25#ifndef _MODIFICATION_HPP_
26#define _MODIFICATION_HPP_
33#include <boost/shared_ptr.hpp>
50 double averageDeltaMass);
79 :
public std::vector<Modification>
190 friend class Peptide::Impl;
KernelTraitsBase< Kernel >::space_type::abscissa_type x
represents a post-translational modification (PTM) modification formula or masses must be provided at...
Modification(double monoisotopicDeltaMass, double averageDeltaMass)
Modification()
constructs a zero-mass modification (provided for MSVC compatibility)
boost::shared_ptr< Impl > impl_
Modification(const Modification &)
bool operator<(const Modification &rhs) const
returns true iff this mod has smaller delta masses
const chemistry::Formula & formula() const
returns the difference formula; throws runtime_error if hasFormula() = false
Modification(const chemistry::Formula &formula)
bool operator==(const Modification &rhs) const
returns true iff delta masses are equal
double averageDeltaMass() const
Modification & operator=(const Modification &)
double monoisotopicDeltaMass() const
bool hasFormula() const
returns true iff the mod was constructed with formula
represents a list of modifications on a single amino acid
bool operator<(const ModificationList &rhs) const
returns true iff the list has fewer modifications or one that's lesser than in the rhs list
ModificationList(const std::vector< Modification > &mods)
double monoisotopicDeltaMass() const
returns the sum of the monoisotopic delta masses of all modifications in the list
double averageDeltaMass() const
returns the sum of the average delta masses of all modifications in the list
bool operator==(const ModificationList &rhs) const
returns true iff the list has equal modifications
ModificationList(const Modification &mod)
maps peptide/protein sequence indexes (0-based) to a modification list
boost::shared_ptr< Impl > impl_
virtual std::pair< iterator, bool > insert(const value_type &x)
If a value_type with the same key as x is not present in the map, then x is inserted into the map....
ModificationMap & operator=(const ModificationMap &)
virtual iterator upper_bound(const key_type &x)
Returns an iterator for the first entry with a key greater than x.
virtual iterator insert(iterator position, const value_type &x)
If a value_type with the same key as x is not present in the map, then x is inserted into the map....
virtual void swap(ModificationMap &)
virtual iterator lower_bound(const key_type &x)
Returns a reference to the first entry with a key greater than or equal to x.
double monoisotopicDeltaMass() const
returns the sum of the monoisotopic delta masses of all modifications in the map
virtual void clear()
Erases all elements from the self.
virtual size_type erase(const key_type &x)
Deletes the element with the key value x from the map, if one exists. Returns 1 if x existed in the m...
virtual bool operator==(const ModificationMap &rhs) const
returns true iff the map has the same modifications
double averageDeltaMass() const
returns the sum of the average delta masses of all modifications in the map
virtual void erase(iterator position)
Deletes the map element pointed to by the iterator position.
virtual void erase(iterator start, iterator finish)
If the iterators start and finish point to the same map and last is reachable from first,...
virtual iterator end()
Returns an iterator pointing to the last element stored in the map; in other words,...
virtual iterator find(const key_type &x)
Searches the map for a pair with the key value x and returns an iterator to that pair if it is found....
ModificationMap(const ModificationMap &other)
virtual std::pair< iterator, iterator > equal_range(const key_type &x)
Returns the pair (lower_bound(x), upper_bound(x)).
virtual reverse_iterator rbegin()
Returns a reverse_iterator pointing to the first element stored in the map. First is defined by the m...
virtual mapped_type & operator[](const key_type &x)
If an element with the key x exists in the map, then a reference to its associated value is returned....
virtual bool operator<(const ModificationMap &rhs) const
returns true iff the map has fewer modified positions or one of the positions is less than in the rhs...
virtual iterator begin()
Returns an iterator pointing to the first element stored in the map. First is defined by the map's co...
virtual reverse_iterator rend()
Returns a reverse_iterator pointing to the last element stored in the map; in other words,...
a wrapper for std::map that will behave properly with polymorphism
BaseType::key_type key_type
BaseType::size_type size_type
BaseType::reverse_iterator reverse_iterator
BaseType::mapped_type mapped_type
BaseType::iterator iterator
BaseType::value_type value_type