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OpenMS
2.6.0
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Go to the documentation of this file.
49 class PeptideIdentification;
85 explicit Mapping(
const std::vector<ProteinIdentification>& prot_ids)
89 void create(
const std::vector<ProteinIdentification>& prot_ids)
91 identifier_to_msrunpath.clear();
92 runpath_to_identifier.clear();
96 prot_id.getPrimaryMSRunPath(filenames);
97 if (filenames.empty())
101 identifier_to_msrunpath[prot_id.getIdentifier()] = filenames;
102 const auto& it = runpath_to_identifier.find(filenames);
103 if (it != runpath_to_identifier.end())
106 "Multiple protein identifications with the same ms-run-path in Consensus/FeatureXML. Check input!\n",
109 runpath_to_identifier[filenames] = prot_id.getIdentifier();
169 return float_data_arrays_;
173 void setFloatDataArrays(
const FloatDataArrays& fda);
176 const StringDataArrays& getStringDataArrays()
const;
179 StringDataArrays& getStringDataArrays();
182 void setStringDataArrays(
const StringDataArrays& sda);
185 const IntegerDataArrays& getIntegerDataArrays()
const;
188 IntegerDataArrays& getIntegerDataArrays();
191 void setIntegerDataArrays(
const IntegerDataArrays& ida);
196 return *std::find_if(integer_data_arrays_.begin(), integer_data_arrays_.end(),
203 return *std::find_if(string_data_arrays_.begin(), string_data_arrays_.end(),
210 return *std::find_if(float_data_arrays_.begin(), float_data_arrays_.end(),
211 [&name](
const FloatDataArray& da) {
return da.getName() == name; } );
217 return *std::find_if(integer_data_arrays_.begin(), integer_data_arrays_.end(),
224 return *std::find_if(string_data_arrays_.begin(), string_data_arrays_.end(),
231 return *std::find_if(float_data_arrays_.begin(), float_data_arrays_.end(),
232 [&name](
const FloatDataArray& da) {
return da.getName() == name; } );
255 static const std::string NamesOfPeakMassType[SIZE_OF_PEAKMASSTYPE];
294 std::pair<int,int> getChargeRange()
const;
303 int getChargeValue_(
String& charge_str)
const;
330 const std::vector<ProteinHit>& getHits()
const;
333 std::vector<ProteinHit>& getHits();
344 void setHits(
const std::vector<ProteinHit>& hits);
347 std::vector<ProteinHit>::iterator findHit(
const String& accession);
350 const std::vector<ProteinGroup>& getProteinGroups()
const;
352 std::vector<ProteinGroup>& getProteinGroups();
357 const std::vector<ProteinGroup>& getIndistinguishableProteins()
const;
359 std::vector<ProteinGroup>& getIndistinguishableProteins();
361 void insertIndistinguishableProteins(
const ProteinGroup& group);
363 void fillIndistinguishableGroupsWithSingletons();
366 double getSignificanceThreshold()
const;
368 void setSignificanceThreshold(
double value);
370 const String& getScoreType()
const;
372 void setScoreType(
const String& type);
374 bool isHigherScoreBetter()
const;
376 void setHigherScoreBetter(
bool higher_is_better);
388 void computeCoverage(
const std::vector<PeptideIdentification>& pep_ids);
397 void computeModifications(
398 const std::vector<PeptideIdentification>& pep_ids,
404 const DateTime& getDateTime()
const;
407 void setDateTime(
const DateTime& date);
409 void setSearchEngine(
const String& search_engine);
411 const String& getSearchEngine()
const;
413 const String getOriginalSearchEngineName()
const;
415 void setSearchEngineVersion(
const String& search_engine_version);
417 const String& getSearchEngineVersion()
const;
419 void setInferenceEngine(
const String& search_engine);
421 const String getInferenceEngine()
const;
423 void setInferenceEngineVersion(
const String& inference_engine_version);
425 const String getInferenceEngineVersion()
const;
435 const String& getIdentifier()
const;
437 void setIdentifier(
const String&
id);
443 void setPrimaryMSRunPath(
const StringList& s,
bool raw =
false);
447 void addPrimaryMSRunPath(
const String& s,
bool raw =
false);
448 void addPrimaryMSRunPath(
const StringList& s,
bool raw =
false);
455 void getPrimaryMSRunPath(
StringList& output,
bool raw =
false)
const;
458 Size nrPrimaryMSRunPaths(
bool raw =
false)
const;
462 bool hasInferenceData()
const;
465 bool hasInferenceEngineAsSearchEngine()
const;
474 std::vector<std::pair<String,String>> getSearchEngineSettingsAsPairs(
const String& se =
"")
const;
Specificity
when querying for valid digestion products, this determines if the specificity of the two peptide end...
Definition: EnzymaticDigestion.h:66
Integer data array class.
Definition: DataArrays.h:52
std::vector< StringDataArray > StringDataArrays
Definition: ProteinIdentification.h:125
Protease digestion_enzyme
The cleavage site information in details (from ProteaseDB)
Definition: ProteinIdentification.h:273
Mapping(const std::vector< ProteinIdentification > &prot_ids)
Definition: ProteinIdentification.h:85
std::vector< FloatDataArray > FloatDataArrays
Definition: ProteinIdentification.h:122
const StringDataArray & getStringDataArrayByName(String name) const
Returns a const reference to the first string meta data array with the given name.
Definition: ProteinIdentification.h:222
PeakMassType
Peak mass type.
Definition: ProteinIdentification.h:247
Invalid value exception.
Definition: Exception.h:335
std::map< String, StringList > identifier_to_msrunpath
Definition: ProteinIdentification.h:80
UInt missed_cleavages
The number of allowed missed cleavages.
Definition: ProteinIdentification.h:268
A more convenient string class.
Definition: String.h:59
std::vector< String > accessions
Accessions of (indistinguishable) proteins that belong to the same group.
Definition: ProteinIdentification.h:134
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
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
Representation of a protein hit.
Definition: ProteinHit.h:58
IntegerDataArrays integer_data_arrays_
Integer data arrays.
Definition: ProteinIdentification.h:243
Definition: ProteinIdentification.h:249
const IntegerDataArray & getIntegerDataArrayByName(String name) const
Returns a const reference to the first integer meta data array with the given name.
Definition: ProteinIdentification.h:215
FloatDataArrays float_data_arrays_
Float data arrays.
Definition: ProteinIdentification.h:237
bool operator<(const QTCluster &q1, const QTCluster &q2)
std::map< StringList, String > runpath_to_identifier
Definition: ProteinIdentification.h:81
Representation of a protein identification run.
Definition: ProteinIdentification.h:70
OpenMS::DataArrays::FloatDataArray FloatDataArray
Float data array vector type.
Definition: ProteinIdentification.h:121
two way mapping from ms-run-path to protID|pepID-identifier
Definition: ProteinIdentification.h:78
String search_engine_
Definition: ProteinIdentification.h:482
bool fragment_mass_tolerance_ppm
Mass tolerance unit of fragment ions (true: ppm, false: Dalton)
Definition: ProteinIdentification.h:270
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
std::vector< ProteinGroup > protein_groups_
Definition: ProteinIdentification.h:493
String charges
The allowed charges for the search.
Definition: ProteinIdentification.h:264
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Definition: ProteinIdentification.h:250
String protein_score_type_
Definition: ProteinIdentification.h:490
std::vector< String > variable_modifications
Allowed variable modifications.
Definition: ProteinIdentification.h:267
PeakMassType mass_type
Mass type of the peaks.
Definition: ProteinIdentification.h:265
FloatDataArray & getFloatDataArrayByName(String name)
Returns a mutable reference to the first float meta data array with the given name.
Definition: ProteinIdentification.h:208
double protein_significance_threshold_
Definition: ProteinIdentification.h:496
String db
The used database.
Definition: ProteinIdentification.h:261
Representation of a digestion enzyme for proteins (protease)
Definition: DigestionEnzymeProtein.h:48
String db_version
The database version.
Definition: ProteinIdentification.h:262
FloatDataArrays & getFloatDataArrays()
Returns a mutable reference to the float meta data arrays.
Definition: ProteinIdentification.h:167
String data array class.
Definition: DataArrays.h:59
double fragment_mass_tolerance
Mass tolerance of fragment ions (Dalton or ppm)
Definition: ProteinIdentification.h:269
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
SearchParameters search_parameters_
Definition: ProteinIdentification.h:484
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
std::vector< String > fixed_modifications
Used fixed modifications.
Definition: ProteinIdentification.h:266
void create(const std::vector< ProteinIdentification > &prot_ids)
Definition: ProteinIdentification.h:89
double precursor_mass_tolerance
Mass tolerance of precursor ions (Dalton or ppm)
Definition: ProteinIdentification.h:271
std::vector< ProteinGroup > indistinguishable_proteins_
Indistinguishable proteins: accessions[0] is "group leader", probability is meaningless.
Definition: ProteinIdentification.h:495
bool operator==(const IDBoostGraph::ProteinGroup &lhs, const IDBoostGraph::ProteinGroup &rhs)
OpenMS::DataArrays::StringDataArray StringDataArray
String data array vector type.
Definition: ProteinIdentification.h:124
StringDataArrays string_data_arrays_
String data arrays.
Definition: ProteinIdentification.h:240
StringDataArray & getStringDataArrayByName(String name)
Returns a mutable reference to the first string meta data array with the given name.
Definition: ProteinIdentification.h:201
bool precursor_mass_tolerance_ppm
Mass tolerance unit of precursor ions (true: ppm, false: Dalton)
Definition: ProteinIdentification.h:272
DateTime date_
Definition: ProteinIdentification.h:485
IntegerDataArray & getIntegerDataArrayByName(String name)
Returns a mutable reference to the first integer meta data array with the given name.
Definition: ProteinIdentification.h:194
double probability
Probability of this group.
Definition: ProteinIdentification.h:131
Search parameters of the DB search.
Definition: ProteinIdentification.h:258
std::vector< IntegerDataArray > IntegerDataArrays
Definition: ProteinIdentification.h:128
EnzymaticDigestion::Specificity enzyme_term_specificity
The number of required cutting-rule matching termini during search (none=0, semi=1,...
Definition: ProteinIdentification.h:274
Float data array class.
Definition: DataArrays.h:45
std::vector< ProteinHit > protein_hits_
Definition: ProteinIdentification.h:492
String taxonomy
The taxonomy restriction.
Definition: ProteinIdentification.h:263
const FloatDataArray & getFloatDataArrayByName(String name) const
Returns a const reference to the first float meta data array with the given name.
Definition: ProteinIdentification.h:229
DateTime Class.
Definition: DateTime.h:54
String search_engine_version_
Definition: ProteinIdentification.h:483
ProteinHit HitType
Hit type definition.
Definition: ProteinIdentification.h:75
OpenMS::DataArrays::IntegerDataArray IntegerDataArray
Integer data array vector type.
Definition: ProteinIdentification.h:127
bool higher_score_better_
Definition: ProteinIdentification.h:491
String id_
Definition: ProteinIdentification.h:481
Bundles multiple (e.g. indistinguishable) proteins in a group.
Definition: ProteinIdentification.h:117