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 String &fixed_modifications, const String &variable_modifications="") | |
| detailed constructor with comma separated list of modifications More... | |
| ModificationDefinitionsSet (const StringList &fixed_modifications, const StringList &variable_modifications=StringList::create("")) | |
| 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 |
| return only the names of the modifications stored in the set More... | |
| std::set< String > | getFixedModificationNames () const |
| return only the names of the fixed modifications More... | |
| std::set< String > | getVariableModificationNames () const |
| return 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... | |
Protected Attributes | |
| std::set< ModificationDefinition > | variable_mods_ |
| std::set< ModificationDefinition > | fixed_mods_ |
| Size | max_mods_per_peptide_ |
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.
default constructor
| ModificationDefinitionsSet | ( | const ModificationDefinitionsSet & | rhs | ) |
copy constructor
| ModificationDefinitionsSet | ( | const String & | fixed_modifications, |
| const String & | variable_modifications = "" |
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| ) |
detailed constructor with comma separated list of modifications
| ModificationDefinitionsSet | ( | const StringList & | fixed_modifications, |
| const StringList & | variable_modifications = StringList::create("") |
||
| ) |
detailed constructor with StringLists
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virtual |
destructor
| 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
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
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| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5 |