OpenMS  3.0.0
DataFilterDialog.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2022.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
27 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Marc Sturm $
33 // --------------------------------------------------------------------------
34 
35 
36 #pragma once
37 
38 // OpenMS_GUI config
39 #include <OpenMS/VISUAL/OpenMS_GUIConfig.h>
40 
42 
43 #include <QDialog>
44 
45 namespace Ui
46 {
47  class DataFilterDialogTemplate;
48 }
49 
50 namespace OpenMS
51 {
56  class OPENMS_GUI_DLLAPI DataFilterDialog :
57  public QDialog
58  {
59  Q_OBJECT
60 
61 public:
64 
66  virtual ~DataFilterDialog();
67 
68 protected slots:
70  void check_();
72  void field_changed_(const QString &);
74  void op_changed_(const QString &);
75 
76 protected:
79 
80 private:
83 
84  Ui::DataFilterDialogTemplate* ui_;
85  };
86 
87 }
LogStream.h
OpenMS::FileTypes::IDXML
OpenMS identification format (.idXML)
Definition: FileTypes.h:64
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
FileHandler.h
FileTypes.h
Size
OpenMS::writtenDigits
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
OpenMS::FalseDiscoveryRate::apply
void apply(std::vector< PeptideIdentification > &fwd_ids, std::vector< PeptideIdentification > &rev_ids) const
Calculates the FDR of two runs, a forward run and a decoy run on peptide level.
OpenMS::DBSuitability::SuitabilityData::getCorrectionFactor
double getCorrectionFactor() const
OpenMS::Ms2IdentificationRate::IdentificationRateData
Structure for storing results.
Definition: Ms2IdentificationRate.h:60
PSMExplainedIonCurrent.h
DBSuitability.h
OpenMS::FASTAFile
This class serves for reading in and writing FASTA files If the protein/gene sequence contains unusua...
Definition: FASTAFile.h:60
OpenMS::DataFilterDialog
Dialog for creating and changing a DataFilter.
Definition: DataFilterDialog.h:56
OpenMS::Constants::k
const double k
Definition: Constants.h:153
OpenMS::DBSuitability::SuitabilityData::suitability_no_rerank
double suitability_no_rerank
Definition: DBSuitability.h:108
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:57
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Ms2IdentificationRate::IdentificationRateData::identification_rate
double identification_rate
Definition: Ms2IdentificationRate.h:64
OpenMS::DataFilters::DataFilter
Representation of a peak/feature filter combining FilterType, FilterOperation and a value (either dou...
Definition: DataFilters.h:75
MzMLFile.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
IdXMLFile.h
OpenMS::Constants::c
const double c
Definition: Constants.h:209
QDialog
OpenMS::DBSuitability::SuitabilityData::num_re_ranked
Size num_re_ranked
Definition: DBSuitability.h:89
OpenMS::FileTypes::MZIDENTML
mzIdentML (HUPO PSI AnalysisXML followup format) (.mzid)
Definition: FileTypes.h:75
OpenMS::DataFilterDialog::filter_
DataFilters::DataFilter & filter_
Reference to the filter that is modified.
Definition: DataFilterDialog.h:78
OpenMS::DBSuitability
This class holds the functionality of calculating the database suitability.
Definition: DBSuitability.h:71
QWidget
OpenMS::PSMExplainedIonCurrent
Definition: PSMExplainedIonCurrent.h:48
OpenMS::QCBase::SpectraMap
Map to find a spectrum via its NativeID.
Definition: QCBase.h:89
OpenMS::IdXMLFile::load
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
OpenMS::DBSuitability::SuitabilityData::getCorrectedNovoHits
double getCorrectedNovoHits() const
OpenMS::MzIdentMLFile
File adapter for MzIdentML files.
Definition: MzIdentMLFile.h:67
OpenMS::FASTAFile::store
void store(const String &filename, const std::vector< FASTAEntry > &data) const
stores the data given by 'data' at the file 'filename'
OpenMS::PSMExplainedIonCurrent::Statistics::average_correctness
double average_correctness
Definition: PSMExplainedIonCurrent.h:62
OpenMS::DBSuitability::SuitabilityData::num_interest
Size num_interest
number of times a deNovo hit scored on top of a database hit
Definition: DBSuitability.h:85
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::PSMExplainedIonCurrent::Statistics
Structure for storing results: average and variance over all PSMs.
Definition: PSMExplainedIonCurrent.h:60
OpenMS::MzMLFile::load
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...
Ui
Definition: SwathWizardBase.h:62
FASTAFile.h
OpenMS::FileHandler
Facilitates file handling by file type recognition.
Definition: FileHandler.h:66
OpenMS::DBSuitability::SuitabilityData::getCorrectedSuitability
double getCorrectedSuitability() const
OpenMS::FileTypes::Type
Type
Actual file types enum.
Definition: FileTypes.h:56
DataFilters.h
OpenMS::FileHandler::getType
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
OpenMS::DefaultParamHandler::setParameters
void setParameters(const Param &param)
Sets the parameters.
OpenMS::PSMExplainedIonCurrent::compute
void compute(FeatureMap &fmap, const MSExperiment &exp, const QCBase::SpectraMap &map_to_spectrum, ToleranceUnit tolerance_unit=ToleranceUnit::AUTO, double tolerance=20)
computes PSMExplainedIonCurrent (only of the first PeptideHit of each PepID)
OpenMS::DefaultParamHandler::getDefaults
const Param & getDefaults() const
Non-mutable access to the default parameters.
Ms2IdentificationRate.h
OpenMS::PSMExplainedIonCurrent::getResults
const std::vector< Statistics > & getResults() const
returns results
OpenMS::Ms2IdentificationRate::compute
void compute(const FeatureMap &feature_map, const MSExperiment &exp, bool assume_all_target=false)
computes Ms2 Identification Rate with FeatureMap
OpenMS::Citation
Stores Citations for individual TOPP tools.
Definition: TOPPBase.h:73
OpenMS::MzIdentMLFile::load
void load(const String &filename, std::vector< ProteinIdentification > &poid, std::vector< PeptideIdentification > &peid)
Loads the identifications from a MzIdentML file.
OpenMS::FalseDiscoveryRate
Calculates false discovery rates (FDR) from identifications.
Definition: FalseDiscoveryRate.h:77
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
OpenMS::DBSuitability::SuitabilityData::cut_off
double cut_off
Definition: DBSuitability.h:93
MSExperiment.h
OPENMS_LOG_ERROR
#define OPENMS_LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:455
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
OpenMS::DBSuitability::SuitabilityData::num_top_db
Size num_top_db
number of times the top hit is considered to be a database hit
Definition: DBSuitability.h:82
OpenMS::Param::copy
Param copy(const std::string &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
OpenMS::DBSuitability::compute
void compute(std::vector< PeptideIdentification > &&pep_ids, const MSExperiment &exp, const std::vector< FASTAFile::FASTAEntry > &original_fasta, const std::vector< FASTAFile::FASTAEntry > &novo_fasta, const ProteinIdentification::SearchParameters &search_params)
Computes suitability of a database used to search a mzML.
OpenMS::FASTAFile::load
void load(const String &filename, std::vector< FASTAEntry > &data) const
loads a FASTA file given by 'filename' and stores the information in 'data' This uses more RAM than r...
OpenMS::PeakFileOptions
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
OpenMS::Ms2IdentificationRate::IdentificationRateData::num_peptide_identification
Size num_peptide_identification
Definition: Ms2IdentificationRate.h:62
OpenMS::Ms2IdentificationRate::getResults
const std::vector< IdentificationRateData > & getResults() const
returns results
OpenMS::DBSuitability::SuitabilityData::num_top_novo
Size num_top_novo
number of times the top hit is considered to be a deNovo hit
Definition: DBSuitability.h:79
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
IDFilter.h
OpenMS::IDFilter::filterHitsByScore
static void filterHitsByScore(std::vector< IdentificationType > &ids, double threshold_score)
Filters peptide or protein identifications according to the score of the hits.
Definition: IDFilter.h:840
OPENMS_LOG_INFO
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
OpenMS::PeakFileOptions::setMSLevels
void setMSLevels(const std::vector< Int > &levels)
sets the desired MS levels for peaks to load
OpenMS::DBSuitability::SuitabilityData
struct to store results
Definition: DBSuitability.h:76
OpenMS::Ms2IdentificationRate
This class is a metric for the QualityControl-ToppTool.
Definition: Ms2IdentificationRate.h:56
PeptideIdentification.h
FalseDiscoveryRate.h
OpenMS::DataFilterDialog::ui_
Ui::DataFilterDialogTemplate * ui_
Definition: DataFilterDialog.h:84
OpenMS::MzMLFile::setOptions
void setOptions(const PeakFileOptions &)
set options for loading/storing
OpenMS::DBSuitability::SuitabilityData::suitability
double suitability
Definition: DBSuitability.h:104
OpenMS::DBSuitability::SuitabilityData::suitability_corr_no_rerank
double suitability_corr_no_rerank
the suitability after correcting the top deNovo hits, if re-ranking would have been disabled
Definition: DBSuitability.h:111
OpenMS::PSMExplainedIonCurrent::Statistics::variance_correctness
double variance_correctness
Definition: PSMExplainedIonCurrent.h:63
OpenMS::QCBase::SpectraMap::calculateMap
void calculateMap(const MSExperiment &exp)
calculate a new map, delete the old one
MzIdentMLFile.h
TOPPBase.h
OpenMS::DBSuitability::getResults
const std::vector< SuitabilityData > & getResults() const
Returns results calculated by this metric.
OpenMS::Ms2IdentificationRate::IdentificationRateData::num_ms2_spectra
Size num_ms2_spectra
Definition: Ms2IdentificationRate.h:63
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:68