| OpenMS 2.5.0

Protected Attributes | List of all members
ModificationDefinition Class Reference
Chemistry

Representation of modification definition. More...

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

## Public Member Functions

Constructor and Destructors
| ModificationDefinition ()
| default constructor More...
| ModificationDefinition (const ModificationDefinition &rhs)
| copy constructor More...
| ModificationDefinition (const String &mod, bool fixed=true, UInt max_occur=0)
| detailed constructor specifying the modification by name More...
| ModificationDefinition (const ResidueModification &mod, bool fixed=true, UInt max_occur=0)
| direct constructor from a residue modification More...
virtual | ~ModificationDefinition ()
| destructor More...
Accessors
void | setFixedModification (bool fixed)
| sets whether this modification definition is fixed or variable (modification must occur vs. can occur) More...
bool | isFixedModification () const
| returns if the modification if fixed true, else false More...
void | setMaxOccurrences (UInt num)
| set the maximal number of occurrences per peptide (unbounded if 0) More...
UInt | getMaxOccurrences () const
| returns the maximal number of occurrences per peptide More...
String | getModificationName () const
| returns the name of the modification More...
void | setModification (const String &modification)
| sets the modification, allowed are unique names provided by ModificationsDB More...
const ResidueModification & | getModification () const
| Returns the modification. More...
Assignment
ModificationDefinition & | operator= (const ModificationDefinition &element)
| assignment operator More...
Predicates
bool | operator== (const ModificationDefinition &rhs) const
| equality operator More...
bool | operator!= (const ModificationDefinition &rhs) const
| inequality operator More...
bool | operator< (const OpenMS::ModificationDefinition &) const
| less than operator for e.g. usage in maps; only mod FullIds are compared! More...

## Protected Attributes

const ResidueModification * | mod_
| the modification More...
bool | fixed_modification_
| fixed (true) or variable (false) More...
UInt | max_occurrences_
| maximal number of occurrences per peptide More...

## Detailed Description

Representation of modification definition.

This class defines a modification type e.g. a input parameter of a search engine. The modification is defined using an unique name of the modification present in the modifications DB instance.

## Constructor & Destructor Documentation

## ◆ ModificationDefinition() [1/4]

ModificationDefinition | ( |  | ) |

default constructor

## ◆ ModificationDefinition() [2/4]

ModificationDefinition | ( | const ModificationDefinition & | rhs | ) |

copy constructor

## ◆ ModificationDefinition() [3/4]

ModificationDefinition | ( | const String & | mod,
|  | bool | fixed = `true`,
|  | UInt | max_occur = `0`
| ) |  |

explicit

detailed constructor specifying the modification by name

## ◆ ModificationDefinition() [4/4]

ModificationDefinition | ( | const ResidueModification & | mod,
|  | bool | fixed = `true`,
|  | UInt | max_occur = `0`
| ) |  |

explicit

direct constructor from a residue modification

## ◆ ~ModificationDefinition()

virtual ~ModificationDefinition | ( |  | ) |

virtual

destructor

## Member Function Documentation

## ◆ getMaxOccurrences()

UInt getMaxOccurrences | ( |  | ) | const

returns the maximal number of occurrences per peptide

## ◆ getModification()

const ResidueModification& getModification | ( |  | ) | const

Returns the modification.

Exceptions

  Exception::InvalidValue | if no modification was set

## ◆ getModificationName()

String getModificationName | ( |  | ) | const

returns the name of the modification

## ◆ isFixedModification()

bool isFixedModification | ( |  | ) | const

returns if the modification if fixed true, else false

## ◆ operator!=()

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

inequality operator

## ◆ operator<()

bool operator< | ( | const OpenMS::ModificationDefinition & |  | ) | const

less than operator for e.g. usage in maps; only mod FullIds are compared!

## ◆ operator=()

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

assignment operator

## ◆ operator==()

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

equality operator

## ◆ setFixedModification()

void setFixedModification | ( | bool | fixed | ) |

sets whether this modification definition is fixed or variable (modification must occur vs. can occur)

## ◆ setMaxOccurrences()

void setMaxOccurrences | ( | UInt | num | ) |

set the maximal number of occurrences per peptide (unbounded if 0)

## ◆ setModification()

void setModification | ( | const String & | modification | ) |

sets the modification, allowed are unique names provided by ModificationsDB

## Member Data Documentation

## ◆ fixed_modification_

bool fixed_modification_

protected

fixed (true) or variable (false)

## ◆ max_occurrences_

UInt max_occurrences_

protected

maximal number of occurrences per peptide

## ◆ mod_

const ResidueModification* mod_

protected

the modification