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H A D | massSearchOligomerTableView.cpp | 281 prop = oligomer->prop("ERROR_MZ"); in selectedOligomersAsPlainText() 316 .arg(oligomer->charge()) in selectedOligomersAsPlainText() 320 .arg(oligomer->name()) in selectedOligomersAsPlainText() 329 .arg(oligomer->isModified()) in selectedOligomersAsPlainText() 348 delete oligomer; in selectedOligomersAsPlainText() 427 Oligomer *oligomer = mp_oligomerList->at(row); in currentChanged() local 434 if (oligomer->startIndex() >= oligomer->polymer()->size() || in currentChanged() 435 oligomer->endIndex() >= oligomer->polymer()->size()) in currentChanged() 458 QString *text = oligomer->monomerText(); in currentChanged() 494 if (oligomer->startIndex() >= oligomer->polymer()->size() || in itemActivated() [all …]
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H A D | fragmentOligomerTableView.cpp | 260 .arg(oligomer->description()) in selectedOligomersAsPlainText() 284 .arg(oligomer->charge()) in selectedOligomersAsPlainText() 288 .arg(oligomer->name()) in selectedOligomersAsPlainText() 297 .arg(oligomer->isModified()) in selectedOligomersAsPlainText() 317 delete oligomer; in selectedOligomersAsPlainText() 397 Oligomer *oligomer = mp_oligomerList->at(row); in currentChanged() local 404 if (oligomer->startIndex() >= oligomer->polymer()->size() || in currentChanged() 405 oligomer->endIndex() >= oligomer->polymer()->size()) in currentChanged() 422 oligomer->polymer()->monomerText(oligomer->startIndex(), in currentChanged() 477 if (oligomer->startIndex() >= oligomer->polymer()->size() || in itemActivated() [all …]
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H A D | cleaveOligomerTableView.cpp | 201 CleaveOligomer *oligomer = in selectedOligomers() local 261 CleaveOligomer *oligomer = in selectedOligomersAsPlainText() local 290 .arg(oligomer->charge()) in selectedOligomersAsPlainText() 294 .arg(oligomer->name()) in selectedOligomersAsPlainText() 322 delete oligomer; in selectedOligomersAsPlainText() 402 CleaveOligomer *oligomer = in currentChanged() local 410 if (oligomer->startIndex() >= oligomer->polymer()->size() || in currentChanged() 411 oligomer->endIndex() >= oligomer->polymer()->size()) in currentChanged() 437 .arg(oligomer->description()); in currentChanged() 478 CleaveOligomer *oligomer = in itemActivated() local [all …]
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H A D | massSearchOligomerTableViewModel.cpp | 188 Oligomer *oligomer = mp_oligomerList->at(row); in data() local 211 valueString = oligomer->name(); in data() 216 .arg(oligomer->startIndex() + 1) in data() 217 .arg(oligomer->endIndex() + 1); in data() 224 Prop *prop = oligomer->prop("ERROR_MZ"); in data() 242 if(oligomer->isModified()) in data() 264 if (!oligomer) in addOligomer() 302 mp_oligomerList->append(oligomer); in addOligomer() 351 Oligomer *oligomer = oligomerList.at(iter); in addOligomers() local 353 mp_oligomerList->append(oligomer); in addOligomers() [all …]
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H A D | fragmentOligomerTableViewModel.cpp | 181 Oligomer *oligomer = mp_oligomerList->at(row); in data() local 191 valueString = oligomer->description(); in data() 195 valueString = oligomer->name(); in data() 200 static_cast<CoordinateList *>(oligomer)->size(); in data() 205 static_cast<CoordinateList *>(oligomer)->at(jter); in data() 222 int charge = oligomer->charge(); in data() 228 if(oligomer->isModified()) in data() 284 Oligomer *oligomer = oligomerList.at(iter); in addOligomers() local 286 mp_oligomerList->append(oligomer); in addOligomers() 356 Oligomer *oligomer = mp_oligomerList->takeAt(iter); in removeOligomers() local [all …]
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H A D | cleaveOligomerTableViewModel.cpp | 189 CleaveOligomer *oligomer = in data() local 200 int partialCleavage = oligomer->partialCleavage(); in data() 206 valueString = oligomer->name(); in data() 211 static_cast<CoordinateList *>(oligomer)->size(); in data() 216 static_cast<CoordinateList *>(oligomer)->at(jter); in data() 233 int charge = oligomer->charge(); in data() 239 if(oligomer->isModified()) in data() 295 CleaveOligomer *oligomer = in addOligomers() local 298 mp_oligomerList->append(oligomer); in addOligomers() 369 CleaveOligomer *oligomer = in removeOligomers() local [all …]
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H A D | mzLabInputOligomerTableViewDlg.cpp | 359 result = oligomer->deionize(); in applyFormula() 373 oligomer->ionize(); in applyFormula() 388 oligomer->ionize(); in applyFormula() 448 result = oligomer->deionize(); in applyMass() 462 oligomer->ionize(); in applyMass() 477 oligomer->ionize(); in applyMass() 572 int result = oligomer->deionize(); in applyThreshold() 577 oligomer->ionize(); in applyThreshold() 652 charge = oligomer->charge(); in applyChargeIncrement() 675 result = oligomer->setCharge(charge); in applyChargeIncrement() [all …]
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H A D | mzLabInputOligomerTableView.cpp | 521 Oligomer *oligomer = 0; in testSimpleTextDataDroppedOrPasted() local 549 if (!oligomer) in testSimpleTextDataDroppedOrPasted() 563 oligomerList->append(oligomer); in testSimpleTextDataDroppedOrPasted() 625 Oligomer *oligomer = 0; in parseOnlyMassLine() local 630 oligomer = in parseOnlyMassLine() 648 return oligomer; in parseOnlyMassLine() 701 Oligomer *oligomer = in parseMassAndChargeLine() local 715 return oligomer; in parseMassAndChargeLine() 802 Oligomer *oligomer = in parseFullLine() local 813 oligomer->setCoordinates(coordinates); in parseFullLine() [all …]
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H A D | mzLabInputOligomerTableViewModel.cpp | 216 Oligomer *oligomer = mp_oligomerList->at(row); in data() local 233 valueString = locale.toString(oligomer->mass(massType), in data() 238 int charge = oligomer->charge(); in data() 244 valueString = oligomer->name(); in data() 250 valueString = oligomer->positionsAsText(); in data() 270 MzLabInputOligomerTableViewModel::addOligomer(Oligomer *oligomer) in addOligomer() argument 272 if (!oligomer) in addOligomer() 310 mp_oligomerList->append(oligomer); in addOligomer() 380 Oligomer *oligomer = mp_oligomerList->takeAt(iter); in removeOligomers() local 382 delete oligomer; in removeOligomers()
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H A D | mzLabOutputOligomerTableView.cpp | 339 (const Oligomer *oligomer) in provideEditorWindowFeedback() argument 341 if(!oligomer) in provideEditorWindowFeedback() 344 const Polymer *polymer = oligomer->polymer(); in provideEditorWindowFeedback() 350 const_cast<Oligomer *>(oligomer)->prop("SEQUENCE_EDITOR_WND"); in provideEditorWindowFeedback() 366 static_cast<CoordinateList *>(const_cast<Oligomer *>(oligomer)); in provideEditorWindowFeedback()
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H A D | mzLabMatchBasedActionsDlg.cpp | 174 Oligomer *oligomer = oligomerList.at(iter); in fillMolecularMassList() local 175 mass = oligomer->molecularMass(massType); in fillMolecularMassList() 347 Oligomer *oligomer = new Oligomer(*listMz1.at(iter)); in performMatchWorkPushButton() local 350 new OligomerPair(listMz1.at(iter), oligomer, in performMatchWorkPushButton()
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H A D | massSearchDlg.cpp | 962 Oligomer *oligomer) in updateProgressDetails() argument 988 if (oligomer) in updateProgressDetails() 990 m_ui.lastOligoNameLineEdit->setText(oligomer->name()); in updateProgressDetails() 992 .arg(oligomer->startIndex() + 1) in updateProgressDetails() 993 .arg(oligomer->endIndex() + 1)); in updateProgressDetails() 997 QString mass = oligomer->mono(locale); in updateProgressDetails() 1000 mass = oligomer->avg(locale); in updateProgressDetails()
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H A D | spectrumCalculationDlg.cpp | 1949 Oligomer *oligomer = mp_oligomerList->at(iter); in executeSpectrumWithCluster() local 1958 static_cast<StringProp *>(oligomer-> in executeSpectrumWithCluster() 2016 double mono = oligomer->mono(); in executeSpectrumWithCluster() 2017 double charge = oligomer->charge(); in executeSpectrumWithCluster() 2128 Oligomer *oligomer = mp_oligomerList->at(iter); in executeSpectrumWithoutCluster() local 2137 mz = oligomer->mono(); in executeSpectrumWithoutCluster() 2139 mz = oligomer->avg(); in executeSpectrumWithoutCluster() 2141 double charge = oligomer->charge(); in executeSpectrumWithoutCluster()
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H A D | mzCalculationDlg.cpp | 457 Oligomer *oligomer = new Oligomer(ionizable, in calculate() local 485 oligomer->appendProp(static_cast<Prop *>(prop)); in calculate() 488 m_oligomerList.append(oligomer); in calculate()
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/dports/science/massxpert/massxpert-c229f4a1abde3c20b83a90e50f9c5d79104dfa5f/lib/ |
H A D | cleaver.cpp | 435 Q_ASSERT(oligomer); in accountCleaveRule() 592 CleaveOligomer *oligomer = in cleavePartial() local 599 partialOligomerList.append(oligomer); in cleavePartial() 629 CleaveOligomer *oligomer = in cleavePartial() local 636 partialOligomerList.append(oligomer); in cleavePartial() 854 oligomer->updateCalcOptions(); in analyzeCrossLinks() 856 oligomerList->append(oligomer); in analyzeCrossLinks() 872 Q_ASSERT(oligomer); in analyzeCrossLinkedOligomer() 884 QString name = oligomer->name(); in analyzeCrossLinkedOligomer() 886 oligomer->setName(name); in analyzeCrossLinkedOligomer() [all …]
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H A D | oligomerList.cpp | 154 Oligomer *oligomer = at(iter); in findOligomerEncompassing() local 156 if(oligomer->encompasses(index)) in findOligomerEncompassing() 161 return oligomer; in findOligomerEncompassing() 194 Oligomer *oligomer = at(iter); in findOligomerEncompassing() local 196 if(oligomer->encompasses(monomer)) in findOligomerEncompassing() 201 return oligomer; in findOligomerEncompassing()
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H A D | cleaveOligomer.cpp | 74 CleaveOligomer::CleaveOligomer(const CleaveOligomer &oligomer) in CleaveOligomer() argument 75 : Oligomer(oligomer), in CleaveOligomer() 76 m_partialCleavage(oligomer.m_partialCleavage) in CleaveOligomer()
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H A D | lib.pro | 43 oligomer.hpp \ 94 oligomer.cpp \
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H A D | xpertedit.tex | 789 oligomer is capped on both its ends; 1222 \pageref{sect:oligomer-data-filtering}. 1274 an isotopic cluster for each oligomer. 1278 Computing isotopic cluster for oligomer 1 1391 of the oligomer, are ignored. 1485 outside of the oligomer; 1537 the cross-links of the oligomer. 1556 \pageref{sect:oligomer-data-filtering}. 1619 \pageref{sect:oligomer-data-filtering}. 1625 \label{sect:oligomer-data-filtering} [all …]
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H A D | xpertminer.tex | 11 \item \mXp-based simulations, like polymer cleavage, oligomer 107 corresponding oligomer and its coordinates in the polymer sequence can 146 oligomer data from these tree view widgets into a m/z list of \xpm, 169 the oligomer name and, finally, the coordinates of the oligomer in 291 that the fragmentation oligomer gets upon its creation is intrinsic to 346 oligomer, and thus its ionization formula); 406 thus getting M=1000; \footnote{Note that if the oligomer is a 407 fragmentation oligomer, the tri-protonated analyte is converted to 408 the canonical oligomer bearing a single charge.}
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H A D | basics-polchem.tex | 564 Thus, the \mXp\ definition of an oligomer might be: \emph{an oligomer 587 the oligomer is calculated by summing the mass of each monomer in the 588 oligomer (since the monomers are not modified, this is easily done) 592 In this way, the oligomer complies with its definition, which states 597 modified oligomer, like our Oligomer 1 in the case of the cyanogen 599 exactly the same way as for the unmodified oligomer. Next, each 600 oligomer is checked for presence or absence of a methionine residue on 704 calculate the mass of an oligomer (by simply adding the masses of its 901 chemical reaction to the oligomer if the right end monomer is
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/dports/science/massxpert/massxpert-c229f4a1abde3c20b83a90e50f9c5d79104dfa5f/debian/ |
H A D | changelog | 172 for each oligomer in the list or not. If not, the mono or avg mass can 214 - Switched to the TableView mass search oligomer display (was using 223 - Switched to the TableView fragmentation oligomer display (was using 270 provided as feedback when an oligomer from the tree/table view was 281 fragment oligomer computed for any given fragmentation pattern. 719 textual mass lists starting from oligomer items in treeviews. 844 searching oligomer data; 861 * Upstream release with main new figure: the oligomer data from a 949 new features of the cleavage- and fragmentation-base oligomer 965 * Reimplemented the cleaver object to use the new oligomer list object
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H A D | TODO | 35 Concept of flying modification, that would automagically apply to any oligomer hovered-on with the …
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H A D | cdd_annot_types.ini | 28 type7=oligomer interface
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H A D | massxpert_fr.ts | 446 any given oligomer with this character or string. By default, '$' is used.</source> 1469 <source>Last oligomer data</source> 5368 <source>No oligomer is selected. Select an oligomer first</source> 6527 Charge of a fragmentation oligomer cannot be 0</source> 6596 Failed to get oligomer's charge.</source> 6603 Failed to set oligomer's charge.</source> 7799 <source>No oligomer is selected. Select an oligomer first</source> 8080 <source>Sorting all oligomer-related sub-spectra...</source> 8112 <source>Elemental composition not found for current oligomer. 8119 <source>Computing isotopic cluster for oligomer %1 [all …]
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