132 return *(*vector_)[position_];
138 return (*vector_)[position_];
161 return (std::tie(vector_, position_) == std::tie(rhs.
vector_, rhs.
position_));
188 const std::vector<const Ribonucleotide*>*
vector_;
221 position_ = position;
253 return *(*vector_)[position_];
259 return (*vector_)[position_];
265 return (*vector_)[position_];
271 return Iterator(vector_, position_ + diff);
282 return Iterator(vector_, position_ - diff);
288 return (std::tie(vector_, position_) == std::tie(rhs.
vector_, rhs.
position_));
515 std::vector<const Ribonucleotide*>
seq_;
ConstIterator of NASequence class.
Definition: NASequence.h:75
ConstIterator(const std::vector< const Ribonucleotide * > *vec_ptr, difference_type position)
detailed constructor with pointer to the vector and offset position
Definition: NASequence.h:92
const_pointer operator->() const
dereference operator
Definition: NASequence.h:136
const value_type * const_pointer
Definition: NASequence.h:80
const ConstIterator operator-(difference_type diff) const
backward jump operator
Definition: NASequence.h:153
ConstIterator & operator=(const ConstIterator &rhs)
assignment operator
Definition: NASequence.h:116
bool operator!=(const ConstIterator &rhs) const
inequality operator
Definition: NASequence.h:165
const ConstIterator operator+(difference_type diff) const
forward jump operator
Definition: NASequence.h:142
ConstIterator()=default
default constructor
ConstIterator & operator--()
decrement operator
Definition: NASequence.h:178
std::random_access_iterator_tag iterator_category
Definition: NASequence.h:83
bool operator==(const ConstIterator &rhs) const
equality comparator
Definition: NASequence.h:159
Ribonucleotide value_type
Definition: NASequence.h:77
ConstIterator & operator++()
increment operator
Definition: NASequence.h:171
ConstIterator(const NASequence::Iterator &rhs)
copy constructor from Iterator
Definition: NASequence.h:104
difference_type position_
Definition: NASequence.h:191
std::vector< const value_type * >::difference_type difference_type
Definition: NASequence.h:81
ConstIterator(const ConstIterator &rhs)
copy constructor
Definition: NASequence.h:99
value_type & reference
Definition: NASequence.h:79
const std::vector< const Ribonucleotide * > * vector_
Definition: NASequence.h:188
const value_type * pointer
Definition: NASequence.h:82
const_reference operator*() const
dereference operator
Definition: NASequence.h:130
virtual ~ConstIterator()
destructor
Definition: NASequence.h:109
difference_type operator-(ConstIterator rhs) const
Definition: NASequence.h:147
const value_type & const_reference
Definition: NASequence.h:78
Iterator of NASequence class.
Definition: NASequence.h:201
const_pointer operator->() const
dereference operator
Definition: NASequence.h:257
const value_type * const_pointer
Definition: NASequence.h:208
pointer operator->()
mutable dereference operator
Definition: NASequence.h:263
const Iterator operator+(difference_type diff) const
forward jump operator
Definition: NASequence.h:269
Iterator & operator--()
decrement operator
Definition: NASequence.h:305
virtual ~Iterator()
destructor
Definition: NASequence.h:230
Iterator(std::vector< const Ribonucleotide * > *vec_ptr, difference_type position)
detailed constructor with pointer to the vector and offset position
Definition: NASequence.h:218
difference_type operator-(Iterator rhs) const
Definition: NASequence.h:274
Iterator & operator=(const Iterator &rhs)
assignment operator
Definition: NASequence.h:237
Ribonucleotide value_type
Definition: NASequence.h:205
bool operator==(const Iterator &rhs) const
equality comparator
Definition: NASequence.h:286
difference_type position_
Definition: NASequence.h:317
std::vector< const value_type * >::difference_type difference_type
Definition: NASequence.h:210
value_type & reference
Definition: NASequence.h:207
Iterator(const Iterator &rhs)
copy constructor
Definition: NASequence.h:225
const value_type * pointer
Definition: NASequence.h:209
const_reference operator*() const
dereference operator
Definition: NASequence.h:251
bool operator!=(const Iterator &rhs) const
inequality operator
Definition: NASequence.h:292
const Iterator operator-(difference_type diff) const
backward jump operator
Definition: NASequence.h:280
Iterator & operator++()
increment operator
Definition: NASequence.h:298
std::vector< const Ribonucleotide * > * vector_
Definition: NASequence.h:314
const value_type & const_reference
Definition: NASequence.h:206
Representation of a nucleic acid sequence.
Definition: NASequence.h:34
ConstIterator cend() const
Definition: NASequence.h:409
virtual ~NASequence()=default
bool operator<(const NASequence &rhs) const
less operator
bool hasThreePrimeMod() const
NASequence getSuffix(Size length) const
Return sequence suffix of the given length (not start index!)
void setSequence(const std::vector< const Ribonucleotide * > &seq)
getter / setter for sequence
std::string toString() const
Iterator begin()
iterators
Definition: NASequence.h:384
bool operator==(const NASequence &rhs) const
destructor
bool hasFivePrimeMod() const
5' and 3' modifications
const std::vector< const Ribonucleotide * > & getSequence() const
Definition: NASequence.h:342
double getMonoWeight(NASFragmentType type=Full, Int charge=0) const
utility functions
friend std::ostream & operator<<(std::ostream &os, const NASequence &seq)
void setThreePrimeMod(const RibonucleotideChainEnd *r)
NASequence getPrefix(Size length) const
Return sequence prefix of the given length (not end index!)
static void parseString_(const String &s, NASequence &nas)
ConstIterator end() const
Definition: NASequence.h:399
const RibonucleotideChainEnd * getThreePrimeMod() const
bool operator!=(const NASequence &rhs) const
not quality
NASequence(std::vector< const Ribonucleotide * > s, const RibonucleotideChainEnd *five_prime, const RibonucleotideChainEnd *three_prime)
full constructor
void set(size_t index, const Ribonucleotide *r)
getter / setter for ribonucleotide elements (easily wrapped using pyOpenMS)
static NASequence fromString(const char *s)
create NASequence object by parsing a C string (character array)
EmpiricalFormula getFormula(NASFragmentType type=Full, Int charge=0) const
Get the formula for a NASequence.
NASFragmentType
an enum of all possible fragment ion types
Definition: NASequence.h:41
@ AminusB
A ion with base loss, added for nucleic acid support.
Definition: NASequence.h:60
@ YIon
MS:1001220 peptide bond up to the C-terminus.
Definition: NASequence.h:50
@ XIon
MS:1001228 amide/C-alpha bond up to the C-terminus.
Definition: NASequence.h:49
@ ZIon
MS:1001230 C-alpha/carbonyl carbon bond.
Definition: NASequence.h:51
@ WIon
W ion, added for nucleic acid support.
Definition: NASequence.h:59
@ BIonMinusH20
MS:1001222 b ion without water.
Definition: NASequence.h:53
@ BIonMinusNH3
MS:1001232 b ion without ammonia.
Definition: NASequence.h:55
@ AIon
MS:1001229 N-terminus up to the C-alpha/carbonyl carbon bond.
Definition: NASequence.h:46
@ Precursor
MS:1001523 Precursor ion.
Definition: NASequence.h:52
@ YIonMinusH20
MS:1001223 y ion without water.
Definition: NASequence.h:54
@ NonIdentified
MS:1001240 Non-identified ion.
Definition: NASequence.h:57
@ BIon
MS:1001224 N-terminus up to the peptide bond.
Definition: NASequence.h:47
@ ThreePrime
only 3' terminus
Definition: NASequence.h:45
@ CIon
MS:1001231 N-terminus up to the amide/C-alpha bond.
Definition: NASequence.h:48
@ YIonMinusNH3
MS:1001233 y ion without ammonia.
Definition: NASequence.h:56
@ Internal
internal, without any termini
Definition: NASequence.h:43
@ Unannotated
no stored annotation
Definition: NASequence.h:58
@ FivePrime
only 5' terminus
Definition: NASequence.h:44
@ DIon
D ion, added for nucleic acid support.
Definition: NASequence.h:61
static NASequence fromString(const String &s)
create NASequence object by parsing an OpenMS string
const Ribonucleotide * get(size_t index)
Definition: NASequence.h:355
static String::ConstIterator parseMod_(const String::ConstIterator str_it, const String &str, NASequence &nas)
Parses modifications in square brackets.
NASequence & operator=(NASequence &&) &=default
Move assignment operator.
ConstIterator cbegin() const
Definition: NASequence.h:404
double getAverageWeight(NASFragmentType type=Full, Int charge=0) const
Get the Average Weight of a NASequence. NB returns the uncharged mass + or - proton masses to match t...
Iterator end()
Definition: NASequence.h:394
std::vector< const Ribonucleotide * > & getSequence()
Definition: NASequence.h:347
NASequence getSubsequence(Size start=0, Size length=Size(-1)) const
Return subsequence with given starting position and length.
const Ribonucleotide *& operator[](size_t index)
getter / setter for sequence elements (C++ container style)
Definition: NASequence.h:361
const RibonucleotideChainEnd * getFivePrimeMod() const
std::vector< const Ribonucleotide * > seq_
Definition: NASequence.h:515
void setFivePrimeMod(const RibonucleotideChainEnd *r)
ConstIterator begin() const
Definition: NASequence.h:389
const Ribonucleotide *const & operator[](size_t index) const
Definition: NASequence.h:366
NASequence & operator=(const NASequence &) &=default
Copy assignment operator.
NASequence(NASequence &&)=default
Move constructor.
NASequence(const NASequence &)=default
default constructor
Representation of a ribonucleotide (modified or unmodified)
Definition: Ribonucleotide.h:26
A more convenient string class.
Definition: String.h:34
const_iterator ConstIterator
Const Iterator.
Definition: String.h:46
int Int
Signed integer type.
Definition: Types.h:72
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:97
bool operator==(const IDBoostGraph::ProteinGroup &lhs, const IDBoostGraph::ProteinGroup &rhs)
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19