ProteoWizard
Functions | Variables
Serializer_MSn_Test.cpp File Reference
#include "Serializer_MSn.hpp"
#include "Serializer_mzML.hpp"
#include "Diff.hpp"
#include "TextWriter.hpp"
#include "pwiz/utility/misc/unit.hpp"
#include "boost/iostreams/positioning.hpp"
#include "pwiz/utility/misc/Std.hpp"
#include <cstring>

Go to the source code of this file.

Functions

void initializeTinyMS1 (MSData &msd)
 
void initializeTinyMS2 (MSData &msd)
 
void testWriteReadMS1 (const MSData &msd)
 
void testWriteReadBMS1 (const MSData &msd)
 
void testWriteReadCMS1 (const MSData &msd)
 
void testWriteReadMS2 (const MSData &msd)
 
void testWriteReadBMS2 (const MSData &msd)
 
void testWriteReadCMS2 (const MSData &msd)
 
void testWriteRead ()
 
int main (int argc, char *argv[])
 

Variables

ostream * os_ = 0
 

Function Documentation

void initializeTinyMS1 ( MSData msd)

Definition at line 39 of file Serializer_MSn_Test.cpp.

References pwiz::msdata::Spectrum::defaultArrayLength, pwiz::msdata::FileDescription::fileContent, pwiz::msdata::MSData::fileDescription, pwiz::msdata::Spectrum::getIntensityArray(), pwiz::msdata::Spectrum::getMZArray(), pwiz::msdata::SpectrumIdentity::id, pwiz::msdata::SpectrumIdentity::index, MS_base_peak_intensity, MS_base_peak_m_z, MS_centroid_spectrum, MS_highest_observed_m_z, MS_lowest_observed_m_z, MS_MS2_file, MS_ms_level, MS_MSn_spectrum, MS_number_of_counts, MS_scan_number_only_nativeID_format, MS_scan_start_time, MS_total_ion_current, pwiz::msdata::MSData::run, pwiz::msdata::Spectrum::scanList, pwiz::msdata::ScanList::scans, pwiz::data::ParamContainer::set(), pwiz::msdata::Spectrum::setMZIntensityArrays(), pwiz::msdata::FileDescription::sourceFilePtrs, pwiz::msdata::Run::spectrumListPtr, and UO_second.

Referenced by testWriteRead().

40 {
42  fc.set(MS_MSn_spectrum);
44 
45  SourceFilePtr sourceFile(new SourceFile);
46  sourceFile->set(MS_scan_number_only_nativeID_format);
47  sourceFile->set(MS_MS2_file);
48  msd.fileDescription.sourceFilePtrs.push_back(sourceFile);
49 
50  shared_ptr<SpectrumListSimple> spectrumList(new SpectrumListSimple);
51  msd.run.spectrumListPtr = spectrumList;
52  spectrumList->spectra.push_back(SpectrumPtr(new Spectrum));
53 
54  Spectrum& s20 = *spectrumList->spectra[0];
55  s20.id = "scan=1";
56  s20.index = 0;
57 
58  s20.set(MS_MSn_spectrum);
59  s20.set(MS_ms_level, 1);
60 
64  s20.set(MS_base_peak_m_z, 0);
65  s20.set(MS_base_peak_intensity, 20);
66  s20.set(MS_total_ion_current, 110);
67 
68  s20.scanList.scans.push_back(Scan());
69  Scan& s20scan = s20.scanList.scans.back();
70  s20scan.set(MS_scan_start_time, 4, UO_second);
71 
72  s20.setMZIntensityArrays(vector<double>(), vector<double>(), MS_number_of_counts);
73  vector<double>& s20_mz = s20.getMZArray()->data;
74  vector<double>& s20_intensity = s20.getIntensityArray()->data;
75 
76  for (int i=0; i<10; i++)
77  s20_mz.push_back(i*2);
78 
79  for (int i=0; i<10; i++)
80  s20_intensity.push_back((10-i)*2);
81 
82  s20.defaultArrayLength = s20_mz.size();
83 
84 } // initializeTinyMS1()
void initializeTinyMS2 ( MSData msd)

Definition at line 86 of file Serializer_MSn_Test.cpp.

References pwiz::msdata::Spectrum::defaultArrayLength, pwiz::msdata::FileDescription::fileContent, pwiz::msdata::MSData::fileDescription, pwiz::msdata::Spectrum::getIntensityArray(), pwiz::msdata::Spectrum::getMZArray(), pwiz::msdata::SpectrumIdentity::id, pwiz::msdata::SpectrumIdentity::index, pwiz::msdata::Precursor::isolationWindow, MS_base_peak_intensity, MS_base_peak_m_z, MS_centroid_spectrum, MS_highest_observed_m_z, MS_isolation_window_target_m_z, MS_lowest_observed_m_z, MS_m_z, MS_MS2_file, MS_ms_level, MS_MSn_spectrum, MS_number_of_counts, MS_possible_charge_state, MS_scan_number_only_nativeID_format, MS_scan_start_time, MS_selected_ion_m_z, MS_total_ion_current, pwiz::msdata::Spectrum::precursors, pwiz::msdata::MSData::run, pwiz::msdata::Spectrum::scanList, pwiz::msdata::ScanList::scans, pwiz::msdata::Precursor::selectedIons, pwiz::data::ParamContainer::set(), pwiz::msdata::Spectrum::setMZIntensityArrays(), pwiz::msdata::FileDescription::sourceFilePtrs, pwiz::msdata::Run::spectrumListPtr, and UO_second.

Referenced by testWriteRead().

87 {
89  fc.set(MS_MSn_spectrum);
91 
92  SourceFilePtr sourceFile(new SourceFile);
93  sourceFile->set(MS_scan_number_only_nativeID_format);
94  sourceFile->set(MS_MS2_file);
95  msd.fileDescription.sourceFilePtrs.push_back(sourceFile);
96 
97  shared_ptr<SpectrumListSimple> spectrumList(new SpectrumListSimple);
98  msd.run.spectrumListPtr = spectrumList;
99  spectrumList->spectra.push_back(SpectrumPtr(new Spectrum));
100 
101  Spectrum& s20 = *spectrumList->spectra[0];
102  s20.id = "scan=1";
103  s20.index = 0;
104 
105  s20.set(MS_MSn_spectrum);
106  s20.set(MS_ms_level, 2);
107 
109  s20.set(MS_lowest_observed_m_z, 0);
110  s20.set(MS_highest_observed_m_z, 18);
111  s20.set(MS_base_peak_m_z, 0);
112  s20.set(MS_base_peak_intensity, 20);
113  s20.set(MS_total_ion_current, 110);
114 
115  s20.precursors.resize(1);
116  Precursor& precursor = s20.precursors.front();
117  precursor.selectedIons.resize(1);
118  precursor.selectedIons[0].set(MS_selected_ion_m_z, 445.34, MS_m_z);
119  precursor.selectedIons[0].set(MS_possible_charge_state, 2);
121 
122  s20.scanList.scans.push_back(Scan());
123  Scan& s20scan = s20.scanList.scans.back();
124  s20scan.set(MS_scan_start_time, 4, UO_second);
125 
126  s20.setMZIntensityArrays(vector<double>(), vector<double>(), MS_number_of_counts);
127  vector<double>& s20_mz = s20.getMZArray()->data;
128  vector<double>& s20_intensity = s20.getIntensityArray()->data;
129 
130  for (int i=0; i<10; i++)
131  s20_mz.push_back(i*2);
132 
133  for (int i=0; i<10; i++)
134  s20_intensity.push_back((10-i)*2);
135 
136  s20.defaultArrayLength = s20_mz.size();
137 
138 } // initializeTinyMS2()
void testWriteReadMS1 ( const MSData msd)

Definition at line 141 of file Serializer_MSn_Test.cpp.

References diff(), pwiz::msdata::DiffConfig::ignoreMetadata, pwiz::msdata::MSn_Type_MS1, os_, pwiz::msdata::Serializer_MSn::read(), unit_assert, and pwiz::msdata::Serializer_MSn::write().

Referenced by testWriteRead().

142 {
143  Serializer_MSn serializer(MSn_Type_MS1);
144 
145  ostringstream oss;
146  serializer.write(oss, msd);
147 
148  if (os_) *os_ << "oss:\n" << oss.str() << endl;
149 
150  MSData msd2;
151  shared_ptr<istream> iss(new istringstream(oss.str()));
152  serializer.read(iss, msd2);
153 
154  DiffConfig config;
155  config.ignoreMetadata = true;
156  Diff<MSData, DiffConfig> diff(msd, msd2, config);
157 
158  if (os_ && diff) *os_ << diff << endl;
159  unit_assert(!diff);
160 }
void testWriteReadBMS1 ( const MSData msd)

Definition at line 162 of file Serializer_MSn_Test.cpp.

References diff(), pwiz::msdata::DiffConfig::ignoreDataProcessing, pwiz::msdata::DiffConfig::ignoreMetadata, pwiz::msdata::MSn_Type_BMS1, os_, pwiz::msdata::Serializer_MSn::read(), unit_assert, and pwiz::msdata::Serializer_MSn::write().

Referenced by testWriteRead().

163 {
164  Serializer_MSn serializer(MSn_Type_BMS1);
165 
166  ostringstream oss;
167  serializer.write(oss, msd);
168 
169  if (os_) *os_ << "oss:\n" << oss.str() << endl;
170 
171  MSData msd2;
172  shared_ptr<istream> iss(new istringstream(oss.str()));
173  serializer.read(iss, msd2);
174 
175  DiffConfig config;
176  config.ignoreMetadata = true;
177  config.ignoreDataProcessing = true;
178  Diff<MSData, DiffConfig> diff(msd, msd2, config);
179  if (os_ && diff) *os_ << diff << endl;
180  unit_assert(!diff);
181 }
void testWriteReadCMS1 ( const MSData msd)

Definition at line 183 of file Serializer_MSn_Test.cpp.

References diff(), pwiz::msdata::DiffConfig::ignoreDataProcessing, pwiz::msdata::DiffConfig::ignoreMetadata, pwiz::msdata::MSn_Type_CMS1, os_, pwiz::msdata::Serializer_MSn::read(), unit_assert, and pwiz::msdata::Serializer_MSn::write().

Referenced by testWriteRead().

184 {
185  Serializer_MSn serializer(MSn_Type_CMS1);
186 
187  ostringstream oss;
188  serializer.write(oss, msd);
189 
190  if (os_) *os_ << "oss:\n" << oss.str() << endl;
191 
192  MSData msd2;
193  shared_ptr<istream> iss(new istringstream(oss.str()));
194  serializer.read(iss, msd2);
195 
196  DiffConfig config;
197  config.ignoreMetadata = true;
198  config.ignoreDataProcessing = true;
199  Diff<MSData, DiffConfig> diff(msd, msd2, config);
200  if (os_ && diff) *os_ << diff << endl;
201  unit_assert(!diff);
202 }
void testWriteReadMS2 ( const MSData msd)

Definition at line 204 of file Serializer_MSn_Test.cpp.

References diff(), pwiz::msdata::DiffConfig::ignoreMetadata, pwiz::msdata::MSn_Type_MS2, os_, pwiz::msdata::Serializer_MSn::read(), unit_assert, and pwiz::msdata::Serializer_MSn::write().

Referenced by testWriteRead().

205 {
206  Serializer_MSn serializer(MSn_Type_MS2);
207 
208  ostringstream oss;
209  serializer.write(oss, msd);
210 
211  if (os_) *os_ << "oss:\n" << oss.str() << endl;
212 
213  MSData msd2;
214  shared_ptr<istream> iss(new istringstream(oss.str()));
215  serializer.read(iss, msd2);
216 
217  DiffConfig config;
218  config.ignoreMetadata = true;
219  Diff<MSData, DiffConfig> diff(msd, msd2, config);
220  if (os_ && diff) *os_ << diff << endl;
221  unit_assert(!diff);
222 }
void testWriteReadBMS2 ( const MSData msd)

Definition at line 224 of file Serializer_MSn_Test.cpp.

References diff(), pwiz::msdata::DiffConfig::ignoreDataProcessing, pwiz::msdata::DiffConfig::ignoreMetadata, pwiz::msdata::MSn_Type_BMS2, os_, pwiz::msdata::Serializer_MSn::read(), unit_assert, and pwiz::msdata::Serializer_MSn::write().

Referenced by testWriteRead().

225 {
226  Serializer_MSn serializer(MSn_Type_BMS2);
227 
228  ostringstream oss;
229  serializer.write(oss, msd);
230 
231  if (os_) *os_ << "oss:\n" << oss.str() << endl;
232 
233  MSData msd2;
234  shared_ptr<istream> iss(new istringstream(oss.str()));
235  serializer.read(iss, msd2);
236 
237  DiffConfig config;
238  config.ignoreMetadata = true;
239  config.ignoreDataProcessing = true;
240  Diff<MSData, DiffConfig> diff(msd, msd2, config);
241  if (os_ && diff) *os_ << diff << endl;
242  unit_assert(!diff);
243 }
void testWriteReadCMS2 ( const MSData msd)

Definition at line 245 of file Serializer_MSn_Test.cpp.

References diff(), pwiz::msdata::DiffConfig::ignoreDataProcessing, pwiz::msdata::DiffConfig::ignoreMetadata, pwiz::msdata::MSn_Type_CMS2, os_, pwiz::msdata::Serializer_MSn::read(), unit_assert, and pwiz::msdata::Serializer_MSn::write().

Referenced by testWriteRead().

246 {
247  Serializer_MSn serializer(MSn_Type_CMS2);
248 
249  ostringstream oss;
250  serializer.write(oss, msd);
251 
252  if (os_) *os_ << "oss:\n" << oss.str() << endl;
253 
254  MSData msd2;
255  shared_ptr<istream> iss(new istringstream(oss.str()));
256  serializer.read(iss, msd2);
257 
258  DiffConfig config;
259  config.ignoreMetadata = true;
260  config.ignoreDataProcessing = true;
261  Diff<MSData, DiffConfig> diff(msd, msd2, config);
262  if (os_ && diff) *os_ << diff << endl;
263  unit_assert(!diff);
264 }
void testWriteRead ( )

Definition at line 266 of file Serializer_MSn_Test.cpp.

References initializeTinyMS1(), initializeTinyMS2(), testWriteReadBMS1(), testWriteReadBMS2(), testWriteReadCMS1(), testWriteReadCMS2(), testWriteReadMS1(), and testWriteReadMS2().

267 {
268  MSData msd1, msd2;
269 
270  initializeTinyMS1(msd1);
271  initializeTinyMS2(msd2);
272 
273  testWriteReadMS1(msd1);
274  testWriteReadBMS1(msd1);
275  testWriteReadCMS1(msd1);
276  testWriteReadMS2(msd2);
277  testWriteReadBMS2(msd2);
278  testWriteReadCMS2(msd2);
279 }
int main ( int  argc,
char *  argv[] 
)

Definition at line 282 of file Serializer_MSn_Test.cpp.

References os_, TEST_EPILOG, TEST_FAILED, TEST_PROLOG, and testWriteRead().

283 {
284  TEST_PROLOG(argc, argv)
285 
286  try
287  {
288  if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout;
289  testWriteRead();
290  }
291  catch (exception& e)
292  {
293  TEST_FAILED(e.what())
294  }
295  catch (...)
296  {
297  TEST_FAILED("Caught unknown exception.")
298  }
299 
301 }

Variable Documentation

ostream* os_ = 0

Definition at line 36 of file Serializer_MSn_Test.cpp.