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SwathFileConsumer.h
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34 
35 #ifndef OPENMS_FORMAT_DATAACCESS_SWATHFILECONSUMER_H
36 #define OPENMS_FORMAT_DATAACCESS_SWATHFILECONSUMER_H
37 
38 #include <boost/cast.hpp>
39 
40 // Datastructures
43 
44 // Consumers
47 
48 // Helpers
51 
54 
55 #ifdef _OPENMP
56 #include <omp.h>
57 #endif
58 
59 namespace OpenMS
60 {
61 
99  class OPENMS_DLLAPI FullSwathFileConsumer :
101  {
102 
103 public:
107 
109  ms1_map_(), // initialize to null
110  consuming_possible_(true),
111  use_external_boundaries_(false),
112  correct_window_counter_(0)
113  {
114  use_external_boundaries_ = !swath_map_boundaries_.empty();
115  }
116 
124  FullSwathFileConsumer(std::vector<OpenSwath::SwathMap> swath_boundaries) :
125  swath_map_boundaries_(swath_boundaries),
126  ms1_map_(), // initialize to null
127  consuming_possible_(true),
128  use_external_boundaries_(false),
129  correct_window_counter_(0)
130  {
131  use_external_boundaries_ = !swath_map_boundaries_.empty();
132  }
133 
135 
137  void setExperimentalSettings(const ExperimentalSettings& exp) {settings_ = exp; }
138 
150  void retrieveSwathMaps(std::vector<OpenSwath::SwathMap>& maps)
151  {
152  consuming_possible_ = false; // make consumption of further spectra / chromatograms impossible
153  ensureMapsAreFilled_();
154  if (ms1_map_)
155  {
158  map.lower = -1;
159  map.upper = -1;
160  map.center = -1;
161  map.ms1 = true;
162  maps.push_back(map);
163  }
164 
165  // Print warning if the lower/upper window could not be determined and we
166  // required manual determination of the boundaries.
167  if (!use_external_boundaries_ && correct_window_counter_ != swath_maps_.size())
168  {
169  std::cout << "WARNING: Could not correctly read the upper/lower limits of the SWATH windows from your input file. Read " <<
170  correct_window_counter_ << " correct (non-zero) window limits (expected " << swath_maps_.size() << " windows)." << std::endl;
171  }
172 
173  size_t nonempty_maps = 0;
174  for (Size i = 0; i < swath_maps_.size(); i++)
175  {
178  map.lower = swath_map_boundaries_[i].lower;
179  map.upper = swath_map_boundaries_[i].upper;
180  map.center = swath_map_boundaries_[i].center;
181  map.ms1 = false;
182  maps.push_back(map);
183  if (map.sptr->getNrSpectra() > 0) {nonempty_maps++;}
184  }
185 
186  if (nonempty_maps != swath_map_boundaries_.size())
187  {
188  std::cout << "WARNING: The number nonempty maps found in the input file (" << nonempty_maps << ") is not equal to the number of provided swath window boundaries (" <<
189  swath_map_boundaries_.size() << "). Please check your input." << std::endl;
190  }
191 
192 
193  }
194 
197  {
198  std::cerr << "Read chromatogram while reading SWATH files, did not expect that!" << std::endl;
199  }
200 
207  {
208  if (!consuming_possible_)
209  {
210  throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__,
211  "FullSwathFileConsumer cannot consume any more spectra after retrieveSwathMaps has been called already");
212  }
213 
214  if (s.getMSLevel() == 1)
215  {
216  consumeMS1Spectrum_(s);
217  }
218  else
219  {
220  if (s.getPrecursors().empty())
221  {
222  throw Exception::InvalidParameter(__FILE__, __LINE__, __PRETTY_FUNCTION__,
223  "Swath scan does not provide a precursor.");
224  }
225 
226  const std::vector<Precursor> prec = s.getPrecursors();
227  double center = prec[0].getMZ();
228  double lower = prec[0].getMZ() - prec[0].getIsolationWindowLowerOffset();
229  double upper = prec[0].getMZ() + prec[0].getIsolationWindowUpperOffset();
230  bool found = false;
231 
232  // Check if enough information is present to infer the swath
233  if (center <= 0.0)
234  {
235  throw Exception::InvalidParameter(__FILE__, __LINE__, __PRETTY_FUNCTION__,
236  "Swath scan does not provide any precursor isolation information.");
237  }
238 
239  // try to match the current scan to one of the already known windows
240  for (Size i = 0; i < swath_map_boundaries_.size(); i++)
241  {
242  // We group by the precursor mz (center of the window) since this
243  // should be present in all SWATH scans.
244  if (std::fabs(center - swath_map_boundaries_[i].center) < 1e-6)
245  {
246  found = true;
247  consumeSwathSpectrum_(s, i);
248  }
249  }
250  if (!found)
251  {
252  if (use_external_boundaries_)
253  {
254  throw Exception::InvalidParameter(__FILE__, __LINE__, __PRETTY_FUNCTION__,
255  String("Encountered SWATH scan with boundary ") + center + " m/z which was not present in the provided windows.");
256  }
257  else
258  {
259  consumeSwathSpectrum_(s, swath_map_boundaries_.size());
260 
261  // we found a new SWATH window
262  if (lower > 0.0 && upper > 0.0)
263  {correct_window_counter_++;}
264 
265  OpenSwath::SwathMap boundary;
266  boundary.lower = lower;
267  boundary.upper = upper;
268  boundary.center = center;
269  swath_map_boundaries_.push_back(boundary);
270 
271  LOG_DEBUG << "Adding Swath centered at " << center
272  << " m/z with an isolation window of " << lower << " to " << upper
273  << " m/z." << std::endl;
274  }
275  }
276  }
277  }
278 
279 protected:
280 
288  virtual void consumeSwathSpectrum_(MapType::SpectrumType& s, size_t swath_nr) = 0;
289 
296  virtual void consumeMS1Spectrum_(MapType::SpectrumType& s) = 0;
297 
303  virtual void ensureMapsAreFilled_() = 0;
304 
306  std::vector<OpenSwath::SwathMap> swath_map_boundaries_;
307 
309  std::vector<boost::shared_ptr<MSExperiment<> > > swath_maps_;
310  boost::shared_ptr<MSExperiment<> > ms1_map_;
311 
313  // (MSExperiment has no constructor using ExperimentalSettings)
315 
318 
321 
324 
325  };
326 
333  class OPENMS_DLLAPI RegularSwathFileConsumer :
334  public FullSwathFileConsumer
335  {
336 
337 public:
341 
343 
344  RegularSwathFileConsumer(std::vector<OpenSwath::SwathMap> known_window_boundaries) :
345  FullSwathFileConsumer(known_window_boundaries) {}
346 
347 protected:
349  {
350  boost::shared_ptr<MSExperiment<Peak1D> > exp(new MSExperiment<Peak1D>(settings_));
351  swath_maps_.push_back(exp);
352  }
353 
355  {
356  while (swath_maps_.size() <= swath_nr)
357  {
358  addNewSwathMap_();
359  }
360 
361  swath_maps_[swath_nr]->addSpectrum(s);
362  }
363 
364  void addMS1Map_()
365  {
366  boost::shared_ptr<MSExperiment<Peak1D> > exp(new MSExperiment<Peak1D>(settings_));
367  ms1_map_ = exp;
368  }
369 
371  {
372  if (!ms1_map_)
373  {
374  addMS1Map_();
375  }
376  ms1_map_->addSpectrum(s);
377  }
378 
380  };
381 
391  class OPENMS_DLLAPI CachedSwathFileConsumer :
392  public FullSwathFileConsumer
393  {
394 
395 public:
399 
400  CachedSwathFileConsumer(String cachedir, String basename, Size nr_ms1_spectra, std::vector<int> nr_ms2_spectra) :
401  ms1_consumer_(NULL),
402  swath_consumers_(),
403  cachedir_(cachedir),
404  basename_(basename),
405  nr_ms1_spectra_(nr_ms1_spectra),
406  nr_ms2_spectra_(nr_ms2_spectra)
407  {}
408 
409  CachedSwathFileConsumer(std::vector<OpenSwath::SwathMap> known_window_boundaries,
410  String cachedir, String basename, Size nr_ms1_spectra, std::vector<int> nr_ms2_spectra) :
411  FullSwathFileConsumer(known_window_boundaries),
412  ms1_consumer_(NULL),
413  swath_consumers_(),
414  cachedir_(cachedir),
415  basename_(basename),
416  nr_ms1_spectra_(nr_ms1_spectra),
417  nr_ms2_spectra_(nr_ms2_spectra)
418  {}
419 
421  {
422  // Properly delete the MSDataCachedConsumer -> free memory and _close_ file stream
423  while (!swath_consumers_.empty())
424  {
425  delete swath_consumers_.back();
426  swath_consumers_.pop_back();
427  }
428  if (ms1_consumer_ != NULL)
429  {
430  delete ms1_consumer_;
431  ms1_consumer_ = NULL;
432  }
433  }
434 
435 protected:
437  {
438  String meta_file = cachedir_ + basename_ + "_" + String(swath_consumers_.size()) + ".mzML";
439  String cached_file = meta_file + ".cached";
440  MSDataCachedConsumer* consumer = new MSDataCachedConsumer(cached_file, true);
441  consumer->setExpectedSize(nr_ms2_spectra_[swath_consumers_.size()], 0);
442  swath_consumers_.push_back(consumer);
443 
444  // maps for meta data
445  boost::shared_ptr<MSExperiment<Peak1D> > exp(new MSExperiment<Peak1D>(settings_));
446  swath_maps_.push_back(exp);
447  }
448 
450  {
451  while (swath_maps_.size() <= swath_nr)
452  {
453  addNewSwathMap_();
454  }
455  swath_consumers_[swath_nr]->consumeSpectrum(s);
456  swath_maps_[swath_nr]->addSpectrum(s); // append for the metadata (actual data is deleted)
457  }
458 
459  void addMS1Map_()
460  {
461  String meta_file = cachedir_ + basename_ + "_ms1.mzML";
462  String cached_file = meta_file + ".cached";
463  ms1_consumer_ = new MSDataCachedConsumer(cached_file, true);
464  ms1_consumer_->setExpectedSize(nr_ms1_spectra_, 0);
465  boost::shared_ptr<MSExperiment<Peak1D> > exp(new MSExperiment<Peak1D>(settings_));
466  ms1_map_ = exp;
467  }
468 
470  {
471  if (ms1_consumer_ == NULL)
472  {
473  addMS1Map_();
474  }
475  ms1_consumer_->consumeSpectrum(s);
476  ms1_map_->addSpectrum(s); // append for the metadata (actual data is deleted)
477  }
478 
480  {
481  size_t swath_consumers_size = swath_consumers_.size();
482  bool have_ms1 = (ms1_consumer_ != NULL);
483 
484  // Properly delete the MSDataCachedConsumer -> free memory and _close_ file stream
485  // The file streams to the cached data on disc can and should be closed
486  // here safely. Since ensureMapsAreFilled_ is called after consuming all
487  // the spectra, there will be no more spectra to append but the client
488  // might already want to read after this call, so all data needs to be
489  // present on disc and the file streams closed.
490  //
491  // TODO merge with destructor code into own function!
492  while (!swath_consumers_.empty())
493  {
494  delete swath_consumers_.back();
495  swath_consumers_.pop_back();
496  }
497  if (ms1_consumer_ != NULL)
498  {
499  delete ms1_consumer_;
500  ms1_consumer_ = NULL;
501  }
502 
503  if (have_ms1)
504  {
505  boost::shared_ptr<MSExperiment<Peak1D> > exp(new MSExperiment<Peak1D>);
506  String meta_file = cachedir_ + basename_ + "_ms1.mzML";
507  // write metadata to disk and store the correct data processing tag
508  CachedmzML().writeMetadata(*ms1_map_, meta_file, true);
509  MzMLFile().load(meta_file, *exp.get());
510  ms1_map_ = exp;
511  }
512 
513 #ifdef _OPENMP
514 #pragma omp parallel for
515 #endif
516  for (SignedSize i = 0; i < boost::numeric_cast<SignedSize>(swath_consumers_size); i++)
517  {
518  boost::shared_ptr<MSExperiment<Peak1D> > exp(new MSExperiment<Peak1D>);
519  String meta_file = cachedir_ + basename_ + "_" + String(i) + ".mzML";
520  // write metadata to disk and store the correct data processing tag
521  CachedmzML().writeMetadata(*swath_maps_[i], meta_file, true);
522  MzMLFile().load(meta_file, *exp.get());
523  swath_maps_[i] = exp;
524  }
525  }
526 
528  std::vector<MSDataCachedConsumer*> swath_consumers_;
529 
533  std::vector<int> nr_ms2_spectra_;
534  };
535 }
536 
537 #endif
CachedSwathFileConsumer(std::vector< OpenSwath::SwathMap > known_window_boundaries, String cachedir, String basename, Size nr_ms1_spectra, std::vector< int > nr_ms2_spectra)
Definition: SwathFileConsumer.h:409
MSExperiment MapType
Definition: SwathFileConsumer.h:104
static OpenSwath::SpectrumAccessPtr getSpectrumAccessOpenMSPtr(boost::shared_ptr< OpenMS::MSExperiment< OpenMS::Peak1D > > exp)
Simple Factory method to get a SpectrumAccess Ptr from an MSExperiment.
void ensureMapsAreFilled_()
Callback function after the reading is complete.
Definition: SwathFileConsumer.h:379
bool use_external_boundaries_
Whether to use external input for SWATH boundaries.
Definition: SwathFileConsumer.h:320
bool consuming_possible_
Whether further spectra can still be consumed.
Definition: SwathFileConsumer.h:317
A more convenient string class.
Definition: String.h:57
void setExperimentalSettings(const ExperimentalSettings &exp)
Set experimental settings (meta-data) of the data to be consumed.
Definition: SwathFileConsumer.h:137
RegularSwathFileConsumer()
Definition: SwathFileConsumer.h:342
RegularSwathFileConsumer(std::vector< OpenSwath::SwathMap > known_window_boundaries)
Definition: SwathFileConsumer.h:344
UInt getMSLevel() const
Returns the MS level.
Definition: MSSpectrum.h:259
void consumeSwathSpectrum_(MapType::SpectrumType &s, size_t swath_nr)
Consume an MS2 spectrum belonging to SWATH "swath_nr".
Definition: SwathFileConsumer.h:449
MapType::SpectrumType SpectrumType
Definition: SwathFileConsumer.h:339
MSDataCachedConsumer * ms1_consumer_
Definition: SwathFileConsumer.h:527
void consumeSwathSpectrum_(MapType::SpectrumType &s, size_t swath_nr)
Consume an MS2 spectrum belonging to SWATH "swath_nr".
Definition: SwathFileConsumer.h:354
MSExperiment settings_
The Experimental settings.
Definition: SwathFileConsumer.h:314
void retrieveSwathMaps(std::vector< OpenSwath::SwathMap > &maps)
Populate the vector of swath maps after consuming all spectra.
Definition: SwathFileConsumer.h:150
MapType::ChromatogramType ChromatogramType
Definition: SwathFileConsumer.h:340
int nr_ms1_spectra_
Definition: SwathFileConsumer.h:532
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:128
void consumeSpectrum(MapType::SpectrumType &s)
* Consume a spectrum which may belong either to an MS1 scan or one of n MS2 (SWATH) scans ...
Definition: SwathFileConsumer.h:206
Transforming and cached writing consumer of MS data.
Definition: MSDataCachedConsumer.h:51
MapType::ChromatogramType ChromatogramType
Definition: SwathFileConsumer.h:398
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
FullSwathFileConsumer()
Definition: SwathFileConsumer.h:108
FullSwathFileConsumer(std::vector< OpenSwath::SwathMap > swath_boundaries)
Constructor.
Definition: SwathFileConsumer.h:124
#define LOG_DEBUG
Macro for general debugging information.
Definition: LogStream.h:459
Abstract base class which can consume spectra coming from SWATH experiment stored in a single file...
Definition: SwathFileConsumer.h:99
std::vector< int > nr_ms2_spectra_
Definition: SwathFileConsumer.h:533
File adapter for MzML files.
Definition: MzMLFile.h:55
A method or algorithm argument contains illegal values.
Definition: Exception.h:634
void consumeChromatogram(MapType::ChromatogramType &)
Consume a chromatogram -> should not happen when dealing with SWATH maps.
Definition: SwathFileConsumer.h:196
void addNewSwathMap_()
Definition: SwathFileConsumer.h:436
~FullSwathFileConsumer()
Definition: SwathFileConsumer.h:134
On-disk cached implementation of FullSwathFileConsumer.
Definition: SwathFileConsumer.h:391
std::vector< OpenSwath::SwathMap > swath_map_boundaries_
A list of Swath map identifiers (lower/upper boundary and center)
Definition: SwathFileConsumer.h:306
void load(const String &filename, MapType &map)
Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled u...
Definition: MzMLFile.h:83
String cachedir_
Definition: SwathFileConsumer.h:530
void addNewSwathMap_()
Definition: SwathFileConsumer.h:348
Data structure to hold one SWATH map with information about upper / lower isolation window and whethe...
Definition: SwathMap.h:46
void addMS1Map_()
Definition: SwathFileConsumer.h:364
std::vector< boost::shared_ptr< MSExperiment<> > > swath_maps_
A list of SWATH maps and the MS1 map.
Definition: SwathFileConsumer.h:309
OpenSwath::SpectrumAccessPtr sptr
Definition: SwathMap.h:48
MapType::ChromatogramType ChromatogramType
Definition: SwathFileConsumer.h:106
void ensureMapsAreFilled_()
Callback function after the reading is complete.
Definition: SwathFileConsumer.h:479
Exception indicating that an invalid parameter was handed over to an algorithm.
Definition: Exception.h:348
In-memory implementation of FullSwathFileConsumer.
Definition: SwathFileConsumer.h:333
void consumeMS1Spectrum_(MapType::SpectrumType &s)
Consume an MS1 spectrum.
Definition: SwathFileConsumer.h:469
MapType::SpectrumType SpectrumType
Definition: SwathFileConsumer.h:397
~CachedSwathFileConsumer()
Definition: SwathFileConsumer.h:420
MSExperiment MapType
Definition: SwathFileConsumer.h:338
void addMS1Map_()
Definition: SwathFileConsumer.h:459
An class that uses on-disk caching to read and write spectra and chromatograms.
Definition: CachedMzML.h:62
The interface of a consumer of spectra and chromatograms.
Definition: IMSDataConsumer.h:68
boost::shared_ptr< MSExperiment<> > ms1_map_
Definition: SwathFileConsumer.h:310
std::vector< MSDataCachedConsumer * > swath_consumers_
Definition: SwathFileConsumer.h:528
void setExpectedSize(Size, Size)
Set expected size of spectra and chromatograms to be consumed.
Definition: MSDataCachedConsumer.h:118
void consumeMS1Spectrum_(MapType::SpectrumType &s)
Consume an MS1 spectrum.
Definition: SwathFileConsumer.h:370
double center
Definition: SwathMap.h:51
void writeMetadata(MapType exp, String out_meta, bool addCacheMetaValue=false)
Write only the meta data of an MSExperiment.
String basename_
Definition: SwathFileConsumer.h:531
const std::vector< Precursor > & getPrecursors() const
returns a const reference to the precursors
double upper
Definition: SwathMap.h:50
bool ms1
Definition: SwathMap.h:52
Description of the experimental settings.
Definition: ExperimentalSettings.h:59
MapType::SpectrumType SpectrumType
Definition: SwathFileConsumer.h:105
MSExperiment MapType
Definition: SwathFileConsumer.h:396
size_t correct_window_counter_
How many windows were correctly annotated (non-zero window limits)
Definition: SwathFileConsumer.h:323
void setExpectedSize(Size, Size)
Set expected size of spectra and chromatograms to be consumed.
Definition: SwathFileConsumer.h:136
double lower
Definition: SwathMap.h:49
CachedSwathFileConsumer(String cachedir, String basename, Size nr_ms1_spectra, std::vector< int > nr_ms2_spectra)
Definition: SwathFileConsumer.h:400

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Nov 1 2016 16:34:46 using doxygen 1.8.11