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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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#include <memory> |
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/////////////////////// Qt includes |
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#include <QString> |
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#include <QObject> |
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#include <QDateTime> |
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#include <QCryptographicHash> |
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/////////////////////// Local includes |
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#include "exportimportconfig.h" |
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#include "Sequence.hpp" |
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#include "IonizeRule.hpp" |
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#include "Ionizable.hpp" |
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#include "Modif.hpp" |
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#include "CalcOptions.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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const int POL_SEQ_FILE_FORMAT_VERSION = 1; |
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class PolChemDef; |
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typedef std::shared_ptr<const PolChemDef> PolChemDefCstSPtr; |
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class IonizeRule; |
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class Ionizable; |
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class CrossLink; |
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class CrossLinkList; |
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//! The Polymer class provides a polymer. |
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/*! A polymer is a sequence(Sequence) to which data are |
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aggregated to make it able to perform a number of tasks. |
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The polymer has a name and a code, so that it is possible to |
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refer to it in printed material... |
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Because Polymer derives from Ionizable, which itself derives from |
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PolChemDefEntity, it holds a pointer to the polymer chemistry |
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definition of the polymer sequence. Without that datum, using the |
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polymer in a complex context would be impossible, as the polymer |
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chemistry definition will provide a huge amount of data required |
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to operate the polymer efficiently. Because Ionizable inherits |
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Ponderable, the polymer has a mono mass and an average mass. |
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The polymer also has modifications(left-end and right-end) to |
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characterize it better. |
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*/ |
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class DECLSPEC Polymer : public QObject, public Sequence, public Ionizable |
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{ |
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Q_OBJECT |
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public: |
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Polymer(PolChemDefCstSPtr pol_chem_def_csp, |
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const QString &name = QString("NOT_SET"), |
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const QString &code = QString("NOT_SET"), |
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const QString &author = QString("NOT SET")); |
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virtual ~Polymer(); |
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void setCode(const QString &); |
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QString code() const; |
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void setAuthor(const QString &); |
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QString author() const; |
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void setFilePath(const QString &); |
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QString filePath() const; |
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void setDateTime(const QString &); |
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QString dateTime() const; |
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bool hasModifiedMonomer(int left_index = -1, int right_index = -1) const; |
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bool setLeftEndModif(const QString & = QString()); |
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bool setLeftEndModif(const Modif &); |
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const Modif &leftEndModif() const; |
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bool isLeftEndModified() const; |
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bool setRightEndModif(const QString & = QString()); |
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bool setRightEndModif(const Modif &); |
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const Modif &rightEndModif() const; |
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bool isRightEndModified() const; |
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const CrossLinkList &crossLinkList() const; |
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CrossLinkList *crossLinkListPtr(); |
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bool crossLinkedMonomerIndexList(int, int, QList<int> *, int *); |
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bool crossLinkList(int, int, QList<CrossLink *> *, int *); |
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virtual bool prepareMonomerRemoval(const Monomer *monomer_p) override; |
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using Ionizable::operator=; |
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virtual bool removeMonomerAt(int index) override; |
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QByteArray md5Sum(int hash_data_specifs) const; |
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// MASS CALCULATION FUNCTIONS |
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///////////////////////////// |
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using Ponderable::accountMasses; |
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bool accountMasses(const CalcOptions &calc_options); |
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static bool accountMasses(Polymer *polymer_p, |
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const CalcOptions &calc_options, |
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double *mono, |
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double *avg); |
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using Ionizable::calculateMasses; |
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bool calculateMasses(const CalcOptions &calc_options, bool reset = true); |
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static bool calculateMasses(Polymer *polymer_p, |
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const CalcOptions &calc_options, |
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double *mono, |
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double *avg, |
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bool reset = true); |
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bool accountCappingMasses(int, int = 1); |
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static bool accountCappingMasses(Polymer *, int, double *, double *, int = 1); |
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bool accountEndModifMasses(int); |
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static bool accountEndModifMasses(Polymer *, int, double *, double *); |
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static bool accountEndModifMasses(Polymer *, int, Ponderable *); |
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bool crossLink(CrossLink *); |
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bool uncrossLink(CrossLink *); |
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///////////////////////////// |
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// MASS CALCULATION FUNCTIONS |
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// ELEMENTAL CALCULATION FUNCTION |
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///////////////////////////////// |
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QString elementalComposition(const IonizeRule &, |
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const CoordinateList &, |
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const CalcOptions &); |
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///////////////////////////////// |
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// ELEMENTAL CALCULATION FUNCTION |
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bool renderXmlCodesElement(const QDomElement &element); |
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static QString xmlPolymerFileGetPolChemDefName(const QString &file_path); |
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bool renderXmlPolymerFile(QString = QString("")); |
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bool renderXmlPolymerModifElement(const QDomElement &, int); |
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bool renderXmlCrossLinksElement(const QDomElement &, int); |
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QString *formatXmlDtd(); |
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QString *formatXmlPolSeqElement(int, const QString & = QString(" ")); |
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QString *formatXmlCrossLinksElement(int, const QString & = QString(" ")); |
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bool writeXmlFile(); |
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using Ionizable::validate; |
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using Sequence::validate; |
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bool validate() override; |
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void debugPutStdErr(); |
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signals: |
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void polymerDestroyedSignal(Polymer *); |
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void crossLinkChangedSignal(Polymer *); |
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void crossLinksPartiallyEncompassedSignal(int) const; |
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protected: |
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//! Code. |
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QString m_code; |
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//! Name of the last user having last modified the polymer sequence. |
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QString m_author; |
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//! File name. |
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QString m_filePath; |
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//! Date and time of the last modification. |
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QDateTime m_dateTime; |
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//! Left end modification. |
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Modif m_leftEndModif; |
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//! Right end modification. |
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Modif m_rightEndModif; |
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//! The list of CrossLink instances. |
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CrossLinkList *mpa_crossLinkList; |
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}; |
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typedef std::shared_ptr<Polymer> PolymerSPtr; |
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typedef std::shared_ptr<const Polymer> PolymerCstSPtr; |
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} // namespace libXpertMass |
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} // namespace MsXpS |
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Q_DECLARE_METATYPE(MsXpS::libXpertMass::Polymer); |
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extern int polymerMetaTypeId; |
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Q_DECLARE_METATYPE(MsXpS::libXpertMass::PolymerSPtr); |
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extern int polymerSPtrMetaTypeId; |
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Q_DECLARE_METATYPE(MsXpS::libXpertMass::PolymerCstSPtr); |
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extern int polymerCstSPtrMetaTypeId; |
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