OpenMS  3.0.0
CompNovoIdentification.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 2002-2022.
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: Timo Sachsenberg $
32 // $Authors: Andreas Bertsch $
33 // --------------------------------------------------------------------------
34 
35 
36 #pragma once
37 
38 // OpenMS includes
40 
41 // stl includes
42 #include <vector>
43 #include <map>
44 
45 namespace OpenMS
46 {
54  class OPENMS_DLLAPI CompNovoIdentification :
56  {
57 
58 public:
59 
65 
68 
70  ~CompNovoIdentification() override;
72 
74  CompNovoIdentification & operator=(const CompNovoIdentification & source);
75 
79  void getIdentifications(std::vector<PeptideIdentification> & ids, const PeakMap & exp) override;
81 
83  void getIdentification(PeptideIdentification & id, const PeakSpectrum & CID_spec, const PeakSpectrum & ETD_spec);
85 
86 
90 
91 protected:
92 
94  void getDecompositionsDAC_(std::set<String> & sequences, Size left, Size right, double peptide_weight, const PeakSpectrum & CID_orig_spec, const PeakSpectrum & ETD_orig_spec, std::map<double, IonScore> & CID_nodes);
95 
97  void reducePermuts_(std::set<String> & permuts, const PeakSpectrum & CID_orig_spec, const PeakSpectrum & ETD_orig_spec, double prefix, double suffix);
98 
100  double estimatePrecursorWeight_(const PeakSpectrum & ETD_spec, Size & charge);
101 
102  };
103 }
104 
OpenMS::ProteinIdentification::SearchParameters::digestion_enzyme
Protease digestion_enzyme
The cleavage site information in details (from ProteaseDB)
Definition: ProteinIdentification.h:273
OpenMS::CompNovoIdentification
run with CompNovoIdentification
Definition: CompNovoIdentification.h:54
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
double
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::CompNovoIdentification::IonScore
CompNovoIonScoringBase::IonScore IonScore
Definition: CompNovoIdentification.h:88
OpenMS::DigestionEnzymeDB::getInstance
static InstanceType * getInstance()
this member function serves as a replacement of the constructor
Definition: DigestionEnzymeDB.h:69
OpenMS::StringUtils::suffix
static String suffix(const String &this_s, size_t length)
Definition: StringUtilsSimple.h:156
OpenMS::File::basename
static String basename(const String &file)
OpenMS::CompNovoIonScoringBase::IsotopeType
IsotopeType
Definition: CompNovoIonScoringBase.h:60
OpenMS::ProteinIdentification::setSearchEngineVersion
void setSearchEngineVersion(const String &search_engine_version)
Sets the search engine version.
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:57
OpenMS::String
A more convenient string class.
Definition: String.h:58
MzMLFile.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::PeakFileOptions::addMSLevel
void addMSLevel(int level)
adds a desired MS level for peaks to load
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::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:70
OpenMS::ParamValue::toBool
bool toBool() const
Conversion to bool.
OpenMS::CompNovoIdentificationBase::Permut
Simple class to store permutations and a score.
Definition: CompNovoIdentificationBase.h:186
OpenMS::MSExperiment::size
Size size() const
Definition: MSExperiment.h:120
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::DateTime::now
static DateTime now()
Returns the current date and time.
OpenMS::CompNovoIonScoringBase::IonScore
Definition: CompNovoIonScoringBase.h:67
OpenMS::ProteinIdentification::SearchParameters::charges
String charges
The allowed charges for the search.
Definition: ProteinIdentification.h:264
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::DateTime::get
void get(UInt &month, UInt &day, UInt &year, UInt &hour, UInt &minute, UInt &second) const
Fills the arguments with the date and the time.
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
ProteaseDB.h
OpenMS::ProteinIdentification::setPrimaryMSRunPath
void setPrimaryMSRunPath(const StringList &s, bool raw=false)
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::CompNovoIdentification::getIdentifications
void getIdentifications(std::vector< PeptideIdentification > &ids, const PeakMap &exp) override
performs an ProteinIdentification run on a PeakMap
OpenMS::CompNovoIdentificationCID::getIdentifications
void getIdentifications(std::vector< PeptideIdentification > &ids, const PeakMap &exp) override
performs an ProteinIdentification run on a PeakMap
CompNovoIdentificationBase.h
CompNovoIdentification.h
OpenMS::DefaultParamHandler::setParameters
void setParameters(const Param &param)
Sets the parameters.
OpenMS::DefaultParamHandler::getDefaults
const Param & getDefaults() const
Non-mutable access to the default parameters.
OpenMS::DefaultParamHandler::getParameters
const Param & getParameters() const
Non-mutable access to the parameters.
OpenMS::ProteinIdentification::setSearchParameters
void setSearchParameters(const SearchParameters &search_parameters)
Sets the search parameters.
OpenMS::ProteinIdentification::SearchParameters::fragment_mass_tolerance
double fragment_mass_tolerance
Mass tolerance of fragment ions (Dalton or ppm)
Definition: ProteinIdentification.h:269
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::CompNovoIdentificationCID
run with CompNovoIdentificationCID
Definition: CompNovoIdentificationCID.h:54
OpenMS::ProteinIdentification::SearchParameters::fixed_modifications
std::vector< String > fixed_modifications
Used fixed modifications.
Definition: ProteinIdentification.h:266
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
OpenMS::ProteinIdentification::setSearchEngine
void setSearchEngine(const String &search_engine)
Sets the search engine type.
OpenMS::CompNovoIdentificationBase
run with CompNovoIdentificationBase
Definition: CompNovoIdentificationBase.h:57
OpenMS::ProteinIdentification::SearchParameters::precursor_mass_tolerance
double precursor_mass_tolerance
Mass tolerance of precursor ions (Dalton or ppm)
Definition: ProteinIdentification.h:271
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
AASequence.h
OpenMS::CompNovoIdentification::Permut
CompNovoIdentificationBase::Permut Permut
Definition: CompNovoIdentification.h:89
OpenMS::Param::copy
Param copy(const std::string &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
OpenMS::PeakFileOptions
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
OpenMS::CompNovoIdentification::IsotopeType
CompNovoIonScoringBase::IsotopeType IsotopeType
Definition: CompNovoIdentification.h:87
OpenMS::ProteinIdentification::setDateTime
void setDateTime(const DateTime &date)
Sets the date of the protein identification run.
OpenMS::PeakFileOptions::clearMSLevels
void clearMSLevels()
clears the MS levels
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::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
OpenMS::StringUtils::prefix
static String prefix(const String &this_s, size_t length)
Definition: StringUtilsSimple.h:147
CompNovoIdentificationCID.h
OpenMS::ProteinIdentification::setIdentifier
void setIdentifier(const String &id)
Sets the identifier.
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OpenMS::ProteinIdentification::SearchParameters
Search parameters of the DB search.
Definition: ProteinIdentification.h:258
OpenMS::Param::getValue
const ParamValue & getValue(const std::string &key) const
Returns a value of a parameter.
OpenMS::DateTime
DateTime Class.
Definition: DateTime.h:58
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::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:68