131 vector_(rhs.vector_),
132 position_(rhs.position_)
138 vector_(rhs.vector_),
139 position_(rhs.position_)
165 return *(*vector_)[position_];
171 return (*vector_)[position_];
194 return (std::tie(vector_, position_) ==
223 const std::vector<const Ribonucleotide*>*
vector_;
254 Iterator(std::vector<const Ribonucleotide*>* vec_ptr,
263 vector_(rhs.vector_),
264 position_(rhs.position_)
290 return *(*vector_)[position_];
296 return (*vector_)[position_];
302 return (*vector_)[position_];
308 return Iterator(vector_, position_ + diff);
319 return Iterator(vector_, position_ - diff);
325 return (std::tie(vector_,position_) ==
370 NASequence(std::vector<const Ribonucleotide*> s,
381 void setSequence(
const std::vector<const Ribonucleotide*>& seq);
417 bool hasFivePrimeMod()
const;
420 bool hasThreePrimeMod()
const;
481 friend OPENMS_DLLAPI std::ostream&
operator<<(std::ostream& os,
512 std::vector<const Ribonucleotide*>
seq_;
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
MS:1001240 Non-identified ion.
Definition: NASequence.h:87
W ion, added for nucleic acid support.
Definition: NASequence.h:89
std::vector< const Ribonucleotide * > & getSequence()
Definition: NASequence.h:388
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
MS:1001230 C-alpha/carbonyl carbon bond.
Definition: NASequence.h:81
Iterator of NASequence class.
Definition: NASequence.h:235
virtual ~ConstIterator()
destructor
Definition: NASequence.h:144
ConstIterator cend() const
Definition: NASequence.h:450
value_type & reference
Definition: NASequence.h:243
difference_type operator-(ConstIterator rhs) const
Definition: NASequence.h:180
ConstIterator & operator--()
decrement operator
Definition: NASequence.h:212
internal, without any termini
Definition: NASequence.h:73
difference_type position_
Definition: NASequence.h:356
bool operator!=(const ConstIterator &rhs) const
inequality operator
Definition: NASequence.h:199
Iterator(const Iterator &rhs)
copy constructor
Definition: NASequence.h:262
const Iterator operator-(difference_type diff) const
backward jump operator
Definition: NASequence.h:317
String toString(const T &i)
fallback template for general purpose using Boost::Karma; more specializations below ...
Definition: StringUtils.h:85
const ConstIterator operator-(difference_type diff) const
backward jump operator
Definition: NASequence.h:186
no stored annotation
Definition: NASequence.h:88
Iterator(std::vector< const Ribonucleotide *> *vec_ptr, difference_type position)
detailed constructor with pointer to the vector and offset position
Definition: NASequence.h:254
ConstIterator begin() const
Definition: NASequence.h:430
D ion, added for nucleic acid support.
Definition: NASequence.h:91
MS:1001228 amide/C-alpha bond up to the C-terminus.
Definition: NASequence.h:79
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Iterator & operator=(const Iterator &rhs)
assignment operator
Definition: NASequence.h:274
const_pointer operator->() const
dereference operator
Definition: NASequence.h:169
MS:1001233 y ion without ammonia.
Definition: NASequence.h:86
MS:1001220 peptide bond up to the C-terminus.
Definition: NASequence.h:80
std::vector< const value_type * >::difference_type difference_type
Definition: NASequence.h:246
const_iterator ConstIterator
Const Iterator.
Definition: String.h:72
const Ribonucleotide *const & operator[](size_t index) const
Definition: NASequence.h:407
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
const value_type & const_reference
Definition: NASequence.h:108
NASFragmentType
an enum of all possible fragment ion types
Definition: NASequence.h:70
const_pointer operator->() const
dereference operator
Definition: NASequence.h:294
bool operator==(const ConstIterator &rhs) const
equality comparator
Definition: NASequence.h:192
MS:1001222 b ion without water.
Definition: NASequence.h:83
ConstIterator & operator=(const ConstIterator &rhs)
assignment operator
Definition: NASequence.h:149
std::vector< const value_type * >::difference_type difference_type
Definition: NASequence.h:111
difference_type position_
Definition: NASequence.h:226
const value_type & const_reference
Definition: NASequence.h:242
only 3' terminus
Definition: NASequence.h:75
const std::vector< const Ribonucleotide * > * vector_
Definition: NASequence.h:223
Size< TNeedle >::Type position(const PatternAuxData< TNeedle > &dh)
Definition: AhoCorasickAmbiguous.h:561
ConstIterator cbegin() const
Definition: NASequence.h:445
bool operator==(const Iterator &rhs) const
equality comparator
Definition: NASequence.h:323
const value_type * const_pointer
Definition: NASequence.h:244
A ion with base loss, added for nucleic acid support.
Definition: NASequence.h:90
Iterator & operator--()
decrement operator
Definition: NASequence.h:343
ConstIterator(const std::vector< const Ribonucleotide *> *vec_ptr, difference_type position)
detailed constructor with pointer to the vector and offset position
Definition: NASequence.h:122
Ribonucleotide value_type
Definition: NASequence.h:107
ConstIterator end() const
Definition: NASequence.h:440
ConstIterator of NASequence class.
Definition: NASequence.h:104
std::random_access_iterator_tag iterator_category
Definition: NASequence.h:113
MS:1001232 b ion without ammonia.
Definition: NASequence.h:85
ConstIterator(const NASequence::Iterator &rhs)
copy constructor from Iterator
Definition: NASequence.h:137
ConstIterator(const ConstIterator &rhs)
copy constructor
Definition: NASequence.h:130
MS:1001229 N-terminus up to the C-alpha/carbonyl carbon bond.
Definition: NASequence.h:76
pointer operator->()
mutable dereference operator
Definition: NASequence.h:300
ConstIterator & operator++()
increment operator
Definition: NASequence.h:205
value_type & reference
Definition: NASequence.h:109
MS:1001224 N-terminus up to the peptide bond.
Definition: NASequence.h:77
bool operator!=(const Iterator &rhs) const
inequality operator
Definition: NASequence.h:330
DPosition< D, TCoordinateType > operator*(DPosition< D, TCoordinateType > position, typename DPosition< D, TCoordinateType >::CoordinateType scalar)
Scalar multiplication (a bit inefficient)
Definition: DPosition.h:427
virtual ~Iterator()
destructor
Definition: NASequence.h:269
only 5' terminus
Definition: NASequence.h:74
const ConstIterator operator+(difference_type diff) const
forward jump operator
Definition: NASequence.h:175
Representation of a ribonucleotide (modified or unmodified)
Definition: Ribonucleotide.h:51
MS:1001223 y ion without water.
Definition: NASequence.h:84
const std::vector< const Ribonucleotide * > & getSequence() const
Definition: NASequence.h:383
A more convenient string class.
Definition: String.h:58
difference_type operator-(Iterator rhs) const
Definition: NASequence.h:311
std::vector< const Ribonucleotide * > * vector_
Definition: NASequence.h:353
Representation of an empirical formula.
Definition: EmpiricalFormula.h:82
const Ribonucleotide *& operator[](size_t index)
getter / setter for sequence elements (C++ container style)
Definition: NASequence.h:402
std::vector< const Ribonucleotide * > seq_
Definition: NASequence.h:512
const value_type * pointer
Definition: NASequence.h:245
const Iterator operator+(difference_type diff) const
forward jump operator
Definition: NASequence.h:306
Iterator & operator++()
increment operator
Definition: NASequence.h:336
const value_type * const_pointer
Definition: NASequence.h:110
MS:1001231 N-terminus up to the amide/C-alpha bond.
Definition: NASequence.h:78
Representation of a nucleic acid sequence.
Definition: NASequence.h:62
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
Ribonucleotide value_type
Definition: NASequence.h:241
MS:1001523 Precursor ion.
Definition: NASequence.h:82
const value_type * pointer
Definition: NASequence.h:112
Iterator end()
Definition: NASequence.h:435
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Iterator begin()
iterators
Definition: NASequence.h:425