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OpenMS
2.6.0
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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;
456 double getMonoWeight(NASFragmentType type = Full,
Int charge = 0)
const;
457 double getAverageWeight(NASFragmentType type = Full,
Int charge = 0)
const;
481 friend OPENMS_DLLAPI std::ostream&
operator<<(std::ostream& os,
512 std::vector<const Ribonucleotide*>
seq_;
const std::vector< const Ribonucleotide * > & getSequence() const
Definition: NASequence.h:383
ConstIterator begin() const
Definition: NASequence.h:430
MS:1001523 Precursor ion.
Definition: NASequence.h:82
ConstIterator of NASequence class.
Definition: NASequence.h:104
const ConstIterator operator-(difference_type diff) const
backward jump operator
Definition: NASequence.h:186
MS:1001233 y ion without ammonia.
Definition: NASequence.h:86
MS:1001232 b ion without ammonia.
Definition: NASequence.h:85
std::vector< const value_type * >::difference_type difference_type
Definition: NASequence.h:246
Iterator(std::vector< const Ribonucleotide * > *vec_ptr, difference_type position)
detailed constructor with pointer to the vector and offset position
Definition: NASequence.h:254
std::vector< const Ribonucleotide * > & getSequence()
Definition: NASequence.h:388
ConstIterator & operator--()
decrement operator
Definition: NASequence.h:212
const typedef value_type * pointer
Definition: NASequence.h:112
const Iterator operator-(difference_type diff) const
backward jump operator
Definition: NASequence.h:317
Representation of a nucleic acid sequence.
Definition: NASequence.h:62
DPosition< D, TCoordinateType > operator*(DPosition< D, TCoordinateType > position, typename DPosition< D, TCoordinateType >::CoordinateType scalar)
Scalar multiplication (a bit inefficient)
Definition: DPosition.h:427
difference_type position_
Definition: NASequence.h:356
D ion, added for nucleic acid support.
Definition: NASequence.h:91
Representation of a ribonucleotide (modified or unmodified)
Definition: Ribonucleotide.h:51
NASFragmentType
an enum of all possible fragment ion types
Definition: NASequence.h:70
ConstIterator(const NASequence::Iterator &rhs)
copy constructor from Iterator
Definition: NASequence.h:137
only 5' terminus
Definition: NASequence.h:74
std::vector< const Ribonucleotide * > seq_
Definition: NASequence.h:512
const Ribonucleotide *const & operator[](size_t index) const
Definition: NASequence.h:407
only 3' terminus
Definition: NASequence.h:75
A more convenient string class.
Definition: String.h:59
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
no stored annotation
Definition: NASequence.h:88
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
MS:1001230 C-alpha/carbonyl carbon bond.
Definition: NASequence.h:81
std::vector< const Ribonucleotide * > * vector_
Definition: NASequence.h:353
const typedef value_type * const_pointer
Definition: NASequence.h:110
std::random_access_iterator_tag iterator_category
Definition: NASequence.h:113
bool operator<(const QTCluster &q1, const QTCluster &q2)
MS:1001223 y ion without water.
Definition: NASequence.h:84
ConstIterator & operator++()
increment operator
Definition: NASequence.h:205
difference_type operator-(Iterator rhs) const
Definition: NASequence.h:311
difference_type position_
Definition: NASequence.h:226
MS:1001231 N-terminus up to the amide/C-alpha bond.
Definition: NASequence.h:78
const_pointer operator->() const
dereference operator
Definition: NASequence.h:294
Ribonucleotide value_type
Definition: NASequence.h:107
ConstIterator cend() const
Definition: NASequence.h:450
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
difference_type operator-(ConstIterator rhs) const
Definition: NASequence.h:180
ConstIterator end() const
Definition: NASequence.h:440
std::vector< const value_type * >::difference_type difference_type
Definition: NASequence.h:111
ConstIterator(const ConstIterator &rhs)
copy constructor
Definition: NASequence.h:130
Ribonucleotide value_type
Definition: NASequence.h:241
const typedef value_type & const_reference
Definition: NASequence.h:242
virtual ~ConstIterator()
destructor
Definition: NASequence.h:144
bool operator==(const Iterator &rhs) const
equality comparator
Definition: NASequence.h:323
bool operator!=(const ConstIterator &rhs) const
inequality operator
Definition: NASequence.h:199
const Ribonucleotide * get(size_t index)
Definition: NASequence.h:396
MS:1001222 b ion without water.
Definition: NASequence.h:83
const ConstIterator operator+(difference_type diff) const
forward jump operator
Definition: NASequence.h:175
value_type & reference
Definition: NASequence.h:109
pointer operator->()
mutable dereference operator
Definition: NASequence.h:300
value_type & reference
Definition: NASequence.h:243
const Ribonucleotide *& operator[](size_t index)
getter / setter for sequence elements (C++ container style)
Definition: NASequence.h:402
bool operator!=(const Iterator &rhs) const
inequality operator
Definition: NASequence.h:330
MS:1001240 Non-identified ion.
Definition: NASequence.h:87
W ion, added for nucleic acid support.
Definition: NASequence.h:89
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
internal, without any termini
Definition: NASequence.h:73
Iterator of NASequence class.
Definition: NASequence.h:235
ConstIterator & operator=(const ConstIterator &rhs)
assignment operator
Definition: NASequence.h:149
MS:1001228 amide/C-alpha bond up to the C-terminus.
Definition: NASequence.h:79
const_pointer operator->() const
dereference operator
Definition: NASequence.h:169
String toString(const T &i)
fallback template for general purpose using Boost::Karma; more specializations below
Definition: StringUtils.h:127
MS:1001224 N-terminus up to the peptide bond.
Definition: NASequence.h:77
Iterator end()
Definition: NASequence.h:435
const std::vector< const Ribonucleotide * > * vector_
Definition: NASequence.h:223
Iterator & operator++()
increment operator
Definition: NASequence.h:336
MS:1001220 peptide bond up to the C-terminus.
Definition: NASequence.h:80
bool operator==(const IDBoostGraph::ProteinGroup &lhs, const IDBoostGraph::ProteinGroup &rhs)
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
Iterator(const Iterator &rhs)
copy constructor
Definition: NASequence.h:262
Iterator & operator--()
decrement operator
Definition: NASequence.h:343
Iterator & operator=(const Iterator &rhs)
assignment operator
Definition: NASequence.h:274
ConstIterator cbegin() const
Definition: NASequence.h:445
bool operator==(const ConstIterator &rhs) const
equality comparator
Definition: NASequence.h:192
A ion with base loss, added for nucleic acid support.
Definition: NASequence.h:90
const typedef value_type * const_pointer
Definition: NASequence.h:244
MS:1001229 N-terminus up to the C-alpha/carbonyl carbon bond.
Definition: NASequence.h:76
const Iterator operator+(difference_type diff) const
forward jump operator
Definition: NASequence.h:306
Size< TNeedle >::Type position(const PatternAuxData< TNeedle > &dh)
Definition: AhoCorasickAmbiguous.h:561
const_iterator ConstIterator
Const Iterator.
Definition: String.h:73
const typedef value_type * pointer
Definition: NASequence.h:245
virtual ~Iterator()
destructor
Definition: NASequence.h:269
const typedef value_type & const_reference
Definition: NASequence.h:108
Iterator begin()
iterators
Definition: NASequence.h:425