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Protected Attributes | List of all members
ModificationDefinitionsSet Class Reference

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

#include <OpenMS/CHEMISTRY/ModificationDefinitionsSet.h>

Public Member Functions

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< ModificationDefinitiongetModifications () 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< StringgetModificationNames () const
 return only the names of the modifications stored in the set More...
 
std::set< StringgetFixedModificationNames () const
 return only the names of the fixed modifications More...
 
std::set< StringgetVariableModificationNames () const
 return only the names of the variable modifications More...
 
Assignment
ModificationDefinitionsSetoperator= (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...
 

Protected Attributes

std::set< ModificationDefinitionvariable_mods_
 
std::set< ModificationDefinitionfixed_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

default constructor

copy constructor

ModificationDefinitionsSet ( const StringList fixed_modifications,
const StringList variable_modifications 
)

detailed constructor with StringLists

virtual ~ModificationDefinitionsSet ( )
virtual

destructor

Member Function Documentation

void addModification ( const ModificationDefinition mod_def)

adds a modification definition to the set

std::set<String> getFixedModificationNames ( ) const

return only the names of the fixed modifications

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

returns the stored fixed modification definitions

Size getMaxModifications ( ) const

return the maximal number of modifications allowed per peptide

std::set<String> getModificationNames ( ) const

return only the names of the modifications stored in the set

std::set<ModificationDefinition> getModifications ( ) const

returns the stored modification definitions

Size getNumberOfFixedModifications ( ) const

returns the number of fixed modifications stored in this set

Size getNumberOfModifications ( ) const

returns the number of modifications stored in this set

Size getNumberOfVariableModifications ( ) const

returns the number of variable modifications stored in this set

std::set<String> getVariableModificationNames ( ) const

return only the names of the variable modifications

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

returns the stored variable modification definitions

bool isCompatible ( const AASequence peptide) const

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

bool operator!= ( const ModificationDefinitionsSet rhs) const

inequality operator

ModificationDefinitionsSet& operator= ( const ModificationDefinitionsSet element)

assignment operator

bool operator== ( const ModificationDefinitionsSet rhs) const

equality operator

void setMaxModifications ( Size  max_mod)

sets the maximal number of modifications allowed per peptide

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

sets the modification definitions

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.

void setModifications ( const StringList fixed_modifications,
const StringList variable_modifications 
)

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

Member Data Documentation

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

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Aug 25 2015 05:54:03 using doxygen 1.8.9.1