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ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h
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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 {
68  struct BinaryDataArray
70  {
72  //DataProcessingPtr dataProcessingPtr;
73 
75  std::vector<double> data;
76  };
77  OPENSWATHALGO_DLLAPI typedef boost::shared_ptr<BinaryDataArray> BinaryDataArrayPtr;
78 
81  {
83  std::size_t index;
85  std::string id;
87  index()
88  {
89  }
90 
91  };
92  OPENSWATHALGO_DLLAPI typedef boost::shared_ptr<ChromatogramMeta> ChromatogramMetaPtr;
93 
95  struct Chromatogram
96  {
98  std::size_t defaultArrayLength;
99 
101  //DataProcessingPtr dataProcessingPtr;
103  //Precursor precursor;
105  //Product product;
106 
108  std::vector<BinaryDataArrayPtr> binaryDataArrayPtrs;
109 
113  {
114  initvec();
115  }
116 
117 private:
118 
119  void initvec()
120  {
121  for (std::size_t i = 0; i < defaultArrayLength; ++i)
122  {
124  binaryDataArrayPtrs[i] = empty;
125  }
126  }
127 
128 public:
131  {
132  return binaryDataArrayPtrs[0];
133  }
134 
136  {
137  binaryDataArrayPtrs[0] = data;
138  }
139 
142  {
143  return binaryDataArrayPtrs[1];
144  }
145 
147  {
148  binaryDataArrayPtrs[1] = data;
149  }
150 
151  };
152  OPENSWATHALGO_DLLAPI typedef boost::shared_ptr<Chromatogram> ChromatogramPtr;
153 
156  {
158  size_t index;
159 
161  std::string id;
162 
163  double RT;
164 
165  int ms_level;
166 
168  index(0)
169  {
170  }
171 
172  };
173 
175  struct Spectrum
176  {
178  std::size_t defaultArrayLength;
179 
181 private:
182  std::vector<BinaryDataArrayPtr> binaryDataArrayPtrs;
183 public:
187  {
188  initvec();
189  }
190 
191 private:
192 
193  void initvec()
194  {
195  for (std::size_t i = 0; i < defaultArrayLength; ++i)
196  {
198  binaryDataArrayPtrs[i] = empty;
199  }
200  }
201 
202 public:
203 
206  {
207  return binaryDataArrayPtrs[0];
208  }
209 
211  {
212  binaryDataArrayPtrs[0] = data;
213  }
214 
217  {
218  return binaryDataArrayPtrs[1];
219  }
220 
222  {
223  binaryDataArrayPtrs[1] = data;
224  }
225 
226  };
227  OPENSWATHALGO_DLLAPI typedef boost::shared_ptr<Spectrum> SpectrumPtr;
228 } //end Namespace OpenSwath
229 
230 #endif // OPENMS_ANALYSIS_OPENSWATH_OPENSWATHALGO_DATAACCESS_DATASTRUCTURES_H
The datastructures used by the OpenSwath interfaces.
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:69
BinaryDataArrayPtr getIntensityArray()
get intensity array (may be null)
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:141
OPENSWATHALGO_DLLAPI typedef boost::shared_ptr< ChromatogramMeta > ChromatogramMetaPtr
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:92
size_t index
the zero-based, consecutive index of the spectrum in the SpectrumList.
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:158
ChromatogramMeta()
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:86
Chromatogram()
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:110
OPENSWATHALGO_DLLAPI typedef boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:152
The structure that captures the generation of a peak list (including the underlying acquisitions) ...
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:175
A single chromatogram.
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:95
int ms_level
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:165
Identifying information for a chromatogram.
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:80
std::vector< BinaryDataArrayPtr > binaryDataArrayPtrs
list of binary data arrays.
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:182
std::string id
a unique identifier for this spectrum.
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:161
std::size_t defaultArrayLength
default length of binary data arrays contained in this element.
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:178
BinaryDataArrayPtr getMZArray() const
get m/z array (may be null)
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:205
Identifying information for a spectrum.
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:155
double RT
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:163
void initvec()
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:193
void setIntensityArray(BinaryDataArrayPtr data)
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:146
OPENSWATHALGO_DLLAPI typedef boost::shared_ptr< Spectrum > SpectrumPtr
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:227
std::size_t defaultArrayLength
default length of binary data arrays contained in this element.
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:98
Spectrum()
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:184
OPENSWATHALGO_DLLAPI typedef boost::shared_ptr< BinaryDataArray > BinaryDataArrayPtr
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:77
void setTimeArray(BinaryDataArrayPtr data)
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:135
SpectrumMeta()
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:167
BinaryDataArrayPtr getTimeArray()
get time array (may be null)
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:130
void initvec()
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:119
BinaryDataArrayPtr getIntensityArray() const
get intensity array (may be null)
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:216
std::size_t index
the zero-based, consecutive index of the chromatogram in the ChromatogramList.
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:83
void setMZArray(BinaryDataArrayPtr data)
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:210
std::string id
a unique identifier for this chromatogram.
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:85
void setIntensityArray(BinaryDataArrayPtr data)
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:221
std::vector< BinaryDataArrayPtr > binaryDataArrayPtrs
this attribute can optionally reference the &#39;id&#39; of the appropriate dataProcessing.
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:108
std::vector< double > data
this optional attribute may reference the &#39;id&#39; attribute of the appropiate dataProcessing.
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:75

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:12 using doxygen 1.8.5