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OpenMS
2.5.0
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50 class ResidueModification;
154 vector_(rhs.vector_),
155 position_(rhs.position_)
161 vector_(rhs.vector_),
162 position_(rhs.position_)
190 return *(*vector_)[position_];
196 return (*vector_)[position_];
287 vector_(rhs.vector_),
288 position_(rhs.position_)
316 return *(*vector_)[position_];
322 return (*vector_)[position_];
328 return (*vector_)[position_];
334 return Iterator(vector_, position_ + diff);
345 return Iterator(vector_, position_ - diff);
429 String toUnmodifiedString() const;
439 String toUniModString() const;
459 String toBracketString(
bool integer_mass = true,
460 bool mass_delta = false,
461 const std::vector<
String> & fixed_modifications = std::vector<
String>()) const;
472 void setNTerminalModification(
const String& modification);
478 const String& getNTerminalModificationName()
const;
485 void setCTerminalModification(
const String& modification);
491 const String& getCTerminalModificationName()
const;
546 bool has(
const Residue& residue)
const;
551 bool hasSubsequence(
const AASequence& peptide)
const;
555 bool hasPrefix(
const AASequence& peptide)
const;
559 bool hasSuffix(
const AASequence& peptide)
const;
562 bool hasNTerminalModification()
const;
565 bool hasCTerminalModification()
const;
568 bool isModified()
const;
611 bool permissive =
true);
622 bool permissive =
true);
670 bool permissive =
true);
Iterator & operator=(const Iterator &rhs)
assignment operator
Definition: AASequence.h:300
ConstIterator for AASequence.
Definition: AASequence.h:123
std::vector< const Residue * > peptide_
Definition: AASequence.h:626
std::vector< const Residue * >::difference_type difference_type
Definition: AASequence.h:132
Representation of a modification.
Definition: ResidueModification.h:76
DPosition< D, TCoordinateType > operator*(DPosition< D, TCoordinateType > position, typename DPosition< D, TCoordinateType >::CoordinateType scalar)
Scalar multiplication (a bit inefficient)
Definition: DPosition.h:427
Iterator end()
Definition: AASequence.h:587
const ResidueModification * c_term_mod_
Definition: AASequence.h:630
A more convenient string class.
Definition: String.h:58
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
difference_type position_
Definition: AASequence.h:382
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
std::vector< const Residue * > * vector_
Definition: AASequence.h:379
with N-terminus and C-terminus
Definition: Residue.h:152
ConstIterator & operator=(const ConstIterator &rhs)
assignment operator
Definition: AASequence.h:174
const typedef Residue & const_reference
Definition: AASequence.h:129
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
const ConstIterator operator+(difference_type diff) const
forward jump operator
Definition: AASequence.h:200
const_pointer operator->() const
dereference operator
Definition: AASequence.h:194
Iterator class for AASequence.
Definition: AASequence.h:258
const typedef Residue * pointer
Definition: AASequence.h:134
difference_type operator-(Iterator rhs) const
Definition: AASequence.h:337
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
const_pointer operator->() const
dereference operator
Definition: AASequence.h:320
ConstIterator & operator--()
decrement operator
Definition: AASequence.h:236
Representation of a residue.
Definition: Residue.h:61
TermSpecificity
Position where the modification is allowed to occur.
Definition: ResidueModification.h:95
bool operator==(const ConstIterator &rhs) const
equality comparator
Definition: AASequence.h:217
ConstIterator & operator++()
increment operator
Definition: AASequence.h:229
pointer operator->()
mutable dereference operator
Definition: AASequence.h:326
const typedef Residue * const_pointer
Definition: AASequence.h:131
ConstIterator(const AASequence::Iterator &rhs)
copy constructor from Iterator
Definition: AASequence.h:160
Iterator(const Iterator &rhs)
copy constructor
Definition: AASequence.h:286
ConstIterator(const std::vector< const Residue * > *vec_ptr, difference_type position)
detailed constructor with pointer to the vector and offset position
Definition: AASequence.h:146
bool operator!=(const Iterator &rhs) const
inequality operator
Definition: AASequence.h:355
Residue & reference
Definition: AASequence.h:265
Iterator & operator++()
increment operator
Definition: AASequence.h:361
const ConstIterator operator-(difference_type diff) const
backward jump operator
Definition: AASequence.h:211
ConstIterator begin() const
Definition: AASequence.h:585
const typedef Residue & const_reference
Definition: AASequence.h:264
ResidueType
Definition: Residue.h:150
difference_type operator-(ConstIterator rhs) const
Definition: AASequence.h:205
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
void setModification(int location, int max_size, String modification, OpenMS::AASequence &aas)
helper function that sets a modification on a AASequence object
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
const std::vector< const Residue * > * vector_
Definition: AASequence.h:247
std::random_access_iterator_tag iterator_category
Definition: AASequence.h:135
ConstIterator(const ConstIterator &rhs)
copy constructor
Definition: AASequence.h:153
std::vector< const Residue * >::difference_type difference_type
Definition: AASequence.h:268
String toString(const T &i)
fallback template for general purpose using Boost::Karma; more specializations below
Definition: StringUtils.h:85
virtual ~ConstIterator()
destructor
Definition: AASequence.h:167
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
bool operator==(const Iterator &rhs) const
equality comparator
Definition: AASequence.h:349
Residue & reference
Definition: AASequence.h:130
const typedef Residue * const_pointer
Definition: AASequence.h:266
ConstIterator end() const
Definition: AASequence.h:589
bool operator!=(const ConstIterator &rhs) const
inequality operator
Definition: AASequence.h:223
Iterator(std::vector< const Residue * > *vec_ptr, difference_type position)
detailed constructor with pointer to the vector and offset position
Definition: AASequence.h:279
Iterator & operator--()
decrement operator
Definition: AASequence.h:368
Iterator begin()
Definition: AASequence.h:583
const Iterator operator+(difference_type diff) const
forward jump operator
Definition: AASequence.h:332
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
std::istream & operator>>(std::istream &os, const AASequence &peptide)
Residue value_type
Definition: AASequence.h:133
Size< TNeedle >::Type position(const PatternAuxData< TNeedle > &dh)
Definition: AhoCorasickAmbiguous.h:561
const_iterator ConstIterator
Const Iterator.
Definition: String.h:72
const typedef Residue * pointer
Definition: AASequence.h:267
const Iterator operator-(difference_type diff) const
backward jump operator
Definition: AASequence.h:343
difference_type position_
Definition: AASequence.h:250
virtual ~Iterator()
destructor
Definition: AASequence.h:293
const ResidueModification * n_term_mod_
Definition: AASequence.h:628