OpenMS
2.5.0
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The MRMFeatureFilter either flags components and/or transitions that do not pass the QC criteria or filters out components and/or transitions that do not pass the QC criteria. More...
#include <OpenMS/ANALYSIS/OPENSWATH/MRMFeatureFilter.h>
Public Member Functions | |
MRMFeatureFilter () | |
Constructor. More... | |
~MRMFeatureFilter () override | |
Destructor. More... | |
void | getDefaultParameters (Param ¶ms) const |
Get the class' default parameters. More... | |
void | updateMembers_ () override |
Synchronize members with param class. More... | |
void | FilterFeatureMap (FeatureMap &features, const MRMFeatureQC &filter_criteria, const TargetedExperiment &transitions) |
Flags or filters features and subordinates in a FeatureMap. More... | |
void | FeatureMapToAttachment (FeatureMap &features, QcMLFile::Attachment &attachment) |
Converts a FeatureMap to a qcMLFile::Attachment. More... | |
double | calculateIonRatio (const Feature &component_1, const Feature &component_2, const String &feature_name) |
Calculates the ion ratio between two transitions. More... | |
double | calculateRTDifference (Feature &component_1, Feature &component_2) |
Calculates the retention time difference between two features. More... | |
double | calculateResolution (Feature &component_1, Feature &component_2) |
Calculates the resolution between two features. More... | |
bool | checkMetaValue (const Feature &component, const String &meta_value_key, const double &meta_value_l, const double &meta_value_u, bool &key_exists) const |
Checks if the metaValue is within the user specified range. More... | |
std::map< String, int > | countLabelsAndTransitionTypes (const Feature &component_group, const TargetedExperiment &transitions) |
Count the number of heavy/light labels and quantifying/detecting/identifying transitions. More... | |
StringList | getUniqueSorted (const StringList &messages) const |
Sorts the messages and returns a copy without duplicates. More... | |
Public Member Functions inherited from DefaultParamHandler | |
DefaultParamHandler (const String &name) | |
Constructor with name that is displayed in error messages. More... | |
DefaultParamHandler (const DefaultParamHandler &rhs) | |
Copy constructor. More... | |
virtual | ~DefaultParamHandler () |
Destructor. More... | |
virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
Assignment operator. More... | |
virtual bool | operator== (const DefaultParamHandler &rhs) const |
Equality operator. More... | |
void | setParameters (const Param ¶m) |
Sets the parameters. More... | |
const Param & | getParameters () const |
Non-mutable access to the parameters. More... | |
const Param & | getDefaults () const |
Non-mutable access to the default parameters. More... | |
const String & | getName () const |
Non-mutable access to the name. More... | |
void | setName (const String &name) |
Mutable access to the name. More... | |
const std::vector< String > & | getSubsections () const |
Non-mutable access to the registered subsections. More... | |
Private Member Functions | |
template<typename T > | |
bool | checkRange (const T &value, const T &value_l, const T &value_u) const |
Private Attributes | |
String | flag_or_filter_ |
flag or filter (i.e., remove) features that do not pass the QC More... | |
bool | report_xic_ |
include the data points for the extracted ion chromatogram (XIC) in the attachment More... | |
bool | report_tic_ |
include the data points for the total ion chromatogram (TIC) in the attachment More... | |
QcMLFile::Attachment | attachment_ |
qcMLFile Attachment More... | |
FeatureMap | features_ |
FeatureMap. More... | |
std::map< String, std::vector< QcMLFile::QualityParameter > > | component_group_qc_report_ |
component group/peptide/compound QCs More... | |
std::map< String, std::vector< QcMLFile::QualityParameter > > | component_qc_report_ |
component/transition QCs More... | |
std::map< std::vector< String >, std::vector< QcMLFile::QualityParameter > > | multi_component_group_qc_report_ |
multi transition QCs More... | |
Additional Inherited Members | |
Protected Member Functions inherited from DefaultParamHandler | |
void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
Protected Attributes inherited from DefaultParamHandler | |
Param | param_ |
Container for current parameters. More... | |
Param | defaults_ |
Container for default parameters. This member should be filled in the constructor of derived classes! More... | |
std::vector< String > | subsections_ |
Container for registered subsections. This member should be filled in the constructor of derived classes! More... | |
String | error_name_ |
Name that is displayed in error messages during the parameter checking. More... | |
bool | check_defaults_ |
If this member is set to false no checking if parameters in done;. More... | |
bool | warn_empty_defaults_ |
If this member is set to false no warning is emitted when defaults are empty;. More... | |
The MRMFeatureFilter either flags components and/or transitions that do not pass the QC criteria or filters out components and/or transitions that do not pass the QC criteria.
MRMFeatureFilter | ( | ) |
Constructor.
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override |
Destructor.
double calculateIonRatio | ( | const Feature & | component_1, |
const Feature & | component_2, | ||
const String & | feature_name | ||
) |
Calculates the ion ratio between two transitions.
component_1 | component of the numerator |
component_2 | component of the denominator |
feature_name | name of the feature to calculate the ratio on e.g., peak_apex, peak_area |
Calculates the resolution between two features.
component_1 | component 1 |
component_2 | component 2 |
Calculates the retention time difference between two features.
component_1 | First eluting component |
component_2 | Second eluting component |
bool checkMetaValue | ( | const Feature & | component, |
const String & | meta_value_key, | ||
const double & | meta_value_l, | ||
const double & | meta_value_u, | ||
bool & | key_exists | ||
) | const |
Checks if the metaValue is within the user specified range.
[in] | component | component of the numerator |
[in] | meta_value_key | Name of the metaValue |
[in] | meta_value_l | Lower bound (inclusive) for the metaValue range |
[in] | meta_value_u | Upper bound (inclusive) for the metaValue range |
[out] | key_exists | true if the given key is found, false otherwise |
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private |
std::map<String,int> countLabelsAndTransitionTypes | ( | const Feature & | component_group, |
const TargetedExperiment & | transitions | ||
) |
Count the number of heavy/light labels and quantifying/detecting/identifying transitions.
component | component_group with subordinates |
transitions | transitions from a TargetedExperiment |
void FeatureMapToAttachment | ( | FeatureMap & | features, |
QcMLFile::Attachment & | attachment | ||
) |
Converts a FeatureMap to a qcMLFile::Attachment.
features | FeatureMap to flag or filter |
attachment | qcML Attachment |
void FilterFeatureMap | ( | FeatureMap & | features, |
const MRMFeatureQC & | filter_criteria, | ||
const TargetedExperiment & | transitions | ||
) |
Flags or filters features and subordinates in a FeatureMap.
features | FeatureMap to flag or filter |
filter_criteria | MRMFeatureQC class defining QC parameters |
transitions | transitions from a TargetedExperiment |
void getDefaultParameters | ( | Param & | params | ) | const |
Get the class' default parameters.
[out] | params | Output parameters |
StringList getUniqueSorted | ( | const StringList & | messages | ) | const |
Sorts the messages and returns a copy without duplicates.
[in] | messages | A StringList containing the failure messages |
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overridevirtual |
Synchronize members with param class.
Reimplemented from DefaultParamHandler.
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private |
qcMLFile Attachment
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private |
component group/peptide/compound QCs
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private |
component/transition QCs
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private |
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private |
flag or filter (i.e., remove) features that do not pass the QC
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private |
multi transition QCs
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private |
include the data points for the total ion chromatogram (TIC) in the attachment
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private |
include the data points for the extracted ion chromatogram (XIC) in the attachment