OpenMS  3.0.0
MzTabBase.h
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31 // $Maintainer: Oliver Alka $
32 // $Authors: Timo Sachsenberg, Oliver Alka $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
40 
41 
42 #include <map>
43 #include <vector>
44 #include <list>
45 #include <algorithm>
46 
47 
48 namespace OpenMS
49 {
58  {
64  };
65 
66  class OPENMS_DLLAPI MzTabDouble
67  {
68 public:
69  MzTabDouble();
70 
71  explicit MzTabDouble(const double v);
72 
73  void set(const double& value);
74 
75  double get() const;
76 
77  String toCellString() const;
78 
79  void fromCellString(const String& s);
80 
81  bool isNull() const;
82 
83  void setNull(bool b);
84 
85  bool isNaN() const;
86 
87  void setNaN();
88 
89  bool isInf() const;
90 
91  void setInf();
92 
93  ~MzTabDouble() = default;
94 
95  bool operator<(const MzTabDouble& rhs) const;
96 
97  bool operator==(const MzTabDouble& rhs) const;
98 
99 protected:
100  double value_;
102  };
103 
104  class OPENMS_DLLAPI MzTabDoubleList
105  {
106 public:
107  MzTabDoubleList() = default;
108 
109  bool isNull() const;
110 
111  void setNull(bool b);
112 
113  String toCellString() const;
114 
115  void fromCellString(const String& s);
116 
117  std::vector<MzTabDouble> get() const;
118 
119  void set(const std::vector<MzTabDouble>& entries);
120 
121  ~MzTabDoubleList() = default;
122 protected:
123  std::vector<MzTabDouble> entries_;
124  };
125 
126  class OPENMS_DLLAPI MzTabInteger
127  {
128 public:
129  MzTabInteger();
130 
131  explicit MzTabInteger(const int v);
132 
133  void set(const Int& value);
134 
135  Int get() const;
136 
137  String toCellString() const;
138 
139  void fromCellString(const String& s);
140 
141  bool isNull() const;
142 
143  void setNull(bool b);
144 
145  bool isNaN() const;
146 
147  void setNaN();
148 
149  bool isInf() const;
150 
151  void setInf();
152 
153  ~MzTabInteger() = default;
154 protected:
157  };
158 
159  class OPENMS_DLLAPI MzTabIntegerList
160  {
161 public:
162  MzTabIntegerList() = default;
163 
164  bool isNull() const;
165 
166  void setNull(bool b);
167 
168  String toCellString() const;
169 
170  void fromCellString(const String& s);
171 
172  std::vector<MzTabInteger> get() const;
173 
174  void set(const std::vector<MzTabInteger>& entries);
175 
176  ~MzTabIntegerList() = default;
177 protected:
178  std::vector<MzTabInteger> entries_;
179  };
180 
181  class OPENMS_DLLAPI MzTabBoolean
182  {
183 public:
184  MzTabBoolean();
185 
186  bool isNull() const;
187 
188  void setNull(bool b);
189 
190  explicit MzTabBoolean(bool v);
191 
192  void set(const bool& value);
193 
194  Int get() const;
195 
196  String toCellString() const;
197 
198  void fromCellString(const String& s);
199 
200  ~MzTabBoolean() = default;
201 protected:
202  int value_;
203  };
204 
205  class OPENMS_DLLAPI MzTabString
206  {
207 public:
208  MzTabString();
209 
210  explicit MzTabString(const String& s);
211 
212  bool isNull() const;
213 
214  void setNull(bool b);
215 
216  void set(const String& value);
217 
218  String get() const;
219 
220  String toCellString() const;
221 
222  void fromCellString(const String& s);
223 
224  ~MzTabString() = default;
225 protected:
227  };
228 
229  typedef std::pair<String, MzTabString> MzTabOptionalColumnEntry; //< column name (not null able), value (null able)
230 
231  class OPENMS_DLLAPI MzTabParameter
232  {
233  public:
234  MzTabParameter();
235 
236  bool isNull() const;
237 
238  void setNull(bool b);
239 
240  void setCVLabel(const String& CV_label);
241 
242  void setAccession(const String& accession);
243 
244  void setName(const String& name);
245 
246  void setValue(const String& value);
247 
248  String getCVLabel() const;
249 
250  String getAccession() const;
251 
252  String getName() const;
253 
254  String getValue() const;
255 
256  String toCellString() const;
257 
258  void fromCellString(const String& s);
259 
260  ~MzTabParameter() = default;
261  protected:
266  };
267 
268  class OPENMS_DLLAPI MzTabParameterList
269  {
270  public:
271  MzTabParameterList() = default;
272 
273  bool isNull() const;
274 
275  void setNull(bool b);
276 
277  String toCellString() const;
278 
279  void fromCellString(const String& s);
280 
281  std::vector<MzTabParameter> get() const;
282 
283  void set(const std::vector<MzTabParameter>& parameters);
284 
285  ~MzTabParameterList() = default;
286 
287  protected:
288  std::vector<MzTabParameter> parameters_;
289  };
290 
291  class OPENMS_DLLAPI MzTabStringList
292  {
293  public:
294  MzTabStringList();
295 
296  bool isNull() const;
297 
298  void setNull(bool b);
299 
301  void setSeparator(char sep);
302 
303  String toCellString() const;
304 
305  void fromCellString(const String& s);
306 
307  std::vector<MzTabString> get() const;
308 
309  void set(const std::vector<MzTabString>& entries);
310 
311  ~MzTabStringList() = default;
312  protected:
313  std::vector<MzTabString> entries_;
314  char sep_;
315  };
316 
317  class OPENMS_DLLAPI MzTabSpectraRef
318  {
319  public:
320  MzTabSpectraRef();
321 
322  bool isNull() const;
323 
324  void setNull(bool b);
325 
326  void setMSFile(Size index);
327 
328  void setSpecRef(const String& spec_ref);
329 
330  String getSpecRef() const;
331 
332  Size getMSFile() const;
333 
334  void setSpecRefFile(const String& spec_ref);
335 
336  String toCellString() const;
337 
338  void fromCellString(const String& s);
339 
340  ~MzTabSpectraRef() = default;
341  protected:
342  Size ms_run_; //< number is specified in the meta data section.
344  };
345 
346  // MTD
347  struct OPENMS_DLLAPI MzTabSoftwareMetaData
348  {
350  std::map<Size, MzTabString> setting;
351  };
352 
353  struct OPENMS_DLLAPI MzTabSampleMetaData
354  {
356  std::map<Size, MzTabParameter> species;
357  std::map<Size, MzTabParameter> tissue;
358  std::map<Size, MzTabParameter> cell_type;
359  std::map<Size, MzTabParameter> disease;
360  std::map<Size, MzTabParameter> custom;
361  };
362 
363  struct OPENMS_DLLAPI MzTabCVMetaData
364  {
369  };
370 
371  struct OPENMS_DLLAPI MzTabInstrumentMetaData
372  {
375  std::map<Size, MzTabParameter> analyzer;
377  };
378 
379  struct OPENMS_DLLAPI MzTabContactMetaData
380  {
384  };
385 
386  class OPENMS_DLLAPI MzTabBase
387  {
388  public:
389  MzTabBase() = default;
390  virtual ~MzTabBase() = default;
391 
392  protected:
394  template <typename SectionRows>
395  std::vector<String> getOptionalColumnNames_(const SectionRows& rows) const
396  {
397  // vector is used to preserve the column order
398  std::vector<String> names;
399  if (!rows.empty())
400  {
401  for (typename SectionRows::const_iterator it = rows.begin(); it != rows.end(); ++it)
402  {
403  for (auto it_opt = it->opt_.cbegin(); it_opt != it->opt_.cend(); ++it_opt)
404  {
405  if (std::find(names.begin(), names.end(), it_opt->first) == names.end())
406  {
407  names.push_back(it_opt->first);
408  }
409  }
410  }
411  }
412  return names;
413  }
414  };
415 } // namespace OpenMS
LogStream.h
OpenMS::MzTabString::value_
String value_
Definition: MzTabBase.h:226
OpenMS::MzTabInstrumentMetaData
Definition: MzTabBase.h:371
OpenMS::MzTabSampleMetaData::species
std::map< Size, MzTabParameter > species
Definition: MzTabBase.h:356
OpenMS::MzTabSampleMetaData::custom
std::map< Size, MzTabParameter > custom
Definition: MzTabBase.h:360
OpenMS::MzTabDouble::value_
double value_
Definition: MzTabBase.h:100
OpenMS::MzTabDouble::state_
MzTabCellStateType state_
Definition: MzTabBase.h:101
OpenMS::MzTabCVMetaData::full_name
MzTabString full_name
Definition: MzTabBase.h:366
OpenMS::MzTabInstrumentMetaData::detector
MzTabParameter detector
Definition: MzTabBase.h:376
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::SIZE_OF_MZTAB_CELLTYPE
Definition: MzTabBase.h:63
OpenMS::operator<
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
OpenMS::MzTabSampleMetaData::description
MzTabString description
Definition: MzTabBase.h:355
OpenMS::MzTabParameter::value_
String value_
Definition: MzTabBase.h:265
OpenMS::MzTabSoftwareMetaData::software
MzTabParameter software
Definition: MzTabBase.h:349
OpenMS::MzTabIntegerList
Definition: MzTabBase.h:159
OpenMS::MzTabContactMetaData::email
MzTabString email
Definition: MzTabBase.h:383
OpenMS::MzTabStringList
Definition: MzTabBase.h:291
OpenMS::MZTAB_CELLSTATE_NULL
Definition: MzTabBase.h:60
OpenMS::MzTabInteger::state_
MzTabCellStateType state_
Definition: MzTabBase.h:156
OpenMS::MzTabSampleMetaData::cell_type
std::map< Size, MzTabParameter > cell_type
Definition: MzTabBase.h:358
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::MzTabSoftwareMetaData
Definition: MzTabBase.h:347
Exception.h
OpenMS::MzTabSampleMetaData
Definition: MzTabBase.h:353
OpenMS::MzTabBase::getOptionalColumnNames_
std::vector< String > getOptionalColumnNames_(const SectionRows &rows) const
Helper function for "get...OptionalColumnNames" functions.
Definition: MzTabBase.h:395
OpenMS::MzTabDouble
Definition: MzTabBase.h:66
OpenMS::MzTabInstrumentMetaData::source
MzTabParameter source
Definition: MzTabBase.h:374
OpenMS::MzTabIntegerList::entries_
std::vector< MzTabInteger > entries_
Definition: MzTabBase.h:178
OpenMS::MZTAB_CELLSTATE_NAN
Definition: MzTabBase.h:61
OpenMS::MZTAB_CELLSTATE_DEFAULT
Definition: MzTabBase.h:59
OpenMS::MzTabDoubleList
Definition: MzTabBase.h:104
OpenMS::MzTabParameterList
Definition: MzTabBase.h:268
OpenMS::MzTabCellStateType
MzTabCellStateType
Base functionality to for MzTab data models.
Definition: MzTabBase.h:57
OpenMS::MzTabBoolean
Definition: MzTabBase.h:181
OpenMS::MzTabSpectraRef::ms_run_
Size ms_run_
Definition: MzTabBase.h:342
OpenMS::MzTabCVMetaData::url
MzTabString url
Definition: MzTabBase.h:368
OpenMS::MzTabParameter
Definition: MzTabBase.h:231
OpenMS::MzTabParameter::CV_label_
String CV_label_
Definition: MzTabBase.h:262
OpenMS::MzTabCVMetaData
Definition: MzTabBase.h:363
OpenMS::MzTabCVMetaData::label
MzTabString label
Definition: MzTabBase.h:365
OpenMS::MzTabInstrumentMetaData::analyzer
std::map< Size, MzTabParameter > analyzer
Definition: MzTabBase.h:375
OpenMS::MzTabStringList::entries_
std::vector< MzTabString > entries_
Definition: MzTabBase.h:313
OpenMS::MZTAB_CELLSTATE_INF
Definition: MzTabBase.h:62
OpenMS::MzTabSampleMetaData::tissue
std::map< Size, MzTabParameter > tissue
Definition: MzTabBase.h:357
OpenMS::MzTabSampleMetaData::disease
std::map< Size, MzTabParameter > disease
Definition: MzTabBase.h:359
OpenMS::MzTabContactMetaData::name
MzTabString name
Definition: MzTabBase.h:381
OpenMS::MzTabBoolean::value_
int value_
Definition: MzTabBase.h:202
OpenMS::Internal::operator==
bool operator==(const IDBoostGraph::ProteinGroup &lhs, const IDBoostGraph::ProteinGroup &rhs)
OpenMS::MzTabStringList::sep_
char sep_
Definition: MzTabBase.h:314
OpenMS::MzTabParameter::name_
String name_
Definition: MzTabBase.h:264
String.h
OpenMS::MzTabDoubleList::entries_
std::vector< MzTabDouble > entries_
Definition: MzTabBase.h:123
OpenMS::MzTabInteger
Definition: MzTabBase.h:126
OpenMS::MzTabContactMetaData::affiliation
MzTabString affiliation
Definition: MzTabBase.h:382
OpenMS::MzTabParameterList::parameters_
std::vector< MzTabParameter > parameters_
Definition: MzTabBase.h:288
OpenMS::MzTabSpectraRef::spec_ref_
String spec_ref_
Definition: MzTabBase.h:343
OpenMS::MzTabCVMetaData::version
MzTabString version
Definition: MzTabBase.h:367
OpenMS::MzTabInstrumentMetaData::name
MzTabParameter name
Definition: MzTabBase.h:373
OpenMS::MzTabInteger::value_
Int value_
Definition: MzTabBase.h:155
OpenMS::MzTabSpectraRef
Definition: MzTabBase.h:317
OpenMS::MzTabContactMetaData
Definition: MzTabBase.h:379
OpenMS::MzTabParameter::accession_
String accession_
Definition: MzTabBase.h:263
OpenMS::MzTabOptionalColumnEntry
std::pair< String, MzTabString > MzTabOptionalColumnEntry
Definition: MzTabBase.h:229
OpenMS::MzTabSoftwareMetaData::setting
std::map< Size, MzTabString > setting
Definition: MzTabBase.h:350
OpenMS::MzTabBase
Definition: MzTabBase.h:386
OpenMS::MzTabString
Definition: MzTabBase.h:205