OpenMS  2.4.0
MzTabFile.h
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34 
35 #pragma once
36 
37 #include <OpenMS/FORMAT/MzTab.h>
38 
43 
44 #include <boost/math/special_functions/fpclassify.hpp>
45 
46 #include <vector>
47 #include <algorithm>
48 
49 namespace OpenMS
50 {
51  class String;
52  class SVOutStream;
58  class OPENMS_DLLAPI MzTabFile
59  {
60 public:
62  MzTabFile();
64  ~MzTabFile();
65 
66  typedef std::map<std::pair<String, String>, std::vector<PeptideHit> > MapAccPepType;
67 
68  // store MzTab file
69  void store(const String& filename, const MzTab& mz_tab) const;
70 
71  // Set store behaviour of optional "reliability" and "uri" columns (default=no)
72  void storeProteinReliabilityColumn(bool store);
73  void storePeptideReliabilityColumn(bool store);
74  void storePSMReliabilityColumn(bool store);
75  void storeSmallMoleculeReliabilityColumn(bool store);
76  void storeProteinUriColumn(bool store);
77  void storePeptideUriColumn(bool store);
78  void storePSMUriColumn(bool store);
79  void storeSmallMoleculeUriColumn(bool store);
80  void storeProteinGoTerms(bool store);
81 
82  // load MzTab file
83  void load(const String& filename, MzTab& mz_tab);
84 
85 protected:
95 
96  void generateMzTabMetaDataSection_(const MzTabMetaData& map, StringList& sl) const;
97 
98  void generateMzTabProteinSection_(const MzTabProteinSectionRows& rows, StringList& sl, const std::vector<String>& optional_columns) const;
99 
100  String generateMzTabProteinHeader_(const MzTabProteinSectionRow& reference_row, const Size n_best_search_engine_scores, const std::vector<String>& optional_columns) const;
101 
102  String generateMzTabProteinSectionRow_(const MzTabProteinSectionRow& row, const std::vector<String>& optional_columns) const;
103 
104  void generateMzTabPeptideSection_(const MzTabPeptideSectionRows& rows, StringList& sl, const std::vector<String>& optional_columns) const;
105 
106  String generateMzTabPeptideHeader_(Size search_ms_runs, Size n_best_search_engine_scores, Size n_search_engine_score, Size assays, Size study_variables, const std::vector<String>& optional_columns) const;
107 
108  String generateMzTabPeptideSectionRow_(const MzTabPeptideSectionRow& row, const std::vector<String>& optional_columns) const;
109 
110  void generateMzTabPSMSection_(const MzTabPSMSectionRows& rows, StringList& sl, const std::vector<String>& optional_columns) const;
111 
112  String generateMzTabPSMHeader_(Size n_search_engine_scores, const std::vector<String>& optional_columns) const;
113 
114  String generateMzTabPSMSectionRow_(const MzTabPSMSectionRow& row, const std::vector<String>& optional_columns) const;
115 
116  void generateMzTabSmallMoleculeSection_(const MzTabSmallMoleculeSectionRows& map, StringList& sl, const std::vector<String>& optional_columns) const;
117 
118  String generateMzTabSmallMoleculeHeader_(Size search_ms_runs, Size n_best_search_engine_scores, Size n_search_engine_score, Size assays, Size study_variables, const std::vector<String>& optional_columns) const;
119 
120  String generateMzTabSmallMoleculeSectionRow_(const MzTabSmallMoleculeSectionRow& row, const std::vector<String>& optional_columns) const;
121 
122  // auxiliary functions
123  // extract two integers from string (e.g. search_engine_score[1]_ms_run[2] -> 1,2)
124  static std::pair<int, int> extractIndexPairsFromBrackets_(const String& s);
125 
126  static void sortPSM_(std::vector<PeptideIdentification>::iterator begin, std::vector<PeptideIdentification>::iterator end);
127 
128  static void keepFirstPSM_(std::vector<PeptideIdentification>::iterator begin, std::vector<PeptideIdentification>::iterator end);
129 
131  static void partitionIntoRuns_(const std::vector<PeptideIdentification>& pep_ids,
132  const std::vector<ProteinIdentification>& pro_ids,
133  std::map<String, std::vector<PeptideIdentification> >& map_run_to_pepids,
134  std::map<String, std::vector<ProteinIdentification> >& map_run_to_proids
135  );
136 
137 
139  static void createProteinToPeptideLinks_(const std::map<String, std::vector<PeptideIdentification> >& map_run_to_pepids, MapAccPepType& map_run_accession_to_pephits);
140 
142  static String extractProteinAccession_(const PeptideHit& peptide_hit);
143 
145  static String extractPeptideModifications_(const PeptideHit& peptide_hit);
146 
148  static String mapSearchEngineToCvParam_(const String& openms_search_engine_name);
149 
150  static String mapSearchEngineScoreToCvParam_(const String& openms_search_engine_name, double score, String score_type);
151 
152  static String extractNumPeptides_(const String& common_identifier, const String& protein_accession,
153  const MapAccPepType& map_run_accession_to_peptides);
154 
155  // mzTab definition of distinct
156  static String extractNumPeptidesDistinct_(String common_identifier, String protein_accession,
157  const MapAccPepType& map_run_accession_to_peptides);
158 
159  // same as distinct but additional constraint of uniqueness (=maps to exactly one Protein)
160  static String extractNumPeptidesUnambiguous_(String common_identifier, String protein_accession,
161  const MapAccPepType& map_run_accession_to_peptides);
162 
163  static std::map<String, Size> extractNumberOfSubSamples_(const std::map<String, std::vector<ProteinIdentification> >& map_run_to_proids);
164 
165  static void writePeptideHeader_(SVOutStream& output, std::map<String, Size> n_sub_samples);
166 
167  static void writeProteinHeader_(SVOutStream& output, std::map<String, Size> n_sub_samples);
168 
169  static void writeProteinData_(SVOutStream& output,
170  const ProteinIdentification& prot_id,
171  Size run_count,
172  String input_filename,
173  bool has_coverage,
174  const MapAccPepType& map_run_accession_to_peptides,
175  const std::map<String, Size>& map_run_to_num_sub
176  );
177 
178  };
179 
180 } // namespace OpenMS
181 
OpenMS::MzTabProteinSectionRow
Definition: MzTab.h:578
OpenMS::FileTypes::IDXML
OpenMS identification format (.idXML)
Definition: FileTypes.h:66
OpenMS::PeptideHit::getCharge
Int getCharge() const
returns the charge of the peptide
ConsensusXMLFile.h
OpenMS::MzTabStringList::setSeparator
void setSeparator(char sep)
OpenMS::MzTabPeptideSectionRow::retention_time
MzTabDoubleList retention_time
Definition: MzTab.h:619
MzTabFile.h
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:150
OpenMS::MzTabFile::store_psm_reliability_
bool store_psm_reliability_
Definition: MzTabFile.h:88
OpenMS::MzTabPSMSectionRow::sequence
MzTabString sequence
Definition: MzTab.h:635
OpenMS::ResidueModification::getUniModAccession
const String getUniModAccession() const
returns the unimod accession if available
FileHandler.h
FileTypes.h
OpenMS::MzTabFile
File adapter for MzTab files.
Definition: MzTabFile.h:58
OpenMS::ModificationsDB::getModification
const ResidueModification & getModification(Size index) const
Returns the modification with the given index.
OpenMS::MzTabParameter::fromCellString
void fromCellString(const String &s) override
OpenMS::Exception::IllegalArgument
A method or algorithm argument contains illegal values.
Definition: Exception.h:648
OpenMS::ResidueModification
Representation of a modification.
Definition: ResidueModification.h:76
OpenMS::MzTabProteinSectionRow::accession
MzTabString accession
Definition: MzTab.h:581
OpenMS::MzTabModification
Definition: MzTab.h:360
OpenMS::Internal::DIntervalBase::minX
CoordinateType minX() const
Accessor for min_ coordinate minimum.
Definition: DIntervalBase.h:240
OpenMS::PeptideHit::getSequence
const AASequence & getSequence() const
returns the peptide sequence without trailing or following spaces
OpenMS::MzTabPSMSectionRows
std::vector< MzTabPSMSectionRow > MzTabPSMSectionRows
Definition: MzTab.h:690
OpenMS::MzTabParameter::setName
void setName(const String &name)
OpenMS::MzTabModification::setModificationIdentifier
void setModificationIdentifier(const MzTabString &mod_id)
OpenMS::ResidueModification::ANYWHERE
Definition: ResidueModification.h:97
OpenMS::String::substitute
String & substitute(char from, char to)
Replaces all occurrences of the character from by the character to.
OpenMS::MzTabMetaData::mz_tab_type
MzTabString mz_tab_type
Definition: MzTab.h:523
OpenMS::MzTabPSMSectionRow::retention_time
MzTabDoubleList retention_time
Definition: MzTab.h:645
OpenMS::MzTabProteinSectionRows
std::vector< MzTabProteinSectionRow > MzTabProteinSectionRows
Definition: MzTab.h:688
OpenMS::Constants::k
const double k
OpenMS::MzTabPeptideSectionRow::opt_
std::vector< MzTabOptionalColumnEntry > opt_
Definition: MzTab.h:629
OpenMS::ProteinIdentification::ProteinGroup::probability
double probability
Probability of this group.
Definition: ProteinIdentification.h:74
OpenMS::String
A more convenient string class.
Definition: String.h:57
OpenMS::MzTabModificationMetaData::modification
MzTabParameter modification
Definition: MzTab.h:464
OpenMS::MzTabFile::store_protein_uri_
bool store_protein_uri_
Definition: MzTabFile.h:90
OpenMS::ModificationsDB::getInstance
static ModificationsDB * getInstance(OpenMS::String unimod_file="CHEMISTRY/unimod.xml", OpenMS::String psimod_file="CHEMISTRY/PSI-MOD.obo", OpenMS::String xlmod_file="CHEMISTRY/XLMOD.obo")
Returns a pointer to the modifications DB (singleton)
Definition: ModificationsDB.h:77
OpenMS::ResidueModification::getId
const String & getId() const
returns the identifier of the modification
PeptideEvidence.h
ConsensusMap.h
OpenMS::MzTabPeptideSectionRow::retention_time_window
MzTabDoubleList retention_time_window
Definition: MzTab.h:620
OpenMS::MzTabMetaData::variable_mod
std::map< Size, MzTabModificationMetaData > variable_mod
Definition: MzTab.h:549
OpenMS::FileTypes::CONSENSUSXML
OpenMS consensus map format (.consensusXML)
Definition: FileTypes.h:67
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::AASequence::getMonoWeight
double getMonoWeight(Residue::ResidueType type=Residue::Full, Int charge=0) const
IdXMLFile.h
FeatureXMLFile.h
OpenMS::ProteinHit
Representation of a protein hit.
Definition: ProteinHit.h:53
OpenMS::Constants::c
const double c
OpenMS::ResidueModification::N_TERM
Definition: ResidueModification.h:99
OpenMS::ProteinHit::getCoverage
double getCoverage() const
returns the coverage (in percent) of the protein hit based upon matched peptides
OpenMS::MzTabProteinSectionRow::best_search_engine_score
std::map< Size, MzTabDouble > best_search_engine_score
Definition: MzTab.h:588
OpenMS::Residue::Full
with N-terminus and C-terminus
Definition: Residue.h:152
OpenMS::MzTabPeptideSectionRow::sequence
MzTabString sequence
Definition: MzTab.h:609
OpenMS::MzTabProteinSectionRow::description
MzTabString description
Definition: MzTab.h:582
OpenMS::ConsensusMap::getPrimaryMSRunPath
void getPrimaryMSRunPath(StringList &toFill) const
returns the MS run path (stored in ColumnHeaders)
OpenMS::ConsensusFeature::HandleSetType
std::set< FeatureHandle, FeatureHandle::IndexLess > HandleSetType
Type definitions.
Definition: ConsensusFeature.h:75
LOG_INFO
#define LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:454
OpenMS::MzTab
Data model of MzTab files. Please see the official MzTab specification at https://code....
Definition: MzTab.h:699
OpenMS::MzTabPeptideSectionRow::modifications
MzTabModificationList modifications
Definition: MzTab.h:618
OpenMS::MzTabPSMSectionRow::opt_
std::vector< MzTabOptionalColumnEntry > opt_
Definition: MzTab.h:655
OpenMS::MzTabMetaData::uri
std::map< Size, MzTabString > uri
Definition: MzTab.h:545
OpenMS::Peak2D::getIntensity
IntensityType getIntensity() const
Definition: Peak2D.h:166
OpenMS::FeatureMap::getPrimaryMSRunPath
void getPrimaryMSRunPath(StringList &toFill) const
get the file path to the first MS run
OpenMS::ModificationsDB
database which holds all residue modifications from UniMod
Definition: ModificationsDB.h:72
OpenMS::AASequence::toString
String toString() const
returns the peptide as string with modifications embedded in brackets
OpenMS::FileTypes::MZIDENTML
mzIdentML (HUPO PSI AnalysisXML followup format) (.mzid)
Definition: FileTypes.h:77
OpenMS::MzTabPSMSectionRow::database
MzTabString database
Definition: MzTab.h:639
OpenMS::AASequence::toUnmodifiedString
String toUnmodifiedString() const
returns the peptide as string without any modifications
OpenMS::MzTabDoubleList::set
void set(const std::vector< MzTabDouble > &entries)
OpenMS::MzTabPeptideSectionRow::peptide_abundance_study_variable
std::map< Size, MzTabDouble > peptide_abundance_study_variable
Definition: MzTab.h:626
OpenMS::MzTabPSMSectionRow::end
MzTabString end
Definition: MzTab.h:654
OpenMS::ResidueModification::PROTEIN_C_TERM
Definition: ResidueModification.h:100
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:61
OpenMS::MzTabProteinSectionRow::database_version
MzTabString database_version
Definition: MzTab.h:586
OpenMS::BaseFeature::getPeptideIdentifications
const std::vector< PeptideIdentification > & getPeptideIdentifications() const
returns a const reference to the PeptideIdentification vector
OpenMS::MzTabFile::store_peptide_uri_
bool store_peptide_uri_
Definition: MzTabFile.h:91
OpenMS::MetaInfoInterface::getMetaValue
const DataValue & getMetaValue(const String &name) const
Returns the value corresponding to a string (or DataValue::EMPTY if not found)
OpenMS::MzTab::setMetaData
void setMetaData(const MzTabMetaData &md)
ListUtils.h
OpenMS::MzTabPeptideSectionRow::peptide_abundance_stdev_study_variable
std::map< Size, MzTabDouble > peptide_abundance_stdev_study_variable
Definition: MzTab.h:627
OpenMS::PeptideIdentification::setHits
void setHits(const std::vector< PeptideHit > &hits)
Sets the peptide hits.
OpenMS::MzTabPSMSectionRow::modifications
MzTabModificationList modifications
Definition: MzTab.h:644
OpenMS::MzTabSpectraRef::setSpecRef
void setSpecRef(String spec_ref)
OpenMS::PeptideIdentification::getHits
const std::vector< PeptideHit > & getHits() const
returns the peptide hits as const
OpenMS::IdXMLFile::load
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
OpenMS::MzTabPSMSectionRow::post
MzTabString post
Definition: MzTab.h:652
OpenMS::MzTabStringList
Definition: MzTab.h:332
OpenMS::MzTabParameterList::fromCellString
void fromCellString(const String &s) override
OpenMS::MzTabPeptideSectionRow::unique
MzTabBoolean unique
Definition: MzTab.h:611
OpenMS::MzTabMetaData
Definition: MzTab.h:516
OpenMS::MzTabMSRunMetaData::id_format
MzTabParameter id_format
Definition: MzTab.h:504
OpenMS::MzTabFile::store_psm_uri_
bool store_psm_uri_
Definition: MzTabFile.h:92
OpenMS::MzIdentMLFile
File adapter for MzIdentML files.
Definition: MzIdentMLFile.h:67
OpenMS::PeptideIdentification::assignRanks
void assignRanks()
Sorts the hits by score and assigns ranks according to the scores.
OpenMS::MzTabProteinSectionRow::opt_
std::vector< MzTabOptionalColumnEntry > opt_
Definition: MzTab.h:603
OpenMS::ProteinHit::getAccession
const String & getAccession() const
returns the accession of the protein
OpenMS::PeptideEvidence::N_TERMINAL_AA
static const char N_TERMINAL_AA
Definition: PeptideEvidence.h:60
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::MzTabStringList::set
void set(const std::vector< MzTabString > &entries)
LOG_DEBUG
#define LOG_DEBUG
Macro for general debugging information.
Definition: LogStream.h:458
PeptideHit.h
OpenMS::MzTabModificationList::set
void set(const std::vector< MzTabModification > &entries)
OpenMS::MzTabParameter::setAccession
void setAccession(const String &accession)
OpenMS::MzTabSpectraRef::setMSFile
void setMSFile(Size index)
OpenMS::PeptideEvidence::UNKNOWN_POSITION
static const int UNKNOWN_POSITION
Definition: PeptideEvidence.h:53
OpenMS::ProteinIdentification::SearchParameters::variable_modifications
std::vector< String > variable_modifications
Allowed variable modifications.
Definition: ProteinIdentification.h:112
OpenMS::FileTypes::FEATUREXML
OpenMS feature file (.featureXML)
Definition: FileTypes.h:65
OpenMS::MzTabPeptideSectionRows
std::vector< MzTabPeptideSectionRow > MzTabPeptideSectionRows
Definition: MzTab.h:689
OpenMS::ResidueModification::getOrigin
char getOrigin() const
Returns the origin (i.e. modified amino acid)
OpenMS::MzTabDouble
Definition: MzTab.h:132
LOG_WARN
#define LOG_WARN
Macro if a warning, a piece of information which should be read by the user, should be logged.
Definition: LogStream.h:450
OpenMS::ResidueModification::C_TERM
Definition: ResidueModification.h:98
OpenMS::SVOutStream
Stream class for writing to comma/tab/...-separated values files.
Definition: SVOutStream.h:54
OpenMS::MetaInfoInterface
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:55
ProteinHit.h
OpenMS::MzTabProteinSectionRow::protein_coverage
MzTabDouble protein_coverage
Definition: MzTab.h:598
OpenMS::MzTabDoubleList
Definition: MzTab.h:154
OpenMS::ConsensusMap::getProteinIdentifications
const std::vector< ProteinIdentification > & getProteinIdentifications() const
non-mutable access to the protein identifications
OpenMS::MzTabParameterList
Definition: MzTab.h:309
OpenMS::ProteinIdentification::SearchParameters::db
String db
The used database.
Definition: ProteinIdentification.h:106
OpenMS::FileHandler
Facilitates file handling by file type recognition.
Definition: FileHandler.h:62
OpenMS::PeptideEvidence::UNKNOWN_AA
static const char UNKNOWN_AA
Definition: PeptideEvidence.h:57
OpenMS::MzTabMetaData::mz_tab_mode
MzTabString mz_tab_mode
Definition: MzTab.h:522
OpenMS::FeatureXMLFile::load
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
OpenMS::ResidueModification::PROTEIN_N_TERM
Definition: ResidueModification.h:101
OpenMS::MzTabBoolean
Definition: MzTab.h:222
ProteinIdentification.h
OpenMS::FileTypes::Type
Type
Actual file types enum.
Definition: FileTypes.h:58
MathFunctions.h
OpenMS::BaseFeature::getCharge
const ChargeType & getCharge() const
Non-mutable access to charge state.
OpenMS::MzTabPeptideSectionRow::mass_to_charge
MzTabDouble mass_to_charge
Definition: MzTab.h:622
OpenMS::ConsensusFeature
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:69
OpenMS::MzTabPSMSectionRow::pre
MzTabString pre
Definition: MzTab.h:651
OpenMS::ProteinHit::getScore
float getScore() const
returns the score of the protein hit
OpenMS::AASequence::size
Size size() const
returns the number of residues
OpenMS::MzTabMSRunMetaData::format
MzTabParameter format
Definition: MzTab.h:502
OpenMS::MzTabParameter
Definition: MzTab.h:270
OpenMS::MzTabFile::store
void store(const String &filename, const MzTab &mz_tab) const
OpenMS::FileHandler::getType
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
OpenMS::MzTabMetaData::psm_search_engine_score
std::map< Size, MzTabParameter > psm_search_engine_score
Definition: MzTab.h:530
OpenMS::ProteinIdentification::SearchParameters::db_version
String db_version
The database version.
Definition: ProteinIdentification.h:107
OpenMS::DBoundingBox< 2 >
OpenMS::MzTabFile::store_peptide_reliability_
bool store_peptide_reliability_
Definition: MzTabFile.h:87
MzTab.h
OpenMS::MzTabPSMSectionRow::accession
MzTabString accession
Definition: MzTab.h:637
OpenMS::MzTab::setProteinSectionRows
void setProteinSectionRows(const MzTabProteinSectionRows &psd)
OpenMS::AASequence::isModified
bool isModified() const
returns true if any of the residues or termini are modified
OpenMS::PeptideHit::extractProteinAccessionsSet
std::set< String > extractProteinAccessionsSet() const
extracts the set of non-empty protein accessions from peptide evidences
OpenMS::MzTabPSMSectionRow::charge
MzTabInteger charge
Definition: MzTab.h:646
seqan::find
bool find(TFinder &finder, const Pattern< TNeedle, FuzzyAC > &me, PatternAuxData< TNeedle > &dh)
Definition: AhoCorasickAmbiguous.h:884
OpenMS::String::toUpper
String & toUpper()
Converts the string to uppercase.
OpenMS::MzTabPeptideSectionRow::search_engine_score_ms_run
std::map< Size, std::map< Size, MzTabDouble > > search_engine_score_ms_run
Definition: MzTab.h:616
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:75
OpenMS::FeatureMap::getUnassignedPeptideIdentifications
const std::vector< PeptideIdentification > & getUnassignedPeptideIdentifications() const
non-mutable access to the unassigned peptide identifications
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:73
OpenMS::Peak2D::getRT
CoordinateType getRT() const
Returns the RT coordinate (index 0)
Definition: Peak2D.h:208
OpenMS::MzTab::setPSMSectionRows
void setPSMSectionRows(const MzTabPSMSectionRows &psd)
OpenMS::ProteinIdentification::ProteinGroup::accessions
std::vector< String > accessions
Accessions of (indistinguishable) proteins that belong to the same group.
Definition: ProteinIdentification.h:77
MetaInfoInterfaceUtils.h
OpenMS::MzTabProteinSectionRow::ambiguity_members
MzTabStringList ambiguity_members
Definition: MzTab.h:594
OpenMS::ProteinIdentification::SearchParameters::fixed_modifications
std::vector< String > fixed_modifications
Used fixed modifications.
Definition: ProteinIdentification.h:111
OpenMS::MzTabPeptideSectionRow::best_search_engine_score
std::map< Size, MzTabDouble > best_search_engine_score
Definition: MzTab.h:615
OpenMS::MzIdentMLFile::load
void load(const String &filename, std::vector< ProteinIdentification > &poid, std::vector< PeptideIdentification > &peid)
Loads the identifications from a MzIdentML file.
ModificationsDB.h
OpenMS::MzTabMSRunMetaData
Definition: MzTab.h:500
OpenMS::FeatureMap::setProteinIdentifications
void setProteinIdentifications(const std::vector< ProteinIdentification > &protein_identifications)
sets the protein identifications
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
OpenMS::MzTabPeptideSectionRow::peptide_abundance_std_error_study_variable
std::map< Size, MzTabDouble > peptide_abundance_std_error_study_variable
Definition: MzTab.h:628
OpenMS::AASequence::hasCTerminalModification
bool hasCTerminalModification() const
predicate which is true if the peptide is C-term modified
OpenMS::ConsensusMap::getColumnHeaders
const ColumnHeaders & getColumnHeaders() const
Non-mutable access to the file descriptions.
OpenMS::PeptideHit::getPeptideEvidences
const std::vector< PeptideEvidence > & getPeptideEvidences() const
returns information on peptides (potentially) identified by this PSM
OpenMS::MzTabPeptideSectionRow::accession
MzTabString accession
Definition: MzTab.h:610
OpenMS::MzTabPSMSectionRow::unique
MzTabBoolean unique
Definition: MzTab.h:638
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:93
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
OpenMS::Feature::getConvexHull
ConvexHull2D & getConvexHull() const
Returns the overall convex hull of the feature (calculated from the convex hulls of the mass traces)
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::MzTabModificationList
Definition: MzTab.h:390
OpenMS::MetaInfoInterface::metaValueExists
bool metaValueExists(const String &name) const
Returns whether an entry with the given name exists.
OpenMS::MzTabModification::setPositionsAndParameters
void setPositionsAndParameters(const std::vector< std::pair< Size, MzTabParameter > > &ppp)
OpenMS::PeptideHit::getScore
double getScore() const
returns the PSM score
OpenMS::MzTabPSMSectionRow::calc_mass_to_charge
MzTabDouble calc_mass_to_charge
Definition: MzTab.h:648
OpenMS::MzTabMetaData::protein_search_engine_score
std::map< Size, MzTabParameter > protein_search_engine_score
Definition: MzTab.h:528
OpenMS::ProteinHit::getDescription
String getDescription() const
returns the description of the protein
OpenMS::MetaInfoInterface::getKeys
void getKeys(std::vector< String > &keys) const
Fills the given vector with a list of all keys for which a value is set.
OpenMS::MzTabPSMSectionRow::search_engine_score
std::map< Size, MzTabDouble > search_engine_score
Definition: MzTab.h:642
OpenMS::FeatureXMLFile
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
OpenMS::MzTabPSMSectionRow::PSM_ID
MzTabInteger PSM_ID
Definition: MzTab.h:636
OpenMS::MzTabPSMSectionRow::search_engine
MzTabParameterList search_engine
Definition: MzTab.h:641
OpenMS::MzTabMetaData::peptide_search_engine_score
std::map< Size, MzTabParameter > peptide_search_engine_score
Definition: MzTab.h:529
OpenMS::PeptideEvidence::C_TERMINAL_AA
static const char C_TERMINAL_AA
Definition: PeptideEvidence.h:61
OpenMS::DataValue::toString
String toString() const
Conversion to String.
OpenMS::ConvexHull2D::getBoundingBox
DBoundingBox< 2 > getBoundingBox() const
returns the bounding box of the feature hull points
OpenMS::MzTabFile::store_protein_goterms_
bool store_protein_goterms_
Definition: MzTabFile.h:94
OpenMS::MzTabPSMSectionRow::start
MzTabString start
Definition: MzTab.h:653
OpenMS::Internal::DIntervalBase::maxX
CoordinateType maxX() const
Accessor for min_ coordinate maximum.
Definition: DIntervalBase.h:252
OpenMS::MzTabFile::store_smallmolecule_reliability_
bool store_smallmolecule_reliability_
Definition: MzTabFile.h:89
OpenMS::MzTabProteinSectionRow::database
MzTabString database
Definition: MzTab.h:585
OpenMS::MzTabPeptideSectionRow::charge
MzTabInteger charge
Definition: MzTab.h:621
OpenMS::MzTabInteger
Definition: MzTab.h:178
OpenMS::MzTabModificationMetaData::position
MzTabString position
Definition: MzTab.h:466
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:107
OpenMS::Exception::BaseException::what
const char * what() const noexcept override
Returns the error message of the exception.
OpenMS::AASequence::hasNTerminalModification
bool hasNTerminalModification() const
predicate which is true if the peptide is N-term modified
OpenMS::Exception::MissingInformation
Not all required information provided.
Definition: Exception.h:195
OpenMS::Peak2D::getMZ
CoordinateType getMZ() const
Returns the m/z coordinate (index 1)
Definition: Peak2D.h:196
OpenMS::ProteinIdentification::ProteinGroup
Bundles multiple (e.g. indistinguishable) proteins in a group.
Definition: ProteinIdentification.h:71
OpenMS::MzTabPeptideSectionRow
Definition: MzTab.h:607
OpenMS::MzTabSpectraRef
Definition: MzTab.h:413
OpenMS::MzTabSmallMoleculeSectionRow
Definition: MzTab.h:659
OpenMS::MzTabMetaData::ms_run
std::map< Size, MzTabMSRunMetaData > ms_run
Definition: MzTab.h:557
OpenMS::MzTabMSRunMetaData::location
MzTabString location
Definition: MzTab.h:503
PeptideIdentification.h
OpenMS::ProteinIdentification::SearchParameters
Search parameters of the DB search.
Definition: ProteinIdentification.h:103
OpenMS::MzTabModificationMetaData
Definition: MzTab.h:462
OpenMS::MzTabPSMSectionRow::database_version
MzTabString database_version
Definition: MzTab.h:640
OpenMS::AASequence::getCTerminalModification
const ResidueModification * getCTerminalModification() const
returns a pointer to the C-terminal modification, or zero if none is set
OpenMS::MzTabOptionalColumnEntry
std::pair< String, MzTabString > MzTabOptionalColumnEntry
Definition: MzTab.h:575
OpenMS::MzTabModificationMetaData::site
MzTabString site
Definition: MzTab.h:465
OpenMS::ResidueModification::getTermSpecificity
TermSpecificity getTermSpecificity() const
returns terminal specificity
OpenMS::MzTabFile::MapAccPepType
std::map< std::pair< String, String >, std::vector< PeptideHit > > MapAccPepType
Definition: MzTabFile.h:66
OpenMS::AASequence::getNTerminalModification
const ResidueModification * getNTerminalModification() const
returns a pointer to the N-terminal modification, or zero if none is set
OpenMS::MzTabPSMSectionRow::spectra_ref
MzTabSpectraRef spectra_ref
Definition: MzTab.h:650
MzIdentMLFile.h
TOPPBase.h
OpenMS::MzTabFile::store_smallmolecule_uri_
bool store_smallmolecule_uri_
Definition: MzTabFile.h:93
OpenMS::MzTabParameter::setCVLabel
void setCVLabel(const String &CV_label)
OpenMS::FeatureMap::getProteinIdentifications
const std::vector< ProteinIdentification > & getProteinIdentifications() const
non-mutable access to the protein identifications
OpenMS::MzTabPSMSectionRow
Definition: MzTab.h:633
OpenMS::ConsensusXMLFile
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:61
OpenMS::MzTabPSMSectionRow::exp_mass_to_charge
MzTabDouble exp_mass_to_charge
Definition: MzTab.h:647
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:63
OpenMS::MzTabString
Definition: MzTab.h:244
OpenMS::MzTab::setPeptideSectionRows
void setPeptideSectionRows(const MzTabPeptideSectionRows &psd)
OpenMS::MzTabFile::store_protein_reliability_
bool store_protein_reliability_
Definition: MzTabFile.h:86
OpenMS::MzTabMetaData::fixed_mod
std::map< Size, MzTabModificationMetaData > fixed_mod
Definition: MzTab.h:547
OpenMS::MzTabMetaData::description
MzTabString description
Definition: MzTab.h:526
OpenMS::MzTabSmallMoleculeSectionRows
std::vector< MzTabSmallMoleculeSectionRow > MzTabSmallMoleculeSectionRows
Definition: MzTab.h:691
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:54
StringListUtils.h