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OpenMS
2.6.0
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39 #include <OpenMS/VISUAL/OpenMS_GUIConfig.h>
47 class DataFilterDialogTemplate;
72 void field_changed_(
const QString &);
74 void op_changed_(
const QString &);
84 Ui::DataFilterDialogTemplate*
ui_;
OpenMS identification format (.idXML)
Definition: FileTypes.h:66
Base class for TOPP applications.
Definition: TOPPBase.h:144
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
constexpr Int writtenDigits(const FloatingPointType &=FloatingPointType())
Number of digits commonly used for writing a floating point type (a.k.a. precision)....
Definition: Types.h:294
Structure for storing results.
Definition: Ms2IdentificationRate.h:60
This class serves for reading in and writing FASTA files.
Definition: FASTAFile.h:64
Dialog for creating and changing a DataFilter.
Definition: DataFilterDialog.h:56
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:59
double identification_rate
Definition: Ms2IdentificationRate.h:64
Representation of a peak/feature filter combining FilterType, FilterOperation and a value.
Definition: DataFilters.h:74
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
Size num_top_novo
number of times the top hit is considered to be a deNovo hit
Definition: DBSuitability.h:74
void compute(std::vector< PeptideIdentification > pep_ids)
Computes suitability of a database used to search a mzML.
mzIdentML (HUPO PSI AnalysisXML followup format) (.mzid)
Definition: FileTypes.h:77
DataFilters::DataFilter & filter_
Reference to the filter that is modified.
Definition: DataFilterDialog.h:78
This class holds the functionality of calculating the database suitability.
Definition: DBSuitability.h:66
Size num_top_db
number of times the top hit is considered to be a database hit
Definition: DBSuitability.h:77
double suitability
Definition: DBSuitability.h:99
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
File adapter for MzIdentML files.
Definition: MzIdentMLFile.h:67
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
struct to store results
Definition: DBSuitability.h:71
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 num_interest
number of times a deNovo hit scored on top of a database hit
Definition: DBSuitability.h:80
Definition: SwathWizardBase.h:62
Facilitates file handling by file type recognition.
Definition: FileHandler.h:62
Type
Actual file types enum.
Definition: FileTypes.h:58
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
void setParameters(const Param ¶m)
Sets the parameters.
const Param & getDefaults() const
Non-mutable access to the default parameters.
void compute(const FeatureMap &feature_map, const MSExperiment &exp, bool assume_all_target=false)
computes Ms2 Identification Rate with FeatureMap
Stores Citations for individual TOPP tools.
Definition: TOPPBase.h:70
void load(const String &filename, std::vector< ProteinIdentification > &poid, std::vector< PeptideIdentification > &peid)
Loads the identifications from a MzIdentML file.
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
#define OPENMS_LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:455
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
static void load(const String &filename, std::vector< FASTAEntry > &data)
loads a FASTA file given by 'filename' and stores the information in 'data'
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
Size num_peptide_identification
Definition: Ms2IdentificationRate.h:62
const std::vector< IdentificationRateData > & getResults() const
returns results
Size num_re_ranked
Definition: DBSuitability.h:84
Management and storage of parameters / INI files.
Definition: Param.h:73
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
void setMSLevels(const std::vector< Int > &levels)
sets the desired MS levels for peaks to load
This class is a metric for the QualityControl-ToppTool.
Definition: Ms2IdentificationRate.h:56
Ui::DataFilterDialogTemplate * ui_
Definition: DataFilterDialog.h:84
void setOptions(const PeakFileOptions &)
set options for loading/storing
const std::vector< SuitabilityData > & getResults() const
Returns results calculated by this metric.
Size num_ms2_spectra
Definition: Ms2IdentificationRate.h:63
Used to load and store idXML files.
Definition: IdXMLFile.h:63
static void store(const String &filename, const std::vector< FASTAEntry > &data)
stores the data given by 'data' at the file 'filename'