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