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| MascotGenericFile () |
| constructor More...
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| ~MascotGenericFile () override |
| destructor More...
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void | updateMembers_ () override |
| docu in base class More...
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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 execution (optionally a compact format is used: no zero-intensity peaks, limited number of decimal places) More...
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void | store (std::ostream &os, const String &filename, const PeakMap &experiment, bool compact=false) |
| store the experiment data in a MascotGenericFile; the output is written to the given stream, the filename will be noted in the file (optionally a compact format is used: no zero-intensity peaks, limited number of decimal places) More...
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template<typename MapType > |
void | load (const String &filename, MapType &exp) |
| loads a Mascot Generic File into a PeakMap More...
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std::pair< String, String > | getHTTPPeakListEnclosure (const String &filename) const |
| enclosing Strings of the peak list body for HTTP submission More...
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| ProgressLogger () |
| Constructor. More...
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| ~ProgressLogger () |
| Destructor. More...
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| ProgressLogger (const ProgressLogger &other) |
| Copy constructor. More...
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ProgressLogger & | operator= (const ProgressLogger &other) |
| Assignment Operator. More...
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void | setLogType (LogType type) const |
| Sets the progress log that should be used. The default type is NONE! More...
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LogType | getLogType () const |
| Returns the type of progress log being used. More...
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void | startProgress (SignedSize begin, SignedSize end, const String &label) const |
| Initializes the progress display. More...
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void | setProgress (SignedSize value) const |
| Sets the current progress. More...
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void | endProgress () const |
| Ends the progress display. More...
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void | nextProgress () const |
| increment progress by 1 (according to range begin-end) More...
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Public Member Functions inherited from DefaultParamHandler |
| DefaultParamHandler (const String &name) |
| Constructor with name that is displayed in error messages. More...
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| DefaultParamHandler (const DefaultParamHandler &rhs) |
| Copy constructor. More...
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virtual | ~DefaultParamHandler () |
| Destructor. More...
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virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
| Assignment operator. More...
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virtual bool | operator== (const DefaultParamHandler &rhs) const |
| Equality operator. More...
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void | setParameters (const Param ¶m) |
| Sets the parameters. More...
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const Param & | getParameters () const |
| Non-mutable access to the parameters. More...
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const Param & | getDefaults () const |
| Non-mutable access to the default parameters. More...
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const String & | getName () const |
| Non-mutable access to the name. More...
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void | setName (const String &name) |
| Mutable access to the name. More...
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const std::vector< String > & | getSubsections () const |
| Non-mutable access to the registered subsections. More...
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void | writeParameterHeader_ (const String &name, std::ostream &os) |
| writes a parameter header More...
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void | writeModifications_ (const std::vector< String > &mods, std::ostream &os, bool variable_mods=false) |
| write a list of (fixed or variable) modifications More...
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void | writeHeader_ (std::ostream &os) |
| writes the full header More...
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void | writeSpectrum_ (std::ostream &os, const PeakSpectrum &spec, const String &filename, const String &native_id_type_accession) |
| writes the spectrum More...
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void | writeMSExperiment_ (std::ostream &os, const String &filename, const PeakMap &experiment) |
| writes the MSExperiment More...
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template<typename SpectrumType > |
bool | getNextSpectrum_ (std::ifstream &is, SpectrumType &spectrum, Size &line_number, const Size &spectrum_number) |
| reads a spectrum block, the section between 'BEGIN IONS' and 'END IONS' of a MGF file More...
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Protected Member Functions inherited from DefaultParamHandler |
void | defaultsToParam_ () |
| Updates the parameters after the defaults have been set in the constructor. More...
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Read/write Mascot generic files (MGF).
For details of the format, see http://www.matrixscience.com/help/data_file_help.html#GEN.