35 #ifndef OPENMS_CHEMISTRY_AASEQUENCE_H
36 #define OPENMS_CHEMISTRY_AASEQUENCE_H
51 class ResidueModification;
106 position_ = position;
111 vector_(rhs.vector_),
112 position_(rhs.position_)
118 vector_(rhs.vector_),
119 position_(rhs.position_)
147 return *(*vector_)[position_];
153 return (*vector_)[position_];
239 position_ = position;
244 vector_(rhs.vector_),
245 position_(rhs.position_)
273 return *(*vector_)[position_];
279 return (*vector_)[position_];
285 return (*vector_)[position_];
291 return Iterator(vector_, position_ + diff);
302 return Iterator(vector_, position_ - diff);
368 String toUnmodifiedString()
const;
374 void setNTerminalModification(
const String& modification);
377 const String& getNTerminalModification()
const;
380 void setCTerminalModification(
const String& modification);
383 const String& getCTerminalModification()
const;
438 bool has(
const Residue& residue)
const;
443 bool hasSubsequence(
const AASequence& peptide)
const;
447 bool hasPrefix(
const AASequence& peptide)
const;
451 bool hasSuffix(
const AASequence& peptide)
const;
454 bool hasNTerminalModification()
const;
457 bool hasCTerminalModification()
const;
460 bool isModified()
const;
463 bool isModified(
Size index)
const;
504 bool permissive =
true);
513 bool permissive =
true);
529 bool permissive =
true);
Iterator & operator=(const Iterator &rhs)
assignment operator
Definition: AASequence.h:257
virtual ~ConstIterator()
destructor
Definition: AASequence.h:124
A more convenient string class.
Definition: String.h:57
difference_type position_
Definition: AASequence.h:207
const Residue & const_reference
Definition: AASequence.h:221
ConstIterator & operator=(const ConstIterator &rhs)
assignment operator
Definition: AASequence.h:131
Iterator end()
Definition: AASequence.h:482
Residue & reference
Definition: AASequence.h:87
Representation of a modification.
Definition: ResidueModification.h:65
difference_type operator-(ConstIterator rhs) const
Definition: AASequence.h:162
const Residue * const_pointer
Definition: AASequence.h:88
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:128
Representation of a peptide/protein sequence.
Definition: AASequence.h:70
Iterator begin()
Definition: AASequence.h:478
std::vector< const Residue * > * vector_
Definition: AASequence.h:336
Iterator & operator++()
increment operator
Definition: AASequence.h:318
std::random_access_iterator_tag iterator_category
Definition: AASequence.h:92
Representation of a residue.
Definition: Residue.h:62
difference_type position_
Definition: AASequence.h:339
const_iterator ConstIterator
Const Iterator.
Definition: String.h:71
ConstIterator(const ConstIterator &rhs)
copy constructor
Definition: AASequence.h:110
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:90
bool operator!=(const ConstIterator &rhs) const
inequality operator
Definition: AASequence.h:180
Iterator(const Iterator &rhs)
copy constructor
Definition: AASequence.h:243
const_pointer operator->() const
dereference operator
Definition: AASequence.h:277
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
pointer operator->()
mutable dereference operator
Definition: AASequence.h:283
DPosition< D, TCoordinateType > operator*(DPosition< D, TCoordinateType > position, typename DPosition< D, TCoordinateType >::CoordinateType scalar)
Scalar multiplication (a bit inefficient)
Definition: DPosition.h:421
const Iterator operator-(difference_type diff) const
backward jump operator
Definition: AASequence.h:300
Definition: Residue.h:361
std::vector< const Residue * >::difference_type difference_type
Definition: AASequence.h:225
ConstIterator for AASequence.
Definition: AASequence.h:80
const ConstIterator operator-(difference_type diff) const
backward jump operator
Definition: AASequence.h:168
const Iterator operator+(difference_type diff) const
forward jump operator
Definition: AASequence.h:289
bool operator!=(const Iterator &rhs) const
inequality operator
Definition: AASequence.h:312
Iterator & operator--()
decrement operator
Definition: AASequence.h:325
Residue & reference
Definition: AASequence.h:222
const Residue * const_pointer
Definition: AASequence.h:223
std::vector< const Residue * > peptide_
Definition: AASequence.h:516
std::vector< const Residue * >::difference_type difference_type
Definition: AASequence.h:89
std::istream & operator>>(std::istream &os, const AASequence &peptide)
ConstIterator & operator--()
decrement operator
Definition: AASequence.h:193
ResidueType
Definition: Residue.h:359
ConstIterator(const AASequence::Iterator &rhs)
copy constructor from Iterator
Definition: AASequence.h:117
const ResidueModification * n_term_mod_
Definition: AASequence.h:518
bool operator==(const ConstIterator &rhs) const
equality comparator
Definition: AASequence.h:174
const ResidueModification * c_term_mod_
Definition: AASequence.h:520
const ConstIterator operator+(difference_type diff) const
forward jump operator
Definition: AASequence.h:157
difference_type operator-(Iterator rhs) const
Definition: AASequence.h:294
Iterator class for AASequence.
Definition: AASequence.h:215
ConstIterator(const std::vector< const Residue * > *vec_ptr, difference_type position)
detailed constructor with pointer to the vector and offset position
Definition: AASequence.h:103
const Residue * pointer
Definition: AASequence.h:224
Iterator(std::vector< const Residue * > *vec_ptr, difference_type position)
detailed constructor with pointer to the vector and offset position
Definition: AASequence.h:236
const Residue & const_reference
Definition: AASequence.h:86
const_pointer operator->() const
dereference operator
Definition: AASequence.h:151
String toString(T i)
toString functions (single argument)
Definition: StringUtils.h:68
const Residue * pointer
Definition: AASequence.h:91
const std::vector< const Residue * > * vector_
Definition: AASequence.h:204
int Int
Signed integer type.
Definition: Types.h:96
ConstIterator end() const
Definition: AASequence.h:484
bool operator==(const Iterator &rhs) const
equality comparator
Definition: AASequence.h:306
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:51
ConstIterator begin() const
Definition: AASequence.h:480
virtual ~Iterator()
destructor
Definition: AASequence.h:250
ConstIterator & operator++()
increment operator
Definition: AASequence.h:186