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/dports/science/massxpert/massxpert-c229f4a1abde3c20b83a90e50f9c5d79104dfa5f/gui/
H A DmassSearchOligomerTableView.cpp281 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()
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H A DfragmentOligomerTableView.cpp260 .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()
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H A DcleaveOligomerTableView.cpp201 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
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H A DmassSearchOligomerTableViewModel.cpp188 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()
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H A DfragmentOligomerTableViewModel.cpp181 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
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H A DcleaveOligomerTableViewModel.cpp189 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
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H A DmzLabInputOligomerTableViewDlg.cpp359 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()
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H A DmzLabInputOligomerTableView.cpp521 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()
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H A DmzLabInputOligomerTableViewModel.cpp216 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()
H A DmzLabOutputOligomerTableView.cpp339 (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()
H A DmzLabMatchBasedActionsDlg.cpp174 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()
H A DmassSearchDlg.cpp962 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()
H A DspectrumCalculationDlg.cpp1949 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()
H A DmzCalculationDlg.cpp457 Oligomer *oligomer = new Oligomer(ionizable, in calculate() local
485 oligomer->appendProp(static_cast<Prop *>(prop)); in calculate()
488 m_oligomerList.append(oligomer); in calculate()
/dports/science/massxpert/massxpert-c229f4a1abde3c20b83a90e50f9c5d79104dfa5f/lib/
H A Dcleaver.cpp435 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()
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H A DoligomerList.cpp154 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()
H A DcleaveOligomer.cpp74 CleaveOligomer::CleaveOligomer(const CleaveOligomer &oligomer) in CleaveOligomer() argument
75 : Oligomer(oligomer), in CleaveOligomer()
76 m_partialCleavage(oligomer.m_partialCleavage) in CleaveOligomer()
H A Dlib.pro43 oligomer.hpp \
94 oligomer.cpp \
/dports/science/massxpert/massxpert-c229f4a1abde3c20b83a90e50f9c5d79104dfa5f/usermanual/
H A Dxpertedit.tex789 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}
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H A Dxpertminer.tex11 \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.}
H A Dbasics-polchem.tex564 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
/dports/science/massxpert/massxpert-c229f4a1abde3c20b83a90e50f9c5d79104dfa5f/debian/
H A Dchangelog172 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
/dports/science/massxpert/massxpert-c229f4a1abde3c20b83a90e50f9c5d79104dfa5f/
H A DTODO35 Concept of flying modification, that would automagically apply to any oligomer hovered-on with the …
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/cn3d/data/
H A Dcdd_annot_types.ini28 type7=oligomer interface
/dports/science/massxpert/massxpert-c229f4a1abde3c20b83a90e50f9c5d79104dfa5f/i18n/
H A Dmassxpert_fr.ts446 any given oligomer with this character or string. By default, &apos;$&apos; 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&apos;s charge.</source>
6603 Failed to set oligomer&apos;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
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