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34 
35 #ifndef OPENMS_ANALYSIS_OPENSWATH_OPENSWATHALGO_DATAACCESS_DATASTRUCTURES_H
36 #define OPENMS_ANALYSIS_OPENSWATH_OPENSWATHALGO_DATAACCESS_DATASTRUCTURES_H
37 
38 #include <string>
39 #include <vector>
40 #include <boost/shared_ptr.hpp>
41 
42 #include <OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/OpenSwathAlgoConfig.h>
43 
44 namespace OpenSwath
45 {
67  struct OPENSWATHALGO_DLLAPI OSBinaryDataArray
69  {
71  //DataProcessingPtr dataProcessingPtr;
72 
74  std::vector<double> data;
75  };
77  typedef boost::shared_ptr<BinaryDataArray> BinaryDataArrayPtr;
78 
80  struct OPENSWATHALGO_DLLAPI OSChromatogramMeta
81  {
83  std::size_t index;
85  std::string id;
87  index()
88  {
89  }
90 
91  };
93  typedef boost::shared_ptr<ChromatogramMeta> ChromatogramMetaPtr;
94 
96  struct OPENSWATHALGO_DLLAPI OSChromatogram
97  {
99  std::size_t defaultArrayLength;
100 
102  //DataProcessingPtr dataProcessingPtr;
104  //Precursor precursor;
106  //Product product;
107 
109  std::vector<BinaryDataArrayPtr> binaryDataArrayPtrs;
110 
112  defaultArrayLength(2),
113  binaryDataArrayPtrs(defaultArrayLength)
114  {
115  initvec();
116  }
117 
118 private:
119 
120  void initvec()
121  {
122  for (std::size_t i = 0; i < defaultArrayLength; ++i)
123  {
124  BinaryDataArrayPtr empty(new BinaryDataArray);
125  binaryDataArrayPtrs[i] = empty;
126  }
127  }
128 
129 public:
131  BinaryDataArrayPtr getTimeArray()
132  {
133  return binaryDataArrayPtrs[0];
134  }
135 
136  void setTimeArray(BinaryDataArrayPtr data)
137  {
138  binaryDataArrayPtrs[0] = data;
139  }
140 
142  BinaryDataArrayPtr getIntensityArray()
143  {
144  return binaryDataArrayPtrs[1];
145  }
146 
147  void setIntensityArray(BinaryDataArrayPtr data)
148  {
149  binaryDataArrayPtrs[1] = data;
150  }
151 
152  };
154  typedef boost::shared_ptr<Chromatogram> ChromatogramPtr;
155 
157  struct OPENSWATHALGO_DLLAPI OSSpectrumMeta
158  {
160  size_t index;
161 
163  std::string id;
164 
165  double RT;
166 
167  int ms_level;
168 
170  index(0)
171  {
172  }
173 
174  };
176  typedef boost::shared_ptr<SpectrumMeta> SpectrumMetaPtr;
177 
179  struct OPENSWATHALGO_DLLAPI OSSpectrum
180  {
182  std::size_t defaultArrayLength;
183 
185 private:
186  std::vector<BinaryDataArrayPtr> binaryDataArrayPtrs;
187 public:
189  defaultArrayLength(2),
190  binaryDataArrayPtrs(defaultArrayLength)
191  {
192  initvec();
193  }
194 
195 private:
196 
197  void initvec()
198  {
199  for (std::size_t i = 0; i < defaultArrayLength; ++i)
200  {
201  BinaryDataArrayPtr empty(new BinaryDataArray);
202  binaryDataArrayPtrs[i] = empty;
203  }
204  }
205 
206 public:
207 
209  BinaryDataArrayPtr getMZArray() const
210  {
211  return binaryDataArrayPtrs[0];
212  }
213 
214  void setMZArray(BinaryDataArrayPtr data)
215  {
216  binaryDataArrayPtrs[0] = data;
217  }
218 
220  BinaryDataArrayPtr getIntensityArray() const
221  {
222  return binaryDataArrayPtrs[1];
223  }
224 
225  void setIntensityArray(BinaryDataArrayPtr data)
226  {
227  binaryDataArrayPtrs[1] = data;
228  }
229 
230  };
232  typedef boost::shared_ptr<Spectrum> SpectrumPtr;
233 } //end Namespace OpenSwath
234 
235 #endif // OPENMS_ANALYSIS_OPENSWATH_OPENSWATHALGO_DATAACCESS_DATASTRUCTURES_H
void setTimeArray(BinaryDataArrayPtr data)
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:136
std::size_t defaultArrayLength
default length of binary data arrays contained in this element.
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:99
BinaryDataArrayPtr getTimeArray()
get time array (may be null)
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:131
Identifying information for a spectrum.
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:157
OSChromatogramMeta ChromatogramMeta
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:92
void initvec()
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:120
std::string id
a unique identifier for this chromatogram.
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:85
OSBinaryDataArray BinaryDataArray
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:76
boost::shared_ptr< ChromatogramMeta > ChromatogramMetaPtr
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:93
int ms_level
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:167
std::size_t defaultArrayLength
default length of binary data arrays contained in this element.
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:182
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:232
OSChromatogram Chromatogram
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:153
void setMZArray(BinaryDataArrayPtr data)
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:214
std::vector< BinaryDataArrayPtr > binaryDataArrayPtrs
list of binary data arrays.
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:186
The structure that captures the generation of a peak list (including the underlying acquisitions) ...
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:179
boost::shared_ptr< SpectrumMeta > SpectrumMetaPtr
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:176
boost::shared_ptr< BinaryDataArray > BinaryDataArrayPtr
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:77
OSChromatogram()
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:111
std::size_t index
the zero-based, consecutive index of the chromatogram in the ChromatogramList.
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:83
std::vector< BinaryDataArrayPtr > binaryDataArrayPtrs
this attribute can optionally reference the &#39;id&#39; of the appropriate dataProcessing.
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:109
void setIntensityArray(BinaryDataArrayPtr data)
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:225
double RT
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:165
BinaryDataArrayPtr getIntensityArray()
get intensity array (may be null)
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:142
Definition: MRMScoring.h:51
BinaryDataArrayPtr getMZArray() const
get m/z array (may be null)
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:209
void initvec()
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:197
void setIntensityArray(BinaryDataArrayPtr data)
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:147
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:154
OSSpectrumMeta SpectrumMeta
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:175
OSSpectrum Spectrum
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:231
A single chromatogram.
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:96
OSSpectrumMeta()
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:169
Identifying information for a chromatogram.
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:80
std::vector< double > data
this optional attribute may reference the &#39;id&#39; attribute of the appropriate dataProcessing.
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:74
OSSpectrum()
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:188
BinaryDataArrayPtr getIntensityArray() const
get intensity array (may be null)
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:220
size_t index
the zero-based, consecutive index of the spectrum in the SpectrumList.
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:160
std::string id
a unique identifier for this spectrum.
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:163
OSChromatogramMeta()
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:86
The datastructures used by the OpenSwath interfaces.
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:68

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Nov 1 2016 16:34:46 using doxygen 1.8.11