| 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 | /////////////////////// Std lib includes | ||
| 35 | #include <memory> | ||
| 36 | |||
| 37 | /////////////////////// Qt includes | ||
| 38 | #include <QDebug> | ||
| 39 | |||
| 40 | |||
| 41 | /////////////////////// IsoSpec | ||
| 42 | #include <IsoSpec++/isoSpec++.h> | ||
| 43 | #include <IsoSpec++/element_tables.h> | ||
| 44 | |||
| 45 | |||
| 46 | // extern const int elem_table_atomicNo[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]; | ||
| 47 | // extern const double | ||
| 48 | // elem_table_probability[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]; | ||
| 49 | // extern const double elem_table_mass[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]; | ||
| 50 | // extern const int elem_table_massNo[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]; | ||
| 51 | // extern const int | ||
| 52 | // elem_table_extraNeutrons[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]; | ||
| 53 | // extern const char* elem_table_element[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]; | ||
| 54 | // extern const char* elem_table_symbol[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]; | ||
| 55 | // extern const bool elem_table_Radioactive[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]; | ||
| 56 | // extern const double | ||
| 57 | // elem_table_log_probability[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]; | ||
| 58 | |||
| 59 | /////////////////////// pappsomspp includes | ||
| 60 | #include "pappsomspp/trace/trace.h" | ||
| 61 | #include "pappsomspp/types.h" | ||
| 62 | |||
| 63 | |||
| 64 | /////////////////////// Local includes | ||
| 65 | #include "globals.hpp" | ||
| 66 | #include "PeakCentroid.hpp" | ||
| 67 | #include "Formula.hpp" | ||
| 68 | #include "IsotopicClusterGenerator.hpp" | ||
| 69 | #include "IsotopicDataLibraryHandler.hpp" | ||
| 70 | #include "IsotopicDataUserConfigHandler.hpp" | ||
| 71 | #include "IsotopicDataManualConfigHandler.hpp" | ||
| 72 | |||
| 73 | |||
| 74 | namespace MsXpS | ||
| 75 | { | ||
| 76 | |||
| 77 | namespace libXpertMass | ||
| 78 | { | ||
| 79 | |||
| 80 | |||
| 81 | /*! | ||
| 82 | \class MsXpS::libXpertMass::IsotopicClusterGenerator | ||
| 83 | \inmodule libXpertMass | ||
| 84 | \ingroup XpertMassMassCalculations | ||
| 85 | \inheaderfile IsotopicClusterGenerator.hpp | ||
| 86 | |||
| 87 | \brief The IsotopicClusterGenerator class provides the features needed to model | ||
| 88 | isotopic clusters starting from (elemental-composition, charge) pairs. | ||
| 89 | |||
| 90 | The modelling uses the member isotopic data. The generated isotopic clusters | ||
| 91 | only contain cluster centroid peaks. If peaks should have a profile, then they | ||
| 92 | need to be shaped. | ||
| 93 | |||
| 94 | \sa IsotopicClusterShaper, MassPeakShaper | ||
| 95 | */ | ||
| 96 | |||
| 97 | /*! | ||
| 98 | \enum MsXpS::libXpertMass::IsotopicDataType | ||
| 99 | |||
| 100 | This enum specifies the type of isotopic data. | ||
| 101 | |||
| 102 | \value NOT_SET: Not configured. | ||
| 103 | . | ||
| 104 | \value LIBRARY_CONFIG: The isotopic data are loaded intact from the IsoSpec | ||
| 105 | library data and are considered pristine natural abundance data. | ||
| 106 | . | ||
| 107 | \value USER_CONFIG: The isotopic data are in the same format as for | ||
| 108 | LIBRARY_CONFIG but might have been modified by the user to configure new | ||
| 109 | abundances. | ||
| 110 | . | ||
| 111 | \value MANUAL_CONFIG: The isotopic data are in a specific format, different | ||
| 112 | than the two above, that actually crafts the isotopes starting from scratch. | ||
| 113 | */ | ||
| 114 | |||
| 115 | /*! | ||
| 116 | \typealias FormulaChargePair | ||
| 117 | |||
| 118 | Alias for std::pair<QString, int>. | ||
| 119 | */ | ||
| 120 | |||
| 121 | /*! | ||
| 122 | \typealias IsotopicClusterChargePair | ||
| 123 | |||
| 124 | Alias for std::pair<pappso::TraceCstSPtr, int>. | ||
| 125 | */ | ||
| 126 | |||
| 127 | /*! | ||
| 128 | \typedef IsotopicClusterGeneratorSPtr | ||
| 129 | \relates IsotopicClusterGenerator. | ||
| 130 | |||
| 131 | Synonym for std::shared_ptr<IsotopicClusterGenerator>. | ||
| 132 | */ | ||
| 133 | ✗ | IsotopicClusterGenerator::IsotopicClusterGenerator() | |
| 134 | { | ||
| 135 | ✗ | } | |
| 136 | |||
| 137 | /*! | ||
| 138 | \typedef IsotopicClusterGeneratorCstSPtr | ||
| 139 | \relates IsotopicClusterGenerator. | ||
| 140 | |||
| 141 | Synonym for std::shared_ptr<const IsotopicClusterGenerator>. | ||
| 142 | */ | ||
| 143 | |||
| 144 | /*! | ||
| 145 | \variable MsXpS::libXpertMass::IsotopicClusterGenerator::msp_isotopicData | ||
| 146 | |||
| 147 | \brief The isotopic data needed for the computations. | ||
| 148 | */ | ||
| 149 | |||
| 150 | /*! | ||
| 151 | \variable MsXpS::libXpertMass::IsotopicClusterGenerator::m_isotopicDataType | ||
| 152 | |||
| 153 | \brief The \l IsotopicDataType type of data. | ||
| 154 | */ | ||
| 155 | |||
| 156 | /*! | ||
| 157 | \variable MsXpS::libXpertMass::IsotopicClusterGenerator::m_maxSummedProbability | ||
| 158 | |||
| 159 | \brief The summed probability of all the isotopic cluster peaks. The | ||
| 160 | computation stops when this probability is reached. | ||
| 161 | */ | ||
| 162 | |||
| 163 | /*! | ||
| 164 | \variable MsXpS::libXpertMass::IsotopicClusterGenerator::m_normalizeIntensity | ||
| 165 | |||
| 166 | \brief The most intense cluster peak's intensity that is used to normalize all | ||
| 167 | the other cluster peaks. | ||
| 168 | */ | ||
| 169 | |||
| 170 | /*! | ||
| 171 | \variable MsXpS::libXpertMass::IsotopicClusterGenerator::m_sortType | ||
| 172 | |||
| 173 | \brief The type of sorting required for the generated cluster peak centroids. | ||
| 174 | */ | ||
| 175 | |||
| 176 | /*! | ||
| 177 | \variable MsXpS::libXpertMass::IsotopicClusterGenerator::m_sortOrder | ||
| 178 | |||
| 179 | \brief The order of the sorting for the generated cluster peak centroids. | ||
| 180 | */ | ||
| 181 | |||
| 182 | /*! | ||
| 183 | \variable MsXpS::libXpertMass::IsotopicClusterGenerator::m_formulaChargePairs | ||
| 184 | |||
| 185 | \brief The set of (elemental composition, charge) pairs. | ||
| 186 | */ | ||
| 187 | |||
| 188 | /*! | ||
| 189 | \variable MsXpS::libXpertMass::IsotopicClusterGenerator::m_isotopicClusterChargePairs | ||
| 190 | |||
| 191 | \brief The set of (isotopic cluster, charge) pairs. | ||
| 192 | */ | ||
| 193 | |||
| 194 | |||
| 195 | /*! | ||
| 196 | \brief Constructs a IsotopicClusterGenerator instance. | ||
| 197 | |||
| 198 | \list | ||
| 199 | \li \a isotopic_data_sp: The isotopic data used for the calculations. | ||
| 200 | \endlist | ||
| 201 | */ | ||
| 202 | ✗ | IsotopicClusterGenerator::IsotopicClusterGenerator( | |
| 203 | ✗ | libXpertMass::IsotopicDataSPtr isotopic_data_sp) | |
| 204 | ✗ | : msp_isotopicData(isotopic_data_sp) | |
| 205 | { | ||
| 206 | ✗ | } | |
| 207 | |||
| 208 | /*! | ||
| 209 | \brief Destructs this IsotopicClusterGenerator instance. | ||
| 210 | */ | ||
| 211 | ✗ | IsotopicClusterGenerator::~IsotopicClusterGenerator() | |
| 212 | { | ||
| 213 | // qDebug(); | ||
| 214 | ✗ | } | |
| 215 | |||
| 216 | /*! | ||
| 217 | \brief Sets the isotopic data type to \a isotopic_data_type. | ||
| 218 | */ | ||
| 219 | void | ||
| 220 | ✗ | IsotopicClusterGenerator::setIsotopicDataType( | |
| 221 | IsotopicDataType isotopic_data_type) | ||
| 222 | { | ||
| 223 | ✗ | m_isotopicDataType = isotopic_data_type; | |
| 224 | ✗ | } | |
| 225 | |||
| 226 | |||
| 227 | /*! | ||
| 228 | \brief Sets the isotopic data to \a isotopic_data_sp. | ||
| 229 | */ | ||
| 230 | void | ||
| 231 | ✗ | IsotopicClusterGenerator::setIsotopicData( | |
| 232 | libXpertMass::IsotopicDataSPtr isotopic_data_sp) | ||
| 233 | { | ||
| 234 | ✗ | msp_isotopicData = isotopic_data_sp; | |
| 235 | ✗ | } | |
| 236 | |||
| 237 | |||
| 238 | /*! | ||
| 239 | \brief Returns the isotopic data. | ||
| 240 | */ | ||
| 241 | libXpertMass::IsotopicDataSPtr | ||
| 242 | ✗ | IsotopicClusterGenerator::getIsotopicData() const | |
| 243 | { | ||
| 244 | ✗ | return msp_isotopicData; | |
| 245 | } | ||
| 246 | |||
| 247 | |||
| 248 | /*! | ||
| 249 | \brief Adds the (elemental composition, charge) pair \a | ||
| 250 | formula_charge_pair to the member list of FormulaChargePair instances. | ||
| 251 | |||
| 252 | The member list of FormulaChargePair instances is first cleared. | ||
| 253 | */ | ||
| 254 | void | ||
| 255 | ✗ | IsotopicClusterGenerator::setFormulaChargePair( | |
| 256 | FormulaChargePair &formula_charge_pair) | ||
| 257 | { | ||
| 258 | ✗ | m_formulaChargePairs.clear(); | |
| 259 | ✗ | m_formulaChargePairs.push_back(formula_charge_pair); | |
| 260 | |||
| 261 | // qDebug() << formula_charge_pair.first << formula_charge_pair.second; | ||
| 262 | ✗ | } | |
| 263 | |||
| 264 | /*! | ||
| 265 | \brief Adds the (elemental composition, charge) pair \a | ||
| 266 | formula_charge_pair to the member list of FormulaChargePair instances. | ||
| 267 | */ | ||
| 268 | void | ||
| 269 | ✗ | IsotopicClusterGenerator::appendFormulaChargePair( | |
| 270 | FormulaChargePair &formula_charge_pair) | ||
| 271 | { | ||
| 272 | ✗ | m_formulaChargePairs.push_back(formula_charge_pair); | |
| 273 | |||
| 274 | // qDebug() << formula_charge_pair.first << formula_charge_pair.second; | ||
| 275 | ✗ | } | |
| 276 | |||
| 277 | /*! | ||
| 278 | \brief Adds the (elemental composition, charge) pairs \a | ||
| 279 | formula_charge_pairs to the member list of FormulaChargePair instances. | ||
| 280 | |||
| 281 | The member list of FormulaChargePair instances is first cleared. | ||
| 282 | */ | ||
| 283 | void | ||
| 284 | ✗ | IsotopicClusterGenerator::setFormulaChargePairs( | |
| 285 | const std::vector<FormulaChargePair> &formula_charge_pairs) | ||
| 286 | { | ||
| 287 | ✗ | m_formulaChargePairs.clear(); | |
| 288 | |||
| 289 | ✗ | m_formulaChargePairs.assign(formula_charge_pairs.begin(), | |
| 290 | formula_charge_pairs.end()); | ||
| 291 | |||
| 292 | // qDebug() << "Set" << m_formulaChargePairs.size() << "formula/charge pairs"; | ||
| 293 | // for(auto pair : m_formulaChargePairs) | ||
| 294 | // qDebug() << pair.first << "/" << pair.second; | ||
| 295 | ✗ | } | |
| 296 | |||
| 297 | /*! | ||
| 298 | \brief Sets the summed probability maximum value to \a max_probability. | ||
| 299 | */ | ||
| 300 | void | ||
| 301 | ✗ | IsotopicClusterGenerator::setMaxSummedProbability(double max_probability) | |
| 302 | { | ||
| 303 | ✗ | m_maxSummedProbability = max_probability; | |
| 304 | ✗ | } | |
| 305 | |||
| 306 | /*! | ||
| 307 | \brief Sets the normalization intensity to \a normalize_intensity. | ||
| 308 | */ | ||
| 309 | void | ||
| 310 | ✗ | IsotopicClusterGenerator::setNormalizationIntensity(int normalize_intensity) | |
| 311 | { | ||
| 312 | ✗ | m_normalizeIntensity = normalize_intensity; | |
| 313 | ✗ | } | |
| 314 | |||
| 315 | /*! | ||
| 316 | \brief Sets the \a sort_type. | ||
| 317 | */ | ||
| 318 | void | ||
| 319 | ✗ | IsotopicClusterGenerator::setSortType(pappso::SortType sort_type) | |
| 320 | { | ||
| 321 | ✗ | m_sortType = sort_type; | |
| 322 | ✗ | } | |
| 323 | |||
| 324 | /*! | ||
| 325 | \brief Sets the \a sort_order. | ||
| 326 | */ | ||
| 327 | void | ||
| 328 | ✗ | IsotopicClusterGenerator::setSortOrder(pappso::SortOrder sort_order) | |
| 329 | { | ||
| 330 | ✗ | m_sortOrder = sort_order; | |
| 331 | ✗ | } | |
| 332 | |||
| 333 | /*! | ||
| 334 | \brief Validates the elemental composition \a formula. | ||
| 335 | |||
| 336 | The \a formula needs to be fully indexed, that is, even an atom present only | ||
| 337 | once needs to be indexed with '1', like this \c H2O1. | ||
| 338 | |||
| 339 | Returns true if validation was successful, false otherwise. | ||
| 340 | |||
| 341 | \sa Formula::validate() | ||
| 342 | */ | ||
| 343 | bool | ||
| 344 | ✗ | IsotopicClusterGenerator::validateFormula(Formula &formula) | |
| 345 | { | ||
| 346 | // qDebug() << "Checking formula:" << formula.toString() | ||
| 347 | //<< "against an isotopic data set of " << msp_isotopicData->size() | ||
| 348 | //<< "isotopes"; | ||
| 349 | |||
| 350 | // Check the syntax of the formula. Note that we need an obligatory count | ||
| 351 | // index even for elements that are present a single time (H2O1 note the | ||
| 352 | // 1). | ||
| 353 | |||
| 354 | // IsoSpec requires that even single-count element be qualified with an | ||
| 355 | // index (H2O1) | ||
| 356 | |||
| 357 | ✗ | formula.setForceCountIndex(true); | |
| 358 | |||
| 359 | // We have to validate because the formula might be "C5H6N3-O1", in which case | ||
| 360 | // if would fail the simple checkSyntax() call (that call needs to be used on | ||
| 361 | // already split parts of a formula). | ||
| 362 | |||
| 363 | ✗ | if(!formula.validate( | |
| 364 | ✗ | msp_isotopicData, true /*store atom count*/, true /*reset counts*/)) | |
| 365 | ✗ | return false; | |
| 366 | |||
| 367 | ✗ | return true; | |
| 368 | } | ||
| 369 | |||
| 370 | /*! | ||
| 371 | \brief Validates all the elemental compositions in this | ||
| 372 | IsotopicClusterGenerator instance. | ||
| 373 | |||
| 374 | Each \l FormulaChargePair in m_formulaChargePairs is validated for its | ||
| 375 | elemental composition by first creating a \l Formula out of it. | ||
| 376 | |||
| 377 | Returns true if validation was successful, false otherwise. | ||
| 378 | |||
| 379 | \sa validateFormula, Formula::validate() | ||
| 380 | */ | ||
| 381 | bool | ||
| 382 | ✗ | IsotopicClusterGenerator::validateAllFormulas() | |
| 383 | { | ||
| 384 | ✗ | for(FormulaChargePair &pair : m_formulaChargePairs) | |
| 385 | { | ||
| 386 | ✗ | Formula formula(pair.first); | |
| 387 | |||
| 388 | ✗ | if(!validateFormula(formula)) | |
| 389 | ✗ | return false; | |
| 390 | ✗ | } | |
| 391 | |||
| 392 | ✗ | return true; | |
| 393 | } | ||
| 394 | |||
| 395 | /*! | ||
| 396 | \brief Runs the IsoSpec-based isotopic calculations. | ||
| 397 | |||
| 398 | \list | ||
| 399 | |||
| 400 | \li \a element_count: the number of elements in the chemical composition. | ||
| 401 | \li \a charge: the charge of the analyte. | ||
| 402 | |||
| 403 | \li \a per_element_isotopes_count_array_p: pointer to int array. This array | ||
| 404 | lists the number of isotopes that each element has. Typically, C has 2, O has 3, | ||
| 405 | P has 1... | ||
| 406 | |||
| 407 | \li \a per_element_symbol_count_array_p: pointer to int array. This array lists | ||
| 408 | the count of atoms of each element. Typically H20 will have 2 for H and 1 for O. | ||
| 409 | |||
| 410 | \li \a per_element_isotope_masses_arrays_p_p: pointer to pointer to double array | ||
| 411 | (array of arrays of double). Each array contains a new sub-array for each | ||
| 412 | symbol. The sub-array contains the isotopic masses for one of the element | ||
| 413 | symbols. | ||
| 414 | |||
| 415 | \li \a per_element_isotope_probs_arrays_p_p: pointer to pointer to double array | ||
| 416 | (array of arrays of double). Each array contains a new sub-array for each | ||
| 417 | symbol. The sub-array contains the isotopic probs for one of the element | ||
| 418 | symbols. | ||
| 419 | |||
| 420 | \endlist | ||
| 421 | |||
| 422 | Returns a pappso::Trace with the calculated isotopic cluster. | ||
| 423 | */ | ||
| 424 | pappso::TraceSPtr | ||
| 425 | ✗ | IsotopicClusterGenerator::runIsotopicDataCalculations( | |
| 426 | std::size_t element_count, | ||
| 427 | int charge, | ||
| 428 | int *per_element_isotopes_count_array_p, | ||
| 429 | int *per_element_symbol_count_array_p, | ||
| 430 | double **per_element_isotope_masses_arrays_p_p, | ||
| 431 | double **per_element_isotope_probs_arrays_p_p) | ||
| 432 | { | ||
| 433 | // We get all the isotopic data relevant to the isotopic cluster modelling | ||
| 434 | // calculation as performed by the IsoSpec library. | ||
| 435 | |||
| 436 | ✗ | if(per_element_isotopes_count_array_p == nullptr || | |
| 437 | ✗ | per_element_symbol_count_array_p == nullptr || | |
| 438 | ✗ | per_element_isotope_masses_arrays_p_p == nullptr || | |
| 439 | per_element_isotope_probs_arrays_p_p == nullptr) | ||
| 440 | ✗ | qFatal("Programming error. The pointers cannot be nullptr."); | |
| 441 | |||
| 442 | |||
| 443 | ✗ | if(m_maxSummedProbability <= 0 || m_maxSummedProbability > 1) | |
| 444 | { | ||
| 445 | ✗ | qDebug() << "The maximum summed probability has an incorrect value:" | |
| 446 | ✗ | << m_maxSummedProbability; | |
| 447 | ✗ | return nullptr; | |
| 448 | } | ||
| 449 | |||
| 450 | IsoSpec::IsoLayeredGenerator iso( | ||
| 451 | ✗ | IsoSpec::Iso(element_count, | |
| 452 | per_element_isotopes_count_array_p, | ||
| 453 | per_element_symbol_count_array_p, | ||
| 454 | per_element_isotope_masses_arrays_p_p, | ||
| 455 | ✗ | per_element_isotope_probs_arrays_p_p), | |
| 456 | // The three values below are from the documentation (default values in the | ||
| 457 | // constructor). We have added them 20230329 because we discovered that they | ||
| 458 | // were needed on minGW64, otherwise we would experience crashes. | ||
| 459 | 1000, | ||
| 460 | 1000, | ||
| 461 | true, | ||
| 462 | ✗ | m_maxSummedProbability); | |
| 463 | |||
| 464 | // qDebug() << "iso's mono peak mass:" << iso.getMonoisotopicPeakMass(); | ||
| 465 | |||
| 466 | // Each time we run a calculation, we do store the results in a new | ||
| 467 | // IsotopicCluster. | ||
| 468 | |||
| 469 | ✗ | pappso::TraceSPtr isotopic_cluster_sp = std::make_shared<pappso::Trace>(); | |
| 470 | |||
| 471 | // We store the results as std::vector<std::shared_ptr<libmass:PeakCentroid>> | ||
| 472 | // because we'll want to sort the values according to the user's requirements. | ||
| 473 | |||
| 474 | ✗ | double effective_summed_probs = 0; | |
| 475 | |||
| 476 | // Iterate in all the cluster configurations and output all the ones that | ||
| 477 | // summatively make a total probability <= to the probability set by the | ||
| 478 | // user. | ||
| 479 | |||
| 480 | /////////////// ATTENTION //////////////// | ||
| 481 | // The loop below is tricky, | ||
| 482 | |||
| 483 | ✗ | while(iso.advanceToNextConfiguration()) | |
| 484 | { | ||
| 485 | ✗ | double iso_prob = iso.prob(); | |
| 486 | ✗ | double iso_mz = iso.mass() / charge; | |
| 487 | |||
| 488 | // qDebug() << "For current configuration (charge accounted for):" << | ||
| 489 | // iso_mz | ||
| 490 | //<< iso_prob | ||
| 491 | //<< "and effective_probs_sum : " << effective_summed_probs; | ||
| 492 | |||
| 493 | // Create a peak centroid and store it (remark that we change the mass | ||
| 494 | // of the ion into m/z because the user had set the charge corresponding | ||
| 495 | // to the formula for which the isotopic cluster is being computed. | ||
| 496 | |||
| 497 | ✗ | isotopic_cluster_sp->push_back(pappso::DataPoint(iso_mz, iso_prob)); | |
| 498 | |||
| 499 | // qDebug() << "Pushed back new peak centroid:" << iso_mz << "/" << | ||
| 500 | // iso_prob; | ||
| 501 | |||
| 502 | // We do this increment at the end of the block. Indeed, if we had set up | ||
| 503 | // at the top of the block, then, if the very first centroid had already a | ||
| 504 | // prob > m_maxSummedProbability, then we would end up with an empty | ||
| 505 | // cluster! | ||
| 506 | |||
| 507 | ✗ | effective_summed_probs += iso_prob; | |
| 508 | |||
| 509 | ✗ | if(effective_summed_probs > m_maxSummedProbability) | |
| 510 | { | ||
| 511 | // qDebug() << "Reached the max value: effective_summed_probs:" | ||
| 512 | //<< effective_summed_probs | ||
| 513 | //<< "and m_maxSummedProbability:" << m_maxSummedProbability | ||
| 514 | //<< "BREAKING."; | ||
| 515 | ✗ | break; | |
| 516 | } | ||
| 517 | else | ||
| 518 | { | ||
| 519 | // qDebug() << "Not yet reached the max value: effective_summed_probs | ||
| 520 | // : " | ||
| 521 | //<< effective_summed_probs | ||
| 522 | //<< "and m_maxSummedProbability:" << m_maxSummedProbability; | ||
| 523 | } | ||
| 524 | } | ||
| 525 | |||
| 526 | // Now perform the normalization to the Gaussian apex intensity value if | ||
| 527 | // so is requested by the user For this we first need to find | ||
| 528 | // what is the most intensity peak centroid. Then, we'll normalize against | ||
| 529 | // it by dividing all intensity that that most intense value and | ||
| 530 | // multiplying by the requested gaussian apex intensity value. | ||
| 531 | |||
| 532 | // qDebug() << "Now asking for normalization."; | ||
| 533 | |||
| 534 | // Just a debug check. | ||
| 535 | // qDebug() << "Before normalizing, first data point:" | ||
| 536 | //<< isotopic_cluster_sp->front().toString(); | ||
| 537 | |||
| 538 | ✗ | normalizeIntensities(isotopic_cluster_sp); | |
| 539 | |||
| 540 | // Just a debug check. | ||
| 541 | // qDebug() << "After normalizing, first data point:" | ||
| 542 | //<< isotopic_cluster_sp->front().toString(); | ||
| 543 | |||
| 544 | // Now check if the user requests to kind of sorting of the PeakCentroid | ||
| 545 | // instances. | ||
| 546 | |||
| 547 | ✗ | sortPeakCentroids(isotopic_cluster_sp); | |
| 548 | |||
| 549 | // qDebug() << "Now returning a cluster of size:" << | ||
| 550 | // isotopic_cluster_sp->size(); | ||
| 551 | |||
| 552 | ✗ | return isotopic_cluster_sp; | |
| 553 | ✗ | } | |
| 554 | |||
| 555 | /*! | ||
| 556 | \brief Calculates the isotopic cluster's peak centroids for \a | ||
| 557 | formula_charge_pair. | ||
| 558 | |||
| 559 | \list 1 | ||
| 560 | \li The elemental composition formula string is converted to a \l Formula and | ||
| 561 | validated. | ||
| 562 | \li The proper isotopic data handler is allocated (\l IsotopicDataType). | ||
| 563 | \li The number of symbols in the elemental composition is determined. | ||
| 564 | \li The int arrays and arrays of double arrays are allocated. | ||
| 565 | \li The arrays are filled-in with \l configureIsotopicData(). | ||
| 566 | \li The calculations are performed on these arrays with \l | ||
| 567 | runIsotopicDataCalculations(). | ||
| 568 | \endlist | ||
| 569 | |||
| 570 | Returns the results of the computation in the form of a | ||
| 571 | IsotopicClusterChargePair instance. | ||
| 572 | */ | ||
| 573 | IsotopicClusterChargePair | ||
| 574 | ✗ | IsotopicClusterGenerator::generateIsotopicClusterCentroids( | |
| 575 | FormulaChargePair formula_charge_pair) | ||
| 576 | { | ||
| 577 | // qDebug() << "Starting generation of isotopic cluster for formula:" | ||
| 578 | //<< formula_charge_pair.first; | ||
| 579 | |||
| 580 | ✗ | Formula formula(formula_charge_pair.first); | |
| 581 | |||
| 582 | // The check will generate useful data inside the Formula! | ||
| 583 | ✗ | if(!validateFormula(formula)) | |
| 584 | ✗ | return std::pair(std::make_shared<const pappso::Trace>(), 0); | |
| 585 | |||
| 586 | // Use the correct handler! | ||
| 587 | |||
| 588 | ✗ | std::unique_ptr<IsotopicDataBaseHandler> isotopic_data_handler_up = nullptr; | |
| 589 | |||
| 590 | ✗ | if(m_isotopicDataType == IsotopicDataType::LIBRARY_CONFIG) | |
| 591 | { | ||
| 592 | isotopic_data_handler_up = | ||
| 593 | ✗ | std::make_unique<IsotopicDataLibraryHandler>(msp_isotopicData); | |
| 594 | } | ||
| 595 | ✗ | else if(m_isotopicDataType == IsotopicDataType::USER_CONFIG) | |
| 596 | { | ||
| 597 | isotopic_data_handler_up = | ||
| 598 | ✗ | std::make_unique<IsotopicDataUserConfigHandler>(msp_isotopicData); | |
| 599 | } | ||
| 600 | ✗ | else if(m_isotopicDataType == IsotopicDataType::MANUAL_CONFIG) | |
| 601 | { | ||
| 602 | isotopic_data_handler_up = | ||
| 603 | ✗ | std::make_unique<IsotopicDataManualConfigHandler>(msp_isotopicData); | |
| 604 | } | ||
| 605 | else | ||
| 606 | ✗ | qFatal("Programming error. The isotopic data type is not correct."); | |
| 607 | |||
| 608 | |||
| 609 | // At this point we need to create the arrays exactly as we do in the user | ||
| 610 | // manual config. So we need to know how many different chemical element | ||
| 611 | // symbols we have in the formula. | ||
| 612 | |||
| 613 | std::map<QString, double> symbol_double_count_map = | ||
| 614 | ✗ | formula.getSymbolCountMap(); | |
| 615 | |||
| 616 | ✗ | std::size_t element_count = symbol_double_count_map.size(); | |
| 617 | |||
| 618 | // qDebug() << "Number of different symbols in the formula:" << element_count; | ||
| 619 | |||
| 620 | ✗ | if(!element_count) | |
| 621 | { | ||
| 622 | ✗ | qDebug() << "There is not a single element in the Formula."; | |
| 623 | ✗ | return std::pair(std::make_shared<const pappso::Trace>(), 0); | |
| 624 | } | ||
| 625 | |||
| 626 | // qDebug() << "The validated formula has a symbol/count map size:" | ||
| 627 | //<< element_count; | ||
| 628 | |||
| 629 | // We have to copy the symbol/count map obtained by validating | ||
| 630 | // the formula into the isotopic data handler. That map is essential for the | ||
| 631 | // crafting by the handler of the different IsoSpec arrays. | ||
| 632 | |||
| 633 | // At this point, all the elements defined by the user have been completed and | ||
| 634 | // we'll have to create the static arrays that are needed by IsoSpec. | ||
| 635 | |||
| 636 | // We now need to construct the C arrays for IsoSpec. The arrays need to | ||
| 637 | // be filled-in very accurately. | ||
| 638 | |||
| 639 | // This array lists the number of isotopes that each element has. | ||
| 640 | // Typically, C has 2, O has 3, P has 1... | ||
| 641 | ✗ | int *per_element_isotopes_count_array_p = nullptr; | |
| 642 | |||
| 643 | // This array lists the count of atoms of each element. | ||
| 644 | // Typically H20 will have 2 for H and 1 for O. | ||
| 645 | ✗ | int *per_element_symbol_count_array_p = nullptr; | |
| 646 | |||
| 647 | // These are arrays of arrays! Each array contains a new sub-array for each | ||
| 648 | // symbol. The sub-array contains the isotopic masses (or probs) for one of | ||
| 649 | // the element symbols. The sub-arrays are allocated by the handler below. | ||
| 650 | ✗ | double **per_element_isotope_masses_arrays_p_p = nullptr; | |
| 651 | ✗ | double **per_element_isotope_probs_arrays_p_p = nullptr; | |
| 652 | |||
| 653 | // The isotopic cluster calculations do not understand | ||
| 654 | // formulas with double counts for the symbols!! | ||
| 655 | // We thus need to convert the symbol_count_map that is | ||
| 656 | // <QString,double>-based to a map that has its second | ||
| 657 | // member, not of double type but of int type. | ||
| 658 | |||
| 659 | ✗ | std::map<QString, int> symbol_int_count_map; | |
| 660 | std::map<QString, double>::const_iterator iter = | ||
| 661 | ✗ | symbol_double_count_map.begin(); | |
| 662 | |||
| 663 | ✗ | while(iter != symbol_double_count_map.end()) | |
| 664 | { | ||
| 665 | ✗ | symbol_int_count_map[iter->first] = static_cast<int>(iter->second); | |
| 666 | |||
| 667 | // qDebug() << "Old " << iter->first << "double version:" << iter->second | ||
| 668 | // << "new int version:" << symbol_int_count_map[iter->first]; | ||
| 669 | |||
| 670 | ✗ | ++iter; | |
| 671 | } | ||
| 672 | |||
| 673 | // We pass the array pointers by reference. | ||
| 674 | ✗ | if(!configureIsotopicData(symbol_int_count_map, | |
| 675 | per_element_isotopes_count_array_p, | ||
| 676 | per_element_symbol_count_array_p, | ||
| 677 | per_element_isotope_masses_arrays_p_p, | ||
| 678 | per_element_isotope_probs_arrays_p_p)) | ||
| 679 | { | ||
| 680 | ✗ | qDebug() << "Failed to actually prepare the isotopic data tables for the " | |
| 681 | ✗ | "computation."; | |
| 682 | |||
| 683 | ✗ | return std::pair(std::make_shared<const pappso::Trace>(), 0); | |
| 684 | } | ||
| 685 | |||
| 686 | // At this point we have all the arrays needed to work. | ||
| 687 | |||
| 688 | pappso::TraceSPtr isotopic_cluster_sp = | ||
| 689 | runIsotopicDataCalculations(element_count, | ||
| 690 | formula_charge_pair.second, | ||
| 691 | per_element_isotopes_count_array_p, | ||
| 692 | per_element_symbol_count_array_p, | ||
| 693 | per_element_isotope_masses_arrays_p_p, | ||
| 694 | ✗ | per_element_isotope_probs_arrays_p_p); | |
| 695 | |||
| 696 | // FIXME | ||
| 697 | // To avoid a memory leak, we need to delete the mass and prob heap-allocated | ||
| 698 | // arrays. | ||
| 699 | |||
| 700 | // delete[] per_element_isotopes_count_array_p; | ||
| 701 | // delete[] per_element_symbol_count_array_p; | ||
| 702 | |||
| 703 | // for(std::size_t iter = 0; iter < element_count; ++iter) | ||
| 704 | //{ | ||
| 705 | // delete[] per_element_isotope_masses_arrays_p_p[iter]; | ||
| 706 | // delete[] per_element_isotope_probs_arrays_p_p[iter]; | ||
| 707 | //} | ||
| 708 | |||
| 709 | ✗ | if(isotopic_cluster_sp == nullptr) | |
| 710 | ✗ | qDebug() << "Failed to compute an isotopic cluster for formula:" | |
| 711 | ✗ | << formula_charge_pair.first; | |
| 712 | |||
| 713 | // Just a debug check. | ||
| 714 | // qDebug() << "After normalizing, first data point:" | ||
| 715 | //<< isotopic_cluster_sp->front().toString(); | ||
| 716 | |||
| 717 | // qDebug() << "Done generating cluster for formula:" | ||
| 718 | //<< formula_charge_pair.first; | ||
| 719 | |||
| 720 | ✗ | return std::pair(isotopic_cluster_sp, formula_charge_pair.second); | |
| 721 | ✗ | } | |
| 722 | |||
| 723 | |||
| 724 | /*! | ||
| 725 | \brief Configures the isotopic data in a set of arrays for the (symbol,count) | ||
| 726 | pairs in \a symbol_count_map. | ||
| 727 | |||
| 728 | \list | ||
| 729 | |||
| 730 | \li \a per_element_isotopes_count_array_p: pointer to int array. This array | ||
| 731 | lists | ||
| 732 | the number of isotopes that each element has. Typically, C has 2, O has 3, P has | ||
| 733 | 1... | ||
| 734 | |||
| 735 | \li \a per_element_symbol_count_array_p: pointer to int array. This array lists | ||
| 736 | the count of atoms of each element. Typically H20 will have 2 for H and 1 for O. | ||
| 737 | |||
| 738 | \li \a per_element_isotope_masses_arrays_p_p: pointer to pointer to double array | ||
| 739 | (array of arrays of double). Each array contains a new sub-array for each | ||
| 740 | symbol. The sub-array contains the isotopic masses for one of the element | ||
| 741 | symbols. | ||
| 742 | |||
| 743 | \li \a per_element_isotope_probs_arrays_p_p: pointer to pointer to double array | ||
| 744 | (array of arrays of double). Each array contains a new sub-array for each | ||
| 745 | symbol. The sub-array contains the isotopic probs for one of the element | ||
| 746 | symbols. | ||
| 747 | |||
| 748 | \endlist | ||
| 749 | |||
| 750 | Returns a pappso::Trace with the calculated isotopic cluster. | ||
| 751 | */ | ||
| 752 | bool | ||
| 753 | ✗ | IsotopicClusterGenerator::configureIsotopicData( | |
| 754 | std::map<QString, int> &symbol_count_map, | ||
| 755 | int *&per_element_isotopes_count_array_p, | ||
| 756 | int *&per_element_symbol_count_array_p, | ||
| 757 | double **&per_element_isotope_masses_arrays_p_p, | ||
| 758 | double **&per_element_isotope_probs_arrays_p_p) | ||
| 759 | { | ||
| 760 | // Start by allocating the arrays we'll have to feed in this configuration | ||
| 761 | // work. | ||
| 762 | |||
| 763 | // However, we need to ensure that we actually have some stuff to work on. | ||
| 764 | // That stuff is kind of a formula in the form of the std::map<QString, int> | ||
| 765 | // m_symbolCountMap that pairs the symbols of the atoms in the formula and | ||
| 766 | // the count for each symbol. | ||
| 767 | |||
| 768 | ✗ | if(!symbol_count_map.size()) | |
| 769 | ✗ | return false; | |
| 770 | |||
| 771 | // qDebug() << "The isotopic data have" << msp_isotopicData->size() | ||
| 772 | //<< "isotopes"; | ||
| 773 | |||
| 774 | // Example used in the comments below: glucose, C6H12O6. | ||
| 775 | |||
| 776 | // How many isotopes of each element symbols are there? | ||
| 777 | // C:2, H:2, O:3 | ||
| 778 | ✗ | per_element_isotopes_count_array_p = new int[symbol_count_map.size()]; | |
| 779 | |||
| 780 | // How many atoms of each chemical element symbol are there? | ||
| 781 | // C:6, H:12, O:6 | ||
| 782 | ✗ | per_element_symbol_count_array_p = new int[symbol_count_map.size()]; | |
| 783 | |||
| 784 | // Each subarray contains the mass of one of the isotopes for the element | ||
| 785 | // symbol. | ||
| 786 | // First array for C (two masses), second array for H (two masses), third | ||
| 787 | // array for O (three masses). | ||
| 788 | ✗ | per_element_isotope_masses_arrays_p_p = new double *[symbol_count_map.size()]; | |
| 789 | |||
| 790 | // Each subarray contains the prob of one of the isotopes for the element | ||
| 791 | // symbol. | ||
| 792 | // First array for C (two probs), second array for H (two probs), third | ||
| 793 | // array for O (three probs). | ||
| 794 | ✗ | per_element_isotope_probs_arrays_p_p = new double *[symbol_count_map.size()]; | |
| 795 | |||
| 796 | // Index that will allow to address the right slot in the arrays being | ||
| 797 | // filled with isotopic data. | ||
| 798 | ✗ | int current_symbol_index = 0; | |
| 799 | |||
| 800 | ✗ | for(auto item : symbol_count_map) | |
| 801 | { | ||
| 802 | ✗ | QString symbol = item.first; | |
| 803 | ✗ | int symbol_count = item.second; | |
| 804 | |||
| 805 | // qDebug() << "Iterating in symbol/count:" << symbol << "/" << | ||
| 806 | // symbol_count; | ||
| 807 | |||
| 808 | // Immediately fill-in the symbol count value. | ||
| 809 | ✗ | per_element_symbol_count_array_p[current_symbol_index] = symbol_count; | |
| 810 | |||
| 811 | // Now get iterator bounding the isotopes for this symbol. | ||
| 812 | |||
| 813 | std::pair<std::vector<IsotopeSPtr>::const_iterator, | ||
| 814 | std::vector<IsotopeSPtr>::const_iterator> | ||
| 815 | ✗ | iter_pair = msp_isotopicData->getIsotopesBySymbol(symbol); | |
| 816 | |||
| 817 | // Handy shortcuts | ||
| 818 | ✗ | std::vector<IsotopeSPtr>::const_iterator iter = iter_pair.first; | |
| 819 | ✗ | std::vector<IsotopeSPtr>::const_iterator iter_end = iter_pair.second; | |
| 820 | |||
| 821 | ✗ | std::size_t isotope_count = std::distance(iter, iter_end); | |
| 822 | |||
| 823 | // qDebug() << "For symbol:" << symbol << "there are:" << isotope_count | ||
| 824 | //<< "isotopes"; | ||
| 825 | |||
| 826 | // Sanity check | ||
| 827 | ✗ | if(isotope_count != msp_isotopicData->getIsotopeCountBySymbol(symbol)) | |
| 828 | ✗ | qFatal( | |
| 829 | "Programming error. The is something wrong with the isotopic " | ||
| 830 | "data."); | ||
| 831 | |||
| 832 | // Fill-in the isotope count for the current symbol. | ||
| 833 | ✗ | per_element_isotopes_count_array_p[current_symbol_index] = isotope_count; | |
| 834 | |||
| 835 | // Fill-in the isotopes (mass/prob). For each element symbol in the | ||
| 836 | // symbol/count map, we allocate a double array the size of the number | ||
| 837 | // of isotopes so as to store the mass of each isotope (same for the | ||
| 838 | // probs later). Once we have done that fill-in, we can set the address | ||
| 839 | // of the array of the array of array below. | ||
| 840 | |||
| 841 | // Allocate a double array for the masses and another one for the probs. | ||
| 842 | |||
| 843 | ✗ | double *masses_p = new double[isotope_count]; | |
| 844 | ✗ | double *probs_p = new double[isotope_count]; | |
| 845 | |||
| 846 | ✗ | int current_isotope_index = 0; | |
| 847 | |||
| 848 | ✗ | while(iter != iter_end) | |
| 849 | { | ||
| 850 | ✗ | IsotopeSPtr isotope_sp = *iter; | |
| 851 | |||
| 852 | // qDebug() << "For symbol" << symbol << "iterating with index" | ||
| 853 | //<< current_isotope_index << "with Isotope *" | ||
| 854 | //<< isotope_sp.get(); | ||
| 855 | |||
| 856 | ✗ | masses_p[current_isotope_index] = isotope_sp->getMass(); | |
| 857 | ✗ | probs_p[current_isotope_index] = isotope_sp->getProbability(); | |
| 858 | |||
| 859 | // Increment the iterator | ||
| 860 | ✗ | ++iter; | |
| 861 | // Increment the isotope index so that we fill next array cell. | ||
| 862 | ✗ | ++current_isotope_index; | |
| 863 | ✗ | } | |
| 864 | |||
| 865 | // At this time the masses and probs for the isotopes of current symbol | ||
| 866 | // have been filled-in. | ||
| 867 | |||
| 868 | ✗ | per_element_isotope_masses_arrays_p_p[current_symbol_index] = masses_p; | |
| 869 | ✗ | per_element_isotope_probs_arrays_p_p[current_symbol_index] = probs_p; | |
| 870 | |||
| 871 | // We need to increment this index so as to address the right slot in | ||
| 872 | // the arrays! | ||
| 873 | ✗ | ++current_symbol_index; | |
| 874 | ✗ | } | |
| 875 | |||
| 876 | // At this point we have documented all the isotopic data required to | ||
| 877 | // perform a calculation with IsoSpec. | ||
| 878 | |||
| 879 | ✗ | return true; | |
| 880 | } | ||
| 881 | |||
| 882 | /*! | ||
| 883 | \brief Normalizes the intensities of the isotopic cluster's peak centroids in | ||
| 884 | \a isotopic_cluster_sp. | ||
| 885 | |||
| 886 | If normalization is asked for, the most intense peak centroid in \a | ||
| 887 | isotopic_cluster_sp is determined. That intensity becomes the | ||
| 888 | m_normalizeIntensity value and all the other peak centroids' intensities are | ||
| 889 | normalized. | ||
| 890 | |||
| 891 | \note The normalization occurs \e{in place}. | ||
| 892 | */ | ||
| 893 | void | ||
| 894 | ✗ | IsotopicClusterGenerator::normalizeIntensities( | |
| 895 | pappso::TraceSPtr &isotopic_cluster_sp) | ||
| 896 | { | ||
| 897 | |||
| 898 | // qDebug() << "The normalize_intensity is:" << m_normalizeIntensity; | ||
| 899 | |||
| 900 | // The most intense peak centroid's intensity value needs to be set to the | ||
| 901 | // requested value and the same change ratio needs to be applied to all the | ||
| 902 | // other peak centroids. | ||
| 903 | |||
| 904 | // No normalization is asked for. | ||
| 905 | ✗ | if(m_normalizeIntensity == std::numeric_limits<int>::min()) | |
| 906 | { | ||
| 907 | // qDebug() << "No normalization was asked for. Skipping."; | ||
| 908 | ✗ | return; | |
| 909 | } | ||
| 910 | |||
| 911 | ✗ | if(!isotopic_cluster_sp->size()) | |
| 912 | { | ||
| 913 | ✗ | qDebug() << "The isotopic cluster has not a single data point."; | |
| 914 | ✗ | return; | |
| 915 | } | ||
| 916 | // First get the most intense centroid. | ||
| 917 | |||
| 918 | ✗ | double max_found_intensity = 0; | |
| 919 | |||
| 920 | // qDebug() << "isotopic_cluster_sp->size():" << isotopic_cluster_sp->size(); | ||
| 921 | |||
| 922 | ✗ | pappso::Trace::iterator vector_iterator = std::max_element( | |
| 923 | ✗ | isotopic_cluster_sp->begin(), | |
| 924 | ✗ | isotopic_cluster_sp->end(), | |
| 925 | ✗ | [](const pappso::DataPoint first, const pappso::DataPoint second) { | |
| 926 | ✗ | return first.y < second.y; | |
| 927 | }); | ||
| 928 | |||
| 929 | ✗ | if(vector_iterator == isotopic_cluster_sp->end()) | |
| 930 | ✗ | qFatal("Programming error"); | |
| 931 | |||
| 932 | ✗ | max_found_intensity = (*vector_iterator).y; | |
| 933 | |||
| 934 | ✗ | if(!max_found_intensity) | |
| 935 | ✗ | qFatal("The maximum intensity of the whole isotopic cluster is 0."); | |
| 936 | |||
| 937 | // qDebug().noquote() << "Peak centroid with maximum intensity: " | ||
| 938 | //<< vector_iterator->toString(); | ||
| 939 | |||
| 940 | // Calculate the ratio between the final requested intensity and the greatest | ||
| 941 | // intensity. That ratio will be multiplied to intensity of the each peak | ||
| 942 | // centroid, which is why we call it a factor. | ||
| 943 | |||
| 944 | ✗ | double intensity_factor = m_normalizeIntensity / max_found_intensity; | |
| 945 | |||
| 946 | // qDebug() << "Will multiply this intensity factor to each data point's " | ||
| 947 | //"intensity value:" | ||
| 948 | //<< intensity_factor; | ||
| 949 | |||
| 950 | // Just a debug check. | ||
| 951 | // qDebug() << "Before normalizing, first data point:" | ||
| 952 | //<< isotopic_cluster_sp->front().toString(); | ||
| 953 | |||
| 954 | ✗ | std::for_each( | |
| 955 | ✗ | isotopic_cluster_sp->begin(), | |
| 956 | ✗ | isotopic_cluster_sp->end(), | |
| 957 | ✗ | [intensity_factor](pappso::DataPoint &data_point) // modify in-place | |
| 958 | { | ||
| 959 | // qDebug() << "Before normalization:" << | ||
| 960 | // data_point.toString(); | ||
| 961 | |||
| 962 | ✗ | double normalized_intensity = data_point.y * intensity_factor; | |
| 963 | |||
| 964 | ✗ | data_point.y = normalized_intensity; | |
| 965 | |||
| 966 | // qDebug() << "After normalization:" << | ||
| 967 | // data_point.toString(); | ||
| 968 | ✗ | }); | |
| 969 | |||
| 970 | // At this point the centroids' intensity have been normalized. | ||
| 971 | |||
| 972 | // Just a debug check. | ||
| 973 | // qDebug() << "After normalizing, first data point:" | ||
| 974 | //<< isotopic_cluster_sp->front().toString(); | ||
| 975 | } | ||
| 976 | |||
| 977 | /*! | ||
| 978 | \brief Sorts the peak centroids of the isotopic cluster \a isotopic_cluster_sp. | ||
| 979 | |||
| 980 | The sort is performed according to \l m_sortType. | ||
| 981 | */ | ||
| 982 | void | ||
| 983 | ✗ | IsotopicClusterGenerator::sortPeakCentroids( | |
| 984 | pappso::TraceSPtr &isotopic_cluster_sp) | ||
| 985 | { | ||
| 986 | ✗ | if(m_sortType == pappso::SortType::no_sort) | |
| 987 | ✗ | return; | |
| 988 | |||
| 989 | ✗ | return isotopic_cluster_sp->sort(m_sortType, m_sortOrder); | |
| 990 | } | ||
| 991 | |||
| 992 | /*! | ||
| 993 | \brief Returns a string containing a space-separated set of m/z, intensity | ||
| 994 | pairs, representing the isotopic cluster in \a isotopic_cluster_sp. | ||
| 995 | */ | ||
| 996 | QString | ||
| 997 | ✗ | IsotopicClusterGenerator::clusterToString( | |
| 998 | const pappso::TraceCstSPtr &isotopic_cluster_sp) const | ||
| 999 | { | ||
| 1000 | |||
| 1001 | // Export the results as a string. Note how we do export the relative | ||
| 1002 | // intensity. If there was normalization, that value was updated, otherwise it | ||
| 1003 | // had been initialized identical to the intensity upon creation of the | ||
| 1004 | // PeakCentroid instances in the vector. | ||
| 1005 | |||
| 1006 | ✗ | QString text; | |
| 1007 | |||
| 1008 | ✗ | for(const pappso::DataPoint &dp : *isotopic_cluster_sp) | |
| 1009 | { | ||
| 1010 | ✗ | text += QString("%1 %2\n").arg(dp.x, 0, 'f', 30).arg(dp.y, 0, 'f', 30); | |
| 1011 | } | ||
| 1012 | |||
| 1013 | // qDebug().noquote() << "Cluster to string: " << text; | ||
| 1014 | |||
| 1015 | ✗ | return text; | |
| 1016 | ✗ | } | |
| 1017 | |||
| 1018 | |||
| 1019 | /*! | ||
| 1020 | \brief Returns a string containing a space-separated set of m/z, intensity | ||
| 1021 | pairs, representing the isotopic clusters in the member isotopic clusters \l | ||
| 1022 | m_isotopicClusterChargePairs. | ||
| 1023 | */ | ||
| 1024 | QString | ||
| 1025 | ✗ | IsotopicClusterGenerator::clustersToString() const | |
| 1026 | { | ||
| 1027 | |||
| 1028 | // Export the results as a string. Note how we do export the relative | ||
| 1029 | // intensity. If there was normalization, that value was updated, otherwise it | ||
| 1030 | // had been initialized identical to the intensity upon creation of the | ||
| 1031 | // PeakCentroid instances in the vector. | ||
| 1032 | |||
| 1033 | ✗ | QString text; | |
| 1034 | |||
| 1035 | ✗ | for(auto isotopic_cluster_charge_pair : m_isotopicClusterChargePairs) | |
| 1036 | { | ||
| 1037 | ✗ | text += clusterToString(isotopic_cluster_charge_pair.first); | |
| 1038 | ✗ | } | |
| 1039 | |||
| 1040 | // qDebug().noquote() << text; | ||
| 1041 | |||
| 1042 | ✗ | return text; | |
| 1043 | ✗ | } | |
| 1044 | |||
| 1045 | /*! | ||
| 1046 | \brief Starts the computations. | ||
| 1047 | |||
| 1048 | The member m_isotopicClusterChargePairs are first cleared. | ||
| 1049 | |||
| 1050 | Returns the count of IsotopicClusterChargePair instances generated upon the | ||
| 1051 | calculations. | ||
| 1052 | */ | ||
| 1053 | std::size_t | ||
| 1054 | ✗ | IsotopicClusterGenerator::run() | |
| 1055 | { | ||
| 1056 | // Iterate in all the formula/charge pairs and for each compute an isotopic | ||
| 1057 | // cluster. | ||
| 1058 | |||
| 1059 | ✗ | m_isotopicClusterChargePairs.clear(); | |
| 1060 | |||
| 1061 | ✗ | for(auto formula_charge_pair : m_formulaChargePairs) | |
| 1062 | { | ||
| 1063 | IsotopicClusterChargePair pair = | ||
| 1064 | ✗ | generateIsotopicClusterCentroids(formula_charge_pair); | |
| 1065 | |||
| 1066 | ✗ | if(!pair.first->size()) | |
| 1067 | { | ||
| 1068 | ✗ | qFatal("The isotopic cluster is empty for formula: %s", | |
| 1069 | ✗ | formula_charge_pair.first.toLatin1().data()); | |
| 1070 | } | ||
| 1071 | |||
| 1072 | ✗ | m_isotopicClusterChargePairs.push_back(pair); | |
| 1073 | ✗ | } | |
| 1074 | |||
| 1075 | ✗ | return m_isotopicClusterChargePairs.size(); | |
| 1076 | } | ||
| 1077 | |||
| 1078 | /*! | ||
| 1079 | \brief Returns the member list ofIsotopicClusterChargePair instances. | ||
| 1080 | */ | ||
| 1081 | const std::vector<IsotopicClusterChargePair> & | ||
| 1082 | ✗ | IsotopicClusterGenerator::getIsotopicClusterChargePairs() const | |
| 1083 | { | ||
| 1084 | ✗ | return m_isotopicClusterChargePairs; | |
| 1085 | } | ||
| 1086 | |||
| 1087 | } // namespace libXpertMass | ||
| 1088 | |||
| 1089 | } // namespace MsXpS | ||
| 1090 |