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OpenMS
2.6.0
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Go to the documentation of this file.
45 #define OPENSWATH_PRECONDITION(condition, message)\
46 assert( (condition) && (message));
48 #define OPENMS_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:66
Base class for TOPP applications.
Definition: TOPPBase.h:144
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:863
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
const AASequence & getSequence() const
returns the peptide sequence without trailing or following spaces
static String basename(const String &file)
Returns the basename of the file (without the path).
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:75
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:59
File not found exception.
Definition: Exception.h:523
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
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
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
const std::vector< PeptideHit > & getHits() const
returns the peptide hits as const
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:46
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:62
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:58
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)
Returns the path of the file (without the file name).
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:73
bool hasCTerminalModification() const
predicate which is true if the peptide is C-term modified
A required parameter was not given.
Definition: TOPPBase.h:111
#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:63
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
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
ExitCodes
Exit codes.
Definition: TOPPBase.h:149
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:662
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
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:63
static String typeToName(Type type)
Returns the name/extension of the type.
double getRT() const
returns the RT of the MS2 spectrum where the identification occurred
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