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);
403 AASequence& operator=(const AASequence&) = default;
406 AASequence& operator=(AASequence&&) = default;
429 String toUnmodifiedString() const;
439 String toUniModString() const;
459 String toBracketString(
bool integer_mass = true,
460 bool mass_delta = false,
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);
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
ConstIterator & operator--()
decrement operator
Definition: AASequence.h:236
const ConstIterator operator-(difference_type diff) const
backward jump operator
Definition: AASequence.h:211
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
const ConstIterator operator+(difference_type diff) const
forward jump operator
Definition: AASequence.h:200
const Residue * pointer
Definition: AASequence.h:134
difference_type position_
Definition: AASequence.h:382
const ResidueModification * c_term_mod_
Definition: AASequence.h:630
const Residue & const_reference
Definition: AASequence.h:264
const ResidueModification * n_term_mod_
Definition: AASequence.h:628
ConstIterator & operator=(const ConstIterator &rhs)
assignment operator
Definition: AASequence.h:174
TermSpecificity
Position where the modification is allowed to occur.
Definition: ResidueModification.h:95
Residue & reference
Definition: AASequence.h:130
String toString(const T &i)
fallback template for general purpose using Boost::Karma; more specializations below ...
Definition: StringUtils.h:85
std::vector< const Residue * >::difference_type difference_type
Definition: AASequence.h:268
const Residue * const_pointer
Definition: AASequence.h:266
const Iterator operator-(difference_type diff) const
backward jump operator
Definition: AASequence.h:343
const Iterator operator+(difference_type diff) const
forward jump operator
Definition: AASequence.h:332
ConstIterator(const AASequence::Iterator &rhs)
copy constructor from Iterator
Definition: AASequence.h:160
bool operator!=(const ConstIterator &rhs) const
inequality operator
Definition: AASequence.h:223
bool operator!=(const Iterator &rhs) const
inequality operator
Definition: AASequence.h:355
Representation of a residue.
Definition: Residue.h:61
Iterator(std::vector< const Residue *> *vec_ptr, difference_type position)
detailed constructor with pointer to the vector and offset position
Definition: AASequence.h:279
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Iterator begin()
Definition: AASequence.h:583
difference_type operator-(Iterator rhs) const
Definition: AASequence.h:337
ConstIterator for AASequence.
Definition: AASequence.h:123
ConstIterator end() const
Definition: AASequence.h:589
Representation of a modification.
Definition: ResidueModification.h:76
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
Residue value_type
Definition: AASequence.h:133
difference_type position_
Definition: AASequence.h:250
const_iterator ConstIterator
Const Iterator.
Definition: String.h:72
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
const Residue * const_pointer
Definition: AASequence.h:131
virtual ~ConstIterator()
destructor
Definition: AASequence.h:167
pointer operator->()
mutable dereference operator
Definition: AASequence.h:326
Iterator & operator++()
increment operator
Definition: AASequence.h:361
Size< TNeedle >::Type position(const PatternAuxData< TNeedle > &dh)
Definition: AhoCorasickAmbiguous.h:561
difference_type operator-(ConstIterator rhs) const
Definition: AASequence.h:205
Iterator & operator=(const Iterator &rhs)
assignment operator
Definition: AASequence.h:300
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
with N-terminus and C-terminus
Definition: Residue.h:152
void setModification(int location, int max_size, String modification, OpenMS::AASequence &aas)
helper function that sets a modification on a AASequence object
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
Iterator end()
Definition: AASequence.h:587
std::random_access_iterator_tag iterator_category
Definition: AASequence.h:135
const Residue & const_reference
Definition: AASequence.h:129
bool operator==(const ConstIterator &rhs) const
equality comparator
Definition: AASequence.h:217
virtual ~Iterator()
destructor
Definition: AASequence.h:293
DPosition< D, TCoordinateType > operator*(DPosition< D, TCoordinateType > position, typename DPosition< D, TCoordinateType >::CoordinateType scalar)
Scalar multiplication (a bit inefficient)
Definition: DPosition.h:427
ResidueType
Definition: Residue.h:150
std::vector< const Residue * > * vector_
Definition: AASequence.h:379
Iterator class for AASequence.
Definition: AASequence.h:258
Iterator & operator--()
decrement operator
Definition: AASequence.h:368
std::vector< const Residue * >::difference_type difference_type
Definition: AASequence.h:132
A more convenient string class.
Definition: String.h:58
std::vector< const Residue * > peptide_
Definition: AASequence.h:626
const_pointer operator->() const
dereference operator
Definition: AASequence.h:320
Representation of an empirical formula.
Definition: EmpiricalFormula.h:82
const_pointer operator->() const
dereference operator
Definition: AASequence.h:194
const std::vector< const Residue * > * vector_
Definition: AASequence.h:247
Iterator(const Iterator &rhs)
copy constructor
Definition: AASequence.h:286
Residue & reference
Definition: AASequence.h:265
std::istream & operator>>(std::istream &os, const AASequence &peptide)
ConstIterator begin() const
Definition: AASequence.h:585
ConstIterator & operator++()
increment operator
Definition: AASequence.h:229
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
const Residue * pointer
Definition: AASequence.h:267
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
bool operator==(const Iterator &rhs) const
equality comparator
Definition: AASequence.h:349
ConstIterator(const ConstIterator &rhs)
copy constructor
Definition: AASequence.h:153