ProteoWizard
TextWriter.hpp
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1 //
2 // $Id$
3 //
4 //
5 // Original author: Matt Chambers <matt.chambers .@. vanderbilt.edu>
6 //
7 // Copyright 2009 Vanderbilt University - Nashville, TN 37232
8 //
9 // Licensed under the Apache License, Version 2.0 (the "License");
10 // you may not use this file except in compliance with the License.
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13 // http://www.apache.org/licenses/LICENSE-2.0
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18 // See the License for the specific language governing permissions and
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21 
22 
23 #ifndef _TRADATA_TEXTWRITER_HPP_
24 #define _TRADATA_TEXTWRITER_HPP_
25 
26 
28 #include "TraData.hpp"
29 #include "boost/lexical_cast.hpp"
30 #include <iostream>
31 #include <string>
32 #include <vector>
33 
34 
35 namespace pwiz {
36 namespace tradata {
37 
38 
40 using std::string;
41 
42 
44 {
45  public:
46 
47  TextWriter(std::ostream& os, int depth = 0)
48  : os_(os), depth_(depth), indent_(depth*2, ' ')
49  {}
50 
51  TextWriter child() {return TextWriter(os_, depth_+1);}
52 
53  TextWriter& operator()(const std::string& text)
54  {
55  os_ << indent_ << text << std::endl;
56  return *this;
57  }
58 
59  TextWriter& operator()(const CVParam& cvParam)
60  {
61  os_ << indent_ << "cvParam: " << cvTermInfo(cvParam.cvid).name;
62  if (!cvParam.value.empty())
63  os_ << ", " << cvParam.value;
64  if (cvParam.units != CVID_Unknown)
65  os_ << ", " << cvParam.unitsName();
66  os_ << std::endl;
67  return *this;
68  }
69 
70  TextWriter& operator()(const UserParam& userParam)
71  {
72  os_ << indent_ << "userParam: " << userParam.name;
73  if (!userParam.value.empty()) os_ << ", " << userParam.value;
74  if (!userParam.type.empty()) os_ << ", " << userParam.type;
75  if (userParam.units != CVID_Unknown) os_ << ", " << cvTermInfo(userParam.units).name;
76  os_ << std::endl;
77  return *this;
78  }
79 
80  template<typename object_type>
81  TextWriter& operator()(const std::string& label, const std::vector<object_type>& v)
82  {
83  (*this)(label);
84  for_each(v.begin(), v.end(), child());
85  return *this;
86  }
87 
88  template<typename object_type>
89  TextWriter& operator()(const std::string& label, const object_type& v)
90  {
91  (*this)(label)(boost::lexical_cast<std::string>(v));
92  return *this;
93  }
94 
95 
97  {
98  (*this)("tradata:");
99  child()("version: " + msd.version());
100  if (!msd.cvs.empty())
101  child()("cvList: ", msd.cvs);
102  if (!msd.contactPtrs.empty())
103  child()("contactList: ", msd.contactPtrs);
104  if (!msd.publications.empty())
105  child()("publicationList: ", msd.publications);
106  if (!msd.instrumentPtrs.empty())
107  child()("instrumentList: ", msd.instrumentPtrs);
108  if (!msd.softwarePtrs.empty())
109  child()("softwareList: ", msd.softwarePtrs);
110  if (!msd.proteinPtrs.empty())
111  child()("proteinList: ", msd.proteinPtrs);
112  if (!msd.peptidePtrs.empty())
113  child()("peptideList: ", msd.peptidePtrs);
114  if (!msd.compoundPtrs.empty())
115  child()("compoundList: ", msd.compoundPtrs);
116  if (!msd.transitions.empty())
117  child()("transitionList: ", msd.transitions);
118  if (!msd.targets.empty())
119  child()(msd.targets);
120 
121  return *this;
122  }
123 
125  {
126  (*this)("cv:");
127  child()
128  ("id: " + cv.id)
129  ("fullName: " + cv.fullName)
130  ("version: " + cv.version)
131  ("URI: " + cv.URI);
132  return *this;
133  }
134 
135  TextWriter& operator()(const ParamContainer& paramContainer)
136  {
137  for_each(paramContainer.cvParams.begin(), paramContainer.cvParams.end(), *this);
138  for_each(paramContainer.userParams.begin(), paramContainer.userParams.end(), *this);
139  return *this;
140  }
141 
142  TextWriter& operator()(const Publication& publication)
143  {
144  (*this)("publication:");
145  child()
146  ("id: " + publication.id)
147  (static_cast<const ParamContainer&>(publication));
148  return *this;
149  }
150 
151  TextWriter& operator()(const Software& software)
152  {
153  (*this)("software:");
154  child()
155  ("id: " + software.id)
156  ("version: " + software.version)
157  (static_cast<const ParamContainer&>(software));
158  return *this;
159  }
160 
161  TextWriter& operator()(const Contact& contact)
162  {
163  (*this)("contact:");
164  child()(static_cast<const ParamContainer&>(contact));
165  return *this;
166  }
167 
168  TextWriter& operator()(const RetentionTime& retentionTime)
169  {
170  (*this)("retentionTime:");
171  child()(static_cast<const ParamContainer&>(retentionTime));
172  if (retentionTime.softwarePtr.get() &&
173  !retentionTime.softwarePtr->empty())
174  child()("softwareRef: " + retentionTime.softwarePtr->id);
175  return *this;
176  }
177 
178  TextWriter& operator()(const Prediction& prediction)
179  {
180  (*this)("prediction:");
181  child()(static_cast<const ParamContainer&>(prediction));
182  return *this;
183  }
184 
185  TextWriter& operator()(const Evidence& evidence)
186  {
187  (*this)("evidence:");
188  child()(static_cast<const ParamContainer&>(evidence));
189  return *this;
190  }
191 
192  TextWriter& operator()(const Validation& validation)
193  {
194  (*this)("validation:");
195  child()(static_cast<const ParamContainer&>(validation));
196  return *this;
197  }
198 
199  TextWriter& operator()(const Protein& protein)
200  {
201  (*this)("protein:");
202  child()("id: " + protein.id)
203  ("sequence: " + protein.sequence);
204  child()(static_cast<const ParamContainer&>(protein));
205  return *this;
206  }
207 
209  {
210  (*this)("modification:");
211  child()("location: ", lexical_cast<string>(modification.location))
212  ("monoisotopicMassDelta: " + lexical_cast<string>(modification.monoisotopicMassDelta))
213  ("averageMassDelta: " + lexical_cast<string>(modification.averageMassDelta));
214  child()(static_cast<const ParamContainer&>(modification));
215  return *this;
216  }
217 
219  {
220  (*this)("peptide:");
221  child()("id: " + peptide.id)
222  ("sequence: " + peptide.sequence)
223  (peptide.evidence);
224 
225  if (!peptide.proteinPtrs.empty())
226  child()("proteinRefs:", peptide.proteinPtrs);
227  if (!peptide.modifications.empty())
228  child()("modifications:", peptide.modifications);
229  if (!peptide.retentionTimes.empty())
230  child()("retentionTimes:", peptide.retentionTimes);
231 
232  child()(static_cast<const ParamContainer&>(peptide));
233  return *this;
234  }
235 
236  TextWriter& operator()(const Compound& compound)
237  {
238  (*this)("compound:");
239  child()("id: " + compound.id)
240  ("retentionTimes:", compound.retentionTimes);
241  child()(static_cast<const ParamContainer&>(compound));
242  return *this;
243  }
244 
245  TextWriter& operator()(const Precursor& precursor)
246  {
247  (*this)("precursor:");
248  child()(static_cast<const ParamContainer&>(precursor));
249  return *this;
250  }
251 
252  TextWriter& operator()(const Product& product)
253  {
254  (*this)("product:");
255  child()(static_cast<const ParamContainer&>(product));
256  return *this;
257  }
258 
259  TextWriter& operator()(const Transition& transition)
260  {
261  (*this)("transition:");
262  child()("id: ", transition.id);
263  if (!transition.precursor.empty())
264  child()(transition.precursor);
265  if (!transition.product.empty())
266  child()(transition.product);
267  if (!transition.prediction.empty())
268  child()(transition.prediction);
269  if (!transition.interpretationList.empty())
270  child()("interpretationList: ", transition.interpretationList);
271  if (!transition.configurationList.empty())
272  child()("configurationList: ", transition.configurationList);
273  if (transition.peptidePtr.get() && !transition.peptidePtr->empty())
274  child()("peptideRef: " + transition.peptidePtr->id);
275  if (transition.compoundPtr.get() && !transition.compoundPtr->empty())
276  child()("compoundRef: " + transition.compoundPtr->id);
277  return *this;
278  }
279 
280  TextWriter& operator()(const Target& target)
281  {
282  (*this)("target:");
283  child()("id: ", target.id);
284  if (!target.precursor.empty())
285  child()(target.precursor);
286  if (!target.configurationList.empty())
287  child()("configurationList: ", target.configurationList);
288  if (target.peptidePtr.get() && !target.peptidePtr->empty())
289  child()("peptideRef: " + target.peptidePtr->id);
290  if (target.compoundPtr.get() && !target.compoundPtr->empty())
291  child()("compoundRef: " + target.compoundPtr->id);
292  return *this;
293  }
294 
295  TextWriter& operator()(const TargetList& targetList)
296  {
297  (*this)("targetList:");
298  child()(static_cast<const ParamContainer&>(targetList));
299  if (!targetList.targetExcludeList.empty())
300  child()("targetExcludeList: ", targetList.targetExcludeList);
301  if (!targetList.targetIncludeList.empty())
302  child()("targetIncludeList: ", targetList.targetIncludeList);
303  return *this;
304  }
305 
306  // if no other overload matches, assume the object is a shared_ptr of a valid overloaded type
307  template<typename object_type>
308  TextWriter& operator()(const boost::shared_ptr<object_type>& p)
309  {
310  return p.get() ? (*this)(*p) : *this;
311  }
312 
313  private:
314  std::ostream& os_;
315  int depth_;
316  std::string indent_;
317 };
318 
319 
320 } // namespace tradata
321 } // namespace pwiz
322 
323 
324 #endif // _TRADATA_TEXTWRITER_HPP_
325 
pwiz::data::UserParam
Uncontrolled user parameters (essentially allowing free text). Before using these,...
Definition: ParamTypes.hpp:185
pwiz::tradata::Contact
Definition: TraData.hpp:46
pwiz::tradata::TargetList
List of precursor m/z targets to include or exclude.
Definition: TraData.hpp:334
pwiz::cv::CV::fullName
std::string fullName
the usual name for the resource (e.g. The PSI-MS Controlled Vocabulary).
Definition: cv.hpp:14924
pwiz::tradata::Target::id
std::string id
String label for this target.
Definition: TraData.hpp:311
pwiz::tradata::TraData::instrumentPtrs
std::vector< InstrumentPtr > instrumentPtrs
List of instruments on which transitions are validated.
Definition: TraData.hpp:366
pwiz::data::UserParam::type
std::string type
the datatype of the parameter, where appropriate (e.g.: xsd:float).
Definition: ParamTypes.hpp:194
os_
ostream * os_
Definition: ChromatogramList_FilterTest.cpp:40
pwiz::tradata::TextWriter::operator()
TextWriter & operator()(const Target &target)
Definition: TextWriter.hpp:280
pwiz::tradata::TextWriter::operator()
TextWriter & operator()(const Publication &publication)
Definition: TextWriter.hpp:142
pwiz::tradata::Precursor::empty
bool empty() const
returns true iff contains no params
pwiz::data::unimod::modification
const PWIZ_API_DECL Modification & modification(CVID cvid)
find a modification by CVID
pwiz::tradata::TextWriter::operator()
TextWriter & operator()(const Protein &protein)
Definition: TextWriter.hpp:199
pwiz::tradata::Product
Product (Q3) of the transition.
Definition: TraData.hpp:266
pwiz::tradata::Target::precursor
Precursor precursor
Precursor (Q1) of the target.
Definition: TraData.hpp:320
pwiz
Definition: ChromatogramList_Filter.hpp:36
pwiz::tradata::TargetList::targetIncludeList
std::vector< Target > targetIncludeList
List of precursor m/z targets to include.
Definition: TraData.hpp:340
pwiz::cv::CV
Information about an ontology or CV source and a short 'lookup' tag to refer to.
Definition: cv.hpp:14915
pwiz::cv::CV::URI
std::string URI
the URI for the resource.
Definition: cv.hpp:14921
pwiz::tradata::Transition::precursor
Precursor precursor
Precursor (Q1) of the transition.
Definition: TraData.hpp:285
pwiz::proteome::Protein::id
std::string id
Definition: ProteomeData.hpp:42
pwiz::tradata::Compound
Chemical compound other than a peptide for which one or more transitions.
Definition: TraData.hpp:240
pwiz::tradata::Software::id
std::string id
Identifier for the software to be used for referencing within a document.
Definition: TraData.hpp:73
pwiz::tradata::TextWriter::operator()
TextWriter & operator()(const Contact &contact)
Definition: TextWriter.hpp:161
pwiz::tradata::TargetList::targetExcludeList
std::vector< Target > targetExcludeList
List of precursor m/z targets to exclude.
Definition: TraData.hpp:337
pwiz::tradata::Evidence
Information about empirical mass spectrometer observations of the peptide.
Definition: TraData.hpp:116
pwiz::data::ParamContainer::userParams
std::vector< UserParam > userParams
a collection of uncontrolled user terms
Definition: ParamTypes.hpp:253
pwiz::tradata::Target::peptidePtr
PeptidePtr peptidePtr
Reference to a peptide for which this target is the trigger.
Definition: TraData.hpp:314
pwiz::tradata::TextWriter::operator()
TextWriter & operator()(const Validation &validation)
Definition: TextWriter.hpp:192
pwiz::tradata::Target
A peptide or compound that is to be included or excluded from a target list of precursor m/z values.
Definition: TraData.hpp:308
pwiz::tradata::TextWriter::operator()
TextWriter & operator()(const Transition &transition)
Definition: TextWriter.hpp:259
pwiz::proteome::Modification
represents a post-translational modification (PTM) modification formula or masses must be provided at...
Definition: Modification.hpp:41
pwiz::tradata::TraData::contactPtrs
std::vector< ContactPtr > contactPtrs
List of contacts referenced in the generation or validation of transitions.
Definition: TraData.hpp:360
pwiz::tradata::TraData::cvs
std::vector< CV > cvs
List of controlled vocabularies used in a TraML document note: one of the <cv> elements in this list ...
Definition: TraData.hpp:357
pwiz::cv::CV::id
std::string id
the short label to be used as a reference tag with which to refer to this particular Controlled Vocab...
Definition: cv.hpp:14918
pwiz::tradata::TextWriter::indent_
std::string indent_
Definition: TextWriter.hpp:316
pwiz::data::UserParam::units
CVID units
an optional CV parameter for the unit term associated with the value, if any (e.g....
Definition: ParamTypes.hpp:197
pwiz::tradata::Publication
Definition: TraData.hpp:60
pwiz::proteome::Peptide
represents a peptide or polypeptide (a sequence of amino acids)
Definition: Peptide.hpp:61
PWIZ_API_DECL
#define PWIZ_API_DECL
Definition: Export.hpp:32
pwiz::tradata::Transition::configurationList
std::vector< Configuration > configurationList
List of insutrument configurations used in the validation or optimization of the transitions.
Definition: TraData.hpp:300
pwiz::cv::CV::version
std::string version
the version of the CV from which the referred-to terms are drawn.
Definition: cv.hpp:14927
pwiz::tradata::TextWriter::operator()
TextWriter & operator()(const CV &cv)
Definition: TextWriter.hpp:124
pwiz::tradata::Transition::id
std::string id
String label for this transition.
Definition: TraData.hpp:276
pwiz::tradata::TextWriter::operator()
TextWriter & operator()(const std::string &label, const object_type &v)
Definition: TextWriter.hpp:89
pwiz::tradata::TraData::publications
std::vector< Publication > publications
List of publications from which the transitions were collected or wherein they are published.
Definition: TraData.hpp:363
pwiz::tradata::Software::version
std::string version
Version of the software program described.
Definition: TraData.hpp:76
pwiz::tradata::TextWriter::child
TextWriter child()
Definition: TextWriter.hpp:51
pwiz::cv::cv
const PWIZ_API_DECL CV & cv(const std::string &prefix)
returns a CV object for the specified namespace (prefix); currently supported namespaces are: MS UO
Export.hpp
pwiz::tradata::Compound::id
std::string id
Identifier for the compound to be used for referencing within a document.
Definition: TraData.hpp:243
pwiz::identdata::peptide
PWIZ_API_DECL proteome::Peptide peptide(const Peptide &peptide)
creates a proteome::Peptide from an identdata::Peptide
pwiz::tradata::Prediction::empty
bool empty() const
returns true iff all members are empty and contain no params
pwiz::data::CVParam::unitsName
std::string unitsName() const
convenience function to return string for the units
pwiz::tradata::TextWriter::operator()
TextWriter & operator()(const Peptide &peptide)
Definition: TextWriter.hpp:218
pwiz::tradata::TextWriter::operator()
TextWriter & operator()(const Evidence &evidence)
Definition: TextWriter.hpp:185
pwiz::tradata::Prediction
Information about a prediction for a suitable transition using some software.
Definition: TraData.hpp:102
pwiz::tradata::TextWriter::operator()
TextWriter & operator()(const TraData &msd)
Definition: TextWriter.hpp:96
pwiz::tradata::TraData
Definition: TraData.hpp:350
pwiz::tradata::TextWriter::operator()
TextWriter & operator()(const ParamContainer &paramContainer)
Definition: TextWriter.hpp:135
pwiz::cv::CVTermInfo::name
std::string name
Definition: cv.hpp:14947
pwiz::data::CVParam::units
CVID units
Definition: ParamTypes.hpp:48
pwiz::tradata::TextWriter::operator()
TextWriter & operator()(const std::string &text)
Definition: TextWriter.hpp:53
CVID_Unknown
CVID_Unknown
Definition: cv.hpp:114
pwiz::data::ParamContainer
The base class for elements that may contain cvParams, userParams, or paramGroup references.
Definition: ParamTypes.hpp:244
pwiz::tradata::Transition::interpretationList
std::vector< Interpretation > interpretationList
List of possible interprations of fragment ions for a transition.
Definition: TraData.hpp:297
pwiz::tradata::TextWriter::operator()
TextWriter & operator()(const boost::shared_ptr< object_type > &p)
Definition: TextWriter.hpp:308
pwiz::data::CVParam::value
std::string value
Definition: ParamTypes.hpp:47
pwiz::tradata::Compound::retentionTimes
std::vector< RetentionTime > retentionTimes
List of retention time information entries.
Definition: TraData.hpp:246
pwiz::tradata::TargetList::empty
bool empty() const
returns true iff all members are empty and contain no params
pwiz::data::UserParam::value
std::string value
the value for the parameter, where appropriate.
Definition: ParamTypes.hpp:191
pwiz::tradata::TextWriter::operator()
TextWriter & operator()(const RetentionTime &retentionTime)
Definition: TextWriter.hpp:168
pwiz::cv::cvTermInfo
const PWIZ_API_DECL CVTermInfo & cvTermInfo(CVID cvid)
returns CV term info for the specified CVID
pwiz::tradata::TextWriter::depth_
int depth_
Definition: TextWriter.hpp:315
pwiz::tradata::Software
Definition: TraData.hpp:70
pwiz::tradata::TraData::transitions
std::vector< Transition > transitions
List of transitions.
Definition: TraData.hpp:379
pwiz::tradata::TextWriter::operator()
TextWriter & operator()(const Modification &modification)
Definition: TextWriter.hpp:208
pwiz::tradata::TextWriter::TextWriter
TextWriter(std::ostream &os, int depth=0)
Definition: TextWriter.hpp:47
pwiz::tradata::TraData::proteinPtrs
std::vector< ProteinPtr > proteinPtrs
List of proteins for which one or more transitions are intended to identify.
Definition: TraData.hpp:372
pwiz::proteome::Protein
Definition: ProteomeData.hpp:36
TraData.hpp
pwiz::proteome::Peptide::sequence
const std::string & sequence() const
returns the sequence of amino acids making up the peptide
pwiz::tradata::RetentionTime::softwarePtr
SoftwarePtr softwarePtr
Software used to determine the retention time.
Definition: TraData.hpp:94
pwiz::tradata::TextWriter::os_
std::ostream & os_
Definition: TextWriter.hpp:314
pwiz::tradata::TextWriter::operator()
TextWriter & operator()(const Product &product)
Definition: TextWriter.hpp:252
boost::lexical_cast
toType lexical_cast(const std::string &str, bool &success)
Definition: optimized_lexical_cast.hpp:70
pwiz::tradata::Target::compoundPtr
CompoundPtr compoundPtr
Reference to a compound for which this target is the trigger.
Definition: TraData.hpp:317
pwiz::tradata::TraData::targets
TargetList targets
List of precursor m/z targets to include or exclude.
Definition: TraData.hpp:382
pwiz::tradata::TextWriter::operator()
TextWriter & operator()(const Software &software)
Definition: TextWriter.hpp:151
pwiz::tradata::TraData::version
const std::string & version() const
returns the version of this traML document; for a document created programmatically,...
pwiz::tradata::TextWriter::operator()
TextWriter & operator()(const std::string &label, const std::vector< object_type > &v)
Definition: TextWriter.hpp:81
pwiz::tradata::Transition::product
Product product
Product (Q3) of the transition.
Definition: TraData.hpp:288
pwiz::proteome::TextWriter
Definition: TextWriter.hpp:39
pwiz::tradata::TraData::compoundPtrs
std::vector< CompoundPtr > compoundPtrs
Definition: TraData.hpp:376
pwiz::tradata::Validation
Information about the state of validation of a transition on a given instrument model.
Definition: TraData.hpp:124
pwiz::tradata::TextWriter::operator()
TextWriter & operator()(const Compound &compound)
Definition: TextWriter.hpp:236
pwiz::tradata::Target::configurationList
std::vector< Configuration > configurationList
List of instrument configurations used in the validation or optimization of the target.
Definition: TraData.hpp:326
pwiz::util::virtual_map::empty
virtual bool empty() const
Returns true if the map is empty, false otherwise.
Definition: virtual_map.hpp:153
pwiz::tradata::Product::empty
bool empty() const
returns true iff contains no params
pwiz::data::CVParam::cvid
CVID cvid
Definition: ParamTypes.hpp:46
pwiz::proteome::Peptide::modifications
ModificationMap & modifications()
the map of sequence offsets (0-based) to modifications; modifications can be added or removed from th...
pwiz::tradata::Transition::prediction
Prediction prediction
Information about a prediction for a suitable transition using some software.
Definition: TraData.hpp:291
pwiz::tradata::Precursor
Precursor (Q1) of the transition.
Definition: TraData.hpp:258
pwiz::tradata::TextWriter::operator()
TextWriter & operator()(const UserParam &userParam)
Definition: TextWriter.hpp:70
pwiz::tradata::TextWriter::operator()
TextWriter & operator()(const Precursor &precursor)
Definition: TextWriter.hpp:245
pwiz::tradata::TextWriter::operator()
TextWriter & operator()(const Prediction &prediction)
Definition: TextWriter.hpp:178
pwiz::tradata::Publication::id
std::string id
Identifier for the publication to be used for referencing within a document.
Definition: TraData.hpp:63
pwiz::tradata::RetentionTime
Definition: TraData.hpp:91
pwiz::tradata::TextWriter::operator()
TextWriter & operator()(const TargetList &targetList)
Definition: TextWriter.hpp:295
pwiz::tradata::TraData::softwarePtrs
std::vector< SoftwarePtr > softwarePtrs
List of software packages used in the generation of one of more transitions described in the document...
Definition: TraData.hpp:369
pwiz::data::CVParam
represents a tag-value pair, where the tag comes from the controlled vocabulary
Definition: ParamTypes.hpp:44
pwiz::tradata::Transition
Definition: TraData.hpp:273
pwiz::tradata::Transition::peptidePtr
PeptidePtr peptidePtr
Reference to a peptide which this transition is intended to identify.
Definition: TraData.hpp:279
pwiz::tradata::TextWriter::operator()
TextWriter & operator()(const CVParam &cvParam)
Definition: TextWriter.hpp:59
pwiz::tradata::Transition::compoundPtr
CompoundPtr compoundPtr
Reference to a compound for this transition.
Definition: TraData.hpp:282
pwiz::data::UserParam::name
std::string name
the name for the parameter.
Definition: ParamTypes.hpp:188
pwiz::tradata::TraData::peptidePtrs
std::vector< PeptidePtr > peptidePtrs
List of compounds (including peptides) for which one or more transitions are intended to identify.
Definition: TraData.hpp:375
pwiz::data::ParamContainer::cvParams
std::vector< CVParam > cvParams
a collection of controlled vocabulary terms
Definition: ParamTypes.hpp:250