
OpenMS::IdXMLFile::store
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.
OpenMS::ResidueModification
Representation of a modification.
Definition: ResidueModification.h:76
OpenMS::MzCalibration::mz_ref_
double mz_ref_
Definition: MzCalibration.h:90
OpenMS::ModificationDefinitionsSet
Representation of a set of modification definitions.
Definition: ModificationDefinitionsSet.h:58
OpenMS::ProteinIdentification::PeakMassType
PeakMassType
Peak mass type.
Definition: ProteinIdentification.h:247
OpenMS::File::basename
static String basename(const String &file)
Returns the basename of the file (without the path).
OpenMS::FileTypes::PEPXML
TPP pepXML file (.pepXML)
Definition: FileTypes.h:75
OpenMS::ProteinIdentification::SearchParameters::missed_cleavages
UInt missed_cleavages
The number of allowed missed cleavages.
Definition: ProteinIdentification.h:268
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:55
OpenMS::String
A more convenient string class.
Definition: String.h:59
MzMLFile.h
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:249
OpenMS::IntList
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
OpenMS::File::getUniqueName
static String getUniqueName(bool include_hostname=true)
Returns a string, consisting of date, time, hostname, process id, and a incrementing number....
OpenMS::operator<
bool operator<(const QTCluster &q1, const QTCluster &q2)
ListUtils.h
OpenMS::QCBase::SpectraMap
Map to find a spectrum via its NativeID.
Definition: QCBase.h:77
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:270
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:193
OpenMS::ModificationsDB::getInstance
static ModificationsDB * getInstance()
Returns a pointer to the modifications DB (singleton)
OpenMS::File::exists
static bool exists(const String &file)
Method used to test if a file exists.
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::ProteinIdentification::AVERAGE
Definition: ProteinIdentification.h:250
OpenMS::ProteinIdentification::SearchParameters::variable_modifications
std::vector< String > variable_modifications
Allowed variable modifications.
Definition: ProteinIdentification.h:267
OpenMS::ProteinIdentification::SearchParameters::mass_type
PeakMassType mass_type
Mass type of the peaks.
Definition: ProteinIdentification.h:265
OpenMS::ResidueModification::getOrigin
char getOrigin() const
Returns the origin (i.e. modified amino acid)
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...
int
OpenMS::SpectrumMetaDataLookup::readSpectra
void readSpectra(const SpectrumContainer &spectra, const String &scan_regexp=default_scan_regexp, bool get_precursor_rt=false)
Read spectra and store their meta data.
Definition: SpectrumMetaDataLookup.h:213
OpenMS::ProteinIdentification::SearchParameters::db
String db
The used database.
Definition: ProteinIdentification.h:261
OpenMS::QCBase
This class serves as an abstract base class for all QC classes.
Definition: QCBase.h:54
QProcess
ModificationDefinitionsSet.h
OpenMS::ResidueModification::getDiffMonoMass
double getDiffMonoMass() const
returns the diff monoisotopic mass, or 0.0 if not set
PepXMLFile.h
OpenMS::String::toQString
QString toQString() const
Conversion to Qt QString.
OpenMS::ProteinIdentification::SearchParameters::fragment_mass_tolerance
double fragment_mass_tolerance
Mass tolerance of fragment ions (Dalton or ppm)
Definition: ProteinIdentification.h:269
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::ProteinIdentification::SearchParameters::fixed_modifications
std::vector< String > fixed_modifications
Used fixed modifications.
Definition: ProteinIdentification.h:266
ModificationsDB.h
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
OpenMS::ProteinIdentification::SearchParameters::precursor_mass_tolerance
double precursor_mass_tolerance
Mass tolerance of precursor ions (Dalton or ppm)
Definition: ProteinIdentification.h:271
OpenMS::SpectrumMetaDataLookup
Helper class for looking up spectrum meta data.
Definition: SpectrumMetaDataLookup.h:142
OpenMS::File::absolutePath
static String absolutePath(const String &file)
Replaces the relative path in the argument with the absolute path.
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:97
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
OpenMS::MSExperiment::getSpectra
const std::vector< MSSpectrum > & getSpectra() const
returns the spectrum list
OpenMS::PepXMLFile::load
void load(const String &filename, std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides, const String &experiment_name, const SpectrumMetaDataLookup &lookup)
Loads peptide sequences with modifications out of a PepXML file.
String.h
OpenMS::ModificationsDB::getAllSearchModifications
void getAllSearchModifications(std::vector< String > &modifications) const
Collects all modifications that can be used for identification searches.
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:272
OpenMS::File::getTempDirectory
static String getTempDirectory()
The current OpenMS temporary data path (for temporary files)
OpenMS::PepXMLFile
Used to load and store PepXML files.
Definition: PepXMLFile.h:63
OpenMS::MzCalibration
QC metric calculating (un)calibrated m/z error.
Definition: MzCalibration.h:58
OpenMS::ResidueModification::getTermSpecificityName
String getTermSpecificityName(TermSpecificity term_spec=NUMBER_OF_TERM_SPECIFICITY) const
Returns the name of the terminal specificity.
OpenMS::ProteinIdentification::SearchParameters
Search parameters of the DB search.
Definition: ProteinIdentification.h:258
OpenMS::ResidueModification::getTermSpecificity
TermSpecificity getTermSpecificity() const
returns terminal specificity
OpenMS::ModificationsDB::getModification
const ResidueModification * getModification(Size index) const
Returns the modification with the given index. note: out-of-bounds check is only performed in debug m...
File.h
OpenMS::MzCalibration::mz_raw_
double mz_raw_
Definition: MzCalibration.h:89
OpenMS::DefaultParamHandler::writeParametersToMetaValues
static void writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &prefix="")
Writes all parameters to meta values.
TOPPBase.h
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:63
QCBase.h
OpenMS::FileHandler::swapExtension
static String swapExtension(const String &filename, const FileTypes::Type new_type)
Tries to find and remove a known file extension, and append the new one.