OpenMS  3.0.0
AreaIterator.h
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31 // $Maintainer: Timo Sachsenberg$
32 // $Authors: Marc Sturm $
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34 
35 #pragma once
36 
37 // OpenMS includes
38 #include <OpenMS/CONCEPT/Types.h>
40 
41 // STL includes
42 #include <iterator>
43 
44 namespace OpenMS
45 {
46  namespace Internal
47  {
56  template <class ValueT, class ReferenceT, class PointerT, class SpectrumIteratorT, class PeakIteratorT>
57  class AreaIterator :
58  public std::iterator<std::forward_iterator_tag, ValueT>
59  {
60 public:
61  typedef double CoordinateType;
62  typedef ValueT PeakType;
63  typedef SpectrumIteratorT SpectrumIteratorType;
64  typedef PeakIteratorT PeakIteratorType;
65 
69  typedef ValueT value_type;
72  typedef ReferenceT reference;
74  typedef PointerT pointer;
76  typedef unsigned int difference_type;
78 
81  first_(first),
82  current_scan_(begin),
83  end_scan_(end),
84  low_mz_(low_mz),
85  high_mz_(high_mz),
86  is_end_(false)
87  {
88  nextScan_();
89  }
90 
93  first_(),
94  current_scan_(),
95  end_scan_(),
96  current_peak_(),
97  end_peak_(),
98  low_mz_(0.0),
99  high_mz_(0.0),
100  is_end_(true)
101  {}
102 
105  {}
106 
108  AreaIterator(const AreaIterator & rhs) :
109  first_(rhs.first_),
111  end_scan_(rhs.end_scan_),
113  end_peak_(rhs.end_peak_),
114  low_mz_(rhs.low_mz_),
115  high_mz_(rhs.high_mz_),
116  is_end_(rhs.is_end_)
117  {}
118 
121  {
122  if (&rhs == this) return *this;
123 
124  is_end_ = rhs.is_end_;
125  //only copy iterators, if the assigned iterator is not the end iterator
126  if (!is_end_)
127  {
128  first_ = rhs.first_;
130  end_scan_ = rhs.end_scan_;
132  end_peak_ = rhs.end_peak_;
133  low_mz_ = rhs.low_mz_;
134  high_mz_ = rhs.high_mz_;
135  }
136 
137  return *this;
138  }
139 
141  bool operator==(const AreaIterator & rhs) const
142  {
143  //Both end iterators => equal
144  if (is_end_ && rhs.is_end_) return true;
145 
146  //Normal and end iterator => not equal
147  if (!is_end_ && rhs.is_end_) return false;
148 
149  if (is_end_ && !rhs.is_end_) return false;
150 
151  //Equality of pointed to peak addresses
152  return &(*current_peak_) == &(*(rhs.current_peak_));
153  }
154 
156  bool operator!=(const AreaIterator & rhs) const
157  {
158  return !(*this == rhs);
159  }
160 
163  {
164  //no increment if this is the end iterator
165  if (is_end_) return *this;
166 
167  ++current_peak_;
168  // test whether we arrived at the end of the current scan
169  if (current_peak_ == end_peak_)
170  {
171  ++current_scan_;
172  nextScan_();
173  }
174  return *this;
175  }
176 
179  {
180  AreaIterator tmp(*this);
181  ++(*this);
182  return tmp;
183  }
184 
187  {
188  return current_peak_.operator*();
189  }
190 
193  {
194  return current_peak_.operator->();
195  }
196 
199  {
200  return current_scan_->getRT();
201  }
202 
204  inline PeakIndex getPeakIndex() const
205  {
206  if (is_end_)
207  {
208  return PeakIndex();
209  }
210  else
211  {
213  }
214  }
215 
216 private:
217  //Advances to the iterator to the next valid peak in the next valid spectrum
218  void nextScan_()
219  {
220  while (true)
221  {
222  //if (current_scan_ != end_scan_) std::cout << "RT: " << current_scan_->getRT() << std::endl;
223  while (current_scan_ != end_scan_ && current_scan_->getMSLevel() != 1)
224  {
225  ++current_scan_;
226  }
227  if (current_scan_ == end_scan_)
228  {
229  is_end_ = true;
230  return;
231  }
232  current_peak_ = current_scan_->MZBegin(low_mz_);
233  end_peak_ = current_scan_->MZEnd(high_mz_);
234  if (current_peak_ != end_peak_)
235  {
236  return;
237  }
238  ++current_scan_;
239  }
240  }
241 
257  bool is_end_;
258 
259  };
260 
261  }
262 }
263 
OpenMS::Internal::AreaIterator::pointer
PointerT pointer
The pointer type as returned by operator->()
Definition: AreaIterator.h:74
PeakIndex.h
double
OpenMS::Internal::AreaIterator
Forward iterator for an area of peaks in an experiment.
Definition: AreaIterator.h:57
Types.h
OpenMS::Internal::AreaIterator::current_scan_
SpectrumIteratorType current_scan_
Iterator to the current spectrum.
Definition: AreaIterator.h:245
OpenMS::Internal::AreaIterator::~AreaIterator
~AreaIterator()
Destructor.
Definition: AreaIterator.h:104
OpenMS::Internal::AreaIterator::is_end_
bool is_end_
Flag that indicates that this iterator is the end iterator.
Definition: AreaIterator.h:257
OpenMS::Internal::AreaIterator::AreaIterator
AreaIterator()
Default constructor (for the end iterator)
Definition: AreaIterator.h:92
OpenMS::Internal::AreaIterator::SpectrumIteratorType
SpectrumIteratorT SpectrumIteratorType
Definition: AreaIterator.h:63
OpenMS::Internal::AreaIterator::reference
ReferenceT reference
The reference type as returned by operator*()
Definition: AreaIterator.h:72
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::Internal::AreaIterator::value_type
ValueT value_type
The iterator's value type.
Definition: AreaIterator.h:70
OpenMS::Internal::AreaIterator::AreaIterator
AreaIterator(SpectrumIteratorType first, SpectrumIteratorType begin, SpectrumIteratorType end, CoordinateType low_mz, CoordinateType high_mz)
Constructor for the begin iterator.
Definition: AreaIterator.h:80
OpenMS::PeakIndex
Index of a peak or feature.
Definition: PeakIndex.h:50
OpenMS::Internal::AreaIterator::operator->
pointer operator->() const
Dereferencing of this pointer yields the underlying peak.
Definition: AreaIterator.h:192
OpenMS::Internal::AreaIterator::first_
SpectrumIteratorType first_
Iterator to the first scan of the map (needed to calculate the index)
Definition: AreaIterator.h:243
OpenMS::Internal::AreaIterator::PeakIteratorType
PeakIteratorT PeakIteratorType
Definition: AreaIterator.h:64
OpenMS::Internal::AreaIterator::end_peak_
PeakIteratorType end_peak_
Past-the-end iterator of peaks in the current spectrum.
Definition: AreaIterator.h:251
OpenMS::Internal::AreaIterator::nextScan_
void nextScan_()
Definition: AreaIterator.h:218
OpenMS::Internal::AreaIterator::operator!=
bool operator!=(const AreaIterator &rhs) const
Test for inequality.
Definition: AreaIterator.h:156
OpenMS::Internal::AreaIterator::operator++
AreaIterator & operator++()
Step forward by one (prefix operator)
Definition: AreaIterator.h:162
OpenMS::Internal::AreaIterator::getPeakIndex
PeakIndex getPeakIndex() const
returns the PeakIndex corresponding to the current iterator position
Definition: AreaIterator.h:204
OpenMS::Internal::AreaIterator::operator*
reference operator*() const
Dereferencing of this pointer yields the underlying peak.
Definition: AreaIterator.h:186
OpenMS::Internal::AreaIterator::end_scan_
SpectrumIteratorType end_scan_
Past-the-end iterator of spectra.
Definition: AreaIterator.h:247
OpenMS::Internal::AreaIterator::operator=
AreaIterator & operator=(const AreaIterator &rhs)
Assignment operator.
Definition: AreaIterator.h:120
OpenMS::Internal::AreaIterator::low_mz_
CoordinateType low_mz_
low m/z boundary
Definition: AreaIterator.h:253
OpenMS::Internal::AreaIterator::current_peak_
PeakIteratorType current_peak_
Iterator to the current peak.
Definition: AreaIterator.h:249
OpenMS::Internal::AreaIterator::PeakType
ValueT PeakType
Definition: AreaIterator.h:62
OpenMS::Internal::AreaIterator::AreaIterator
AreaIterator(const AreaIterator &rhs)
Copy constructor.
Definition: AreaIterator.h:108
OpenMS::Internal::AreaIterator::getRT
CoordinateType getRT() const
returns the retention time of the current scan
Definition: AreaIterator.h:198
OpenMS::Internal::AreaIterator::difference_type
unsigned int difference_type
The difference type.
Definition: AreaIterator.h:76
OpenMS::Internal::AreaIterator::operator++
AreaIterator operator++(int)
Step forward by one (postfix operator)
Definition: AreaIterator.h:178
OpenMS::Internal::AreaIterator::operator==
bool operator==(const AreaIterator &rhs) const
Test for equality.
Definition: AreaIterator.h:141
OpenMS::Internal::AreaIterator::high_mz_
CoordinateType high_mz_
high m/z boundary
Definition: AreaIterator.h:255
OpenMS::Internal::AreaIterator::CoordinateType
double CoordinateType
Definition: AreaIterator.h:61