ProteoWizard
Functions
MSDataTest.cpp File Reference
#include "MSData.hpp"
#include "pwiz/utility/misc/unit.hpp"
#include "pwiz/utility/misc/Std.hpp"

Go to the source code of this file.

Functions

void testSpectrumListSimple ()
 
void testChromatograms ()
 
void testIDParsing ()
 
void testAllDataProcessing ()
 
int main (int argc, char *argv[])
 

Function Documentation

◆ testSpectrumListSimple()

void testSpectrumListSimple ( )

Definition at line 33 of file MSDataTest.cpp.

34{
35 // fill in SpectrumListSimple
36
37 shared_ptr<SpectrumListSimple> spectrumListSimple(new SpectrumListSimple);
38
39 unit_assert(spectrumListSimple->empty());
40 spectrumListSimple->dp = DataProcessingPtr(new DataProcessing("dp"));
41 unit_assert(!spectrumListSimple->empty());
42
43 SpectrumPtr spectrum0(new Spectrum);
44 spectrum0->index = 0;
45 spectrum0->id = "sample=1 period=1 cycle=123 experiment=2";
46
47 // add m/z values 0,...,9
49 for (unsigned int i=0; i<10; i++) bd_mz->data.push_back(i);
50 bd_mz->cvParams.push_back(MS_m_z_array);
51 double* buffer = &bd_mz->data[0];
52
53 // add intensity values 10,...,1
54 BinaryDataArrayPtr bd_intensity(new BinaryDataArray);
55 for (unsigned int i=0; i<10; i++) bd_intensity->data.push_back(10-i);
56 bd_intensity->cvParams.push_back(MS_intensity_array);
57
58 spectrum0->binaryDataArrayPtrs.push_back(bd_mz);
59 spectrum0->binaryDataArrayPtrs.push_back(bd_intensity);
60 spectrum0->defaultArrayLength = 10;
61
62 SpectrumPtr spectrum1(new Spectrum);
63 spectrum1->index = 1;
64 spectrum1->id = "sample=1 period=1 cycle=345 experiment=2";
65 spectrum1->cvParams.push_back(MS_MSn_spectrum);
66 spectrum1->cvParams.push_back(CVParam(MS_ionization_type, 420));
67
68 spectrumListSimple->spectra.push_back(spectrum0);
69 spectrumListSimple->spectra.push_back(spectrum1);
70
71 // let an MSData object hold onto it as a SpectrumListPtr
72
73 MSData data;
74 data.run.spectrumListPtr = spectrumListSimple;
75
76 // test SpectrumList interface
77
78 // verify index()
79 const SpectrumList& spectrumList = *data.run.spectrumListPtr;
80 unit_assert_operator_equal(2, spectrumList.size());
81 unit_assert_operator_equal(0, spectrumList.find("sample=1 period=1 cycle=123 experiment=2"));
82 unit_assert_operator_equal(1, spectrumList.find("sample=1 period=1 cycle=345 experiment=2"));
83
84 // verify findAbbreviated()
85 unit_assert_operator_equal(0, spectrumList.findAbbreviated("1.1.123.2"));
86 unit_assert_operator_equal(1, spectrumList.findAbbreviated("1.1.345.2"));
87
88 // verify findNameValue
89
90 IndexList result = spectrumList.findNameValue("cycle", "123");
91 unit_assert(result.size()==1 && result[0]==0);
92
93 result = spectrumList.findNameValue("cycle", "345");
94 unit_assert(result.size()==1 && result[0]==1);
95
96 // verify spectrumIdentity()
97
98 const SpectrumIdentity& identity0 = spectrumList.spectrumIdentity(0);
99 unit_assert(identity0.index == spectrum0->index);
100 unit_assert(identity0.id == spectrum0->id);
101
102 const SpectrumIdentity& identity1 = spectrumList.spectrumIdentity(1);
103 unit_assert(identity1.index == spectrum1->index);
104 unit_assert(identity1.id == spectrum1->id);
105
106 // verify spectrum 0
107 SpectrumPtr spectrum = spectrumList.spectrum(0);
108 unit_assert(spectrum->index == spectrum0->index);
109 unit_assert(spectrum->id == spectrum0->id);
110
111 // verify no extra copying of binary data arrays
112 unit_assert(spectrum->binaryDataArrayPtrs.size() == 2);
113 unit_assert(&(spectrum->binaryDataArrayPtrs[0]->data[0]) == buffer);
114
115 // verify getMZIntensityPairs()
116
117 unit_assert(spectrum->binaryDataArrayPtrs[0]->hasCVParam(MS_m_z_array) == true);
118 unit_assert(spectrum->binaryDataArrayPtrs[1]->hasCVParam(MS_intensity_array) == true);
119
120 vector<MZIntensityPair> mziPairs;
121 spectrum->getMZIntensityPairs(mziPairs);
122 unit_assert(mziPairs.size() == 10);
123
124 vector<double> doubleArray;
125 unit_assert(spectrum->defaultArrayLength == 10);
126 doubleArray.resize(spectrum->defaultArrayLength*2);
127 spectrum->getMZIntensityPairs(reinterpret_cast<MZIntensityPair*>(&doubleArray[0]),
128 spectrum->defaultArrayLength);
129
130 for (unsigned int i=0; i<10; i++)
131 {
132 const MZIntensityPair& p = mziPairs[i];
133 unit_assert(p.mz == i);
134 unit_assert(p.intensity == 10-i);
135 unit_assert(doubleArray[2*i] == i);
136 unit_assert(doubleArray[2*i+1] == 10-i);
137 }
138
139 // verify setMZIntensityPairs()
140 spectrum->binaryDataArrayPtrs.clear();
141 unit_assert(spectrum->binaryDataArrayPtrs.empty());
142 vector<MZIntensityPair> mziPairs2;
143 for (unsigned int i=0; i<10; i++)
144 mziPairs2.push_back(MZIntensityPair(2*i, 3*i));
145 spectrum->setMZIntensityPairs(mziPairs2, MS_number_of_detector_counts);
146 unit_assert(spectrum->binaryDataArrayPtrs.size() == 2);
147 unit_assert(spectrum->binaryDataArrayPtrs[0]->hasCVParam(MS_m_z_array) == true);
148 unit_assert(spectrum->binaryDataArrayPtrs[1]->hasCVParam(MS_intensity_array) == true);
149 unit_assert(spectrum->binaryDataArrayPtrs[1]->cvParam(MS_intensity_array).units == MS_number_of_detector_counts);
150 unit_assert(spectrum->binaryDataArrayPtrs[0]->data.size() == 10);
151 unit_assert(spectrum->binaryDataArrayPtrs[1]->data.size() == 10);
152 for (unsigned int i=0; i<10; i++)
153 unit_assert(spectrum->binaryDataArrayPtrs[0]->data[i] == 2*i &&
154 spectrum->binaryDataArrayPtrs[1]->data[i] == 3*i);
155
156 // verify spectrum 1
157 spectrum = spectrumList.spectrum(1);
158 unit_assert(spectrum->index == spectrum1->index);
159 unit_assert(spectrum->id == spectrum1->id);
160
161 // verify DataProcessingPtr
162
163 unit_assert(spectrumList.dataProcessingPtr().get() &&
164 spectrumList.dataProcessingPtr()->id == "dp");
165}
Interface for accessing spectra, which may be stored in memory or backed by a data file (RAW,...
Definition MSData.hpp:661
virtual const boost::shared_ptr< const DataProcessing > dataProcessingPtr() const
returns the data processing affecting spectra retrieved through this interface
virtual IndexList findNameValue(const std::string &name, const std::string &value) const
find all spectrum indexes with specified name/value pair
virtual size_t findAbbreviated(const std::string &abbreviatedId, char delimiter='.') const
find an abbreviated id (e.g. "1.1.123.2" for "sample=1 period=1 cycle=123 experiment=2") in the spect...
virtual size_t size() const =0
returns the number of spectra
virtual SpectrumPtr spectrum(size_t index, bool getBinaryData=false) const =0
retrieve a spectrum by index
virtual size_t find(const std::string &id) const
find id in the spectrum index (returns size() on failure)
virtual const SpectrumIdentity & spectrumIdentity(size_t index) const =0
access to a spectrum index
MS_intensity_array
intensity array: A data array of intensity values.
Definition cv.hpp:2151
MS_MSn_spectrum
MSn spectrum: MSn refers to multi-stage MS2 experiments designed to record product ion spectra where ...
Definition cv.hpp:2364
MS_m_z_array
m/z array: A data array of m/z values.
Definition cv.hpp:2148
MS_number_of_detector_counts
number of detector counts: The number of counted events observed in one or a group of elements of a d...
Definition cv.hpp:741
MS_ionization_type
ionization type: The method by which gas phase ions are generated from the sample.
Definition cv.hpp:285
boost::shared_ptr< DataProcessing > DataProcessingPtr
Definition MSData.hpp:288
boost::shared_ptr< BinaryDataArray > BinaryDataArrayPtr
Definition MSData.hpp:417
boost::shared_ptr< Spectrum > SpectrumPtr
Definition MSData.hpp:573
represents a tag-value pair, where the tag comes from the controlled vocabulary
The structure into which encoded binary data goes. Byte ordering is always little endian (Intel style...
Definition MSData.hpp:405
Description of the way in which a particular software was used.
Definition MSData.hpp:274
This is the root element of ProteoWizard; it represents the mzML element, defined as: intended to cap...
Definition MSData.hpp:850
Run run
a run in mzML should correspond to a single, consecutive and coherent set of scans on an instrument.
Definition MSData.hpp:886
The data point type of a mass spectrum.
Definition MSData.hpp:423
SpectrumListPtr spectrumListPtr
all mass spectra and the acquisitions underlying them are described and attached here....
Definition MSData.hpp:827
The structure that captures the generation of a peak list (including the underlying acquisitions)
Definition MSData.hpp:506
Identifying information for a spectrum.
Definition MSData.hpp:471
std::string id
a unique identifier for this spectrum. It should be expected that external files may use this identif...
Definition MSData.hpp:476
size_t index
the zero-based, consecutive index of the spectrum in the SpectrumList.
Definition MSData.hpp:473
Simple writeable in-memory implementation of SpectrumList.
Definition MSData.hpp:717
#define unit_assert(x)
Definition unit.hpp:85
#define unit_assert_operator_equal(expected, actual)
Definition unit.hpp:92

References pwiz::msdata::SpectrumList::dataProcessingPtr(), pwiz::msdata::SpectrumList::find(), pwiz::msdata::SpectrumList::findAbbreviated(), pwiz::msdata::SpectrumList::findNameValue(), pwiz::msdata::SpectrumIdentity::id, pwiz::msdata::SpectrumIdentity::index, pwiz::msdata::MZIntensityPair::intensity, MS_intensity_array, MS_ionization_type, MS_m_z_array, MS_MSn_spectrum, MS_number_of_detector_counts, pwiz::msdata::MZIntensityPair::mz, pwiz::msdata::MSData::run, pwiz::msdata::SpectrumList::size(), pwiz::msdata::SpectrumList::spectrum(), pwiz::msdata::SpectrumList::spectrumIdentity(), pwiz::msdata::Run::spectrumListPtr, unit_assert, and unit_assert_operator_equal.

Referenced by main().

◆ testChromatograms()

void testChromatograms ( )

Definition at line 168 of file MSDataTest.cpp.

169{
171
172 for (int i=0; i<3; i++)
173 {
174 vector<TimeIntensityPair> pairs;
175 for (int j=0; j<10; j++) pairs.push_back(TimeIntensityPair(j, 10*i+j));
176 cls.chromatograms.push_back(ChromatogramPtr(new Chromatogram));
177 cls.chromatograms.back()->setTimeIntensityPairs(pairs, UO_second, MS_number_of_detector_counts);
178 }
179
180 DataProcessingPtr dp(new DataProcessing("dp"));
181 cls.dp = dp;
182
183 ChromatogramList& cl = cls;
184
185 unit_assert(cl.size() == 3);
186
187 for (size_t i=0; i<3; i++)
188 {
189 vector<TimeIntensityPair> result;
190 cl.chromatogram(i)->getTimeIntensityPairs(result);
191 unit_assert(result.size() == 10);
192 for (size_t j=0; j<10; j++)
193 unit_assert(result[j].time==j && result[j].intensity==10*i+j);
194 }
195
196 unit_assert(cl.dataProcessingPtr().get() &&
197 cl.dataProcessingPtr()->id == "dp");
198}
Interface for accessing chromatograms, which may be stored in memory or backed by a data file (RAW,...
Definition MSData.hpp:757
virtual size_t size() const =0
returns the number of chromatograms
virtual ChromatogramPtr chromatogram(size_t index, bool getBinaryData=false) const =0
retrieve a chromatogram by index
virtual const boost::shared_ptr< const DataProcessing > dataProcessingPtr() const
returns the data processing affecting spectra retrieved through this interface
UO_second
second: A time unit which is equal to the duration of 9 192 631 770 periods of the radiation correspo...
Definition cv.hpp:13833
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition MSData.hpp:624
A single chromatogram.
Definition MSData.hpp:578
Simple writeable in-memory implementation of ChromatogramList.
Definition MSData.hpp:791
std::vector< ChromatogramPtr > chromatograms
Definition MSData.hpp:792
The data point type of a chromatogram.
Definition MSData.hpp:447

References pwiz::msdata::ChromatogramList::chromatogram(), pwiz::msdata::ChromatogramListSimple::chromatograms, pwiz::msdata::ChromatogramList::dataProcessingPtr(), pwiz::msdata::ChromatogramListSimple::dp, MS_number_of_detector_counts, pwiz::msdata::ChromatogramList::size(), unit_assert, and UO_second.

Referenced by main().

◆ testIDParsing()

void testIDParsing ( )

Definition at line 201 of file MSDataTest.cpp.

202{
203 string id = "hair=blue favorite=420 age=36.175 upsideDown=1";
204
205 map<string,string> parsedID = id::parse(id);
206 unit_assert(parsedID.size() == 4);
207
208 unit_assert(id::value(id, "hair") == "blue");
209 unit_assert(id::valueAs<int>(id, "favorite") == 420);
210 unit_assert_equal(id::valueAs<double>(id, "age"), 36.175, 1e-6);
211 unit_assert(id::valueAs<bool>(id, "upsideDown") == true);
212
213 unit_assert(id::abbreviate(id) == "blue.420.36.175.1");
214 unit_assert(id::abbreviate(id, ',') == "blue,420,36.175,1");
215
216 id = "controllerType=0 controllerNumber=1 scan=123";
221 unit_assert(id::abbreviate(id) == "0.1.123");
222 unit_assert(id::abbreviate(id, ',') == "0,1,123");
223
225
226 id = "spectrum=123";
230
231 id = "scan=123";
240 unit_assert(id::abbreviate(id) == "123");
241 unit_assert(id::abbreviate(id, ',') == "123");
242
243 id = "sample=1 period=2 cycle=123 experiment=3";
246 unit_assert(id::abbreviate(id) == "1.2.123.3");
247 unit_assert(id::abbreviate(id, ',') == "1,2,123,3");
248}
MS_spectrum_identifier_nativeID_format
spectrum identifier nativeID format: Native format defined by spectrum=xsd:nonNegativeInteger.
Definition cv.hpp:3003
MS_Thermo_nativeID_format
Thermo nativeID format: Native format defined by controllerType=xsd:nonNegativeInteger controllerNumb...
Definition cv.hpp:2976
MS_WIFF_nativeID_format
WIFF nativeID format: Native format defined by sample=xsd:nonNegativeInteger period=xsd:nonNegativeIn...
Definition cv.hpp:2982
MS_scan_number_only_nativeID_format
scan number only nativeID format: Native format defined by scan=xsd:nonNegativeInteger.
Definition cv.hpp:3000
MS_Bruker_BAF_nativeID_format
Bruker BAF nativeID format: Native format defined by scan=xsd:nonNegativeInteger.
Definition cv.hpp:2988
CVID_Unknown
Definition cv.hpp:114
MS_multiple_peak_list_nativeID_format
multiple peak list nativeID format: Native format defined by index=xsd:nonNegativeInteger.
Definition cv.hpp:2994
MS_no_nativeID_format
no nativeID format: No nativeID format indicates that the file tagged with this term does not contain...
Definition cv.hpp:3171
MS_Bruker_Agilent_YEP_nativeID_format
Bruker/Agilent YEP nativeID format: Native format defined by scan=xsd:nonNegativeInteger.
Definition cv.hpp:2985
PWIZ_API_DECL std::string translateScanNumberToNativeID(CVID nativeIDFormat, const std::string &scanNumber)
translates a "scan number" to a string that is correct for the given nativeID format; semantic validi...
PWIZ_API_DECL std::map< std::string, std::string > parse(const std::string &id)
parses an id string into a map<string,string>
PWIZ_API_DECL std::string abbreviate(const std::string &id, char delimiter='.')
abbreviates a nativeID ("name1=value1 name2=value2" translates to "value1.value2")
PWIZ_API_DECL std::string value(const std::string &id, const std::string &name)
convenience function to extract a named value from an id string
PWIZ_API_DECL std::string translateNativeIDToScanNumber(CVID nativeIDFormat, const std::string &id)
translates a nativeID in the given nativeID format to a simple integer "scan number"; some nativeID f...
#define unit_assert_equal(x, y, epsilon)
Definition unit.hpp:99

References pwiz::msdata::id::abbreviate(), CVID_Unknown, MS_Bruker_Agilent_YEP_nativeID_format, MS_Bruker_BAF_nativeID_format, MS_multiple_peak_list_nativeID_format, MS_no_nativeID_format, MS_scan_number_only_nativeID_format, MS_spectrum_identifier_nativeID_format, MS_Thermo_nativeID_format, MS_WIFF_nativeID_format, pwiz::msdata::id::parse(), pwiz::msdata::id::translateNativeIDToScanNumber(), pwiz::msdata::id::translateScanNumberToNativeID(), unit_assert, unit_assert_equal, and pwiz::msdata::id::value().

Referenced by main().

◆ testAllDataProcessing()

void testAllDataProcessing ( )

Definition at line 251 of file MSDataTest.cpp.

252{
253 MSData msd;
255 msd.run.spectrumListPtr = sl;
256
257 DataProcessingPtr realDeal(new DataProcessing("dp"));
258 DataProcessingPtr poser(new DataProcessing("dp"));
259
260 msd.dataProcessingPtrs.push_back(realDeal);
261 sl->dp = poser;
262
263 // test allDataProcessingPtrs()
264 vector<DataProcessingPtr> all = msd.allDataProcessingPtrs();
265 unit_assert_operator_equal(1, all.size());
266 unit_assert_operator_equal(realDeal, all[0]);
267}
boost::shared_ptr< SpectrumListSimple > SpectrumListSimplePtr
Definition MSData.hpp:731
std::vector< DataProcessingPtr > allDataProcessingPtrs() const
return dataProcessingPtrs augmented by the dataProcessingPtr() set in SpectrumList and/or Chromatogra...
std::vector< DataProcessingPtr > dataProcessingPtrs
list and descriptions of data processing applied to this data.
Definition MSData.hpp:880

References pwiz::msdata::MSData::allDataProcessingPtrs(), pwiz::msdata::MSData::dataProcessingPtrs, pwiz::msdata::MSData::run, pwiz::msdata::Run::spectrumListPtr, and unit_assert_operator_equal.

Referenced by main().

◆ main()

int main ( int  argc,
char *  argv[] 
)

Definition at line 270 of file MSDataTest.cpp.

271{
272 TEST_PROLOG(argc, argv)
273
274 try
275 {
280 }
281 catch (exception& e)
282 {
283 TEST_FAILED(e.what())
284 }
285 catch (...)
286 {
287 TEST_FAILED("Caught unknown exception.")
288 }
289
291}
void testSpectrumListSimple()
void testIDParsing()
void testChromatograms()
void testAllDataProcessing()
#define TEST_EPILOG
Definition unit.hpp:183
#define TEST_FAILED(x)
Definition unit.hpp:177
#define TEST_PROLOG(argc, argv)
Definition unit.hpp:175

References TEST_EPILOG, TEST_FAILED, TEST_PROLOG, testAllDataProcessing(), testChromatograms(), testIDParsing(), and testSpectrumListSimple().