| Line | Branch | Exec | Source |
|---|---|---|---|
| 1 | /* BEGIN software license | ||
| 2 | * | ||
| 3 | * MsXpertSuite - mass spectrometry software suite | ||
| 4 | * ----------------------------------------------- | ||
| 5 | * Copyright (C) 2009--2020 Filippo Rusconi | ||
| 6 | * | ||
| 7 | * http://www.msxpertsuite.org | ||
| 8 | * | ||
| 9 | * This file is part of the MsXpertSuite project. | ||
| 10 | * | ||
| 11 | * The MsXpertSuite project is the successor of the massXpert project. This | ||
| 12 | * project now includes various independent modules: | ||
| 13 | * | ||
| 14 | * - massXpert, model polymer chemistries and simulate mass spectrometric data; | ||
| 15 | * - mineXpert, a powerful TIC chromatogram/mass spectrum viewer/miner; | ||
| 16 | * | ||
| 17 | * This program is free software: you can redistribute it and/or modify | ||
| 18 | * it under the terms of the GNU General Public License as published by | ||
| 19 | * the Free Software Foundation, either version 3 of the License, or | ||
| 20 | * (at your option) any later version. | ||
| 21 | * | ||
| 22 | * This program is distributed in the hope that it will be useful, | ||
| 23 | * but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| 24 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| 25 | * GNU General Public License for more details. | ||
| 26 | * | ||
| 27 | * You should have received a copy of the GNU General Public License | ||
| 28 | * along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| 29 | * | ||
| 30 | * END software license | ||
| 31 | */ | ||
| 32 | |||
| 33 | |||
| 34 | /////////////////////// StdLib includes | ||
| 35 | #include <cmath> | ||
| 36 | #include <algorithm> | ||
| 37 | #include <limits> // for std::numeric_limits | ||
| 38 | |||
| 39 | |||
| 40 | /////////////////////// Qt includes | ||
| 41 | |||
| 42 | |||
| 43 | /////////////////////// pappsomspp includes | ||
| 44 | #include <pappsomspp/massspectrum/massspectrum.h> | ||
| 45 | #include <pappsomspp/processing/combiners/massspectrumpluscombiner.h> | ||
| 46 | #include <pappsomspp/processing/combiners/tracepluscombiner.h> | ||
| 47 | #include <pappsomspp/trace/trace.h> | ||
| 48 | #include <pappsomspp/processing/filters/filternormalizeintensities.h> | ||
| 49 | #include <pappsomspp/utils.h> | ||
| 50 | |||
| 51 | |||
| 52 | /////////////////////// Local includes | ||
| 53 | #include "globals.hpp" | ||
| 54 | #include "MassDataCborMassSpectrumHandler.hpp" | ||
| 55 | #include "IsotopicClusterShaper.hpp" | ||
| 56 | #include "MassPeakShaper.hpp" | ||
| 57 | |||
| 58 | |||
| 59 | namespace MsXpS | ||
| 60 | { | ||
| 61 | |||
| 62 | namespace libXpertMass | ||
| 63 | { | ||
| 64 | |||
| 65 | |||
| 66 | /*! | ||
| 67 | \class MsXpS::libXpertMass::IsotopicClusterShaper | ||
| 68 | \inmodule libXpertMass | ||
| 69 | \ingroup XpertMassMassCalculations | ||
| 70 | \inheaderfile IsotopicClusterShaper.hpp | ||
| 71 | |||
| 72 | \brief The IsotopicClusterShaper class provides the features needed to shape | ||
| 73 | sets of (peak centroid m/z, intensity) pairs associated to a given charge | ||
| 74 | into a mass spectral pappso;:Trace. | ||
| 75 | |||
| 76 | Each set of (peak centroid m/z, intensity) pairs corresponds to an isotopic | ||
| 77 | cluster that is associated to a charge. | ||
| 78 | |||
| 79 | The configuration of the peak shaping process is held in a specific \l | ||
| 80 | MassPeakShaperConfig class. | ||
| 81 | |||
| 82 | The output of the computation is a pappso::Trace obtained by combining all the | ||
| 83 | different shapes obtained for the different peak centroids of all the sets of | ||
| 84 | (peak centroid m/z, intensity) pairs. If binning was requested, the obtained | ||
| 85 | Trace is the result of a combination accounting for the required bin size, | ||
| 86 | otherwise the obtained Trace is the result of the mere addition of all the | ||
| 87 | points in the different traces. | ||
| 88 | |||
| 89 | \sa MassPeakShaperConfig | ||
| 90 | */ | ||
| 91 | |||
| 92 | /*! | ||
| 93 | \variable MsXpS::libXpertMass::IsotopicClusterShaper::m_isotopicClusterChargePairs | ||
| 94 | |||
| 95 | \brief Vector of pappso::Trace instances in pair with charges. | ||
| 96 | */ | ||
| 97 | |||
| 98 | /*! | ||
| 99 | \variable MsXpS::libXpertMass::IsotopicClusterShaper::m_config | ||
| 100 | |||
| 101 | \brief The configuration driving the mass peak shaping process. | ||
| 102 | */ | ||
| 103 | |||
| 104 | /*! | ||
| 105 | \variable MsXpS::libXpertMass::IsotopicClusterShaper::m_mapTrace | ||
| 106 | |||
| 107 | \brief The map relating a m/z value to its intensity. | ||
| 108 | |||
| 109 | This map is a variant of pappso::Trace that is designed to allow for easy mass | ||
| 110 | spectrum combination. It is generally used only for computations and is | ||
| 111 | converted to a pappso::Trace once all the computations have been carried out. | ||
| 112 | */ | ||
| 113 | |||
| 114 | /*! | ||
| 115 | \variable MsXpS::libXpertMass::IsotopicClusterShaper::m_finalTrace | ||
| 116 | |||
| 117 | \brief The pappso::Trace holding the final results of the computations. | ||
| 118 | */ | ||
| 119 | |||
| 120 | /*! | ||
| 121 | \variable MsXpS::libXpertMass::IsotopicClusterShaper::m_mzIntegrationParams | ||
| 122 | |||
| 123 | \brief The configuration of the mass spectral combinations (for | ||
| 124 | example, determines the bins, if binning is required). | ||
| 125 | */ | ||
| 126 | |||
| 127 | /*! | ||
| 128 | \variable MsXpS::libXpertMass::IsotopicClusterShaper::m_mostIntensePeakMz | ||
| 129 | |||
| 130 | \brief The most intense peak encountered during the calculations. | ||
| 131 | */ | ||
| 132 | |||
| 133 | /*! | ||
| 134 | \variable MsXpS::libXpertMass::IsotopicClusterShaper::m_smallestMz | ||
| 135 | |||
| 136 | \brief The smallest m/z value encountered during the calculations. | ||
| 137 | |||
| 138 | This value is required for the crafting of the bins. | ||
| 139 | */ | ||
| 140 | |||
| 141 | /*! | ||
| 142 | \variable MsXpS::libXpertMass::IsotopicClusterShaper::m_greatestMz | ||
| 143 | |||
| 144 | \brief The greatest m/z value encountered during the calculations. | ||
| 145 | |||
| 146 | This value is required for the crafting of the bins. | ||
| 147 | */ | ||
| 148 | |||
| 149 | /*! | ||
| 150 | \variable MsXpS::libXpertMass::IsotopicClusterShaper::m_normalizeIntensity | ||
| 151 | |||
| 152 | \brief The value by which all the peak shapes need to be normalized. | ||
| 153 | */ | ||
| 154 | |||
| 155 | /*! | ||
| 156 | \brief Constructs a IsotopicClusterShaper instance. | ||
| 157 | |||
| 158 | \list | ||
| 159 | \li \a isotopic_cluster: The peak centroids belonging to an isotopic cluster | ||
| 160 | in the form of a pappso::Trace. | ||
| 161 | \li \a charge: The charge of the analyte below the isotopic cluster peaks. | ||
| 162 | \li \a config: The mass peak shaping process configuration. | ||
| 163 | \endlist | ||
| 164 | |||
| 165 | Each pappso::DataPoint in the \a isotopic_cluster pappso::Trace corresponds to | ||
| 166 | a (m/z, intensity) peak centroid belonging to the isotopic cluster. | ||
| 167 | */ | ||
| 168 | ✗ | IsotopicClusterShaper::IsotopicClusterShaper( | |
| 169 | const pappso::Trace &isotopic_cluster, | ||
| 170 | int charge, | ||
| 171 | ✗ | const MassPeakShaperConfig &config) | |
| 172 | ✗ | : m_config(config) | |
| 173 | { | ||
| 174 | // No need to reset, we are constructing. | ||
| 175 | ✗ | setIsotopicCluster(isotopic_cluster, charge, false); | |
| 176 | ✗ | } | |
| 177 | |||
| 178 | |||
| 179 | /*! | ||
| 180 | \brief Constructs a IsotopicClusterShaper instance. | ||
| 181 | |||
| 182 | \list | ||
| 183 | \li \a isotopic_cluster_charge_pairs: The pairs associating a pappso::Trace | ||
| 184 | instance to its corresponding charge. | ||
| 185 | \li \a config: The mass peak shaping process configuration. | ||
| 186 | \endlist | ||
| 187 | |||
| 188 | In this constructor, a set of sets of (m/z, charge) peak centroids is passed as | ||
| 189 | argument. The pappso::Trace instances in \a isotopic_cluster_charge_pairs might | ||
| 190 | correspond to all the isotopic clusters representing a given analyte at | ||
| 191 | different charges. | ||
| 192 | */ | ||
| 193 | ✗ | IsotopicClusterShaper::IsotopicClusterShaper( | |
| 194 | const std::vector<IsotopicClusterChargePair> &isotopic_cluster_charge_pairs, | ||
| 195 | ✗ | const MassPeakShaperConfig &config) | |
| 196 | ✗ | : m_config(config) | |
| 197 | { | ||
| 198 | // No need to reset, we are constructing. | ||
| 199 | ✗ | setIsotopicClusterChargePairs(isotopic_cluster_charge_pairs, false); | |
| 200 | ✗ | } | |
| 201 | |||
| 202 | /*! | ||
| 203 | \brief Destructs this IsotopicClusterShaper instance. | ||
| 204 | */ | ||
| 205 | ✗ | IsotopicClusterShaper::~IsotopicClusterShaper() | |
| 206 | { | ||
| 207 | ✗ | } | |
| 208 | |||
| 209 | /*! | ||
| 210 | \brief Sets the peak shaping process \a{config}uration. | ||
| 211 | */ | ||
| 212 | void | ||
| 213 | ✗ | IsotopicClusterShaper::setConfig(MassPeakShaperConfig config) | |
| 214 | { | ||
| 215 | ✗ | m_config = config; | |
| 216 | ✗ | } | |
| 217 | |||
| 218 | |||
| 219 | /*! | ||
| 220 | \brief Gets the peak shaping process configuration. | ||
| 221 | */ | ||
| 222 | MassPeakShaperConfig | ||
| 223 | ✗ | IsotopicClusterShaper::getConfig() const | |
| 224 | { | ||
| 225 | ✗ | return m_config; | |
| 226 | } | ||
| 227 | |||
| 228 | |||
| 229 | /*! | ||
| 230 | \brief Sets the intensity normalization value to \a max_intensity. | ||
| 231 | */ | ||
| 232 | void | ||
| 233 | ✗ | IsotopicClusterShaper::setNormalizeIntensity(int max_intensity) | |
| 234 | { | ||
| 235 | ✗ | m_normalizeIntensity = max_intensity; | |
| 236 | ✗ | } | |
| 237 | |||
| 238 | |||
| 239 | /*! | ||
| 240 | \brief Gets the intensity normalization value. | ||
| 241 | */ | ||
| 242 | int | ||
| 243 | ✗ | IsotopicClusterShaper::getNormalizeIntensity() const | |
| 244 | { | ||
| 245 | ✗ | return m_normalizeIntensity; | |
| 246 | } | ||
| 247 | |||
| 248 | /*! | ||
| 249 | \brief Runs the mass peak shaping process for all the \l | ||
| 250 | IsotopicClusterChargePair objects in \l m_isotopicClusterChargePairs. | ||
| 251 | |||
| 252 | If \a reset is true, the member \l m_mapTrace and \l m_finalTrace are cleared | ||
| 253 | before starting the computations. The \l m_config member is first | ||
| 254 | \l{MassPeakShaperConfig::resolve()}d to check that all the parameters have been | ||
| 255 | properly set and are valid. | ||
| 256 | |||
| 257 | Returns the obtained pappso::Trace corresponding to the combination of all the | ||
| 258 | individual traces obtained for the various isotopic clusters and their | ||
| 259 | corresponding charge. | ||
| 260 | */ | ||
| 261 | pappso::Trace & | ||
| 262 | ✗ | IsotopicClusterShaper::run(bool reset) | |
| 263 | { | ||
| 264 | ✗ | if(reset) | |
| 265 | { | ||
| 266 | // Clear the map trace that will receive the results of the combinations. | ||
| 267 | ✗ | m_mapTrace.clear(); | |
| 268 | ✗ | m_finalTrace.clear(); | |
| 269 | } | ||
| 270 | |||
| 271 | ✗ | if(!m_config.resolve()) | |
| 272 | { | ||
| 273 | ✗ | qDebug() << "The peak shaper configuration failed to resolve."; | |
| 274 | ✗ | return m_finalTrace; | |
| 275 | } | ||
| 276 | |||
| 277 | // This class works on a vector of pairs containing the following: | ||
| 278 | // 1. a pappso::TraceCstSPtr | ||
| 279 | // 2. a charge | ||
| 280 | |||
| 281 | // We will process each pair in turn. If the integration requires bin, then | ||
| 282 | // each shaped isotopic cluster will be combined into a mass spectrum. | ||
| 283 | // Otherwise a trace combiner will be used. | ||
| 284 | |||
| 285 | // When setting the data (either by construction or using the set<> functions, | ||
| 286 | // we had monitored the smallest and the greatest m/z value over the whole set | ||
| 287 | // of the DataPoint objects in the isotopic clusters (centroid data). This is | ||
| 288 | // because we need, in case binning is required, these values to craft the | ||
| 289 | // bins. | ||
| 290 | |||
| 291 | // We will need to perform combinations, positive combinations. | ||
| 292 | // This mass spectrum combiner is in case we need binning. | ||
| 293 | ✗ | pappso::MassSpectrumPlusCombiner mass_spectrum_plus_combiner; | |
| 294 | |||
| 295 | // This trace combiner is in case do *not* need binning. | ||
| 296 | ✗ | pappso::TracePlusCombiner trace_plus_combiner(-1); | |
| 297 | |||
| 298 | // Configure the mass spectrum combiner in case we need binning. | ||
| 299 | |||
| 300 | ✗ | if(m_config.withBins()) | |
| 301 | { | ||
| 302 | // Bins were requested. | ||
| 303 | |||
| 304 | // qDebug() << "Bins are required."; | ||
| 305 | |||
| 306 | // Get the bin size out of the configuration. | ||
| 307 | |||
| 308 | ✗ | double bin_size = m_config.getBinSize(); | |
| 309 | |||
| 310 | // qDebug() << "The bin size in the config is:" << bin_size; | ||
| 311 | |||
| 312 | // Because we had monitored the m/z values of all the shapes generated | ||
| 313 | // above, we know the smallest and greatest m/z value that were | ||
| 314 | // encountered in all that peak shaping activity. We thus can create the | ||
| 315 | // bins faithfully. | ||
| 316 | |||
| 317 | ✗ | MassPeakWidthLogic logic = m_config.getMassPeakWidthLogic(); | |
| 318 | |||
| 319 | // The m_smallestMz and m_greatestMz values have been determined by | ||
| 320 | // looking into the unshaped isotopic clusters passed to this object | ||
| 321 | // either by construction or with functions. These two mz values are thus | ||
| 322 | // peak centroids, not data points belonging to a shaped peak since we | ||
| 323 | // have not yet started shaping the peaks. This means that we cannot | ||
| 324 | // create bins start / ending at these values because we would loose the | ||
| 325 | // first half of the first shaped peak centroid and the second half of the | ||
| 326 | // last shaped peak centroid (a shaped peak goes left *and* right of the | ||
| 327 | // peak centroid otherwise there would be no shape). | ||
| 328 | // | ||
| 329 | // This is why we provide a confortable margin fo the bin creation below | ||
| 330 | // by removing 1 Th on the left of the smallest mz and by adding 1 Th on | ||
| 331 | // right of the greatest mz. | ||
| 332 | |||
| 333 | ✗ | if(logic == MassPeakWidthLogic::FWHM) | |
| 334 | { | ||
| 335 | ✗ | m_mzIntegrationParams = pappso::MzIntegrationParams( | |
| 336 | ✗ | m_smallestMz - 1, | |
| 337 | ✗ | m_greatestMz + 1, | |
| 338 | pappso::BinningType::ARBITRARY, | ||
| 339 | -1, | ||
| 340 | pappso::PrecisionFactory::getDaltonInstance(bin_size), | ||
| 341 | 1, | ||
| 342 | ✗ | true); | |
| 343 | } | ||
| 344 | ✗ | else if(logic == MassPeakWidthLogic::RESOLUTION) | |
| 345 | { | ||
| 346 | ✗ | double resolution = m_config.getResolution(); | |
| 347 | |||
| 348 | ✗ | m_mzIntegrationParams = pappso::MzIntegrationParams( | |
| 349 | ✗ | m_smallestMz - 1, | |
| 350 | ✗ | m_greatestMz + 1, | |
| 351 | pappso::BinningType::ARBITRARY, | ||
| 352 | -1, | ||
| 353 | pappso::PrecisionFactory::getResInstance(resolution), | ||
| 354 | m_config.getBinSizeDivisor(), | ||
| 355 | ✗ | true); | |
| 356 | } | ||
| 357 | else | ||
| 358 | ✗ | qFatal( | |
| 359 | "Programming error. By this time, the mass peak width logic should " | ||
| 360 | "have been defined."); | ||
| 361 | |||
| 362 | // qDebug() << "The mz integration params:" | ||
| 363 | //<< m_mzIntegrationParams.toString(); | ||
| 364 | |||
| 365 | // Now compute the bins. | ||
| 366 | |||
| 367 | ✗ | std::vector<double> bins = m_mzIntegrationParams.createBins(); | |
| 368 | // qDebug() << "The bins:" << bins; | ||
| 369 | |||
| 370 | ✗ | mass_spectrum_plus_combiner.setBins(bins); | |
| 371 | // qDebug() << "Set bins to the mass spectrum combiner:" | ||
| 372 | //<< mass_spectrum_plus_combiner.getBins().size(); | ||
| 373 | ✗ | } | |
| 374 | |||
| 375 | ✗ | std::size_t peak_centroid_count = 0; | |
| 376 | ✗ | std::size_t isotopic_cluster_count = 0; | |
| 377 | |||
| 378 | // Iterate in the isotopic cluster/charge pairs. | ||
| 379 | ✗ | for(auto isotopic_cluster_charge_pair : m_isotopicClusterChargePairs) | |
| 380 | { | ||
| 381 | ✗ | int charge = isotopic_cluster_charge_pair.second; | |
| 382 | |||
| 383 | // Iterate in the data points of the current centroid data isotopic | ||
| 384 | // cluster. | ||
| 385 | ✗ | for(auto data_point : *isotopic_cluster_charge_pair.first) | |
| 386 | { | ||
| 387 | // Note the division by m_charge below! | ||
| 388 | |||
| 389 | pappso::Trace trace = MassPeakShaper::computePeakShape( | ||
| 390 | ✗ | data_point.x / charge, data_point.y, m_config); | |
| 391 | |||
| 392 | // qDebug() << "The shaped isotopic cluster has size:" << | ||
| 393 | // trace.size(); | ||
| 394 | |||
| 395 | ✗ | if(trace.size()) | |
| 396 | { | ||
| 397 | ✗ | if(m_config.withBins()) | |
| 398 | ✗ | mass_spectrum_plus_combiner.combine(m_mapTrace, trace); | |
| 399 | else | ||
| 400 | ✗ | trace_plus_combiner.combine(m_mapTrace, trace); | |
| 401 | |||
| 402 | // qDebug() << qSetRealNumberPrecision(15) | ||
| 403 | //<< "The map trace for combination has size:" | ||
| 404 | //<< m_mapTrace.size() | ||
| 405 | //<< "and starting m/z:" << m_mapTrace.begin()->first | ||
| 406 | //<< "and ending m/z:" | ||
| 407 | //<< std::prev(m_mapTrace.end())->first; | ||
| 408 | |||
| 409 | ✗ | ++peak_centroid_count; | |
| 410 | } | ||
| 411 | ✗ | } | |
| 412 | ✗ | ++isotopic_cluster_count; | |
| 413 | ✗ | } | |
| 414 | |||
| 415 | // qDebug() << QString( | ||
| 416 | //"Successfully processed %1 isotopic clusters for a total of %2 " | ||
| 417 | //"shaped peak centroids") | ||
| 418 | //.arg(isotopic_cluster_count) | ||
| 419 | //.arg(peak_centroid_count); | ||
| 420 | |||
| 421 | // The user might have asked that the most intense m/z peak centroid be used | ||
| 422 | // for normalization. In that case that peak centroid's intensity is brought | ||
| 423 | // to m_normalizeIntensity and the ratio between its current intensity and | ||
| 424 | // m_normalizeIntensity is used to normalize all the other data points in the | ||
| 425 | // trace. | ||
| 426 | |||
| 427 | ✗ | if(m_normalizeIntensity != 1) | |
| 428 | { | ||
| 429 | |||
| 430 | // qDebug() << "Now normalizing to intensity = " << m_normalizeIntensity; | ||
| 431 | |||
| 432 | ✗ | pappso::Trace trace = m_mapTrace.toTrace(); | |
| 433 | m_finalTrace = | ||
| 434 | ✗ | trace.filter(pappso::FilterNormalizeIntensities(m_normalizeIntensity)); | |
| 435 | |||
| 436 | // double max_int = normalized_trace.maxYDataPoint().y; | ||
| 437 | // qDebug() << "After normalization max int:" << max_int; | ||
| 438 | ✗ | } | |
| 439 | else | ||
| 440 | ✗ | m_finalTrace = m_mapTrace.toTrace(); | |
| 441 | |||
| 442 | // qDebug() << "Returning a trace of size:" << m_finalTrace.size(); | ||
| 443 | |||
| 444 | // pappso::Utils::writeToFile(m_finalTrace.toString(), "/tmp/mass/trace.txt"); | ||
| 445 | |||
| 446 | ✗ | return m_finalTrace; | |
| 447 | ✗ | } | |
| 448 | |||
| 449 | /*! | ||
| 450 | \brief Handles the \a isotopic_cluster_sp input isotopic cluster as a | ||
| 451 | pappso::Trace. | ||
| 452 | |||
| 453 | \a isotopic_cluster_sp is associated to a \a charge. If \a reset is true, the | ||
| 454 | member vector of \l IsotopicClusterChargePair instances is cleared before the | ||
| 455 | computations. | ||
| 456 | |||
| 457 | This function is the workhorse for all the functions used to set the initial | ||
| 458 | data for the computations. Its main task is to scrutinize the data in \a | ||
| 459 | isotopic_cluster_sp and update the \l m_smallestMz, \l m_greatestMz and \l | ||
| 460 | m_mostIntensePeakMz values based on the data passed as argument. | ||
| 461 | */ | ||
| 462 | void | ||
| 463 | ✗ | IsotopicClusterShaper::setIsotopicCluster( | |
| 464 | pappso::TraceCstSPtr isotopic_cluster_sp, int charge, bool reset) | ||
| 465 | { | ||
| 466 | ✗ | if(reset) | |
| 467 | ✗ | m_isotopicClusterChargePairs.clear(); | |
| 468 | |||
| 469 | ✗ | double min_x = isotopic_cluster_sp->minX(); | |
| 470 | ✗ | m_smallestMz = std::min(m_smallestMz, min_x); | |
| 471 | |||
| 472 | ✗ | double max_x = isotopic_cluster_sp->maxX(); | |
| 473 | ✗ | m_greatestMz = std::max(m_greatestMz, max_x); | |
| 474 | |||
| 475 | ✗ | m_mostIntensePeakMz = isotopic_cluster_sp->maxYDataPoint().x; | |
| 476 | |||
| 477 | // qDebug() << qSetRealNumberPrecision(15) << "m_smallestMz:" << m_smallestMz | ||
| 478 | //<< "m_greatestMz:" << m_greatestMz | ||
| 479 | //<< "m_mostIntensePeakMz:" << m_mostIntensePeakMz; | ||
| 480 | |||
| 481 | ✗ | m_isotopicClusterChargePairs.push_back( | |
| 482 | ✗ | IsotopicClusterChargePair(isotopic_cluster_sp, charge)); | |
| 483 | |||
| 484 | ✗ | m_config.setReferencePeakMz(m_mostIntensePeakMz); | |
| 485 | ✗ | } | |
| 486 | |||
| 487 | |||
| 488 | /*! | ||
| 489 | \brief Handles the \a isotopic_cluster_sp input isotopic cluster as a | ||
| 490 | pappso::Trace. | ||
| 491 | |||
| 492 | \a isotopic_cluster_sp is associated to a \a charge. | ||
| 493 | |||
| 494 | The member vector of \l IsotopicClusterChargePair instances is cleared before | ||
| 495 | the computations. | ||
| 496 | */ | ||
| 497 | void | ||
| 498 | ✗ | IsotopicClusterShaper::setIsotopicCluster( | |
| 499 | pappso::TraceCstSPtr isotopic_cluster_sp, int charge) | ||
| 500 | { | ||
| 501 | ✗ | setIsotopicCluster(isotopic_cluster_sp, charge, true); | |
| 502 | ✗ | } | |
| 503 | |||
| 504 | |||
| 505 | /*! | ||
| 506 | \brief Handles the \a isotopic_cluster input isotopic cluster as a | ||
| 507 | pappso::Trace. | ||
| 508 | |||
| 509 | \a isotopic_cluster is associated to a \a charge. If \a reset is true, the | ||
| 510 | member vector of \l IsotopicClusterChargePair instances is cleared before the | ||
| 511 | computations. | ||
| 512 | */ | ||
| 513 | void | ||
| 514 | ✗ | IsotopicClusterShaper::setIsotopicCluster(const pappso::Trace &isotopic_cluster, | |
| 515 | int charge, | ||
| 516 | bool reset) | ||
| 517 | { | ||
| 518 | ✗ | setIsotopicCluster( | |
| 519 | ✗ | std::make_shared<const pappso::Trace>(isotopic_cluster), charge, reset); | |
| 520 | ✗ | } | |
| 521 | |||
| 522 | |||
| 523 | /*! | ||
| 524 | \brief Handles the \a isotopic_cluster input isotopic cluster as a | ||
| 525 | pappso::Trace. | ||
| 526 | |||
| 527 | \a isotopic_cluster is associated to a \a charge. | ||
| 528 | |||
| 529 | The member vector of \l IsotopicClusterChargePair instances is cleared before | ||
| 530 | the computations. | ||
| 531 | */ | ||
| 532 | void | ||
| 533 | ✗ | IsotopicClusterShaper::setIsotopicCluster(const pappso::Trace &isotopic_cluster, | |
| 534 | int charge) | ||
| 535 | { | ||
| 536 | ✗ | setIsotopicCluster( | |
| 537 | ✗ | std::make_shared<const pappso::Trace>(isotopic_cluster), charge, true); | |
| 538 | ✗ | } | |
| 539 | |||
| 540 | |||
| 541 | /*! | ||
| 542 | \brief Handles the \a isotopic_cluster_charge_pair input isotopic cluster as a | ||
| 543 | IsotopicClusterChargePair. | ||
| 544 | |||
| 545 | The member vector of \l IsotopicClusterChargePair instances is cleared before | ||
| 546 | the computations. | ||
| 547 | */ | ||
| 548 | void | ||
| 549 | ✗ | IsotopicClusterShaper::setIsotopicCluster( | |
| 550 | IsotopicClusterChargePair isotopic_cluster_charge_pair) | ||
| 551 | { | ||
| 552 | ✗ | setIsotopicCluster(isotopic_cluster_charge_pair.first, | |
| 553 | isotopic_cluster_charge_pair.second, | ||
| 554 | true); | ||
| 555 | ✗ | } | |
| 556 | |||
| 557 | |||
| 558 | /*! | ||
| 559 | \brief Handles the \a isotopic_cluster_charge_pair input isotopic cluster as a | ||
| 560 | IsotopicClusterChargePair. | ||
| 561 | |||
| 562 | If \a reset is true, the member vector of \l IsotopicClusterChargePair instances | ||
| 563 | is cleared before the computations. | ||
| 564 | */ | ||
| 565 | void | ||
| 566 | ✗ | IsotopicClusterShaper::setIsotopicCluster( | |
| 567 | IsotopicClusterChargePair isotopic_cluster_charge_pair, bool reset) | ||
| 568 | { | ||
| 569 | ✗ | setIsotopicCluster(isotopic_cluster_charge_pair.first, | |
| 570 | isotopic_cluster_charge_pair.second, | ||
| 571 | reset); | ||
| 572 | ✗ | } | |
| 573 | |||
| 574 | |||
| 575 | /*! | ||
| 576 | \brief Handles the \a isotopic_cluster_charge_pairs input isotopic cluster as a | ||
| 577 | vector of IsotopicClusterChargePair instances. | ||
| 578 | |||
| 579 | If \a reset is true, the member vector of \l IsotopicClusterChargePair | ||
| 580 | instances is cleared before the computations. | ||
| 581 | */ | ||
| 582 | void | ||
| 583 | ✗ | IsotopicClusterShaper::setIsotopicClusterChargePairs( | |
| 584 | const std::vector<IsotopicClusterChargePair> &isotopic_cluster_charge_pairs, | ||
| 585 | bool reset) | ||
| 586 | { | ||
| 587 | ✗ | for(auto cluster_charge_pair : isotopic_cluster_charge_pairs) | |
| 588 | ✗ | setIsotopicCluster( | |
| 589 | ✗ | cluster_charge_pair.first, cluster_charge_pair.second, reset); | |
| 590 | |||
| 591 | // qDebug() << qSetRealNumberPrecision(15) << "m_smallestMz:" << m_smallestMz | ||
| 592 | //<< "m_greatestMz:" << m_greatestMz | ||
| 593 | //<< "m_mostIntensePeakMz:" << m_mostIntensePeakMz; | ||
| 594 | ✗ | } | |
| 595 | |||
| 596 | |||
| 597 | /*! | ||
| 598 | \brief Handles the \a isotopic_cluster_charge_pairs input isotopic cluster as a | ||
| 599 | vector of IsotopicClusterChargePair instances. | ||
| 600 | |||
| 601 | The member vector of \l IsotopicClusterChargePair instances is cleared before | ||
| 602 | the computations. | ||
| 603 | */ | ||
| 604 | void | ||
| 605 | ✗ | IsotopicClusterShaper::setIsotopicClusterChargePairs( | |
| 606 | const std::vector<IsotopicClusterChargePair> &isotopic_cluster_charge_pairs) | ||
| 607 | { | ||
| 608 | ✗ | setIsotopicClusterChargePairs(isotopic_cluster_charge_pairs, true); | |
| 609 | |||
| 610 | // qDebug() << qSetRealNumberPrecision(15) << "m_smallestMz:" << m_smallestMz | ||
| 611 | //<< "m_greatestMz:" << m_greatestMz | ||
| 612 | //<< "m_mostIntensePeakMz:" << m_mostIntensePeakMz; | ||
| 613 | ✗ | } | |
| 614 | |||
| 615 | /*! | ||
| 616 | \brief Adds an isotopic cluster in the form of the \a isotopic_cluster | ||
| 617 | pappso::Trace associated to the corresponding \a charge. | ||
| 618 | |||
| 619 | The member vector of \l IsotopicClusterChargePair instances is \e{not} cleared | ||
| 620 | before the computations. | ||
| 621 | */ | ||
| 622 | void | ||
| 623 | ✗ | IsotopicClusterShaper::appendIsotopicCluster( | |
| 624 | const pappso::Trace &isotopic_cluster, int charge) | ||
| 625 | { | ||
| 626 | // Do not clear the isotopic clusters! | ||
| 627 | |||
| 628 | ✗ | setIsotopicCluster(isotopic_cluster, charge, false); | |
| 629 | ✗ | } | |
| 630 | |||
| 631 | |||
| 632 | /*! | ||
| 633 | \brief Adds isotopic clusters in the form of the \a | ||
| 634 | isotopic_cluster_charge_pairs vector of IsotopicClusterChargePair instances. | ||
| 635 | |||
| 636 | The member vector of \l IsotopicClusterChargePair instances is \e{not} cleared | ||
| 637 | before the computations. | ||
| 638 | */ | ||
| 639 | void | ||
| 640 | ✗ | IsotopicClusterShaper::appendIsotopicClusterChargePairs( | |
| 641 | const std::vector<IsotopicClusterChargePair> &isotopic_cluster_charge_pairs) | ||
| 642 | { | ||
| 643 | ✗ | setIsotopicClusterChargePairs(isotopic_cluster_charge_pairs, false); | |
| 644 | |||
| 645 | // qDebug() << "m_smallestMz:" << m_smallestMz << "m_greatestMz:" << | ||
| 646 | // m_greatestMz | ||
| 647 | //<< "m_mostIntensePeakMz:" << m_mostIntensePeakMz; | ||
| 648 | ✗ | } | |
| 649 | |||
| 650 | /*! | ||
| 651 | \brief Returns the final result of all the computations as a string. | ||
| 652 | */ | ||
| 653 | QString | ||
| 654 | ✗ | IsotopicClusterShaper::shapeToString() | |
| 655 | { | ||
| 656 | ✗ | return m_finalTrace.toString(); | |
| 657 | } | ||
| 658 | |||
| 659 | } // namespace libXpertMass | ||
| 660 | |||
| 661 | } // namespace MsXpS | ||
| 662 |