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OpenMS
3.0.0
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45 #define OPENSWATH_PRECONDITION(condition, message)\
46 assert( (condition) && (message));
48 #define OPENSWATH_POSTCONDITION(condition, message)\
49 assert( (condition) && (message));
Size findByRT(double rt) const
Look up spectrum by retention time (RT).
OpenMS identification format (.idXML)
Definition: FileTypes.h:64
Base class for TOPP applications.
Definition: TOPPBase.h:147
const String & getModificationName() const
returns the name (ID) of the modification, or an empty string if none is set
static void keepNBestHits(std::vector< IdentificationType > &ids, Size n)
Filters peptide or protein identifications according to the score of the hits, keeping the n best hit...
Definition: IDFilter.h:881
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 on an amino acid residue.
Definition: ResidueModification.h:78
const AASequence & getSequence() const
returns the peptide sequence without trailing or following spaces
static String & toUpper(String &this_s)
Definition: StringUtilsSimple.h:557
static String basename(const String &file)
void sortSpectra(bool sort_mz=true)
Sorts the data points by retention time.
static FileTypes::Type getTypeByFileName(const String &filename)
Determines the file type from a file name.
TPP pepXML file (.pepXML)
Definition: FileTypes.h:73
File adapter for MzML files.
Definition: MzMLFile.h:57
A more convenient string class.
Definition: String.h:58
File not found exception.
Definition: Exception.h:509
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
void addMSLevel(int level)
adds a desired MS level for peaks to load
String toString() const
returns the peptide as string with modifications embedded in brackets
String toUnmodifiedString() const
returns the peptide as string without any modifications or (e.g., "PEPTIDER")
#define OPENMS_LOG_WARN
Macro if a warning, a piece of information which should be read by the user, should be logged.
Definition: LogStream.h:460
bool hasPrefix(const String &string) const
true if String begins with string, false otherwise
bool hasSubstring(const String &string) const
true if String contains the string, false otherwise
const String & getCTerminalModificationName() const
returns the name (ID) of the C-terminal modification, or an empty string if none is set
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
void setModification(Size index, const String &modification)
static ModificationsDB * getInstance()
Returns a pointer to the modifications DB (singleton)
static bool exists(const String &file)
Method used to test if a file exists.
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
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...
Size findByNativeID(const String &native_id) const
Look up spectrum by native ID.
double rt_tolerance
Tolerance for look-up by retention time.
Definition: SpectrumLookup.h:78
void setNTerminalModification(const String &modification)
Facilitates file handling by file type recognition.
Definition: FileHandler.h:66
const Residue & getResidue(Size index) const
returns a pointer to the residue at position index
Helper class for looking up spectra based on different attributes.
Definition: SpectrumLookup.h:67
double getDiffMonoMass() const
returns the diff monoisotopic mass, or 0.0 if not set
Type
Actual file types enum.
Definition: FileTypes.h:56
void readSpectra(const SpectrumContainer &spectra, const String &scan_regexp=default_scan_regexp)
Read and index spectra for later look-up.
Definition: SpectrumLookup.h:103
Size size() const
returns the number of residues
void store(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids, const String &mz_file="", const String &mz_name="", bool peptideprophet_analyzed=false, double rt_tolerance=0.01)
Stores idXML as PepXML file.
void setCTerminalModification(const String &modification)
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
bool split(const char splitter, std::vector< String > &substrings, bool quote_protect=false) const
Splits a string into substrings using splitter as delimiter.
QString toQString() const
Conversion to Qt QString.
static String path(const String &file)
bool isModified() const
returns true if any of the residues or termini are modified
const String & getScoreType() const
returns the peptide score type
void setSequence(const AASequence &sequence)
sets the peptide sequence
const String & getNTerminalModificationName() const
returns the name (ID) of the N-terminal modification, or an empty string if none is set
This class handles csv files. Currently only loading is implemented.
Definition: CsvFile.h:49
static bool canRun(const String &java_executable, bool verbose_on_error=true)
Determine if Java is installed and reachable.
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
bool hasCTerminalModification() const
predicate which is true if the peptide is C-term modified
A required parameter was not given.
Definition: TOPPBase.h:114
#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.
Class representing a temporary directory.
Definition: File.h:64
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
Collection of utility functions for management of vectors.
Definition: ListUtils.h:77
const std::vector< MSSpectrum > & getSpectra() const
returns the spectrum list
double getScore() const
returns the PSM score
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
static String number(double d, UInt n)
Definition: StringUtils.h:196
ExitCodes
Exit codes.
Definition: TOPPBase.h:152
void getAllSearchModifications(std::vector< String > &modifications) const
Collects all modifications that can be used for identification searches.
void clearMSLevels()
clears the MS levels
String & remove(char what)
Remove all occurrences of the character what.
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
bool hasNTerminalModification() const
predicate which is true if the peptide is N-term modified
Used to load and store PepXML files.
Definition: PepXMLFile.h:63
static AASequence fromString(const String &s, bool permissive=true)
create AASequence object by parsing an OpenMS string
Element could not be found exception.
Definition: Exception.h:674
Search parameters of the DB search.
Definition: ProteinIdentification.h:258
bool isModified() const
true if the residue is a modified one
const ResidueModification * getModification(Size index) const
Returns the modification with the given index. note: out-of-bounds check is only performed in debug m...
const std::string LOCALIZED_MODIFICATIONS_USERPARAM
Definition: Constants.h:265
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
Size findByScanNumber(Size scan_number) const
Look up spectrum by scan number (extracted from the native ID).
Used to load and store idXML files.
Definition: IdXMLFile.h:68
static String typeToName(Type type)
Returns the name/extension of the type.
void setScore(double score)
sets the PSM score
static String swapExtension(const String &filename, const FileTypes::Type new_type)
Tries to find and remove a known file extension, and append the new one.
Representation of a peptide hit.
Definition: PeptideHit.h:55