35 #ifndef OPENMS_FORMAT_DATAACCESS_SWATHFILECONSUMER_H
36 #define OPENMS_FORMAT_DATAACCESS_SWATHFILECONSUMER_H
38 #include <boost/cast.hpp>
110 consuming_possible_(true),
111 use_external_boundaries_(false),
112 correct_window_counter_(0)
114 use_external_boundaries_ = !swath_map_boundaries_.empty();
125 swath_map_boundaries_(swath_boundaries),
127 consuming_possible_(true),
128 use_external_boundaries_(false),
129 correct_window_counter_(0)
131 use_external_boundaries_ = !swath_map_boundaries_.empty();
152 consuming_possible_ =
false;
153 ensureMapsAreFilled_();
167 if (!use_external_boundaries_ && correct_window_counter_ != swath_maps_.size())
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;
173 size_t nonempty_maps = 0;
174 for (
Size i = 0; i < swath_maps_.size(); i++)
178 map.
lower = swath_map_boundaries_[i].lower;
179 map.
upper = swath_map_boundaries_[i].upper;
180 map.
center = swath_map_boundaries_[i].center;
183 if (map.
sptr->getNrSpectra() > 0) {nonempty_maps++;}
186 if (nonempty_maps != swath_map_boundaries_.size())
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;
198 std::cerr <<
"Read chromatogram while reading SWATH files, did not expect that!" << std::endl;
208 if (!consuming_possible_)
211 "FullSwathFileConsumer cannot consume any more spectra after retrieveSwathMaps has been called already");
216 consumeMS1Spectrum_(s);
223 "Swath scan does not provide a precursor.");
227 double center = prec[0].getMZ();
228 double lower = prec[0].getMZ() - prec[0].getIsolationWindowLowerOffset();
229 double upper = prec[0].getMZ() + prec[0].getIsolationWindowUpperOffset();
236 "Swath scan does not provide any precursor isolation information.");
240 for (
Size i = 0; i < swath_map_boundaries_.size(); i++)
244 if (std::fabs(center - swath_map_boundaries_[i].center) < 1e-6)
247 consumeSwathSpectrum_(s, i);
252 if (use_external_boundaries_)
255 String(
"Encountered SWATH scan with boundary ") + center +
" m/z which was not present in the provided windows.");
259 consumeSwathSpectrum_(s, swath_map_boundaries_.size());
262 if (lower > 0.0 && upper > 0.0)
263 {correct_window_counter_++;}
266 boundary.
lower = lower;
267 boundary.
upper = upper;
269 swath_map_boundaries_.push_back(boundary);
271 LOG_DEBUG <<
"Adding Swath centered at " << center
272 <<
" m/z with an isolation window of " << lower <<
" to " << upper
273 <<
" m/z." << std::endl;
303 virtual void ensureMapsAreFilled_() = 0;
351 swath_maps_.push_back(exp);
356 while (swath_maps_.size() <= swath_nr)
361 swath_maps_[swath_nr]->addSpectrum(s);
376 ms1_map_->addSpectrum(s);
405 nr_ms1_spectra_(nr_ms1_spectra),
406 nr_ms2_spectra_(nr_ms2_spectra)
410 String cachedir,
String basename,
Size nr_ms1_spectra, std::vector<int> nr_ms2_spectra) :
416 nr_ms1_spectra_(nr_ms1_spectra),
417 nr_ms2_spectra_(nr_ms2_spectra)
423 while (!swath_consumers_.empty())
425 delete swath_consumers_.back();
426 swath_consumers_.pop_back();
428 if (ms1_consumer_ != NULL)
430 delete ms1_consumer_;
431 ms1_consumer_ = NULL;
438 String meta_file = cachedir_ + basename_ +
"_" +
String(swath_consumers_.size()) +
".mzML";
439 String cached_file = meta_file +
".cached";
441 consumer->
setExpectedSize(nr_ms2_spectra_[swath_consumers_.size()], 0);
442 swath_consumers_.push_back(consumer);
446 swath_maps_.push_back(exp);
451 while (swath_maps_.size() <= swath_nr)
455 swath_consumers_[swath_nr]->consumeSpectrum(s);
456 swath_maps_[swath_nr]->addSpectrum(s);
461 String meta_file = cachedir_ + basename_ +
"_ms1.mzML";
462 String cached_file = meta_file +
".cached";
464 ms1_consumer_->setExpectedSize(nr_ms1_spectra_, 0);
471 if (ms1_consumer_ == NULL)
475 ms1_consumer_->consumeSpectrum(s);
476 ms1_map_->addSpectrum(s);
481 size_t swath_consumers_size = swath_consumers_.size();
482 bool have_ms1 = (ms1_consumer_ != NULL);
492 while (!swath_consumers_.empty())
494 delete swath_consumers_.back();
495 swath_consumers_.pop_back();
497 if (ms1_consumer_ != NULL)
499 delete ms1_consumer_;
500 ms1_consumer_ = NULL;
506 String meta_file = cachedir_ + basename_ +
"_ms1.mzML";
514 #pragma omp parallel for
516 for (
SignedSize i = 0; i < boost::numeric_cast<SignedSize>(swath_consumers_size); i++)
519 String meta_file = cachedir_ + basename_ +
"_" +
String(i) +
".mzML";
523 swath_maps_[i] = exp;
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
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