OpenMS
AASequence.h
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1 // Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Timo Sachsenberg $
6 // $Authors: Andreas Bertsch, Timo Sachsenberg $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
13 #include <OpenMS/CONCEPT/Types.h>
16 
17 #include <vector>
18 #include <iosfwd>
19 #include <map>
20 
21 namespace OpenMS
22 {
23 
85  class OPENMS_DLLAPI AASequence
86  {
87 public:
88 
89  class Iterator;
90 
95  class OPENMS_DLLAPI ConstIterator
96  {
97  public:
98  // TODO Iterator constructor for ConstIterator
99 
100  typedef const Residue& const_reference;
101  typedef Residue& reference;
102  typedef const Residue* const_pointer;
103  typedef std::vector<const Residue*>::difference_type difference_type;
105  typedef const Residue* pointer;
106  typedef std::random_access_iterator_tag iterator_category;
107 
112  ConstIterator() = default;
113 
115  ConstIterator(const std::vector<const Residue*>* vec_ptr, difference_type position)
116  : vector_{vec_ptr},
117  position_{position}
118  {
119  }
120 
122  ConstIterator(const ConstIterator& rhs) = default;
123 
126  vector_(rhs.vector_),
127  position_(rhs.position_)
128  {
129  }
130 
132  virtual ~ConstIterator() = default;
133 
135 
137  ConstIterator& operator=(const ConstIterator& rhs) = default;
138 
144  {
145  return *(*vector_)[position_];
146  }
147 
150  {
151  return (*vector_)[position_];
152  }
153 
156  {
157  return ConstIterator(vector_, position_ + diff);
158  }
159 
161  {
162  return position_ - rhs.position_;
163  }
164 
167  {
168  return ConstIterator(vector_, position_ - diff);
169  }
170 
172  bool operator==(const ConstIterator& rhs) const
173  {
174  return vector_ == rhs.vector_ && position_ == rhs.position_;
175  }
176 
178  bool operator!=(const ConstIterator& rhs) const
179  {
180  return vector_ != rhs.vector_ || position_ != rhs.position_;
181  }
182 
185  {
186  ++position_;
187  return *this;
188  }
189 
192  {
193  --position_;
194  return *this;
195  }
196 
198 
199 protected:
200 
201  // pointer to the AASequence vector
202  const std::vector<const Residue*>* vector_ {};
203 
204  // position in the AASequence vector
205  difference_type position_ {};
206  };
207 
208 
213  class OPENMS_DLLAPI Iterator
214  {
215 public:
216 
218 
219  typedef const Residue& const_reference;
220  typedef Residue& reference;
221  typedef const Residue* const_pointer;
222  typedef const Residue* pointer;
223  typedef std::vector<const Residue*>::difference_type difference_type;
224 
229  Iterator() = default;
230 
232  Iterator(std::vector<const Residue*>* vec_ptr, difference_type position)
233  : vector_ {vec_ptr},
234  position_{position}
235  {
236  }
237 
239  Iterator(const Iterator& rhs) = default;
240 
242  virtual ~Iterator() = default;
243 
245 
248  {
249  if (this != &rhs)
250  {
251  position_ = rhs.position_;
252  vector_ = rhs.vector_;
253  }
254  return *this;
255  }
256 
262  {
263  return *(*vector_)[position_];
264  }
265 
268  {
269  return (*vector_)[position_];
270  }
271 
274  {
275  return (*vector_)[position_];
276  }
277 
280  {
281  return Iterator(vector_, position_ + diff);
282  }
283 
285  {
286  return position_ - rhs.position_;
287  }
288 
291  {
292  return Iterator(vector_, position_ - diff);
293  }
294 
296  bool operator==(const Iterator& rhs) const
297  {
298  return vector_ == rhs.vector_ && position_ == rhs.position_;
299  }
300 
302  bool operator!=(const Iterator& rhs) const
303  {
304  return vector_ != rhs.vector_ || position_ != rhs.position_;
305  }
306 
309  {
310  ++position_;
311  return *this;
312  }
313 
316  {
317  --position_;
318  return *this;
319  }
320 
322 
323 protected:
324 
325  // pointer to the AASequence vector
326  std::vector<const Residue*>* vector_ {};
327 
328  // position in the AASequence vector
329  difference_type position_ {};
330  };
331 
335 
338 
340  AASequence(const AASequence&) = default;
341 
343  AASequence(AASequence&&) noexcept = default;
344 
346  virtual ~AASequence();
348 
350  AASequence& operator=(const AASequence&) = default;
351 
353  AASequence& operator=(AASequence&&) = default; // TODO: add noexcept (gcc 4.8 bug)
354 
356  bool empty() const;
357 
361 
373  String toString() const;
374 
376  String toUnmodifiedString() const;
377 
386  String toUniModString() const;
387 
406  String toBracketString(bool integer_mass = true,
407  bool mass_delta = false,
408  const std::vector<String> & fixed_modifications = std::vector<String>()) const;
409 
412  void setModification(Size index, const String& modification);
413 
415  void setModification(Size index, const Residue* modification);
416 
418  void setModification(Size index, const ResidueModification* modification);
419 
422  void setModification(Size index, const ResidueModification& modification);
423 
425  void setModificationByDiffMonoMass(Size index, double diffMonoMass);
426 
429  void setNTerminalModification(const String& modification);
430 
432  void setNTerminalModification(const ResidueModification* modification);
433 
435  void setNTerminalModification(const ResidueModification& mod);
436 
438  void setNTerminalModificationByDiffMonoMass(double diffMonoMass, bool protein_term);
439 
441  const String& getNTerminalModificationName() const;
442 
444  const ResidueModification* getNTerminalModification() const;
445 
448  void setCTerminalModification(const String& modification);
449 
451  void setCTerminalModification(const ResidueModification* modification);
452 
454  void setCTerminalModification(const ResidueModification& mod);
455 
457  void setCTerminalModificationByDiffMonoMass(double diffMonoMass, bool protein_term);
458 
460  const String& getCTerminalModificationName() const;
461 
463  const ResidueModification* getCTerminalModification() const;
464 
466  const Residue& getResidue(Size index) const;
467 
469  EmpiricalFormula getFormula(Residue::ResidueType type = Residue::Full, Int charge = 0) const;
470 
472  double getAverageWeight(Residue::ResidueType type = Residue::Full, Int charge = 0) const;
473 
478  double getMonoWeight(Residue::ResidueType type = Residue::Full, Int charge = 0) const;
479 
485  double getMZ(Int charge, Residue::ResidueType type = Residue::Full) const;
486 
488  const Residue& operator[](Size index) const;
489 
491  AASequence operator+(const AASequence& peptide) const;
492 
494  AASequence& operator+=(const AASequence&);
495 
497  AASequence operator+(const Residue* residue) const;
498 
500  AASequence& operator+=(const Residue*);
501 
503  Size size() const;
504 
506  AASequence getPrefix(Size index) const;
507 
509  AASequence getSuffix(Size index) const;
510 
512  AASequence getSubsequence(Size index, UInt number) const;
513 
515  void getAAFrequencies(std::map<String, Size>& frequency_table) const;
516 
518 
523  bool has(const Residue& residue) const;
524 
527  bool hasSubsequence(const AASequence& peptide) const;
528 
531  bool hasPrefix(const AASequence& peptide) const;
532 
535  bool hasSuffix(const AASequence& peptide) const;
536 
538  bool hasNTerminalModification() const;
539 
541  bool hasCTerminalModification() const;
542 
544  bool isModified() const;
545 
547  bool operator==(const AASequence& rhs) const;
548 
550  bool operator<(const AASequence& rhs) const;
551 
553  bool operator!=(const AASequence& rhs) const;
555 
559  inline Iterator begin() { return Iterator(&peptide_, 0); }
560 
561  inline ConstIterator begin() const { return ConstIterator(&peptide_, 0); }
562 
563  inline Iterator end() { return Iterator(&peptide_, (Int) peptide_.size()); }
564 
565  inline ConstIterator end() const { return ConstIterator(&peptide_, (Int) peptide_.size()); }
567 
572  friend OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const AASequence& peptide);
573 
575  friend OPENMS_DLLAPI std::istream& operator>>(std::istream& is, const AASequence& peptide);
577 
586  static AASequence fromString(const String& s,
587  bool permissive = true);
588 
597  static AASequence fromString(const char* s,
598  bool permissive = true);
599 
600  protected:
601 
602  std::vector<const Residue*> peptide_;
603 
605 
607 
622  const String& str,
623  AASequence& aas,
624  const ResidueModification::TermSpecificity& specificity);
625 
640  const String& str,
641  AASequence& aas,
642  const ResidueModification::TermSpecificity& specificity);
643 
644  static void parseString_(const String& peptide, AASequence& aas,
645  bool permissive = true);
646  };
647 
648  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const AASequence& peptide);
649 
650  OPENMS_DLLAPI std::istream& operator>>(std::istream& os, const AASequence& peptide);
651 
652 } // namespace OpenMS
653 
654 
ConstIterator for AASequence.
Definition: AASequence.h:96
const_pointer operator->() const
dereference operator
Definition: AASequence.h:149
ConstIterator(const ConstIterator &rhs)=default
copy constructor
const ConstIterator operator-(difference_type diff) const
backward jump operator
Definition: AASequence.h:166
Residue value_type
Definition: AASequence.h:104
virtual ~ConstIterator()=default
destructor
ConstIterator(const std::vector< const Residue * > *vec_ptr, difference_type position)
detailed constructor with pointer to the vector and offset position
Definition: AASequence.h:115
bool operator!=(const ConstIterator &rhs) const
inequality operator
Definition: AASequence.h:178
ConstIterator(const AASequence::Iterator &rhs)
copy constructor from Iterator
Definition: AASequence.h:125
const ConstIterator operator+(difference_type diff) const
forward jump operator
Definition: AASequence.h:155
ConstIterator()=default
default constructor
ConstIterator & operator--()
decrement operator
Definition: AASequence.h:191
std::random_access_iterator_tag iterator_category
Definition: AASequence.h:106
bool operator==(const ConstIterator &rhs) const
equality comparator
Definition: AASequence.h:172
const std::vector< const Residue * > * vector_
Definition: AASequence.h:202
ConstIterator & operator++()
increment operator
Definition: AASequence.h:184
const Residue * const_pointer
Definition: AASequence.h:102
std::vector< const Residue * >::difference_type difference_type
Definition: AASequence.h:103
difference_type position_
Definition: AASequence.h:205
const Residue * pointer
Definition: AASequence.h:105
Residue & reference
Definition: AASequence.h:101
const Residue & const_reference
Definition: AASequence.h:100
const_reference operator*() const
dereference operator
Definition: AASequence.h:143
ConstIterator & operator=(const ConstIterator &rhs)=default
assignment operator
difference_type operator-(ConstIterator rhs) const
Definition: AASequence.h:160
Iterator class for AASequence.
Definition: AASequence.h:214
const_pointer operator->() const
dereference operator
Definition: AASequence.h:267
Iterator()=default
default constructor
pointer operator->()
mutable dereference operator
Definition: AASequence.h:273
virtual ~Iterator()=default
destructor
const Iterator operator+(difference_type diff) const
forward jump operator
Definition: AASequence.h:279
Iterator & operator--()
decrement operator
Definition: AASequence.h:315
Iterator(const Iterator &rhs)=default
copy constructor
std::vector< const Residue * > * vector_
Definition: AASequence.h:326
difference_type operator-(Iterator rhs) const
Definition: AASequence.h:284
Iterator & operator=(const Iterator &rhs)
assignment operator
Definition: AASequence.h:247
Iterator(std::vector< const Residue * > *vec_ptr, difference_type position)
detailed constructor with pointer to the vector and offset position
Definition: AASequence.h:232
bool operator==(const Iterator &rhs) const
equality comparator
Definition: AASequence.h:296
const Residue * const_pointer
Definition: AASequence.h:221
std::vector< const Residue * >::difference_type difference_type
Definition: AASequence.h:223
difference_type position_
Definition: AASequence.h:329
const Residue * pointer
Definition: AASequence.h:222
Residue & reference
Definition: AASequence.h:220
const Residue & const_reference
Definition: AASequence.h:219
const_reference operator*() const
dereference operator
Definition: AASequence.h:261
bool operator!=(const Iterator &rhs) const
inequality operator
Definition: AASequence.h:302
const Iterator operator-(difference_type diff) const
backward jump operator
Definition: AASequence.h:290
Iterator & operator++()
increment operator
Definition: AASequence.h:308
Representation of a peptide/protein sequence.
Definition: AASequence.h:86
std::vector< const Residue * > peptide_
Definition: AASequence.h:602
AASequence(const AASequence &)=default
Copy constructor.
static String::ConstIterator parseModSquareBrackets_(const String::ConstIterator str_it, const String &str, AASequence &aas, const ResidueModification::TermSpecificity &specificity)
Parses modifications in square brackets (a mass)
ConstIterator end() const
Definition: AASequence.h:565
static AASequence fromString(const char *s, bool permissive=true)
create AASequence object by parsing a C string (character array)
static String::ConstIterator parseModRoundBrackets_(const String::ConstIterator str_it, const String &str, AASequence &aas, const ResidueModification::TermSpecificity &specificity)
Parses modifications in round brackets (an identifier)
static void parseString_(const String &peptide, AASequence &aas, bool permissive=true)
friend std::ostream & operator<<(std::ostream &os, const AASequence &peptide)
writes a peptide to an output stream
const ResidueModification * c_term_mod_
Definition: AASequence.h:606
static AASequence fromString(const String &s, bool permissive=true)
create AASequence object by parsing an OpenMS string
Iterator end()
Definition: AASequence.h:563
AASequence(AASequence &&) noexcept=default
Move constructor.
const ResidueModification * n_term_mod_
Definition: AASequence.h:604
ConstIterator begin() const
Definition: AASequence.h:561
AASequence()
Default constructor.
friend std::istream & operator>>(std::istream &is, const AASequence &peptide)
reads a peptide from an input stream
Representation of an empirical formula.
Definition: EmpiricalFormula.h:59
Representation of a modification on an amino acid residue.
Definition: ResidueModification.h:53
TermSpecificity
Position where the modification is allowed to occur.
Definition: ResidueModification.h:72
Representation of an amino acid residue.
Definition: Residue.h:37
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
unsigned int UInt
Unsigned integer type.
Definition: Types.h:64
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:97
static bool hasPrefix(const String &this_s, const String &string)
Definition: StringUtilsSimple.h:86
static bool hasSuffix(const String &this_s, const String &string)
Definition: StringUtilsSimple.h:99
static String number(double d, UInt n)
Definition: StringUtils.h:191
static bool has(const String &this_s, Byte byte)
Definition: StringUtilsSimple.h:117
void setModification(int location, int max_size, const String &modification, OpenMS::AASequence &aas)
helper function that sets a modification on a AASequence object
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
std::istream & operator>>(std::istream &os, const AASequence &peptide)
const std::string & toString(const DriftTimeUnit value)