maps peptide/protein sequence indexes (0-based) to a modification list More...
#include <Modification.hpp>
Public Member Functions | |
| ~ModificationMap () | |
| double | monoisotopicDeltaMass () const |
| returns the sum of the monoisotopic delta masses of all modifications in the map | |
| double | averageDeltaMass () const |
| returns the sum of the average delta masses of all modifications in the map | |
| virtual iterator | begin () |
| Returns an iterator pointing to the first element stored in the map. First is defined by the map's comparison operator, Compare. | |
| virtual iterator | end () |
| Returns an iterator pointing to the last element stored in the map; in other words, to the off-the-end value. | |
| virtual reverse_iterator | rbegin () |
| Returns a reverse_iterator pointing to the first element stored in the map. First is defined by the map's comparison operator, Compare. | |
| virtual reverse_iterator | rend () |
| Returns a reverse_iterator pointing to the last element stored in the map; in other words, to the off-the-end value). | |
| 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. Otherwise the pair x,T() is inserted into the map and a reference to the default object T() is returned. | |
| virtual std::pair< iterator, iterator > | equal_range (const key_type &x) |
| Returns the pair (lower_bound(x), upper_bound(x)). | |
| 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. If such a pair is not found the value end() is returned. | |
| virtual iterator | lower_bound (const key_type &x) |
| Returns a reference to the first entry with a key greater than or equal to x. | |
| virtual iterator | upper_bound (const key_type &x) |
| Returns an iterator for the first entry with a key greater than x. | |
| virtual void | clear () |
| Erases all elements from the self. | |
| 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, all elements in the range [start, finish) are deleted from the map. | |
| 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 map, 0 otherwise. | |
| 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. Otherwise, the pair is not inserted. | |
| 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. Otherwise, the pair is not inserted. A position may be supplied as a hint regarding where to do the insertion. If the insertion is done right after position, then it takes amortized constant time. Otherwise it takes O(log N) time. | |
| virtual bool | operator== (const ModificationMap &rhs) const |
| returns true iff the map has the same modifications | |
| 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 map | |
 Public Member Functions inherited from pwiz::util::virtual_map< int, ModificationList > | |
| virtual_map (const key_compare &predicate=key_compare(), const allocator_type &allocator=allocator_type()) | |
| Constructs an empty map that uses the predicate _Pred to order keys, if it is supplied. The map uses the allocator _Alloc for all storage management, if it is supplied. | |
| virtual_map (_Iter _First, _Iter _Last) | |
| Constructs a map containing values in the range [_First, _Last). Creation of the new map is only guaranteed to succeed if the iterators start and finish return values of type pair<class Key, class Value> and all values of Key in the range [_First, _Last) are unique. The map uses the predicate _Pred to order keys, and the allocator _Alloc for all storage management. | |
| virtual_map (_Iter _First, _Iter _Last, const key_compare &_Pred) | |
| Constructs a map containing values in the range [_First, _Last). Creation of the new map is only guaranteed to succeed if the iterators start and finish return values of type pair<class Key, class Value> and all values of Key in the range [_First, _Last) are unique. The map uses the predicate _Pred to order keys, and the allocator _Alloc for all storage management. | |
| virtual_map (_Iter _First, _Iter _Last, const key_compare &_Pred, const allocator_type &_Al) | |
| Constructs a map containing values in the range [_First, _Last). Creation of the new map is only guaranteed to succeed if the iterators start and finish return values of type pair<class Key, class Value> and all values of Key in the range [_First, _Last) are unique. The map uses the predicate _Pred to order keys, and the allocator _Alloc for all storage management. | |
| virtual | ~virtual_map () |
| virtual allocator_type | get_allocator () const |
| Returns a copy of the allocator used by self for storage management. | |
| virtual const_iterator | begin () const |
| Returns a const_iterator pointing to the first element stored in the map. | |
| virtual const_iterator | end () const |
| Returns a const_iterator pointing to the last element stored in the map. | |
| virtual const_reverse_iterator | rbegin () const |
| Returns a const_reverse_iterator pointing to the first element stored in the map. | |
| virtual const_reverse_iterator | rend () const |
| Returns a const_reverse_iterator pointing to the last element stored in the map. | |
| virtual virtual_map< int, ModificationList, key_compare, allocator_type > & | operator= (const virtual_map< int, ModificationList, key_compare, allocator_type > &x) |
| Replaces the contents of *this with a copy of the map x. | |
| virtual size_type | count (const key_type &x) const |
| Returns a 1 if a value with the key x exists in the map. Otherwise returns a 0. | |
| virtual bool | empty () const |
| Returns true if the map is empty, false otherwise. | |
| virtual std::pair < const_iterator, const_iterator > | equal_range (const key_type &x) const |
| Returns the pair (lower_bound(x), upper_bound(x)). | |
| virtual const_iterator | find (const key_type &x) const |
| Same as find above but returns a const_iterator. | |
| void | insert (InputIterator start, InputIterator finish) |
| Copies of each element in the range [start, finish) that possess a unique key (one not already in the map) are inserted into the map. The iterators start and finish must return values of type pair<T1,T2>. This operation takes approximately O(N*log(size()+N)) time. | |
| virtual key_compare | key_comp () const |
| Returns a function object capable of comparing key values using the comparison operation, Compare, of the current map. | |
| virtual const_iterator | lower_bound (const key_type &x) const |
| Same as lower_bound above but returns a const_iterator. | |
| virtual size_type | max_size () const |
| Returns the maximum possible size of the map. This size is only constrained by the number of unique keys that can be represented by the type Key. | |
| virtual size_type | size () const |
| Returns the number of elements in the map. | |
| virtual void | swap (virtual_map< int, ModificationList, key_compare, allocator_type > &x) |
| Swaps the contents of the map x with the current map, *this. | |
| virtual const_iterator | upper_bound (const key_type &x) const |
| Same as upper_bound above, but returns a const_iterator. | |
| virtual value_compare | value_comp () const |
| Returns a function object capable of comparing pair<const Key, T> values using the comparison operation, Compare, of the current map. This function is identical to key_comp for sets. | |
Static Public Member Functions | |
| static int | NTerminus () |
| static int | CTerminus () |
Private Member Functions | |
| ModificationMap () | |
| ModificationMap (const ModificationMap &other) | |
| ModificationMap & | operator= (const ModificationMap &) |
| virtual void | swap (ModificationMap &) |
Private Attributes | |
| boost::shared_ptr< Impl > | impl_ |
Friends | |
| class | Peptide::Impl |
Additional Inherited Members | |
| Public Types inherited from pwiz::util::virtual_map< int, ModificationList > | |
| typedef std::map< int, ModificationList, std::less < int >, std::allocator < std::pair< const int, ModificationList > > > | BaseType |
| typedef BaseType::allocator_type | allocator_type |
| typedef BaseType::key_type | key_type |
| typedef BaseType::value_type | value_type |
| typedef BaseType::key_compare | key_compare |
| typedef BaseType::value_compare | value_compare |
| typedef BaseType::size_type | size_type |
| typedef BaseType::mapped_type | mapped_type |
| typedef BaseType::difference_type | difference_type |
| typedef BaseType::pointer | pointer |
| typedef BaseType::const_pointer | const_pointer |
| typedef BaseType::reference | reference |
| typedef BaseType::const_reference | const_reference |
| typedef BaseType::iterator | iterator |
| typedef BaseType::const_iterator | const_iterator |
| typedef BaseType::reverse_iterator | reverse_iterator |
| typedef BaseType::const_reverse_iterator | const_reverse_iterator |
Detailed Description
maps peptide/protein sequence indexes (0-based) to a modification list
- ModificationMap::NTerminus() returns the index for specifying N terminal mods
- ModificationMap::CTerminus() returns the index for specifying C terminal mods
Definition at line 104 of file Modification.hpp.
Constructor & Destructor Documentation
| pwiz::proteome::ModificationMap::~ModificationMap | ( | ) |
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Member Function Documentation
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Referenced by testConversion().
| double pwiz::proteome::ModificationMap::monoisotopicDeltaMass | ( | ) | const |
returns the sum of the monoisotopic delta masses of all modifications in the map
| double pwiz::proteome::ModificationMap::averageDeltaMass | ( | ) | const |
returns the sum of the average delta masses of all modifications in the map
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Returns an iterator pointing to the first element stored in the map. First is defined by the map's comparison operator, Compare.
Reimplemented from pwiz::util::virtual_map< int, ModificationList >.
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Returns an iterator pointing to the last element stored in the map; in other words, to the off-the-end value.
Reimplemented from pwiz::util::virtual_map< int, ModificationList >.
Referenced by modificationTest().
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Returns a reverse_iterator pointing to the first element stored in the map. First is defined by the map's comparison operator, Compare.
Reimplemented from pwiz::util::virtual_map< int, ModificationList >.
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Returns a reverse_iterator pointing to the last element stored in the map; in other words, to the off-the-end value).
Reimplemented from pwiz::util::virtual_map< int, ModificationList >.
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If an element with the key x exists in the map, then a reference to its associated value is returned. Otherwise the pair x,T() is inserted into the map and a reference to the default object T() is returned.
Reimplemented from pwiz::util::virtual_map< int, ModificationList >.
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Returns the pair (lower_bound(x), upper_bound(x)).
Reimplemented from pwiz::util::virtual_map< int, ModificationList >.
Searches the map for a pair with the key value x and returns an iterator to that pair if it is found. If such a pair is not found the value end() is returned.
Reimplemented from pwiz::util::virtual_map< int, ModificationList >.
Referenced by modificationTest(), and testConversion().
Returns a reference to the first entry with a key greater than or equal to x.
Reimplemented from pwiz::util::virtual_map< int, ModificationList >.
Returns an iterator for the first entry with a key greater than x.
Reimplemented from pwiz::util::virtual_map< int, ModificationList >.
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Erases all elements from the self.
Reimplemented from pwiz::util::virtual_map< int, ModificationList >.
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Deletes the map element pointed to by the iterator position.
Reimplemented from pwiz::util::virtual_map< int, ModificationList >.
If the iterators start and finish point to the same map and last is reachable from first, all elements in the range [start, finish) are deleted from the map.
Reimplemented from pwiz::util::virtual_map< int, ModificationList >.
Deletes the element with the key value x from the map, if one exists. Returns 1 if x existed in the map, 0 otherwise.
Reimplemented from pwiz::util::virtual_map< int, ModificationList >.
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If a value_type with the same key as x is not present in the map, then x is inserted into the map. Otherwise, the pair is not inserted.
Reimplemented from pwiz::util::virtual_map< int, ModificationList >.
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If a value_type with the same key as x is not present in the map, then x is inserted into the map. Otherwise, the pair is not inserted. A position may be supplied as a hint regarding where to do the insertion. If the insertion is done right after position, then it takes amortized constant time. Otherwise it takes O(log N) time.
Reimplemented from pwiz::util::virtual_map< int, ModificationList >.
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returns true iff the map has the same modifications
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returns true iff the map has fewer modified positions or one of the positions is less than in the rhs map
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Friends And Related Function Documentation
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friend |
Definition at line 190 of file Modification.hpp.
Member Data Documentation
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Definition at line 187 of file Modification.hpp.
The documentation for this class was generated from the following file:
- /Users/parag/_Research/pwiz/svn/trunk/pwiz/pwiz/data/proteome/Modification.hpp
