35 #ifndef OPENMS_CHEMISTRY_AASEQUENCE_H 36 #define OPENMS_CHEMISTRY_AASEQUENCE_H 51 class ResidueModification;
141 ConstIterator(
const std::vector<const Residue*>* vec_ptr, difference_type position)
144 position_ = position;
149 vector_(rhs.vector_),
150 position_(rhs.position_)
156 vector_(rhs.vector_),
157 position_(rhs.position_)
185 return *(*vector_)[position_];
191 return (*vector_)[position_];
274 Iterator(std::vector<const Residue*>* vec_ptr, difference_type position)
277 position_ = position;
282 vector_(rhs.vector_),
283 position_(rhs.position_)
311 return *(*vector_)[position_];
317 return (*vector_)[position_];
323 return (*vector_)[position_];
329 return Iterator(vector_, position_ + diff);
340 return Iterator(vector_, position_ - diff);
414 String toUnmodifiedString()
const;
423 String toBracketString(
bool integer_mass =
true,
const std::vector<String> & fixed_modifications = std::vector<String>())
const;
430 void setNTerminalModification(
const String& modification);
433 const String& getNTerminalModificationName()
const;
439 void setCTerminalModification(
const String& modification);
442 const String& getCTerminalModificationName()
const;
497 bool has(
const Residue& residue)
const;
502 bool hasSubsequence(
const AASequence& peptide)
const;
506 bool hasPrefix(
const AASequence& peptide)
const;
510 bool hasSuffix(
const AASequence& peptide)
const;
513 bool hasNTerminalModification()
const;
516 bool hasCTerminalModification()
const;
519 bool isModified()
const;
562 bool permissive =
true);
573 bool permissive =
true);
617 bool permissive =
true);
Iterator & operator=(const Iterator &rhs)
assignment operator
Definition: AASequence.h:295
const Iterator operator+(difference_type diff) const
forward jump operator
Definition: AASequence.h:327
virtual ~ConstIterator()
destructor
Definition: AASequence.h:162
A more convenient string class.
Definition: String.h:57
difference_type position_
Definition: AASequence.h:245
ConstIterator(const std::vector< const Residue *> *vec_ptr, difference_type position)
detailed constructor with pointer to the vector and offset position
Definition: AASequence.h:141
const Residue & const_reference
Definition: AASequence.h:259
bool operator!=(const ConstIterator &rhs) const
inequality operator
Definition: AASequence.h:218
ConstIterator & operator=(const ConstIterator &rhs)
assignment operator
Definition: AASequence.h:169
unsigned int UInt
Unsigned integer type.
Definition: Types.h:95
Iterator end()
Definition: AASequence.h:538
Residue & reference
Definition: AASequence.h:125
Representation of a modification.
Definition: ResidueModification.h:77
const Residue * const_pointer
Definition: AASequence.h:126
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
difference_type operator-(ConstIterator rhs) const
Definition: AASequence.h:200
const_pointer operator->() const
dereference operator
Definition: AASequence.h:189
Representation of a peptide/protein sequence.
Definition: AASequence.h:108
Iterator begin()
Definition: AASequence.h:534
bool operator!=(const Iterator &rhs) const
inequality operator
Definition: AASequence.h:350
ConstIterator end() const
Definition: AASequence.h:540
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
std::vector< const Residue * > * vector_
Definition: AASequence.h:374
Iterator & operator++()
increment operator
Definition: AASequence.h:356
std::random_access_iterator_tag iterator_category
Definition: AASequence.h:130
Representation of a residue.
Definition: Residue.h:62
difference_type position_
Definition: AASequence.h:377
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
bool operator==(const ConstIterator &rhs) const
equality comparator
Definition: AASequence.h:212
const_iterator ConstIterator
Const Iterator.
Definition: String.h:71
ConstIterator(const ConstIterator &rhs)
copy constructor
Definition: AASequence.h:148
void setModification(int location, int max_size, String modification, OpenMS::AASequence &aas)
helper function that sets a modification on a AASequence object
Residue value_type
Definition: AASequence.h:128
Iterator(const Iterator &rhs)
copy constructor
Definition: AASequence.h:281
difference_type operator-(Iterator rhs) const
Definition: AASequence.h:332
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
TermSpecificity
Position where the modification is allowed to occur.
Definition: ResidueModification.h:96
pointer operator->()
mutable dereference operator
Definition: AASequence.h:321
DPosition< D, TCoordinateType > operator*(DPosition< D, TCoordinateType > position, typename DPosition< D, TCoordinateType >::CoordinateType scalar)
Scalar multiplication (a bit inefficient)
Definition: DPosition.h:421
Definition: Residue.h:146
const_pointer operator->() const
dereference operator
Definition: AASequence.h:315
std::vector< const Residue * >::difference_type difference_type
Definition: AASequence.h:263
ConstIterator for AASequence.
Definition: AASequence.h:118
Iterator & operator--()
decrement operator
Definition: AASequence.h:363
Residue & reference
Definition: AASequence.h:260
const Residue * const_pointer
Definition: AASequence.h:261
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
std::vector< const Residue * > peptide_
Definition: AASequence.h:576
std::vector< const Residue * >::difference_type difference_type
Definition: AASequence.h:127
std::istream & operator>>(std::istream &os, const AASequence &peptide)
ConstIterator & operator--()
decrement operator
Definition: AASequence.h:231
ResidueType
Definition: Residue.h:144
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:128
ConstIterator(const AASequence::Iterator &rhs)
copy constructor from Iterator
Definition: AASequence.h:155
bool operator==(const Iterator &rhs) const
equality comparator
Definition: AASequence.h:344
const ResidueModification * n_term_mod_
Definition: AASequence.h:578
const ResidueModification * c_term_mod_
Definition: AASequence.h:580
Iterator class for AASequence.
Definition: AASequence.h:253
const Residue * pointer
Definition: AASequence.h:262
const ConstIterator operator-(difference_type diff) const
backward jump operator
Definition: AASequence.h:206
const Residue & const_reference
Definition: AASequence.h:124
Iterator(std::vector< const Residue *> *vec_ptr, difference_type position)
detailed constructor with pointer to the vector and offset position
Definition: AASequence.h:274
const ConstIterator operator+(difference_type diff) const
forward jump operator
Definition: AASequence.h:195
const Iterator operator-(difference_type diff) const
backward jump operator
Definition: AASequence.h:338
String toString(T i)
toString functions (single argument)
Definition: StringUtils.h:69
const Residue * pointer
Definition: AASequence.h:129
const std::vector< const Residue * > * vector_
Definition: AASequence.h:242
int Int
Signed integer type.
Definition: Types.h:103
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:51
ConstIterator begin() const
Definition: AASequence.h:536
virtual ~Iterator()
destructor
Definition: AASequence.h:288
ConstIterator & operator++()
increment operator
Definition: AASequence.h:224