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OpenMS
2.5.0
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73 void load(
const String & filename,
ProteinIdentification & protein_identification, std::vector<PeptideIdentification> & id_data)
const;
Protease digestion_enzyme
The cleavage site information in details (from ProteaseDB)
Definition: ProteinIdentification.h:236
void setProgress(SignedSize value) const
Sets the current progress.
Base class for TOPP applications.
Definition: TOPPBase.h:144
File adapter for OMSSACSV files.
Definition: OMSSACSVFile.h:54
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.
Representation of a modification.
Definition: ResidueModification.h:76
void getAllOMSSANames(std::vector< String > &all_names) const
returns all the enzyme names available for OMSSA
Definition: ResidueModification.h:97
static ProteaseDB * getInstance()
this member function serves as a replacement of the constructor
Definition: DigestionEnzymeDB.h:69
Representation of a set of modification definitions.
Definition: ModificationDefinitionsSet.h:58
PeakMassType
Peak mass type.
Definition: ProteinIdentification.h:211
void store(const String &filename, const PeakMap &experiment, bool compact=false)
stores the experiment data in a MascotGenericFile that can be used as input for MASCOT shell executio...
Iterator end()
Definition: AASequence.h:587
bool has(const Key &key) const
Test whether the map contains the given key.
Definition: Map.h:108
double getDiffAverageMass() const
returns the difference average mass if set
void setSearchEngineVersion(const String &search_engine_version)
Sets the search engine version.
UInt missed_cleavages
The number of allowed missed cleavages.
Definition: ProteinIdentification.h:231
A more convenient string class.
Definition: String.h:58
Used to load OMSSAXML files.
Definition: OMSSAXMLFile.h:60
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
This class provides some basic file handling methods for text files.
Definition: TextFile.h:46
void addMSLevel(int level)
adds a desired MS level for peaks to load
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Definition: ResidueModification.h:99
Definition: ProteinIdentification.h:213
void startProgress(SignedSize begin, SignedSize end, const String &label) const
Initializes the progress display.
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
static String getUniqueName(bool include_hostname=true)
Returns a string, consisting of date, time, hostname, process id, and a incrementing number....
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
Representation of a protein identification run.
Definition: ProteinIdentification.h:71
profile data
Definition: SpectrumSettings.h:74
void endProgress() const
Ends the progress display.
Size size() const
Definition: MSExperiment.h:127
const EmpiricalFormula & getNeutralLossDiffFormula() const
returns the neutral loss diff formula (if available)
bool fragment_mass_tolerance_ppm
Mass tolerance unit of fragment ions (true: ppm, false: Dalton)
Definition: ProteinIdentification.h:233
static String find(const String &filename, StringList directories=StringList())
Looks up the location of the file filename.
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
Iterator class for AASequence.
Definition: AASequence.h:258
void setModification(Size index, const String &modification)
static ModificationsDB * getInstance()
Returns a pointer to the modifications DB (singleton)
const String & getIdentifier() const
Returns the identifier.
String charges
The allowed charges for the search.
Definition: ProteinIdentification.h:227
const DigestionEnzymeType * getEnzyme(const String &name) const
Definition: DigestionEnzymeDB.h:98
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Definition: ProteinIdentification.h:214
std::vector< String > variable_modifications
Allowed variable modifications.
Definition: ProteinIdentification.h:230
PeakMassType mass_type
Mass type of the peaks.
Definition: ProteinIdentification.h:228
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
char getOrigin() const
Returns the origin (i.e. modified amino acid)
void setPrimaryMSRunPath(const StringList &s, bool raw=false)
TermSpecificity
Position where the modification is allowed to occur.
Definition: ResidueModification.h:95
SpectrumType
Spectrum peak type.
Definition: SpectrumSettings.h:70
Definition: ResidueModification.h:98
String db
The used database.
Definition: ProteinIdentification.h:224
void setNTerminalModification(const String &modification)
Facilitates file handling by file type recognition.
Definition: FileHandler.h:62
bool loadExperiment(const String &filename, MSExperiment &exp, FileTypes::Type force_type=FileTypes::UNKNOWN, ProgressLogger::LogType log=ProgressLogger::NONE, const bool rewrite_source_file=true, const bool compute_hash=true)
Loads a file into an MSExperiment.
double getDiffMonoMass() const
returns the diff monoisotopic mass if set
Type
Actual file types enum.
Definition: FileTypes.h:58
void setCTerminalModification(const String &modification)
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
QString toQString() const
Conversion to Qt QString.
Read/write Mascot generic files (MGF).
Definition: MascotGenericFile.h:61
void setSearchParameters(const SearchParameters &search_parameters)
Sets the search parameters.
double fragment_mass_tolerance
Mass tolerance of fragment ions (Dalton or ppm)
Definition: ProteinIdentification.h:232
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
std::vector< String > fixed_modifications
Used fixed modifications.
Definition: ProteinIdentification.h:229
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
void setSearchEngine(const String &search_engine)
Sets the search engine type.
double precursor_mass_tolerance
Mass tolerance of precursor ions (Dalton or ppm)
Definition: ProteinIdentification.h:234
void setModificationDefinitionsSet(const ModificationDefinitionsSet &rhs)
sets the valid modifications
#define OPENMS_LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:455
static String absolutePath(const String &file)
Replaces the relative path in the argument with the absolute path.
Parse Error exception.
Definition: Exception.h:622
String substr(size_t pos=0, size_t n=npos) const
Wrapper for the STL substr() method. Returns a String object with its contents initialized to a subst...
static String findDatabase(const String &db_name)
const std::vector< MSSpectrum > & getSpectra() const
returns the spectrum list
static bool readable(const String &file)
Return true if the file exists and is readable.
void getAllSearchModifications(std::vector< String > &modifications) const
Collects all modifications that can be used for identification searches.
bool precursor_mass_tolerance_ppm
Mass tolerance unit of precursor ions (true: ppm, false: Dalton)
Definition: ProteinIdentification.h:235
static String getTempDirectory()
The current OpenMS temporary data path (for temporary files)
Iterator begin()
Definition: AASequence.h:583
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
File is empty.
Definition: Exception.h:594
void setHits(const std::vector< ProteinHit > &hits)
Sets the protein hits.
Search parameters of the DB search.
Definition: ProteinIdentification.h:221
String suffix(SizeType length) const
returns the suffix of length length
void load(const String &filename, ProteinIdentification &protein_identification, std::vector< PeptideIdentification > &id_data, bool load_proteins=true, bool load_empty_hits=true)
loads data from a OMSSAXML file
std::vector< String >::const_iterator ConstIterator
Non-mutable iterator.
Definition: TextFile.h:56
TermSpecificity getTermSpecificity() const
returns terminal specificity
String taxonomy
The taxonomy restriction.
Definition: ProteinIdentification.h:226
const ResidueModification * getModification(Size index) const
Returns the modification with the given index. note: out-of-bounds check is only performed in debug m...
std::ifstream infile
Questionable file tested by TEST_FILE_EQUAL.
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
Used to load and store idXML files.
Definition: IdXMLFile.h:63