35 #ifndef OPENMS_CHEMISTRY_AASEQUENCE_H
36 #define OPENMS_CHEMISTRY_AASEQUENCE_H
120 position_ = position;
125 vector_(rhs.vector_),
126 position_(rhs.position_)
132 vector_(rhs.vector_),
133 position_(rhs.position_)
161 return *(*vector_)[position_];
167 return (*vector_)[position_];
253 position_ = position;
258 vector_(rhs.vector_),
259 position_(rhs.position_)
287 return *(*vector_)[position_];
293 return (*vector_)[position_];
299 return (*vector_)[position_];
305 return Iterator(vector_, position_ + diff);
316 return Iterator(vector_, position_ - diff);
390 String toUnmodifiedString()
const;
396 void setNTerminalModification(
const String & modification);
399 const String & getNTerminalModification()
const;
402 void setCTerminalModification(
const String & modification);
405 const String & getCTerminalModification()
const;
408 bool setStringSequence(
const String & sequence);
468 Size getNumberOf(
const String & residue)
const;
484 bool isValid()
const;
487 bool has(
const Residue & residue)
const;
490 bool has(
const String & name)
const;
494 bool hasSubsequence(
const AASequence & peptide)
const;
498 bool hasSubsequence(
const String & peptide)
const;
502 bool hasPrefix(
const AASequence & peptide)
const;
506 bool hasPrefix(
const String & peptide)
const;
510 bool hasSuffix(
const AASequence & peptide)
const;
514 bool hasSuffix(
const String & peptide)
const;
517 bool hasNTerminalModification()
const;
520 bool hasCTerminalModification()
const;
523 bool isModified()
const;
526 bool isModified(
Size index)
const;
529 bool operator==(
const AASequence & rhs)
const;
532 bool operator==(
const String & rhs)
const;
535 bool operator==(
const char * rhs)
const;
541 bool operator!=(
const AASequence & rhs)
const;
544 bool operator!=(
const String & rhs)
const;
547 bool operator!=(
const char * rhs)
const;
578 void parseString_(std::vector<const Residue *> & sequence,
const String & peptide);
String sequence_string_
Definition: AASequence.h:576
Iterator & operator=(const Iterator &rhs)
assignment operator
Definition: AASequence.h:271
virtual ~ConstIterator()
destructor
Definition: AASequence.h:138
std::vector< const Residue * >::difference_type difference_type
Definition: AASequence.h:239
A more convenient string class.
Definition: String.h:56
std::vector< const Residue * > * vector_
Definition: AASequence.h:350
difference_type position_
Definition: AASequence.h:221
const Residue & const_reference
Definition: AASequence.h:235
ConstIterator & operator=(const ConstIterator &rhs)
assignment operator
Definition: AASequence.h:145
Iterator end()
Definition: AASequence.h:557
Residue & reference
Definition: AASequence.h:101
Representation of a modification.
Definition: ResidueModification.h:58
std::ostream & operator<<(std::ostream &os, const ItraqQuantifier::ItraqQuantifierStats &stats)
difference_type operator-(ConstIterator rhs) const
Definition: AASequence.h:176
const Residue * const_pointer
Definition: AASequence.h:102
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:151
Representation of a peptide/protein sequence.
Definition: AASequence.h:84
Iterator begin()
Definition: AASequence.h:553
Iterator & operator++()
increment operator
Definition: AASequence.h:332
std::random_access_iterator_tag iterator_category
Definition: AASequence.h:106
Representation of a residue.
Definition: Residue.h:64
difference_type position_
Definition: AASequence.h:353
ConstIterator(const ConstIterator &rhs)
copy constructor
Definition: AASequence.h:124
void setModification(int location, int max_size, String modification, OpenMS::AASequence &aas)
helper function that sets a modifiction on a AASequence object
Residue value_type
Definition: AASequence.h:104
bool operator!=(const ConstIterator &rhs) const
inequality operator
Definition: AASequence.h:194
Iterator(const Iterator &rhs)
copy constructor
Definition: AASequence.h:257
const_pointer operator->() const
dereference operator
Definition: AASequence.h:291
pointer operator->()
mutable dereference operator
Definition: AASequence.h:297
DPosition< D, TCoordinateType > operator*(DPosition< D, TCoordinateType > position, typename DPosition< D, TCoordinateType >::CoordinateType scalar)
Scalar multiplication (a bit inefficient)
Definition: DPosition.h:415
const Iterator operator-(difference_type diff) const
backward jump operator
Definition: AASequence.h:314
Definition: Residue.h:363
ConstIterator for AASequence.
Definition: AASequence.h:94
const ConstIterator operator-(difference_type diff) const
backward jump operator
Definition: AASequence.h:182
const Iterator operator+(difference_type diff) const
forward jump operator
Definition: AASequence.h:303
bool operator!=(const Iterator &rhs) const
inequality operator
Definition: AASequence.h:326
Iterator & operator--()
decrement operator
Definition: AASequence.h:339
const std::vector< const Residue * > * vector_
Definition: AASequence.h:218
Residue & reference
Definition: AASequence.h:236
bool valid_
Definition: AASequence.h:582
const Residue * const_pointer
Definition: AASequence.h:237
std::vector< const Residue * >::difference_type difference_type
Definition: AASequence.h:103
residue data base which holds residues
Definition: ResidueDB.h:60
std::istream & operator>>(std::istream &os, const AASequence &peptide)
ConstIterator & operator--()
decrement operator
Definition: AASequence.h:207
ResidueType
Definition: Residue.h:361
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:144
ConstIterator(const AASequence::Iterator &rhs)
copy constructor from Iterator
Definition: AASequence.h:131
const ResidueModification * n_term_mod_
Definition: AASequence.h:584
bool operator==(const ConstIterator &rhs) const
equality comparator
Definition: AASequence.h:188
std::vector< const Residue * > peptide_
Definition: AASequence.h:574
const ResidueModification * c_term_mod_
Definition: AASequence.h:586
const ConstIterator operator+(difference_type diff) const
forward jump operator
Definition: AASequence.h:171
difference_type operator-(Iterator rhs) const
Definition: AASequence.h:308
Iterator class for AASequence.
Definition: AASequence.h:229
ConstIterator(const std::vector< const Residue * > *vec_ptr, difference_type position)
detailed constructor with pointer to the vector and offset position
Definition: AASequence.h:117
const Residue * pointer
Definition: AASequence.h:238
Iterator(std::vector< const Residue * > *vec_ptr, difference_type position)
detailed constructor with pointer to the vector and offset position
Definition: AASequence.h:250
const Residue & const_reference
Definition: AASequence.h:100
const_pointer operator->() const
dereference operator
Definition: AASequence.h:165
const Residue * pointer
Definition: AASequence.h:105
int Int
Signed integer type.
Definition: Types.h:100
ConstIterator end() const
Definition: AASequence.h:559
bool operator==(const Iterator &rhs) const
equality comparator
Definition: AASequence.h:320
Map class based on the STL map (containing serveral convenience functions)
Definition: Map.h:50
ConstIterator begin() const
Definition: AASequence.h:555
virtual ~Iterator()
destructor
Definition: AASequence.h:264
ConstIterator & operator++()
increment operator
Definition: AASequence.h:200