| Line | Branch | Exec | Source |
|---|---|---|---|
| 1 | /* BEGIN software license | ||
| 2 | * | ||
| 3 | * MsXpertSuite - mass spectrometry software suite | ||
| 4 | * ----------------------------------------------- | ||
| 5 | * Copyright(C) 2009,...,2018 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 | /////////////////////// Local includes | ||
| 35 | #include "Oligomer.hpp" | ||
| 36 | #include "Polymer.hpp" | ||
| 37 | #include "IonizeRule.hpp" | ||
| 38 | |||
| 39 | |||
| 40 | namespace MsXpS | ||
| 41 | { | ||
| 42 | |||
| 43 | namespace libXpertMass | ||
| 44 | { | ||
| 45 | |||
| 46 | |||
| 47 | /*! | ||
| 48 | \class MsXpS::libXpertMass::Oligomer | ||
| 49 | \inmodule libXpertMass | ||
| 50 | \ingroup PolChemDefBuildingdBlocks | ||
| 51 | \inheaderfile Oligomer.hpp | ||
| 52 | |||
| 53 | \brief The Oligomer class provides abstractions to work with | ||
| 54 | an oligomer molecule (peptide , for example). | ||
| 55 | |||
| 56 | The notion of an oligomer is that it is part of a \l Polymer and is thus | ||
| 57 | defined by a range of \l Monomer indices in this Polymer (the \l Coordinates). | ||
| 58 | |||
| 59 | The start index cannot be less than 0 nor greater than the size of the polymer | ||
| 60 | minus one, and the end index follows the same rule. | ||
| 61 | |||
| 62 | Derived from \l Ionizable (itself derived from \l Ponderable), an oligomer is | ||
| 63 | also characterized by a monoisotopic | ||
| 64 | mass and an average mass. | ||
| 65 | |||
| 66 | All computations about an oligomer (fragmentation, composition, for | ||
| 67 | example, isoelectric point, ...) can only be performed by referring | ||
| 68 | to the sequence of its "enclosing" \l Polymer. Therefore, an Oligomer | ||
| 69 | should never exist after the destruction of its "enclosing" polymer. | ||
| 70 | */ | ||
| 71 | |||
| 72 | /*! | ||
| 73 | \variable MsXpS::libXpertMass::Oligomer::mp_polymer | ||
| 74 | |||
| 75 | \brief The \l Polymer instance of which this Oligomer is part. | ||
| 76 | */ | ||
| 77 | |||
| 78 | /*! | ||
| 79 | \variable MsXpS::libXpertMass::Oligomer::m_description | ||
| 80 | |||
| 81 | \brief The description of the Oligomer. | ||
| 82 | */ | ||
| 83 | |||
| 84 | |||
| 85 | /*! | ||
| 86 | \variable MsXpS::libXpertMass::Oligomer::m_isModified | ||
| 87 | |||
| 88 | \brief Tell if the Oligomer is modified. | ||
| 89 | */ | ||
| 90 | |||
| 91 | /*! | ||
| 92 | \variable MsXpS::libXpertMass::Oligomer::m_crossLinkList | ||
| 93 | |||
| 94 | \brief The list of CrossLink events in the oligomer sequence. | ||
| 95 | */ | ||
| 96 | |||
| 97 | /*! | ||
| 98 | \variable MsXpS::libXpertMass::Oligomer::m_calcOptions | ||
| 99 | |||
| 100 | \brief The calculation options definining how calculations are | ||
| 101 | performed. | ||
| 102 | */ | ||
| 103 | |||
| 104 | /*! | ||
| 105 | \typedef OligomerSPtr | ||
| 106 | \relates Oligomer | ||
| 107 | |||
| 108 | Synonym for std::shared_ptr<Oligomer> OligomerSPtr. | ||
| 109 | */ | ||
| 110 | |||
| 111 | /*! | ||
| 112 | \typedef OligomerCstSPtr | ||
| 113 | \relates Oligomer | ||
| 114 | |||
| 115 | Synonym for std::shared_ptr<const Oligomer> OligomerSPtr. | ||
| 116 | */ | ||
| 117 | |||
| 118 | /*! | ||
| 119 | \brief Constructs an oligomer. | ||
| 120 | |||
| 121 | The Oligomer instance is constructed with these arguments: | ||
| 122 | |||
| 123 | \a polymer: The polymer instance that encloses this Oligomer. Used to intialize | ||
| 124 | the member m_polymer and the Ionizable base class' polymer | ||
| 125 | chemistry definition | ||
| 126 | |||
| 127 | \a name: The name of this Oligomer, used to intialize the Ionizable base class | ||
| 128 | |||
| 129 | \a description: The description of this Oligomer (m_description) | ||
| 130 | |||
| 131 | \a modified: Tells if the Oligomer is modified | ||
| 132 | |||
| 133 | \a ponderable: Used to initialize the Ionizable base class | ||
| 134 | |||
| 135 | \a ionizeRule: Used to initialize the Ionizable base class | ||
| 136 | |||
| 137 | \a calcOptions: Used to initialize the m_calcOptions member | ||
| 138 | |||
| 139 | \a isIonized: Tells if this Oligomer instance is ionized | ||
| 140 | |||
| 141 | \a startIndex: The oligomer's start index coordinate in the enclosing Polymer | ||
| 142 | |||
| 143 | \a endIndex: The oligomer's end index coordinate in the enclosing Polymer | ||
| 144 | */ | ||
| 145 | ✗ | Oligomer::Oligomer(Polymer *polymer, | |
| 146 | const QString &name, | ||
| 147 | const QString &description, | ||
| 148 | bool modified, | ||
| 149 | const Ponderable &ponderable, | ||
| 150 | const IonizeRule &ionizeRule, | ||
| 151 | const CalcOptions &calcOptions, | ||
| 152 | bool isIonized, | ||
| 153 | int startIndex, | ||
| 154 | ✗ | int endIndex) | |
| 155 | : Ionizable( | ||
| 156 | ✗ | polymer->getPolChemDefCstSPtr(), name, ponderable, ionizeRule, isIonized), | |
| 157 | ✗ | mp_polymer(polymer), | |
| 158 | ✗ | m_description(description), | |
| 159 | ✗ | m_isModified{modified}, | |
| 160 | ✗ | m_calcOptions(calcOptions) | |
| 161 | { | ||
| 162 | ✗ | setStartEndIndices(startIndex, endIndex); | |
| 163 | ✗ | } | |
| 164 | |||
| 165 | |||
| 166 | /*! | ||
| 167 | \brief Constructs an oligomer. | ||
| 168 | |||
| 169 | The Oligomer instance is constructed with these arguments: | ||
| 170 | |||
| 171 | \a pol_chem_def_csp: The polymer chemistry definition used to initialize the | ||
| 172 | Ionizable base class | ||
| 173 | |||
| 174 | \a name: The name of this Oligomer, used to intialize the Ionizable base class | ||
| 175 | |||
| 176 | \a description: The description of this Oligomer (m_description) | ||
| 177 | |||
| 178 | \a modified: Tells if the Oligomer is modified | ||
| 179 | |||
| 180 | \a ponderable: Used to initialize the Ionizable base class | ||
| 181 | |||
| 182 | \a ionizeRule: Used to initialize the Ionizable base class | ||
| 183 | |||
| 184 | \a calcOptions: Used to initialize the m_calcOptions member | ||
| 185 | |||
| 186 | \a isIonized: Tells if this Oligomer instance is ionized | ||
| 187 | |||
| 188 | \a startIndex: The oligomer's start index coordinate in the enclosing Polymer | ||
| 189 | |||
| 190 | \a endIndex: The oligomer's end index coordinate in the enclosing Polymer | ||
| 191 | */ | ||
| 192 | ✗ | Oligomer::Oligomer(PolChemDefCstSPtr pol_chem_def_csp, | |
| 193 | const QString &name, | ||
| 194 | const QString &description, | ||
| 195 | bool modified, | ||
| 196 | const Ponderable &ponderable, | ||
| 197 | const IonizeRule &ionizeRule, | ||
| 198 | const CalcOptions &calcOptions, | ||
| 199 | bool isIonized, | ||
| 200 | int startIndex, | ||
| 201 | ✗ | int endIndex) | |
| 202 | : Ionizable(pol_chem_def_csp, name, ponderable, ionizeRule, isIonized), | ||
| 203 | ✗ | mp_polymer(nullptr), | |
| 204 | ✗ | m_description(description), | |
| 205 | ✗ | m_isModified{modified}, | |
| 206 | ✗ | m_calcOptions(calcOptions) | |
| 207 | { | ||
| 208 | ✗ | setStartEndIndices(startIndex, endIndex); | |
| 209 | // if (startIndex < 0) | ||
| 210 | // qDebug() << __FILE__ << __LINE__ | ||
| 211 | // << "Construct with startIndex:" << startIndex; | ||
| 212 | ✗ | } | |
| 213 | |||
| 214 | |||
| 215 | /*! | ||
| 216 | \brief Constructs an oligomer. | ||
| 217 | |||
| 218 | The Oligomer instance is constructed with these arguments: | ||
| 219 | |||
| 220 | \a polymer: The polymer instance that encloses this Oligomer. Used to intialize | ||
| 221 | the member m_polymer and the Ionizable base class' polymer | ||
| 222 | |||
| 223 | \a name: The name of this Oligomer, used to intialize the Ionizable base class | ||
| 224 | |||
| 225 | \a description: The description of this Oligomer (m_description) | ||
| 226 | |||
| 227 | \a modified: Tells if the Oligomer is modified | ||
| 228 | |||
| 229 | \a ponderable: Used to initialize the Ionizable base class | ||
| 230 | |||
| 231 | \a calcOptions: Used to initialize the m_calcOptions member | ||
| 232 | |||
| 233 | \a startIndex: The oligomer's start index coordinate in the enclosing Polymer | ||
| 234 | |||
| 235 | \a endIndex: The oligomer's end index coordinate in the enclosing Polymer | ||
| 236 | */ | ||
| 237 | ✗ | Oligomer::Oligomer(Polymer *polymer, | |
| 238 | const QString &name, | ||
| 239 | const QString &description, | ||
| 240 | bool modified, | ||
| 241 | const Ponderable &ponderable, | ||
| 242 | int startIndex, | ||
| 243 | int endIndex, | ||
| 244 | ✗ | const CalcOptions &calcOptions) | |
| 245 | ✗ | : Ionizable(polymer->getPolChemDefCstSPtr(), name, ponderable), | |
| 246 | ✗ | mp_polymer(polymer), | |
| 247 | ✗ | m_description(description), | |
| 248 | ✗ | m_isModified(modified), | |
| 249 | ✗ | m_calcOptions(calcOptions) | |
| 250 | { | ||
| 251 | ✗ | setStartEndIndices(startIndex, endIndex); | |
| 252 | ✗ | if(startIndex < 0) | |
| 253 | ✗ | qDebug() << __FILE__ << __LINE__ | |
| 254 | ✗ | << "Construct with startIndex:" << startIndex; | |
| 255 | ✗ | } | |
| 256 | |||
| 257 | |||
| 258 | /*! | ||
| 259 | \brief Constructs an oligomer. | ||
| 260 | |||
| 261 | The Oligomer instance is constructed with these arguments: | ||
| 262 | |||
| 263 | \a pol_chem_def_csp: The polymer chemistry definition used to initialize the | ||
| 264 | Ionizable base class | ||
| 265 | |||
| 266 | \a name: The name of this Oligomer, used to intialize the Ionizable base class | ||
| 267 | |||
| 268 | \a description: The description of this Oligomer (m_description) | ||
| 269 | |||
| 270 | \a modified: Tells if the Oligomer is modified | ||
| 271 | |||
| 272 | \a ponderable: Used to initialize the Ionizable base class | ||
| 273 | |||
| 274 | \a calcOptions: Used to initialize the m_calcOptions member | ||
| 275 | |||
| 276 | \a startIndex: The oligomer's start index coordinate in the enclosing Polymer | ||
| 277 | |||
| 278 | \a endIndex: The oligomer's end index coordinate in the enclosing Polymer | ||
| 279 | */ | ||
| 280 | ✗ | Oligomer::Oligomer(PolChemDefCstSPtr pol_chem_def_csp, | |
| 281 | const QString &name, | ||
| 282 | const QString &description, | ||
| 283 | bool modified, | ||
| 284 | const Ponderable &ponderable, | ||
| 285 | const CalcOptions &calcOptions, | ||
| 286 | int startIndex, | ||
| 287 | ✗ | int endIndex) | |
| 288 | : Ionizable(pol_chem_def_csp, name, ponderable), | ||
| 289 | ✗ | mp_polymer(nullptr), | |
| 290 | ✗ | m_description(description), | |
| 291 | ✗ | m_isModified{modified}, | |
| 292 | ✗ | m_calcOptions(calcOptions) | |
| 293 | { | ||
| 294 | ✗ | setStartEndIndices(startIndex, endIndex); | |
| 295 | ✗ | if(startIndex < 0) | |
| 296 | ✗ | qDebug() << __FILE__ << __LINE__ | |
| 297 | ✗ | << "Construct with startIndex:" << startIndex; | |
| 298 | ✗ | } | |
| 299 | |||
| 300 | |||
| 301 | /*! | ||
| 302 | \brief Constructs an oligomer. | ||
| 303 | |||
| 304 | The Oligomer instance is constructed with these arguments: | ||
| 305 | |||
| 306 | \a ionizable: Used to initialize the Ionizable base class | ||
| 307 | |||
| 308 | \a calcOptions: Used to initialize the m_calcOptions member | ||
| 309 | |||
| 310 | \a startIndex: The oligomer's start index coordinate in the enclosing Polymer | ||
| 311 | |||
| 312 | \a endIndex: The oligomer's end index coordinate in the enclosing Polymer | ||
| 313 | */ | ||
| 314 | ✗ | Oligomer::Oligomer(const Ionizable &ionizable, | |
| 315 | const CalcOptions &calcOptions, | ||
| 316 | int startIndex, | ||
| 317 | ✗ | int endIndex) | |
| 318 | : Ionizable(ionizable), | ||
| 319 | ✗ | mp_polymer(nullptr), | |
| 320 | ✗ | m_description("NOT_SET"), | |
| 321 | ✗ | m_calcOptions(calcOptions) | |
| 322 | { | ||
| 323 | ✗ | setStartEndIndices(startIndex, endIndex); | |
| 324 | ✗ | if(startIndex < 0) | |
| 325 | ✗ | qDebug() << __FILE__ << __LINE__ | |
| 326 | ✗ | << "Construct with startIndex:" << startIndex; | |
| 327 | ✗ | } | |
| 328 | |||
| 329 | |||
| 330 | /*! | ||
| 331 | \brief Constructs an oligomer. | ||
| 332 | |||
| 333 | The Oligomer instance is constructed with these arguments: | ||
| 334 | |||
| 335 | \a polymer: Use to initialize the member mp_polymer and also to | ||
| 336 | initialize the Ionizable base class (by using its polymer chemistry definition | ||
| 337 | member). | ||
| 338 | |||
| 339 | \a name: The name of this Oligomer, used to intialize the Ionizable base class | ||
| 340 | |||
| 341 | \a description: The description of this Oligomer (m_description) | ||
| 342 | |||
| 343 | \a modified: Tells if the Oligomer is modified | ||
| 344 | |||
| 345 | \a mono and \a avg: Used to initialize the Ionizable::Ponderable base class | ||
| 346 | |||
| 347 | \a calcOptions: Used to initialize the m_calcOptions member | ||
| 348 | |||
| 349 | \a startIndex: The oligomer's start index coordinate in the enclosing Polymer | ||
| 350 | |||
| 351 | \a endIndex: The oligomer's end index coordinate in the enclosing Polymer | ||
| 352 | */ | ||
| 353 | ✗ | Oligomer::Oligomer(Polymer *polymer, | |
| 354 | const QString &name, | ||
| 355 | const QString &description, | ||
| 356 | bool modified, | ||
| 357 | double mono, | ||
| 358 | double avg, | ||
| 359 | int startIndex, | ||
| 360 | int endIndex, | ||
| 361 | ✗ | const CalcOptions &calcOptions) | |
| 362 | ✗ | : Ionizable(polymer->getPolChemDefCstSPtr(), name, Ponderable(mono, avg)), | |
| 363 | ✗ | mp_polymer(polymer), | |
| 364 | ✗ | m_description(description), | |
| 365 | ✗ | m_isModified{modified}, | |
| 366 | ✗ | m_calcOptions(calcOptions) | |
| 367 | { | ||
| 368 | ✗ | setStartEndIndices(startIndex, endIndex); | |
| 369 | ✗ | if(startIndex < 0) | |
| 370 | ✗ | qDebug() << __FILE__ << __LINE__ | |
| 371 | ✗ | << "Construct with startIndex:" << startIndex; | |
| 372 | ✗ | } | |
| 373 | |||
| 374 | |||
| 375 | /*! | ||
| 376 | \brief Constructs an oligomer. | ||
| 377 | |||
| 378 | The Oligomer instance is constructed with these arguments: | ||
| 379 | |||
| 380 | \a pol_chem_def_csp: The polymer chemistry definition used to initialize the | ||
| 381 | Ionizable base class | ||
| 382 | |||
| 383 | \a name: The name of this Oligomer, used to intialize the Ionizable base class | ||
| 384 | |||
| 385 | \a description: The description of this Oligomer (m_description) | ||
| 386 | |||
| 387 | \a modified: Tells if the Oligomer is modified | ||
| 388 | |||
| 389 | \a calcOptions: Used to initialize the m_calcOptions member | ||
| 390 | |||
| 391 | \a mono and \a avg: Used to initialize the Ionizable::Ponderable base class | ||
| 392 | |||
| 393 | \a startIndex: The oligomer's start index coordinate in the enclosing Polymer | ||
| 394 | |||
| 395 | \a endIndex: The oligomer's end index coordinate in the enclosing Polymer | ||
| 396 | */ | ||
| 397 | ✗ | Oligomer::Oligomer(PolChemDefCstSPtr pol_chem_def_csp, | |
| 398 | const QString &name, | ||
| 399 | const QString &description, | ||
| 400 | bool modified, | ||
| 401 | const CalcOptions &calcOptions, | ||
| 402 | double mono, | ||
| 403 | double avg, | ||
| 404 | int startIndex, | ||
| 405 | ✗ | int endIndex) | |
| 406 | ✗ | : Ionizable(pol_chem_def_csp, name, Ponderable(mono, avg)), | |
| 407 | ✗ | mp_polymer(0), | |
| 408 | ✗ | m_description(description), | |
| 409 | ✗ | m_isModified{modified}, | |
| 410 | ✗ | m_calcOptions(calcOptions) | |
| 411 | { | ||
| 412 | ✗ | setStartEndIndices(startIndex, endIndex); | |
| 413 | ✗ | } | |
| 414 | |||
| 415 | |||
| 416 | /*! | ||
| 417 | \brief Constructs the Oligomer as a copy of \a other. | ||
| 418 | */ | ||
| 419 | ✗ | Oligomer::Oligomer(const Oligomer &other) | |
| 420 | : Sequence(other), | ||
| 421 | CoordinateList(other), | ||
| 422 | Ionizable(other), | ||
| 423 | PropListHolder(other), | ||
| 424 | ✗ | mp_polymer(other.mp_polymer), | |
| 425 | ✗ | m_description(other.m_description), | |
| 426 | ✗ | m_isModified{other.m_isModified}, | |
| 427 | ✗ | m_calcOptions(other.m_calcOptions) | |
| 428 | { | ||
| 429 | ✗ | } | |
| 430 | |||
| 431 | |||
| 432 | /*! | ||
| 433 | \brief Destructs this Oligomer. | ||
| 434 | */ | ||
| 435 | ✗ | Oligomer::~Oligomer() | |
| 436 | { | ||
| 437 | // qDebug() << "~Oligomer()"; | ||
| 438 | ✗ | } | |
| 439 | |||
| 440 | |||
| 441 | /*! | ||
| 442 | \brief Returns the polymer. | ||
| 443 | */ | ||
| 444 | const Polymer * | ||
| 445 | ✗ | Oligomer::polymer() const | |
| 446 | { | ||
| 447 | ✗ | return mp_polymer; | |
| 448 | } | ||
| 449 | |||
| 450 | |||
| 451 | /*! | ||
| 452 | \brief Sets the start and end indices to \a value1 and \a value2 respectively. | ||
| 453 | |||
| 454 | The values are used to construct a Coordinates instance that is allocated on | ||
| 455 | the heap and added to member CoordinateList if that list is empty. If the | ||
| 456 | CoordinateList is not empty, then the values are set to the first Coordinates | ||
| 457 | instance in that list. | ||
| 458 | |||
| 459 | \sa setStartIndex(), setEndIndex() | ||
| 460 | */ | ||
| 461 | void | ||
| 462 | ✗ | Oligomer::setStartEndIndices(int value1, int value2) | |
| 463 | { | ||
| 464 | ✗ | if(!CoordinateList::size()) | |
| 465 | { | ||
| 466 | ✗ | Coordinates *coordinates = new Coordinates(value1, value2); | |
| 467 | ✗ | append(coordinates); | |
| 468 | |||
| 469 | // qDebug() << __FILE__ << __LINE__ | ||
| 470 | // << "[start--end]:" << startIndex() << endIndex(); | ||
| 471 | } | ||
| 472 | else | ||
| 473 | { | ||
| 474 | ✗ | Coordinates *coordinates = first(); | |
| 475 | ✗ | coordinates->setStart(value1); | |
| 476 | ✗ | coordinates->setEnd(value2); | |
| 477 | |||
| 478 | // qDebug() << __FILE__ << __LINE__ | ||
| 479 | // << "[start--end]:" << startIndex() << endIndex(); | ||
| 480 | } | ||
| 481 | ✗ | } | |
| 482 | |||
| 483 | |||
| 484 | /*! | ||
| 485 | \brief Sets the start index to \a value. | ||
| 486 | |||
| 487 | The value is used to construct a Coordinates instance that is allocated on | ||
| 488 | the heap and added to member CoordinateList if that list is empty. If the | ||
| 489 | CoordinateList is not empty, then the value is set to the first Coordinates | ||
| 490 | instance in that list. | ||
| 491 | */ | ||
| 492 | void | ||
| 493 | ✗ | Oligomer::setStartIndex(int value) | |
| 494 | { | ||
| 495 | ✗ | if(value < 0) | |
| 496 | ✗ | qDebug() << __FILE__ << __LINE__ << "setStartIndex with value:" << value; | |
| 497 | |||
| 498 | ✗ | if(!CoordinateList::size()) | |
| 499 | { | ||
| 500 | ✗ | Coordinates *coordinates = new Coordinates(); | |
| 501 | ✗ | coordinates->setStart(value); | |
| 502 | ✗ | append(coordinates); | |
| 503 | } | ||
| 504 | else | ||
| 505 | { | ||
| 506 | ✗ | Coordinates *coordinates = first(); | |
| 507 | ✗ | coordinates->setStart(value); | |
| 508 | } | ||
| 509 | ✗ | } | |
| 510 | |||
| 511 | |||
| 512 | /*! | ||
| 513 | \brief Returns the start index, or -1 if no Coordinates instance is found in | ||
| 514 | the CoordinateList member. | ||
| 515 | |||
| 516 | The start index that is returned is the start index of the first Coordinates | ||
| 517 | instance of the CoordinateList member. | ||
| 518 | */ | ||
| 519 | int | ||
| 520 | ✗ | Oligomer::startIndex() const | |
| 521 | { | ||
| 522 | ✗ | if(!CoordinateList::size()) | |
| 523 | ✗ | return -1; | |
| 524 | |||
| 525 | ✗ | Coordinates *coordinates = first(); | |
| 526 | ✗ | return coordinates->start(); | |
| 527 | } | ||
| 528 | |||
| 529 | |||
| 530 | /*! | ||
| 531 | \brief Sets the end index to \a value. | ||
| 532 | |||
| 533 | The value is used to construct a Coordinates instance that is allocated on | ||
| 534 | the heap and added to member CoordinateList if that list is empty. If the | ||
| 535 | CoordinateList is not empty, then the value is set to the first Coordinates | ||
| 536 | instance in that list. | ||
| 537 | */ | ||
| 538 | void | ||
| 539 | ✗ | Oligomer::setEndIndex(int value) | |
| 540 | { | ||
| 541 | ✗ | if(!CoordinateList::size()) | |
| 542 | { | ||
| 543 | ✗ | Coordinates *coordinates = new Coordinates(); | |
| 544 | ✗ | coordinates->setEnd(value); | |
| 545 | ✗ | append(coordinates); | |
| 546 | } | ||
| 547 | else | ||
| 548 | { | ||
| 549 | ✗ | Coordinates *coordinates = first(); | |
| 550 | ✗ | coordinates->setEnd(value); | |
| 551 | } | ||
| 552 | ✗ | } | |
| 553 | |||
| 554 | |||
| 555 | /*! | ||
| 556 | \brief Returns the end index. | ||
| 557 | |||
| 558 | The end index that is returned is the end index of the first Coordinates | ||
| 559 | instance of the CoordinateList member. | ||
| 560 | */ | ||
| 561 | int | ||
| 562 | ✗ | Oligomer::endIndex() const | |
| 563 | { | ||
| 564 | ✗ | if(!CoordinateList::size()) | |
| 565 | ✗ | return -1; | |
| 566 | |||
| 567 | ✗ | Coordinates *coordinates = first(); | |
| 568 | ✗ | return coordinates->end(); | |
| 569 | } | ||
| 570 | |||
| 571 | /*! | ||
| 572 | \brief Set the description to \a description. | ||
| 573 | */ | ||
| 574 | void | ||
| 575 | ✗ | Oligomer::setDescription(const QString &description) | |
| 576 | { | ||
| 577 | ✗ | m_description = description; | |
| 578 | ✗ | } | |
| 579 | |||
| 580 | /*! | ||
| 581 | \brief Returns the description. | ||
| 582 | */ | ||
| 583 | QString | ||
| 584 | ✗ | Oligomer::description() const | |
| 585 | { | ||
| 586 | ✗ | return m_description; | |
| 587 | } | ||
| 588 | |||
| 589 | /*! | ||
| 590 | \brief Add to the member CoordinateList all the Coordinates instances found in | ||
| 591 | \a list. | ||
| 592 | |||
| 593 | The added Coordinates instances are copies of the instances found in \a list. | ||
| 594 | |||
| 595 | Returns the count of added Coordinates instances allocated on the heap. | ||
| 596 | */ | ||
| 597 | int | ||
| 598 | ✗ | Oligomer::appendCoordinates(CoordinateList *list) | |
| 599 | { | ||
| 600 | ✗ | Q_ASSERT(list); | |
| 601 | |||
| 602 | ✗ | int count = 0; | |
| 603 | |||
| 604 | ✗ | for(int iter = 0; iter < list->size(); ++iter) | |
| 605 | { | ||
| 606 | ✗ | Coordinates *iterCoordinates = list->at(iter); | |
| 607 | |||
| 608 | ✗ | Coordinates *coordinates = new Coordinates(*iterCoordinates); | |
| 609 | |||
| 610 | ✗ | append(coordinates); | |
| 611 | |||
| 612 | ✗ | ++count; | |
| 613 | } | ||
| 614 | |||
| 615 | ✗ | return count; | |
| 616 | } | ||
| 617 | |||
| 618 | /*! | ||
| 619 | \brief Set the IonizeRule member to \a ionize_rule. | ||
| 620 | |||
| 621 | \sa MsXpS::libXpertMass::Ionizable::m_ionizeRule | ||
| 622 | */ | ||
| 623 | void | ||
| 624 | ✗ | Oligomer::setIonizeRule(IonizeRule &ionize_rule) | |
| 625 | { | ||
| 626 | ✗ | m_ionizeRule = ionize_rule; | |
| 627 | ✗ | } | |
| 628 | |||
| 629 | |||
| 630 | /*! | ||
| 631 | \brief Returns a reference to the IonizeRule member. | ||
| 632 | */ | ||
| 633 | IonizeRule & | ||
| 634 | ✗ | Oligomer::ionizeRule() | |
| 635 | { | ||
| 636 | ✗ | return m_ionizeRule; | |
| 637 | } | ||
| 638 | |||
| 639 | /*! | ||
| 640 | \brief Set the calculation options to \a calc_options. | ||
| 641 | |||
| 642 | \sa m_calcOptions | ||
| 643 | */ | ||
| 644 | void | ||
| 645 | ✗ | Oligomer::setCalcOptions(const CalcOptions &calc_options) | |
| 646 | { | ||
| 647 | ✗ | m_calcOptions = calc_options; | |
| 648 | ✗ | } | |
| 649 | |||
| 650 | /*! | ||
| 651 | \brief Returns the calculation options. | ||
| 652 | */ | ||
| 653 | const CalcOptions & | ||
| 654 | ✗ | Oligomer::calcOptions() const | |
| 655 | { | ||
| 656 | ✗ | return m_calcOptions; | |
| 657 | } | ||
| 658 | |||
| 659 | |||
| 660 | /*! | ||
| 661 | \brief Updates the member calculation options with this Oligomer's | ||
| 662 | CoordinateList. | ||
| 663 | |||
| 664 | The data in m_calcOptions that need updating are the CoordinateList elements. | ||
| 665 | */ | ||
| 666 | void | ||
| 667 | ✗ | Oligomer::updateCalcOptions() | |
| 668 | { | ||
| 669 | // The data that need update are the CoordinateList elements | ||
| 670 | // depending on the internal ::OligomerList data. | ||
| 671 | |||
| 672 | ✗ | m_calcOptions.setCoordinateList(*(dynamic_cast<CoordinateList *>(this))); | |
| 673 | ✗ | } | |
| 674 | |||
| 675 | /*! | ||
| 676 | \brief Returns the Monomer in the enclosing Polymer that is located at the | ||
| 677 | start index of this oligomer. | ||
| 678 | |||
| 679 | \sa atRightEnd(), startIndex() | ||
| 680 | */ | ||
| 681 | const Monomer & | ||
| 682 | ✗ | Oligomer::atLeftEnd() const | |
| 683 | { | ||
| 684 | // qDebug() << __FILE__ << __LINE__ << "Going to call at() with value" | ||
| 685 | // << startIndex(); | ||
| 686 | |||
| 687 | ✗ | return *(mp_polymer->at(startIndex())); | |
| 688 | } | ||
| 689 | |||
| 690 | |||
| 691 | /*! | ||
| 692 | \brief Returns the Monomer in the enclosing Polymer that is located at the | ||
| 693 | end index of this oligomer. | ||
| 694 | |||
| 695 | \sa atLeftEnd(), endIndex() | ||
| 696 | */ | ||
| 697 | const Monomer & | ||
| 698 | ✗ | Oligomer::atRightEnd() const | |
| 699 | { | ||
| 700 | // qDebug() << __FILE__ << __LINE__ << "Going to call at() with value" | ||
| 701 | // << endIndex(); | ||
| 702 | |||
| 703 | ✗ | return *(mp_polymer->at(endIndex())); | |
| 704 | } | ||
| 705 | |||
| 706 | /*! | ||
| 707 | \brief Return the Monomer that is located in the enclosing Polymer at \a index. | ||
| 708 | */ | ||
| 709 | const Monomer * | ||
| 710 | ✗ | Oligomer::monomerAt(int index) const | |
| 711 | { | ||
| 712 | ✗ | Q_ASSERT(index >= 0); | |
| 713 | ✗ | Q_ASSERT(index < mp_polymer->size() - 1); | |
| 714 | |||
| 715 | // qDebug() << __FILE__ << __LINE__ << "Going to call at() with value" | ||
| 716 | // << index; | ||
| 717 | |||
| 718 | ✗ | return mp_polymer->at(index); | |
| 719 | } | ||
| 720 | |||
| 721 | /*! | ||
| 722 | \brief Returns the member crossLinkList. | ||
| 723 | */ | ||
| 724 | QList<CrossLink *> * | ||
| 725 | ✗ | Oligomer::crossLinkList() | |
| 726 | { | ||
| 727 | ✗ | return &m_crossLinkList; | |
| 728 | } | ||
| 729 | |||
| 730 | /*! | ||
| 731 | \brief Add the \a cross_link CrossLink to this Oligomer's list of \l{CrossLink}s | ||
| 732 | |||
| 733 | Returns true if the cross-link was added succesfully, or false if \a cross_link | ||
| 734 | was already in the list. | ||
| 735 | */ | ||
| 736 | bool | ||
| 737 | ✗ | Oligomer::addCrossLink(CrossLink *cross_link) | |
| 738 | { | ||
| 739 | // Add the cross-link only if it does not exist already. Return true | ||
| 740 | // only if the crossLink has been added. | ||
| 741 | |||
| 742 | ✗ | if(!m_crossLinkList.contains(cross_link)) | |
| 743 | { | ||
| 744 | ✗ | m_crossLinkList.append(cross_link); | |
| 745 | |||
| 746 | ✗ | return true; | |
| 747 | } | ||
| 748 | |||
| 749 | ✗ | return false; | |
| 750 | } | ||
| 751 | |||
| 752 | |||
| 753 | // ELEMENTAL CALCULATION FUNCTION | ||
| 754 | ///////////////////////////////// | ||
| 755 | |||
| 756 | /*! | ||
| 757 | \brief Returns the elemental composition of this Oligomer instance. | ||
| 758 | */ | ||
| 759 | QString | ||
| 760 | ✗ | Oligomer::elementalComposition() | |
| 761 | { | ||
| 762 | ✗ | return elementalComposition(m_calcOptions, m_ionizeRule); | |
| 763 | } | ||
| 764 | |||
| 765 | |||
| 766 | /*! | ||
| 767 | \brief Returns the elemental composition of this Oligomer instance. | ||
| 768 | |||
| 769 | The computation of the elemental composition is performed as configured in \a | ||
| 770 | calc_options and using the ionization described in \a ionize_rule. | ||
| 771 | */ | ||
| 772 | QString | ||
| 773 | ✗ | Oligomer::elementalComposition(const CalcOptions &calc_options, | |
| 774 | const IonizeRule &ionize_rule) | ||
| 775 | { | ||
| 776 | ✗ | int times = 0; | |
| 777 | |||
| 778 | ✗ | if(calc_options.selectionType() == SELECTION_TYPE_RESIDUAL_CHAINS) | |
| 779 | { | ||
| 780 | ✗ | times = 1; | |
| 781 | |||
| 782 | // qDebug() << __FILE__ << __LINE__ | ||
| 783 | // << "SELECTION_TYPE_RESIDUAL_CHAINS ; times:" << times; | ||
| 784 | } | ||
| 785 | else | ||
| 786 | { | ||
| 787 | // times = CoordinateList::size(); | ||
| 788 | |||
| 789 | // Use the version whereby we can perform a sanity check that | ||
| 790 | // calc_options was updated with the proper CoordinateList | ||
| 791 | // data. | ||
| 792 | |||
| 793 | ✗ | times = calc_options.coordinateList().size(); | |
| 794 | ✗ | if(times != CoordinateList::size()) | |
| 795 | ✗ | qFatal("Fatal error at %s@%d. Aborting.", __FILE__, __LINE__); | |
| 796 | |||
| 797 | // qDebug() << __FILE__ << __LINE__ | ||
| 798 | // << "SELECTION_TYPE_OLIGOMERS ; times:" << times; | ||
| 799 | } | ||
| 800 | |||
| 801 | ✗ | return mp_polymer->elementalComposition( | |
| 802 | ✗ | ionize_rule, *(static_cast<CoordinateList *>(this)), calc_options); | |
| 803 | } | ||
| 804 | |||
| 805 | ///////////////////////////////// | ||
| 806 | // ELEMENTAL CALCULATION FUNCTION | ||
| 807 | |||
| 808 | /*! | ||
| 809 | \brief Calculates the sequence of this Oligomer and sets it to the Sequence | ||
| 810 | base class member m_monomerText. | ||
| 811 | |||
| 812 | Returns the size of m_monomerText. If m_polymer is nullptr, return 0. | ||
| 813 | |||
| 814 | \sa Sequence | ||
| 815 | */ | ||
| 816 | int | ||
| 817 | ✗ | Oligomer::makeMonomerText() | |
| 818 | { | ||
| 819 | // Prepare the text version of the oligomer's sequence by basing | ||
| 820 | // it on the coordinates of *this oligomer and set that text to | ||
| 821 | // m_monomerText. | ||
| 822 | |||
| 823 | ✗ | if(mp_polymer == nullptr) | |
| 824 | ✗ | return 0; | |
| 825 | |||
| 826 | ✗ | QString *text = monomerText(); | |
| 827 | |||
| 828 | ✗ | m_monomerText = *text; | |
| 829 | |||
| 830 | ✗ | delete(text); | |
| 831 | |||
| 832 | ✗ | return m_monomerText.size(); | |
| 833 | } | ||
| 834 | |||
| 835 | /*! | ||
| 836 | \brief Returns a string with the sequence of this Oligomer. | ||
| 837 | |||
| 838 | If mp_polymer is non-nullptr, the sequence is calculated by looking | ||
| 839 | into the Polymer using member Coordinates. | ||
| 840 | |||
| 841 | If mp_polymer is nullptr and if Sequence::m_monomerText is not empty, that is | ||
| 842 | returned. | ||
| 843 | |||
| 844 | If mp_polymer is nullptr and if Sequence::m_monomerText is emtpy, then the | ||
| 845 | sequence is crafted by looking into Sequence::m_monomerList. | ||
| 846 | |||
| 847 | \sa makeMonomerText() | ||
| 848 | */ | ||
| 849 | QString * | ||
| 850 | ✗ | Oligomer::monomerText() | |
| 851 | { | ||
| 852 | // Allocate a new string to hold the text version of *this | ||
| 853 | // oligomer's sequence. | ||
| 854 | |||
| 855 | // There are two situations: | ||
| 856 | |||
| 857 | // 1. The mp_polymer member is non-0, we can get access to it. Ask | ||
| 858 | // the polymer to do the work. This is the most faithful | ||
| 859 | // situation. But the caller must first ensure that the polymer | ||
| 860 | // actually exists. | ||
| 861 | |||
| 862 | // 2. The mp_polymer member is 0, we may have the oligomer | ||
| 863 | // sequence stored in *this oligomer. Test that. | ||
| 864 | |||
| 865 | ✗ | QString *text = new QString(); | |
| 866 | |||
| 867 | ✗ | if(mp_polymer) | |
| 868 | { | ||
| 869 | // For each oligomer(if more than one, which is the case when the | ||
| 870 | // oligomer is actually a cross-linked oligomer), create a string... | ||
| 871 | |||
| 872 | ✗ | int oligomerCount = CoordinateList::size(); | |
| 873 | |||
| 874 | ✗ | for(int iter = 0; iter < oligomerCount; ++iter) | |
| 875 | { | ||
| 876 | ✗ | Coordinates *coordinates = CoordinateList::at(iter); | |
| 877 | |||
| 878 | ✗ | QString *local = mp_polymer->monomerText( | |
| 879 | coordinates->start(), coordinates->end(), true); | ||
| 880 | ✗ | text->append(*local); | |
| 881 | |||
| 882 | // If this is a cross-linked oligomer and we are not appending | ||
| 883 | // text for the __last__ oligomer, then append "~" to let the | ||
| 884 | // user know that the sequences are cross-linked. | ||
| 885 | ✗ | if(oligomerCount > 1 && iter < oligomerCount - 1) | |
| 886 | ✗ | text->append("~"); | |
| 887 | |||
| 888 | ✗ | delete(local); | |
| 889 | } | ||
| 890 | } | ||
| 891 | else | ||
| 892 | { | ||
| 893 | ✗ | if(m_monomerText.size()) | |
| 894 | { | ||
| 895 | ✗ | *text = m_monomerText; | |
| 896 | |||
| 897 | ✗ | return text; | |
| 898 | } | ||
| 899 | else | ||
| 900 | { | ||
| 901 | ✗ | if(m_monomerList.size()) | |
| 902 | ✗ | return Sequence::monomerText(0, m_monomerList.size(), true); | |
| 903 | } | ||
| 904 | } | ||
| 905 | |||
| 906 | ✗ | return text; | |
| 907 | } | ||
| 908 | |||
| 909 | |||
| 910 | /*! | ||
| 911 | \brief Calculates the monoisotopic and average masses. | ||
| 912 | |||
| 913 | The calculation is performed by computing the mono and avg masses | ||
| 914 | of the sequence stretch as described by the start and end indices in | ||
| 915 | the polymer sequence. Default calculation options are used. | ||
| 916 | |||
| 917 | Returns true if calculations were successful, false otherwise. | ||
| 918 | */ | ||
| 919 | bool | ||
| 920 | ✗ | Oligomer::calculateMasses() | |
| 921 | { | ||
| 922 | ✗ | CalcOptions calcOptions; | |
| 923 | |||
| 924 | ✗ | calcOptions.setCapping(CAP_NONE); | |
| 925 | |||
| 926 | ✗ | IonizeRule rule; | |
| 927 | |||
| 928 | ✗ | return calculateMasses(&calcOptions, &rule); | |
| 929 | ✗ | } | |
| 930 | |||
| 931 | /*! | ||
| 932 | \brief Calculates the monoisotopic and average masses. | ||
| 933 | |||
| 934 | The calculation is performed by computing the mono and avg masses | ||
| 935 | of the sequence stretch as described by the start and end indices in | ||
| 936 | the polymer sequence. The calculations are configured by \a calc_options | ||
| 937 | and the ionization is defined in \a ionize_rule. | ||
| 938 | |||
| 939 | Returns true if calculations were successful, false otherwise. | ||
| 940 | */ | ||
| 941 | bool | ||
| 942 | ✗ | Oligomer::calculateMasses(const CalcOptions *calc_options, | |
| 943 | const IonizeRule *ionize_rule) | ||
| 944 | { | ||
| 945 | ✗ | Q_ASSERT(calc_options); | |
| 946 | |||
| 947 | ✗ | CalcOptions localOptions(*calc_options); | |
| 948 | |||
| 949 | // The coordinates of the oligomer are the following: | ||
| 950 | |||
| 951 | // MAMISGMSGRKAS | ||
| 952 | |||
| 953 | // For a tryptic peptide obtained from protein above, we'd have | ||
| 954 | |||
| 955 | // MAMISGMSGR, that is in the oligomer coordinates: | ||
| 956 | |||
| 957 | // [0] MAMISGMSGR [9] | ||
| 958 | |||
| 959 | // When computing the mass of the oligomer, we have to do a | ||
| 960 | |||
| 961 | // for (iter == [0] ; iter < [9 + 1]; ++iter) | ||
| 962 | |||
| 963 | // Which is why we increment add 1 to m_endIndex in the function below. | ||
| 964 | |||
| 965 | // A polymer might be something made of more than one residual chain | ||
| 966 | // in case it is a cross-linked oligomer. Compute the mass fore each | ||
| 967 | // residual chain, without accounting for the cross-links... | ||
| 968 | |||
| 969 | ✗ | m_mono = 0; | |
| 970 | ✗ | m_avg = 0; | |
| 971 | |||
| 972 | // An oligomer _is_ a CoordinateList, and we need that list in the | ||
| 973 | // calcOptions so that we can call the Polymer::accountMasses | ||
| 974 | // function. | ||
| 975 | |||
| 976 | ✗ | localOptions.setCoordinateList(*this); | |
| 977 | |||
| 978 | // We do not want to take into account the cross-links because | ||
| 979 | // we'll be doing this here and because it cannot work if the | ||
| 980 | // cross-links are taken into account from the polymer. | ||
| 981 | |||
| 982 | ✗ | int flags = localOptions.monomerEntities(); | |
| 983 | ✗ | flags &= ~MONOMER_CHEMENT_CROSS_LINK; | |
| 984 | ✗ | localOptions.setMonomerEntities(flags); | |
| 985 | |||
| 986 | ✗ | Polymer::accountMasses(mp_polymer, localOptions, &m_mono, &m_avg); | |
| 987 | |||
| 988 | // qDebug() << __FILE__ << __LINE__ | ||
| 989 | // << "After accounting masses(prior to cross-links):" | ||
| 990 | // << "mono mass is:" << m_mono; | ||
| 991 | |||
| 992 | // At this point, we have added the mass of each constituent | ||
| 993 | // oligomer's residual chain. Let's deal with the cross-links. | ||
| 994 | |||
| 995 | ✗ | for(int iter = 0; iter < m_crossLinkList.size(); ++iter) | |
| 996 | { | ||
| 997 | ✗ | CrossLink *crossLink = m_crossLinkList.at(iter); | |
| 998 | |||
| 999 | ✗ | if(!crossLink->accountMasses(&m_mono, &m_avg)) | |
| 1000 | ✗ | return false; | |
| 1001 | |||
| 1002 | // qDebug() << __FILE__ << __LINE__ | ||
| 1003 | // << "After accounting cross-link:" | ||
| 1004 | // << crossLink->name() | ||
| 1005 | // << "mono mass is:" << m_mono; | ||
| 1006 | } | ||
| 1007 | |||
| 1008 | // If an ionizeRule is provided, use it. Otherwise, ionize | ||
| 1009 | // automatically using the ::Ionizable IonizeRule. | ||
| 1010 | ✗ | if(ionize_rule) | |
| 1011 | { | ||
| 1012 | // Note that if ionizeRule is invalid, then the ionization is | ||
| 1013 | // not performed. | ||
| 1014 | |||
| 1015 | ✗ | if(ionize_rule->isValid()) | |
| 1016 | { | ||
| 1017 | /* | ||
| 1018 | if (ionize(mp_polymer, *ionizeRule) == -1) | ||
| 1019 | The line above is a huge bug. While we should be | ||
| 1020 | ionizing this oligomer, we end up ionizing the polymer ! | ||
| 1021 | */ | ||
| 1022 | |||
| 1023 | ✗ | if(ionize(*ionize_rule) == -1) | |
| 1024 | ✗ | return false; | |
| 1025 | } | ||
| 1026 | } | ||
| 1027 | else | ||
| 1028 | { | ||
| 1029 | ✗ | if(ionize() == -1) | |
| 1030 | ✗ | return false; | |
| 1031 | } | ||
| 1032 | |||
| 1033 | // qDebug() << __FILE__ << __LINE__ | ||
| 1034 | // << "Coming out from the calculateMasses function:" | ||
| 1035 | // << "mono mass is:" << m_mono; | ||
| 1036 | |||
| 1037 | ✗ | return true; | |
| 1038 | ✗ | } | |
| 1039 | |||
| 1040 | /*! | ||
| 1041 | \brief Set the m_isModified status of this Oligomer to \a modified. | ||
| 1042 | */ | ||
| 1043 | void | ||
| 1044 | ✗ | Oligomer::setModified(bool modified) | |
| 1045 | { | ||
| 1046 | ✗ | m_isModified = modified; | |
| 1047 | ✗ | } | |
| 1048 | |||
| 1049 | /*! | ||
| 1050 | \brief Returns the chemical modification status of this Oligomer. | ||
| 1051 | |||
| 1052 | If \a deep is true, the enclosing Polymer must exist (m_polymer cannot be | ||
| 1053 | nullptr) because each monomer of the Polymer is probed for a potential | ||
| 1054 | modification. This function returns true as soon as such a modified monomer is | ||
| 1055 | encountered. | ||
| 1056 | |||
| 1057 | If \a deep is false, the value of m_isModified is returned. | ||
| 1058 | |||
| 1059 | \sa m_isModified, Monomer::isModified() | ||
| 1060 | */ | ||
| 1061 | bool | ||
| 1062 | ✗ | Oligomer::isModified(bool deep /*false*/) | |
| 1063 | { | ||
| 1064 | // Either we truly go to the polymer instance and check if the oligomer is | ||
| 1065 | // modified or we just ask for the member datum, that might have been set, | ||
| 1066 | // for example, during creation of the oligomer in the Cleaver::cleave() | ||
| 1067 | // function. We need the possibility to ask for the member datum because | ||
| 1068 | // there are circumstances where the oligomer exists and not the original | ||
| 1069 | // polymer (for example if the polymer sequence is edited while a set of | ||
| 1070 | // cleavage oligomers is displayed in the cleavage dialog. When the | ||
| 1071 | // tableviewmodel needs to refresh the contents of the cells, it crashes | ||
| 1072 | // because the polymer has been edited and one monomer is missing from the | ||
| 1073 | // sequence of the oligomer as it had been configured in the first place. | ||
| 1074 | |||
| 1075 | ✗ | if(deep) | |
| 1076 | { | ||
| 1077 | ✗ | if(mp_polymer == nullptr) | |
| 1078 | ✗ | qFatal("Programming error."); | |
| 1079 | |||
| 1080 | ✗ | int oligomerCount = CoordinateList::size(); | |
| 1081 | |||
| 1082 | ✗ | for(int iter = 0; iter < oligomerCount; ++iter) | |
| 1083 | { | ||
| 1084 | ✗ | Coordinates *coordinates = CoordinateList::at(iter); | |
| 1085 | |||
| 1086 | ✗ | for(int jter = coordinates->start(); jter < coordinates->end() + 1; | |
| 1087 | ++jter) | ||
| 1088 | { | ||
| 1089 | // qDebug() << __FILE__ << __LINE__ << "Going to call at() | ||
| 1090 | // with value" | ||
| 1091 | // << iter; | ||
| 1092 | |||
| 1093 | ✗ | const Monomer *monomer = mp_polymer->at(jter); | |
| 1094 | |||
| 1095 | ✗ | if(monomer->isModified()) | |
| 1096 | ✗ | return true; | |
| 1097 | } | ||
| 1098 | } | ||
| 1099 | |||
| 1100 | ✗ | return false; | |
| 1101 | } | ||
| 1102 | else | ||
| 1103 | { | ||
| 1104 | ✗ | return m_isModified; | |
| 1105 | } | ||
| 1106 | } | ||
| 1107 | |||
| 1108 | /*! | ||
| 1109 | \brief Returns the size of this Oligomer. | ||
| 1110 | |||
| 1111 | The size is computed by adding the length of all the regions of the | ||
| 1112 | enclosing Polymer as documented in the Coordinates instances in the member | ||
| 1113 | coordinateList. | ||
| 1114 | */ | ||
| 1115 | int | ||
| 1116 | ✗ | Oligomer::size() | |
| 1117 | { | ||
| 1118 | ✗ | int sum = 0; | |
| 1119 | |||
| 1120 | ✗ | int oligomerCount = CoordinateList::size(); | |
| 1121 | |||
| 1122 | // The size of an oligomer is the sum of all its oligomeric | ||
| 1123 | // components as described by the various coordinates. | ||
| 1124 | |||
| 1125 | ✗ | for(int iter = 0; iter < oligomerCount; ++iter) | |
| 1126 | { | ||
| 1127 | ✗ | Coordinates *coordinates = CoordinateList::at(iter); | |
| 1128 | |||
| 1129 | ✗ | sum += coordinates->length(); | |
| 1130 | } | ||
| 1131 | |||
| 1132 | ✗ | return sum; | |
| 1133 | } | ||
| 1134 | |||
| 1135 | /*! | ||
| 1136 | \brief Returns true if this Oligomer spans at least one region of the | ||
| 1137 | enclosing polymer that contains a Monomer at \a index, false otherwise. | ||
| 1138 | */ | ||
| 1139 | bool | ||
| 1140 | ✗ | Oligomer::encompasses(int index) const | |
| 1141 | { | ||
| 1142 | ✗ | int oligomerCount = CoordinateList::size(); | |
| 1143 | |||
| 1144 | ✗ | for(int iter = 0; iter < oligomerCount; ++iter) | |
| 1145 | { | ||
| 1146 | ✗ | Coordinates *coordinates = CoordinateList::at(iter); | |
| 1147 | |||
| 1148 | ✗ | if(index <= coordinates->start() && index >= coordinates->end()) | |
| 1149 | ✗ | return true; | |
| 1150 | } | ||
| 1151 | |||
| 1152 | ✗ | return false; | |
| 1153 | } | ||
| 1154 | |||
| 1155 | |||
| 1156 | /*! | ||
| 1157 | \brief Returns true if this Oligomer spans at least one region of the | ||
| 1158 | enclosing polymer that contains the Monomer \a monomer, false otherwise. | ||
| 1159 | |||
| 1160 | The search is performed by comparing pointers, thus the Monomer to be search \e | ||
| 1161 | is \a monomer. | ||
| 1162 | */ | ||
| 1163 | bool | ||
| 1164 | ✗ | Oligomer::encompasses(const Monomer *monomer) const | |
| 1165 | { | ||
| 1166 | ✗ | int oligomerCount = CoordinateList::size(); | |
| 1167 | |||
| 1168 | ✗ | for(int iter = 0; iter < oligomerCount; ++iter) | |
| 1169 | { | ||
| 1170 | ✗ | Coordinates *coordinates = CoordinateList::at(iter); | |
| 1171 | |||
| 1172 | ✗ | for(int jter = coordinates->start(); jter < coordinates->end() + 1; | |
| 1173 | ++jter) | ||
| 1174 | { | ||
| 1175 | // qDebug() << __FILE__ << __LINE__ << "Going to call at() with | ||
| 1176 | // value" | ||
| 1177 | // << jter; | ||
| 1178 | |||
| 1179 | ✗ | if(mp_polymer->at(jter) == monomer) | |
| 1180 | ✗ | return true; | |
| 1181 | } | ||
| 1182 | } | ||
| 1183 | |||
| 1184 | ✗ | return false; | |
| 1185 | } | ||
| 1186 | |||
| 1187 | } // namespace libXpertMass | ||
| 1188 | |||
| 1189 | } // namespace MsXpS | ||
| 1190 |