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OpenMS
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92 void store(
const String & filename,
const MapType & map)
const;
Base class for TOPP applications.
Definition: TOPPBase.h:150
PeakMap MapType
Definition: MzDataFile.h:57
File adapter for MzData files.
Definition: MzDataFile.h:53
const ResidueModification & getModification(Size index) const
Returns the modification with the given index.
Representation of a modification.
Definition: ResidueModification.h:76
Representation of a set of modification definitions.
Definition: ModificationDefinitionsSet.h:58
PeakMassType
Peak mass type.
Definition: ProteinIdentification.h:93
static String basename(const String &file)
Returns the basename of the file (without the path).
UInt missed_cleavages
The number of allowed missed cleavages.
Definition: ProteinIdentification.h:113
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:57
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
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
static String removeExtension(const String &file)
Definition: ProteinIdentification.h:95
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:58
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)
bool fragment_mass_tolerance_ppm
Mass tolerance unit of fragment ions (true: ppm, false: Dalton)
Definition: ProteinIdentification.h:115
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:175
static bool exists(const String &file)
Method used to test if a file exists.
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Definition: ProteinIdentification.h:96
std::vector< String > variable_modifications
Allowed variable modifications.
Definition: ProteinIdentification.h:112
PeakMassType mass_type
Mass type of the peaks.
Definition: ProteinIdentification.h:110
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 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...
String db
The used database.
Definition: ProteinIdentification.h:106
double getDiffMonoMass() const
returns the diff monoisotopic mass if set
QString toQString() const
Conversion to Qt QString.
double fragment_mass_tolerance
Mass tolerance of fragment ions (Dalton or ppm)
Definition: ProteinIdentification.h:114
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:73
std::vector< String > fixed_modifications
Used fixed modifications.
Definition: ProteinIdentification.h:111
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
double precursor_mass_tolerance
Mass tolerance of precursor ions (Dalton or ppm)
Definition: ProteinIdentification.h:116
void store(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.
static String absolutePath(const String &file)
Replaces the relative path in the argument with the absolute path.
const std::vector< MSSpectrum > & getSpectra() const
returns the spectrum list
PeakFileOptions options_
Options for loading / storing.
Definition: MzDataFile.h:108
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.
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:48
void getPrimaryMSRunPath(StringList &toFill) const
get the file path to the first MS run
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:117
static String getTempDirectory()
The current OpenMS temporary data path (for temporary files)
Used to load and store PepXML files.
Definition: PepXMLFile.h:62
String getTermSpecificityName(TermSpecificity term_spec=NUMBER_OF_TERM_SPECIFICITY) const
Returns the name of the terminal specificity.
Search parameters of the DB search.
Definition: ProteinIdentification.h:103
TermSpecificity getTermSpecificity() const
returns terminal specificity
Used to load and store idXML files.
Definition: IdXMLFile.h:63