| OpenMS 2.5.0

Public Types | Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
IncludeExcludeTarget Class Reference

This class stores a SRM/MRM transition. More...

`#include <OpenMS/ANALYSIS/TARGETED/IncludeExcludeTarget.h>`

Inheritance diagram for IncludeExcludeTarget:

## Public Types

typedef TargetedExperimentHelper::Configuration | Configuration
typedef TargetedExperimentHelper::RetentionTime | RetentionTime

## Public Member Functions

IncludeExcludeTarget & | operator= (const IncludeExcludeTarget &rhs)
| assignment operator More...
Constructors and destructors
| IncludeExcludeTarget ()
| default constructor More...
| IncludeExcludeTarget (const IncludeExcludeTarget &rhs)
| copy constructor More...
| ~IncludeExcludeTarget () override
| destructor More...
Accessors
void | setName (const String &name)
const String & | getName () const
void | setPeptideRef (const String &peptide_ref)
const String & | getPeptideRef () const
void | setCompoundRef (const String &compound_ref)
const String & | getCompoundRef () const
void | setPrecursorMZ (double mz)
| sets the precursor mz (Q1 value) More...
double | getPrecursorMZ () const
void | setPrecursorCVTermList (const CVTermList &list)
void | addPrecursorCVTerm (const CVTerm &cv_term)
const CVTermList & | getPrecursorCVTermList () const
void | setProductMZ (double mz)
double | getProductMZ () const
void | setProductCVTermList (const CVTermList &list)
void | addProductCVTerm (const CVTerm &cv_term)
const CVTermList & | getProductCVTermList () const
void | setInterpretations (const std::vector< CVTermList > &interpretations)
const std::vector< CVTermList > & | getInterpretations () const
void | addInterpretation (const CVTermList &interpretation)
void | setConfigurations (const std::vector< Configuration > &configuration)
const std::vector< Configuration > & | getConfigurations () const
void | addConfiguration (const Configuration &configuration)
void | setPrediction (const CVTermList &prediction)
void | addPredictionTerm (const CVTerm &prediction)
const CVTermList & | getPrediction () const
void | setRetentionTime (RetentionTime rt)
const RetentionTime & | getRetentionTime () const
Predicates
bool | operator== (const IncludeExcludeTarget &rhs) const
| equality operator More...
bool | operator!= (const IncludeExcludeTarget &rhs) const
| inequality operator More...
Public Member Functions inherited from CVTermList
| CVTermList ()=default
| Defaults constructor. More...
| CVTermList (const CVTermList &)=default
| Copy constructor. More...
| CVTermList (CVTermList &&) noexcept
| Move constructor. More...
virtual | ~CVTermList ()
| Destructor. More...
CVTermList & | operator= (const CVTermList &rhs) &=default
| Assignment operator. More...
CVTermList & | operator= (CVTermList &&) &=default
| Move assignment operator. More...
void | setCVTerms (const std::vector< CVTerm > &terms)
| sets the CV terms More...
void | replaceCVTerm (const CVTerm &cv_term)
| replaces the specified CV term More...
void | replaceCVTerms (const std::vector< CVTerm > &cv_terms, const String &accession)
| replaces the specified CV terms using the given accession number More...
void | replaceCVTerms (const Map< String, std::vector< CVTerm > > &cv_term_map)
| replaces all cv terms with a map (can be obtained via getCVTerms) More...
void | consumeCVTerms (const Map< String, std::vector< CVTerm > > &cv_term_map)
| merges the given map into the member map, no duplicate checking More...
const Map< String, std::vector< CVTerm > > & | getCVTerms () const
| returns the accession string of the term More...
void | addCVTerm (const CVTerm &term)
| adds a CV term More...
bool | operator== (const CVTermList &cv_term_list) const
| equality operator More...
bool | operator!= (const CVTermList &cv_term_list) const
| inequality operator More...
bool | hasCVTerm (const String &accession) const
| checks whether the term has a value More...
bool | empty () const
| return true if no terms are available More...
Public Member Functions inherited from MetaInfoInterface
| MetaInfoInterface ()
| Constructor. More...
| MetaInfoInterface (const MetaInfoInterface &rhs)
| Copy constructor. More...
| MetaInfoInterface (MetaInfoInterface &&) noexcept
| Move constructor. More...
| ~MetaInfoInterface ()
| Destructor. More...
MetaInfoInterface & | operator= (const MetaInfoInterface &rhs)
| Assignment operator. More...
MetaInfoInterface & | operator= (MetaInfoInterface &&) noexcept
| Move assignment operator. More...
bool | operator== (const MetaInfoInterface &rhs) const
| Equality operator. More...
bool | operator!= (const MetaInfoInterface &rhs) const
| Equality operator. More...
const DataValue & | getMetaValue (const String &name, const DataValue &default_value=DataValue::EMPTY) const
| Returns the value corresponding to a string, or a default value (default: DataValue::EMPTY) if not found. More...
const DataValue & | getMetaValue (UInt index, const DataValue &default_value=DataValue::EMPTY) const
| Returns the value corresponding to an index, or a default value (default: DataValue::EMPTY) if not found. More...
bool | metaValueExists (const String &name) const
| Returns whether an entry with the given name exists. More...
bool | metaValueExists (UInt index) const
| Returns whether an entry with the given index exists. More...
void | setMetaValue (const String &name, const DataValue &value)
| Sets the DataValue corresponding to a name. More...
void | setMetaValue (UInt index, const DataValue &value)
| Sets the DataValue corresponding to an index. More...
void | removeMetaValue (const String &name)
| Removes the DataValue corresponding to `name` if it exists. More...
void | removeMetaValue (UInt index)
| Removes the DataValue corresponding to `index` if it exists. More...
void | getKeys (std::vector< String > &keys) const
| Fills the given vector with a list of all keys for which a value is set. More...
void | getKeys (std::vector< UInt > &keys) const
| Fills the given vector with a list of all keys for which a value is set. More...
bool | isMetaEmpty () const
| Returns if the MetaInfo is empty. More...
void | clearMetaInfo ()
| Removes all meta values. More...

## Protected Member Functions

void | updateMembers_ ()
Protected Member Functions inherited from MetaInfoInterface
void | createIfNotExists_ ()
| Creates the MetaInfo object if it does not exist. More...

## Protected Attributes

String | name_
double | precursor_mz_
CVTermList | precursor_cv_terms_
double | product_mz_
CVTermList | product_cv_terms_
std::vector< CVTermList > | interpretation_list_
String | peptide_ref_
String | compound_ref_
std::vector< Configuration > | configurations_
CVTermList | prediction_
RetentionTime | rts_
Protected Attributes inherited from CVTermList
Map< String, std::vector< CVTerm > > | cv_terms_
Protected Attributes inherited from MetaInfoInterface
MetaInfo * | meta_
| Pointer to the MetaInfo object (0 by default) More...

## Additional Inherited Members

Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistry & | metaRegistry ()
| Returns a reference to the MetaInfoRegistry. More...

## Detailed Description

This class stores a SRM/MRM transition.

The default values for precursor and product m/z values are set to numeric_limits<double>::max(). Default values for precursor an product charge is set to numeric_limits<Int>::max().

## Member Typedef Documentation

## ◆ Configuration

typedef TargetedExperimentHelper::Configuration Configuration

## ◆ RetentionTime

typedef TargetedExperimentHelper::RetentionTime RetentionTime

## Constructor & Destructor Documentation

## ◆ IncludeExcludeTarget() [1/2]

IncludeExcludeTarget | ( |  | ) |

default constructor

## ◆ IncludeExcludeTarget() [2/2]

IncludeExcludeTarget | ( | const IncludeExcludeTarget & | rhs | ) |

copy constructor

## ◆ ~IncludeExcludeTarget()

~IncludeExcludeTarget | ( |  | ) |

override

destructor

## Member Function Documentation

## ◆ addConfiguration()

void addConfiguration | ( | const Configuration & | configuration | ) |

## ◆ addInterpretation()

void addInterpretation | ( | const CVTermList & | interpretation | ) |

## ◆ addPrecursorCVTerm()

void addPrecursorCVTerm | ( | const CVTerm & | cv_term | ) |

## ◆ addPredictionTerm()

void addPredictionTerm | ( | const CVTerm & | prediction | ) |

## ◆ addProductCVTerm()

void addProductCVTerm | ( | const CVTerm & | cv_term | ) |

## ◆ getCompoundRef()

const String& getCompoundRef | ( |  | ) | const

## ◆ getConfigurations()

const std::vector<Configuration>& getConfigurations | ( |  | ) | const

## ◆ getInterpretations()

const std::vector<CVTermList>& getInterpretations | ( |  | ) | const

## ◆ getName()

const String& getName | ( |  | ) | const

## ◆ getPeptideRef()

const String& getPeptideRef | ( |  | ) | const

## ◆ getPrecursorCVTermList()

const CVTermList& getPrecursorCVTermList | ( |  | ) | const

## ◆ getPrecursorMZ()

double getPrecursorMZ | ( |  | ) | const

## ◆ getPrediction()

const CVTermList& getPrediction | ( |  | ) | const

## ◆ getProductCVTermList()

const CVTermList& getProductCVTermList | ( |  | ) | const

## ◆ getProductMZ()

double getProductMZ | ( |  | ) | const

## ◆ getRetentionTime()

const RetentionTime& getRetentionTime | ( |  | ) | const

## ◆ operator!=()

bool operator!= | ( | const IncludeExcludeTarget & | rhs | ) | const

inequality operator

## ◆ operator=()

IncludeExcludeTarget& operator= | ( | const IncludeExcludeTarget & | rhs | ) |

assignment operator

## ◆ operator==()

bool operator== | ( | const IncludeExcludeTarget & | rhs | ) | const

equality operator

## ◆ setCompoundRef()

void setCompoundRef | ( | const String & | compound_ref | ) |

## ◆ setConfigurations()

void setConfigurations | ( | const std::vector< Configuration > & | configuration | ) |

## ◆ setInterpretations()

void setInterpretations | ( | const std::vector< CVTermList > & | interpretations | ) |

## ◆ setName()

void setName | ( | const String & | name | ) |

## ◆ setPeptideRef()

void setPeptideRef | ( | const String & | peptide_ref | ) |

## ◆ setPrecursorCVTermList()

void setPrecursorCVTermList | ( | const CVTermList & | list | ) |

## ◆ setPrecursorMZ()

void setPrecursorMZ | ( | double | mz | ) |

sets the precursor mz (Q1 value)

## ◆ setPrediction()

void setPrediction | ( | const CVTermList & | prediction | ) |

## ◆ setProductCVTermList()

void setProductCVTermList | ( | const CVTermList & | list | ) |

## ◆ setProductMZ()

void setProductMZ | ( | double | mz | ) |

## ◆ setRetentionTime()

void setRetentionTime | ( | RetentionTime | rt | ) |

## ◆ updateMembers_()

void updateMembers_ | ( |  | ) |

protected

## Member Data Documentation

## ◆ compound_ref_

String compound_ref_

protected

## ◆ configurations_

std::vector<Configuration> configurations_

protected

## ◆ interpretation_list_

std::vector<CVTermList> interpretation_list_

protected

## ◆ name_

String name_

protected

## ◆ peptide_ref_

String peptide_ref_

protected

## ◆ precursor_cv_terms_

CVTermList precursor_cv_terms_

protected

## ◆ precursor_mz_

double precursor_mz_

protected

## ◆ prediction_

CVTermList prediction_

protected

## ◆ product_cv_terms_

CVTermList product_cv_terms_

protected

## ◆ product_mz_

double product_mz_

protected

## ◆ rts_

RetentionTime rts_

protected