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/* BEGIN software license |
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* |
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* MsXpertSuite - mass spectrometry software suite |
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* ----------------------------------------------- |
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* Copyright(C) 2009,...,2018 Filippo Rusconi |
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* |
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* http://www.msxpertsuite.org |
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* |
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* This file is part of the MsXpertSuite project. |
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* |
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* The MsXpertSuite project is the successor of the massXpert project. This |
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* project now includes various independent modules: |
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* |
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* - massXpert, model polymer chemistries and simulate mass spectrometric data; |
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* - mineXpert, a powerful TIC chromatogram/mass spectrum viewer/miner; |
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* |
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* This program is free software: you can redistribute it and/or modify |
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* it under the terms of the GNU General Public License as published by |
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* the Free Software Foundation, either version 3 of the License, or |
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* (at your option) any later version. |
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* |
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* This program is distributed in the hope that it will be useful, |
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* but WITHOUT ANY WARRANTY; without even the implied warranty of |
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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* GNU General Public License for more details. |
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* |
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* You should have received a copy of the GNU General Public License |
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* along with this program. If not, see <http://www.gnu.org/licenses/>. |
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* |
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* END software license |
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*/ |
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#pragma once |
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/////////////////////// Qt includes |
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#include <QString> |
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#include <QList> |
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/////////////////////// Local includes |
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#include "exportimportconfig.h" |
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#include "Formula.hpp" |
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#include "IsotopicData.hpp" |
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#include "Modif.hpp" |
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#include "CrossLinker.hpp" |
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#include "CleaveSpec.hpp" |
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#include "FragSpec.hpp" |
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#include "IonizeRule.hpp" |
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#include "Polymer.hpp" |
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#include "MonomerSpec.hpp" |
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#include "ModifSpec.hpp" |
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#include "CrossLinkerSpec.hpp" |
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#include "PolChemDefSpec.hpp" |
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namespace MsXpS |
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{ |
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namespace libXpertMass |
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{ |
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extern const int POL_CHEM_DEF_FILE_FORMAT_VERSION; |
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class PolChemDef; |
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typedef std::shared_ptr<PolChemDef> PolChemDefSPtr; |
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typedef std::shared_ptr<const PolChemDef> PolChemDefCstSPtr; |
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//! The PolChemDef class provides a polymer chemistry definition. |
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/*! A polymer chemistry definition allows one to characterize in a |
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fine manner the chemistry of a polymer. That means that it should |
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contain: |
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- a list of atoms; |
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- a list of monomers; |
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- a list of modifications; |
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- a list of cross-linkers; |
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- a list of cleavage specifications; |
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- a list of fragmentation specifications; |
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and a number of chemical data, like the left and right cap formulas, |
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the code length(that is the maximum number of characters that might |
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be used to construct a monomer code). |
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Because monomers have to be graphically rendered at some point, in |
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the form of monomer vignettes in the sequence editor, the polymer |
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chemistry definition also contains: |
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- a list of monomer specifications, which tell the sequence editor |
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what file is to be used to render any monomer in the polymer |
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chemistry definition; |
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- a list of modification specifications, which tell the sequence |
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editor what file is to be used to render any chemical |
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modification; |
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*/ |
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class DECLSPEC PolChemDef |
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{ |
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public: |
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PolChemDef(); |
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PolChemDef(const PolChemDefSpec &); |
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virtual ~PolChemDef(); |
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void setVersion(const QString &); |
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QString version() const; |
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void setName(const QString &); |
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QString name() const; |
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void setXmlDataFilePath(const QString &file_path); |
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QString getXmlDataFilePath() const; |
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QString getXmlDataDirPath() const; |
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void setIsotopicDataFilePath(const QString &file_path); |
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QString getIsotopicDataFilePath() const; |
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QString deduceIsotopicDataFilePath() const; |
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void setLeftCap(const Formula &); |
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const Formula &leftCap() const; |
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void setRightCap(const Formula &); |
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const Formula &rightCap() const; |
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void setCodeLength(int); |
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int codeLength() const; |
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bool calculateDelimitedCodes(); |
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const QString &delimitedCodes(); |
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void setIonizeRule(const IonizeRule &); |
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const IonizeRule &ionizeRule() const; |
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IonizeRule *ionizeRulePtr(); |
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void setIsotopicDataSPtr(IsotopicDataSPtr isotopic_data_sp); |
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IsotopicDataCstSPtr getIsotopicDataCstSPtr() const; |
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IsotopicDataSPtr getIsotopicDataSPtr(); |
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const QList<Monomer *> &monomerList() const; |
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QList<Monomer *> *monomerListPtr(); |
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const QList<Modif *> &modifList() const; |
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QList<Modif *> *modifListPtr(); |
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const QList<CrossLinker *> &crossLinkerList() const; |
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QList<CrossLinker *> *crossLinkerListPtr(); |
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const QList<CleaveSpec *> &cleaveSpecList() const; |
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QList<CleaveSpec *> *cleaveSpecListPtr(); |
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const QList<FragSpec *> &fragSpecList() const; |
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QList<FragSpec *> *fragSpecListPtr(); |
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QList<MonomerSpec *> &monomerSpecList() const; |
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QList<MonomerSpec *> *monomerSpecListPtr(); |
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QList<ModifSpec *> &modifSpecList() const; |
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QList<ModifSpec *> *modifSpecListPtr(); |
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bool referenceModifByName(const QString &, Modif *modif = nullptr) const; |
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bool referenceModifByName(const QString &, Modif &modif) const; |
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QList<CrossLinkerSpec *> &crossLinkerSpecList() const; |
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QList<CrossLinkerSpec *> *crossLinkerSpecListPtr(); |
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bool operator==(const PolChemDef &other) const; |
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bool operator!=(const PolChemDef &other) const; |
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bool referenceCrossLinkerByName(const QString &, CrossLinker * = 0) const; |
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static std::size_t loadIsotopicData(PolChemDefSPtr pol_chem_def_sp, |
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const QString &file_path = QString()); |
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static std::size_t writeIsotopicData(PolChemDefSPtr pol_chem_def_sp, |
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const QString &file_path = QString()); |
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static bool renderXmlPolChemDefFile(PolChemDefSPtr pol_chem_def_sp); |
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QString *formatXmlDtd(); |
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bool writeXmlFile(); |
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QStringList *differenceBetweenMonomers(double, MassType); |
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protected: |
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//! Name. |
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/*! Identifies the polymer definition, like "protein" or "dna", for |
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example. |
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*/ |
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QString m_name; |
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//! File path. |
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/*! Fully qualifies the file which contains the polymer chemistry definition. |
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*/ |
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QString m_xmlDataFilePath; |
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QString m_isotopicDataFilePath; |
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//! Left cap formula. |
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/*! Describes how the polymer should be capped on its left end. |
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*/ |
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Formula m_leftCap; |
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//! Right cap formula. |
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/*! Describes how the polymer should be capped on its right end. |
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*/ |
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Formula m_rightCap; |
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//! Code length. |
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/*! Maximum number of characters allowed to construct a monomer |
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code. |
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*/ |
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int m_codeLength; |
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//! Delimited codes string. |
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/*! String made with each code of each monomer separated using '@', |
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like "@Ala@Tyr@Phe@". |
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*/ |
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QString m_delimitedCodes; |
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//! Ionization rule. |
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/*! The ionization rule indicates how the polymer sequence needs be |
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ionized by default. |
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*/ |
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IonizeRule m_ionizeRule; |
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//! Shared pointer to IsotopicData |
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// We will access all the chemical elements data in this class instance. |
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IsotopicDataSPtr msp_isotopicData = nullptr; |
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//! List of monomers. |
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QList<Monomer *> m_monomerList; |
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//! List of modifications. |
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QList<Modif *> m_modifList; |
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//! List of cross-linkers. |
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QList<CrossLinker *> m_crossLinkerList; |
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//! List of cleavage specifications. |
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QList<CleaveSpec *> m_cleaveSpecList; |
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//! List of fragmentation specifications. |
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QList<FragSpec *> m_fragSpecList; |
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//! List of monomer specifications. |
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/*! Each monomer in the polymer chemistry definition has an item in |
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this list indicating where the graphics file is to be found for |
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graphical rendering. |
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*/ |
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mutable QList<MonomerSpec *> m_monomerSpecList; |
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//! List of modification specifications. |
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/*! Each modification in the polymer chemistry definition has an |
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item in this list indicating where the graphics file is to be |
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found for graphical rendering and the graphical mechanism to be |
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used for rendering the modification graphically. |
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*/ |
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mutable QList<ModifSpec *> m_modifSpecList; |
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//! List of cross-link specifications. |
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/*! Each cross-link in the polymer chemistry definition has an item |
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in this list indicating where the graphics file is to be found for |
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graphical rendering. |
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*/ |
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mutable QList<CrossLinkerSpec *> m_crossLinkerSpecList; |
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QList<PolChemDef *> *mp_repositoryList; |
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}; |
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} // namespace libXpertMass |
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} // namespace MsXpS |
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Q_DECLARE_METATYPE(MsXpS::libXpertMass::PolChemDefSPtr); |
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extern int polChemDefSPtrMetaTypeId; |
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Q_DECLARE_METATYPE(MsXpS::libXpertMass::PolChemDefCstSPtr); |
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extern int polChemDefCstSPtrMetaTypeId; |
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