| OpenMS 2.5.0

Public Member Functions | Static Protected Member Functions | Protected Attributes | List of all members
ModificationDefinitionsSet Class Reference
Chemistry

Representation of a set of modification definitions. More...

`#include <OpenMS/CHEMISTRY/ModificationDefinitionsSet.h>`

## Public Member Functions

void | findMatches (std::multimap< double, ModificationDefinition > &matches, double mass, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY, bool consider_fixed=true, bool consider_variable=true, bool is_delta=true, double tolerance=0.01) const
| Finds modifications in the set that match a given (delta) mass. More...
void | inferFromPeptides (const std::vector< PeptideIdentification > &peptides)
| Infers the sets of defined modifications from the modifications present on peptide identifications. More...
Constructor and Destructors
| ModificationDefinitionsSet ()
| default constructor More...
| ModificationDefinitionsSet (const ModificationDefinitionsSet &rhs)
| copy constructor More...
| ModificationDefinitionsSet (const StringList &fixed_modifications, const StringList &variable_modifications)
| detailed constructor with StringLists More...
virtual | ~ModificationDefinitionsSet ()
| destructor More...
Accessors
void | setMaxModifications (Size max_mod)
| sets the maximal number of modifications allowed per peptide More...
Size | getMaxModifications () const
| return the maximal number of modifications allowed per peptide More...
Size | getNumberOfModifications () const
| returns the number of modifications stored in this set More...
Size | getNumberOfFixedModifications () const
| returns the number of fixed modifications stored in this set More...
Size | getNumberOfVariableModifications () const
| returns the number of variable modifications stored in this set More...
void | addModification (const ModificationDefinition &mod_def)
| adds a modification definition to the set More...
void | setModifications (const std::set< ModificationDefinition > &mod_defs)
| sets the modification definitions More...
void | setModifications (const String &fixed_modifications, const String &variable_modifications)
| set the modification definitions from a string More...
void | setModifications (const StringList &fixed_modifications, const StringList &variable_modifications)
| same as above, but using StringList instead of comma separated strings More...
std::set< ModificationDefinition > | getModifications () const
| returns the stored modification definitions More...
const std::set< ModificationDefinition > & | getFixedModifications () const
| returns the stored fixed modification definitions More...
const std::set< ModificationDefinition > & | getVariableModifications () const
| returns the stored variable modification definitions More...
std::set< String > | getModificationNames () const
| returns only the names of the modifications stored in the set More...
void | getModificationNames (StringList &fixed_modifications, StringList &variable_modifications) const
| populates the output lists with the modification names (use e.g. for ProteinIdentification::SearchParameters) More...
std::set< String > | getFixedModificationNames () const
| returns only the names of the fixed modifications More...
std::set< String > | getVariableModificationNames () const
| returns only the names of the variable modifications More...
Assignment
ModificationDefinitionsSet & | operator= (const ModificationDefinitionsSet &element)
| assignment operator More...
Predicates
bool | isCompatible (const AASequence &peptide) const
| returns true if the peptide is compatible with the definitions, e.g. does not contain other modifications More...
bool | operator== (const ModificationDefinitionsSet &rhs) const
| equality operator More...
bool | operator!= (const ModificationDefinitionsSet &rhs) const
| inequality operator More...

## Static Protected Member Functions

static void | addMatches_ (std::multimap< double, ModificationDefinition > &matches, double mass, const String &residue, ResidueModification::TermSpecificity term_spec, const std::set< ModificationDefinition > &source, bool is_delta, double tolerance)
| helper function for findMatches() - finds matching modifications in `source` and adds them to `matches` More...

## Protected Attributes

std::set< ModificationDefinition > | variable_mods_
std::set< ModificationDefinition > | fixed_mods_
Size | max_mods_per_peptide_

## Detailed Description

Representation of a set of modification definitions.

This class enhances the modification definitions as defined in the class ModificationDefinition into a set of definitions. This is also e.g. used as input parameters in search engines.

## Constructor & Destructor Documentation

## ◆ ModificationDefinitionsSet() [1/3]

ModificationDefinitionsSet | ( |  | ) |

default constructor

## ◆ ModificationDefinitionsSet() [2/3]

ModificationDefinitionsSet | ( | const ModificationDefinitionsSet & | rhs | ) |

copy constructor

## ◆ ModificationDefinitionsSet() [3/3]

ModificationDefinitionsSet | ( | const StringList & | fixed_modifications,
|  | const StringList & | variable_modifications
| ) |  |

detailed constructor with StringLists

## ◆ ~ModificationDefinitionsSet()

virtual ~ModificationDefinitionsSet | ( |  | ) |

virtual

destructor

## Member Function Documentation

## ◆ addMatches_()

static void addMatches_ | ( | std::multimap< double, ModificationDefinition > & | matches,
|  | double | mass,
|  | const String & | residue,
|  | ResidueModification::TermSpecificity | term_spec,
|  | const std::set< ModificationDefinition > & | source,
|  | bool | is_delta,
|  | double | tolerance
| ) |  |

static protected

helper function for findMatches() - finds matching modifications in `source` and adds them to `matches`

## ◆ addModification()

void addModification | ( | const ModificationDefinition & | mod_def | ) |

adds a modification definition to the set

## ◆ findMatches()

void findMatches | ( | std::multimap< double, ModificationDefinition > & | matches,
|  | double | mass,
|  | const String & | residue = `""`,
|  | ResidueModification::TermSpecificity | term_spec = `ResidueModification::NUMBER_OF_TERM_SPECIFICITY`,
|  | bool | consider_fixed = `true`,
|  | bool | consider_variable = `true`,
|  | bool | is_delta = `true`,
|  | double | tolerance = `0.01`
| ) |  | const

Finds modifications in the set that match a given (delta) mass.

Parameters

  matches | Matching modifications (output), sorted by mass error
  mass | Query mass
  residue | Query residue
  term_spec | Query term specificity
  consider_variable | Consider the variable modifications?
  consider_fixed | Consider the fixed modifications?
  is_delta | Is `mass` a delta mass (mass difference)?
  tolerance | Numeric tolerance (in Da) for mass matching

Exceptions

  Exception::IllegalArgument | if both `consider_variable` and `consider_fixed` are false

## ◆ getFixedModificationNames()

std::set<String> getFixedModificationNames | ( |  | ) | const

returns only the names of the fixed modifications

## ◆ getFixedModifications()

const std::set<ModificationDefinition>& getFixedModifications | ( |  | ) | const

returns the stored fixed modification definitions

## ◆ getMaxModifications()

Size getMaxModifications | ( |  | ) | const

return the maximal number of modifications allowed per peptide

## ◆ getModificationNames() [1/2]

std::set<String> getModificationNames | ( |  | ) | const

returns only the names of the modifications stored in the set

## ◆ getModificationNames() [2/2]

void getModificationNames | ( | StringList & | fixed_modifications,
|  | StringList & | variable_modifications
| ) |  | const

populates the output lists with the modification names (use e.g. for ProteinIdentification::SearchParameters)

## ◆ getModifications()

std::set<ModificationDefinition> getModifications | ( |  | ) | const

returns the stored modification definitions

## ◆ getNumberOfFixedModifications()

Size getNumberOfFixedModifications | ( |  | ) | const

returns the number of fixed modifications stored in this set

## ◆ getNumberOfModifications()

Size getNumberOfModifications | ( |  | ) | const

returns the number of modifications stored in this set

## ◆ getNumberOfVariableModifications()

Size getNumberOfVariableModifications | ( |  | ) | const

returns the number of variable modifications stored in this set

## ◆ getVariableModificationNames()

std::set<String> getVariableModificationNames | ( |  | ) | const

returns only the names of the variable modifications

## ◆ getVariableModifications()

const std::set<ModificationDefinition>& getVariableModifications | ( |  | ) | const

returns the stored variable modification definitions

## ◆ inferFromPeptides()

void inferFromPeptides | ( | const std::vector< PeptideIdentification > & | peptides | ) |

Infers the sets of defined modifications from the modifications present on peptide identifications.

## ◆ isCompatible()

bool isCompatible | ( | const AASequence & | peptide | ) | const

returns true if the peptide is compatible with the definitions, e.g. does not contain other modifications

## ◆ operator!=()

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

inequality operator

## ◆ operator=()

ModificationDefinitionsSet& operator= | ( | const ModificationDefinitionsSet & | element | ) |

assignment operator

## ◆ operator==()

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

equality operator

## ◆ setMaxModifications()

void setMaxModifications | ( | Size | max_mod | ) |

sets the maximal number of modifications allowed per peptide

## ◆ setModifications() [1/3]

void setModifications | ( | const std::set< ModificationDefinition > & | mod_defs | ) |

sets the modification definitions

## ◆ setModifications() [2/3]

void setModifications | ( | const String & | fixed_modifications,
|  | const String & | variable_modifications
| ) |  |

set the modification definitions from a string

The strings should contain a comma separated list of modifications. The names can be PSI-MOD identifier or any other unique name supported by PSI-MOD. TermSpec definitions and other specific definitions are given by the modifications themselves.

## ◆ setModifications() [3/3]

void setModifications | ( | const StringList & | fixed_modifications,
|  | const StringList & | variable_modifications
| ) |  |

same as above, but using StringList instead of comma separated strings

## Member Data Documentation

## ◆ fixed_mods_

std::set<ModificationDefinition> fixed_mods_

protected

## ◆ max_mods_per_peptide_

Size max_mods_per_peptide_

protected

## ◆ variable_mods_

std::set<ModificationDefinition> variable_mods_

protected