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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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/////////////////////// Local includes |
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#include "MsXpS/libXpertMassCore/FragmentationRule.hpp" |
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#include "MsXpS/libXpertMassCore/PolChemDef.hpp" |
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namespace MsXpS |
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{ |
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namespace libXpertMassCore |
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{ |
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/*! |
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\class MsXpS::libXpertMassCore::FragmentationRule |
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\inmodule libXpertMassCore |
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\ingroup PolChemDefGasPhaseChemicalReactions |
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\inheaderfile FragmentationRule.hpp |
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\brief The FragmentationRule class provides a model for specifying gas phase |
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fragmentation rules for refining fragmentation pathway specifications (\l |
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FragmentationPathway) of \l{Oligomer} \l{Sequence}s. |
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Fragmentation rules characterize in more detail the chemical reaction that |
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governs the fragmentation of the polymer in the gas-phase. The rule is a |
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conditional rule. Its logic is based on the presence of specified monomers |
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right at the place of the fragmentation and before or after that precise |
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location. |
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In saccharide chemistry, fragmentations are a very complex topic. This is |
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because a given monomer will fragment according to a given chemistry if it is |
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preceded in the sequence by a monomer of a given identity and according to |
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another chemistry if its direct environment is different. |
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This paradigm is implemented using a sequence environment logic based on |
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conditions that can be formulated thanks to three monomer codes: |
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\list |
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\li The monomer at which the fragmentation takes place (current code); |
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\li The monomer preceeding the current code (previous code); |
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\li The monomer following the current code (next code); |
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\endlist |
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The use of these codes is typically according to this kind of logic: |
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\e{If current monomer is Glu and previous monomer is Gly and |
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next monomer is Arg, then fragmentation should occur according |
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to this formula : "-H2O"}. |
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\sa FragmentationPathway |
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*/ |
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/*! |
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\variable MsXpS::libXpertMassCore::FragmentationRule::mcsp_polChemDef |
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\brief The PolChemDef (polymer chemistry definition) that is the context in |
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which the Oligomer being fragmented exists. |
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*/ |
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/*! |
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\variable MsXpS::libXpertMassCore::FragmentationRule::m_name |
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\brief The name of the FragmentationRule. |
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*/ |
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/*! |
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\variable MsXpS::libXpertMassCore::FragmentationRule::m_prevCode |
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\brief The \l Monomer code of the Monomer located before the actual |
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fragmentation site. |
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*/ |
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/*! |
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\variable MsXpS::libXpertMassCore::FragmentationRule::m_currCode |
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\brief The \l Monomer code of the Monomer at the actual fragmentation site. |
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*/ |
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/*! |
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\variable MsXpS::libXpertMassCore::FragmentationRule::m_nextCode |
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\brief The \l Monomer code of the Monomer located after the actual fragmentation |
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site. |
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*/ |
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/*! |
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\variable MsXpS::libXpertMassCore::FragmentationRule::m_comment |
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\brief A comment associated to the FragmentationRule. |
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*/ |
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/*! |
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\variable MsXpS::libXpertMassCore::FragmentationRule::m_formula |
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\brief A \l{Formula} instance describing the fragmentation reaction occurring on |
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the Monomer at which the fragmentation occurs. |
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*/ |
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/*! |
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\variable MsXpS::libXpertMassCore::FragmentationRule::m_isValid |
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\brief The validity status of this FragmentationRule instance. |
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*/ |
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/*! |
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\brief Constructs a fragmentation rule with a number of parameters. |
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\list |
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\li \a pol_chem_def_csp Polymer chemistry definition. Cannot be nullptr. |
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\li \a name Name. Cannot be empty. |
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\li \a prev_code Previous monomer code. Defaults to the null string. |
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\li \a current_code Current monomer code. Defaults to the null string. |
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\li \a next_code Next monomer code. Defaults to the null string. |
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\li \a comment Comment. Defaults to the null string. |
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\li \a formula_string Formula. Defaults to the null string. |
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\endlist |
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Upon setting all the member data, this instance is validated and the member |
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m_isValid is set to the result. |
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*/ |
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FragmentationRule::FragmentationRule(PolChemDefCstSPtr pol_chem_def_csp, |
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const QString &name, |
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const QString &prev_code, |
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const QString ¤t_code, |
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const QString &next_code, |
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const QString &comment, |
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const QString &formula_string) |
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: mcsp_polChemDef(pol_chem_def_csp), |
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m_name(name), |
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m_prevCode(prev_code), |
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m_currCode(current_code), |
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m_nextCode(next_code), |
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m_comment(comment), |
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m_formula(formula_string) |
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{ |
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ErrorList error_list; |
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m_isValid = validate(&error_list); |
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if(!m_isValid) |
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qCritical() |
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<< "Upon construction of FragmentationRule, the instance failed to " |
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"validate with errors:" |
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<< Utils::joinErrorList(error_list, ", "); |
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} |
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/*! |
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\brief Constructs a FragmentationRule instance starting from an XML <fgr> \a |
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element according to \a version and using the reference \a pol_chem_def_csp |
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polymer chemistry definition. |
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This is the current format (FAKE fgr): |
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\code |
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<fgr> |
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<name>a-fgr-2</name> |
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<formula>+H100</formula> |
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<prev-mnm-code>F</prev-mnm-code> |
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<curr-mnm-code>D</curr-mnm-code> |
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<next-mnm-code>E</next-mnm-code> |
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<comment>comment here!</comment> |
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</fgr> |
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\endcode |
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The rendering of the CleavageRule instances requires that the PolChemDef be |
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available. |
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\sa renderXmlFgrElement() |
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*/ |
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FragmentationRule::FragmentationRule(PolChemDefCstSPtr pol_chem_def_csp, |
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const QDomElement &element, |
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[[maybe_unused]] int version) |
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: mcsp_polChemDef(pol_chem_def_csp) |
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{ |
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if(mcsp_polChemDef == nullptr || mcsp_polChemDef.get() == nullptr) |
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qCritical() << "Constructing FragmentationRule with no PolChemDef."; |
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if(!renderXmlFgrElement(element)) |
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qCritical() |
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<< "Failed to fully render or validate the FragmentationRule XML element " |
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"for construction of FragmentationRule instance."; |
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} |
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/*! |
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\brief Constructs a FragmentationRule instance as a copy of \a other. |
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Upon setting all the member data, this instance is validated and the member |
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m_isValid is set to the result. |
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*/ |
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FragmentationRule::FragmentationRule(const FragmentationRule &other) |
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: mcsp_polChemDef(other.mcsp_polChemDef), |
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m_name(other.m_name), |
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m_prevCode(other.m_prevCode), |
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m_currCode(other.m_currCode), |
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m_nextCode(other.m_nextCode), |
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m_comment(other.m_comment), |
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m_formula(other.m_formula) |
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{ |
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ErrorList error_list; |
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m_isValid = validate(&error_list); |
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if(!m_isValid) |
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qCritical() |
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<< "Upon construction of FragmentationRule, the instance failed to " |
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"validate with errors:" |
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<< Utils::joinErrorList(error_list, ", "); |
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} |
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/*! |
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\brief Destructs the fragmentation rule. |
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*/ |
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FragmentationRule::~FragmentationRule() |
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{ |
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} |
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/*! |
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\brief Sets the PolChemDef to \a pol_chem_def_csp. |
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*/ |
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void |
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FragmentationRule::setPolchemDefCstSPtr(PolChemDefCstSPtr pol_chem_def_csp) |
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{ |
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mcsp_polChemDef = pol_chem_def_csp; |
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ErrorList error_list; |
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m_isValid = validate(&error_list); |
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if(!m_isValid) |
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qCritical() |
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<< "Upon setting PolChemDef of FragmentationRule, the instance failed to " |
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"validate with errors:" |
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<< Utils::joinErrorList(error_list, ", "); |
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} |
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/*! |
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\brief Returns the PolChemDef. |
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*/ |
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PolChemDefCstSPtr |
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FragmentationRule::getPolchemDefCstSPtr() const |
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{ |
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return mcsp_polChemDef; |
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} |
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/*! |
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\brief Sets the name to \a name. |
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*/ |
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void |
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FragmentationRule::setName(const QString &name) |
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{ |
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m_name = name; |
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ErrorList error_list; |
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m_isValid = validate(&error_list); |
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if(!m_isValid) |
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qCritical() |
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"validate with errors:" |
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<< Utils::joinErrorList(error_list, ", "); |
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} |
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/*! |
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\brief Returns the name. |
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*/ |
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const QString & |
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FragmentationRule::getName() |
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{ |
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return m_name; |
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} |
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/*! |
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\brief Sets the previous monomer \a code. |
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Upon setting the member data, this instance is validated and the member |
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m_isValid is set to the result. |
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*/ |
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void |
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FragmentationRule::setPrevCode(const QString &code) |
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{ |
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m_prevCode = code; |
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ErrorList error_list; |
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m_isValid = validate(&error_list); |
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if(!m_isValid) |
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qCritical() << "Upon setting previous code of FragmentationRule, the " |
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"instance failed to " |
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"validate with errors:" |
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|
2 |
<< Utils::joinErrorList(error_list, ", "); |
| 334 |
|
1 |
} |
| 335 |
|
|
|
| 336 |
|
|
|
| 337 |
|
|
/*! |
| 338 |
|
|
\brief Returns the previous monomer code. |
| 339 |
|
|
*/ |
| 340 |
|
|
const QString & |
| 341 |
|
8 |
FragmentationRule::getPrevCode() const |
| 342 |
|
|
{ |
| 343 |
|
8 |
return m_prevCode; |
| 344 |
|
|
} |
| 345 |
|
|
|
| 346 |
|
|
|
| 347 |
|
|
/*! |
| 348 |
|
|
\brief Sets the current monomer \a code. |
| 349 |
|
|
|
| 350 |
|
|
Upon setting the member data, this instance is validated and the member |
| 351 |
|
|
m_isValid is set to the result. |
| 352 |
|
|
*/ |
| 353 |
|
|
void |
| 354 |
|
1 |
FragmentationRule::setCurrCode(const QString &code) |
| 355 |
|
|
{ |
| 356 |
|
1 |
m_currCode = code; |
| 357 |
|
|
|
| 358 |
|
1 |
ErrorList error_list; |
| 359 |
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|
1 |
m_isValid = validate(&error_list); |
| 360 |
|
|
|
| 361 |
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|
1 |
if(!m_isValid) |
| 362 |
1/2
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|
2 |
qCritical() << "Upon setting current code of FragmentationRule, the " |
| 363 |
|
|
"instance failed to " |
| 364 |
1/2
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|
1 |
"validate with errors:" |
| 365 |
3/6
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|
2 |
<< Utils::joinErrorList(error_list, ", "); |
| 366 |
|
1 |
} |
| 367 |
|
|
|
| 368 |
|
|
|
| 369 |
|
|
/*! |
| 370 |
|
|
\brief Returns the current monomer code. |
| 371 |
|
|
*/ |
| 372 |
|
|
const QString & |
| 373 |
|
8 |
FragmentationRule::getCurrCode() const |
| 374 |
|
|
{ |
| 375 |
|
8 |
return m_currCode; |
| 376 |
|
|
} |
| 377 |
|
|
|
| 378 |
|
|
|
| 379 |
|
|
/*! |
| 380 |
|
|
\brief Sets the next monomer \a code. |
| 381 |
|
|
|
| 382 |
|
|
Upon setting the member data, this instance is validated and the member |
| 383 |
|
|
m_isValid is set to the result. |
| 384 |
|
|
*/ |
| 385 |
|
|
void |
| 386 |
|
1 |
FragmentationRule::setNextCode(const QString &code) |
| 387 |
|
|
{ |
| 388 |
|
1 |
m_nextCode = code; |
| 389 |
|
|
|
| 390 |
|
1 |
ErrorList error_list; |
| 391 |
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|
1 |
m_isValid = validate(&error_list); |
| 392 |
|
|
|
| 393 |
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|
1 |
if(!m_isValid) |
| 394 |
1/2
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|
2 |
qCritical() |
| 395 |
|
|
<< "Upon setting next code of FragmentationRule, the instance failed to " |
| 396 |
1/2
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|
1 |
"validate with errors:" |
| 397 |
3/6
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|
2 |
<< Utils::joinErrorList(error_list, ", "); |
| 398 |
|
1 |
} |
| 399 |
|
|
|
| 400 |
|
|
|
| 401 |
|
|
/*! |
| 402 |
|
|
\brief Returns the next monomer code. |
| 403 |
|
|
*/ |
| 404 |
|
|
const QString & |
| 405 |
|
8 |
FragmentationRule::getNextCode() const |
| 406 |
|
|
{ |
| 407 |
|
8 |
return m_nextCode; |
| 408 |
|
|
} |
| 409 |
|
|
|
| 410 |
|
|
|
| 411 |
|
|
/*! |
| 412 |
|
|
\brief Sets the \a comment. |
| 413 |
|
|
*/ |
| 414 |
|
|
void |
| 415 |
|
1 |
FragmentationRule::setComment(const QString &comment) |
| 416 |
|
|
{ |
| 417 |
|
1 |
m_comment = comment; |
| 418 |
|
1 |
} |
| 419 |
|
|
|
| 420 |
|
|
|
| 421 |
|
|
/*! |
| 422 |
|
|
\brief Returns the comment. |
| 423 |
|
|
*/ |
| 424 |
|
|
const QString & |
| 425 |
|
8 |
FragmentationRule::getComment() const |
| 426 |
|
|
{ |
| 427 |
|
8 |
return m_comment; |
| 428 |
|
|
} |
| 429 |
|
|
|
| 430 |
|
|
/*! |
| 431 |
|
|
\brief Sets the \a formula. |
| 432 |
|
|
|
| 433 |
|
|
Upon setting the member data, this instance is validated and the member |
| 434 |
|
|
m_isValid is set to the result. |
| 435 |
|
|
*/ |
| 436 |
|
|
void |
| 437 |
|
1 |
FragmentationRule::setFormula(const Formula &formula) |
| 438 |
|
|
{ |
| 439 |
|
1 |
m_formula = formula; |
| 440 |
|
|
|
| 441 |
|
1 |
ErrorList error_list; |
| 442 |
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|
1 |
m_isValid = validate(&error_list); |
| 443 |
|
|
|
| 444 |
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|
1 |
if(!m_isValid) |
| 445 |
|
✗ |
qCritical() |
| 446 |
|
|
<< "Upon setting Formula of FragmentationRule, the instance failed to " |
| 447 |
|
✗ |
"validate with errors:" |
| 448 |
|
✗ |
<< Utils::joinErrorList(error_list, ", "); |
| 449 |
|
1 |
} |
| 450 |
|
|
|
| 451 |
|
|
/*! |
| 452 |
|
|
\brief Sets the member Formula using \a formula_string. |
| 453 |
|
|
|
| 454 |
|
|
Upon setting the member data, this instance is validated and the member |
| 455 |
|
|
m_isValid is set to the result. |
| 456 |
|
|
*/ |
| 457 |
|
|
void |
| 458 |
|
✗ |
FragmentationRule::setFormula(const QString &formula_string) |
| 459 |
|
|
{ |
| 460 |
|
✗ |
m_formula = Formula(formula_string); |
| 461 |
|
|
|
| 462 |
|
✗ |
ErrorList error_list; |
| 463 |
|
✗ |
m_isValid = validate(&error_list); |
| 464 |
|
|
|
| 465 |
|
✗ |
if(!m_isValid) |
| 466 |
|
✗ |
qCritical() |
| 467 |
|
|
<< "Upon setting Formula of FragmentationRule, the instance failed to " |
| 468 |
|
✗ |
"validate with errors:" |
| 469 |
|
✗ |
<< Utils::joinErrorList(error_list, ", "); |
| 470 |
|
✗ |
} |
| 471 |
|
|
|
| 472 |
|
|
/*! |
| 473 |
|
|
\brief Returns a const reference to the member \l Formula. |
| 474 |
|
|
*/ |
| 475 |
|
|
const Formula & |
| 476 |
|
8 |
FragmentationRule::getFormulaCstRef() const |
| 477 |
|
|
{ |
| 478 |
|
8 |
return m_formula; |
| 479 |
|
|
} |
| 480 |
|
|
|
| 481 |
|
|
/*! |
| 482 |
|
|
\brief Returns a reference to the member \l Formula. |
| 483 |
|
|
*/ |
| 484 |
|
|
Formula & |
| 485 |
|
✗ |
FragmentationRule::getFormulaRef() |
| 486 |
|
|
{ |
| 487 |
|
✗ |
return m_formula; |
| 488 |
|
|
} |
| 489 |
|
|
|
| 490 |
|
|
//////////////// OPERATORS ///////////////////// |
| 491 |
|
|
/*! |
| 492 |
|
|
\brief Assigns \a other to this FragmentationRule instance. |
| 493 |
|
|
|
| 494 |
|
|
Upon setting the member data, this instance is validated and the member |
| 495 |
|
|
m_isValid is set to the result. |
| 496 |
|
|
|
| 497 |
|
|
Returns a reference to this fragmentation rule. |
| 498 |
|
|
*/ |
| 499 |
|
|
FragmentationRule & |
| 500 |
|
1 |
FragmentationRule::operator=(const FragmentationRule &other) |
| 501 |
|
|
{ |
| 502 |
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|
1 |
if(&other == this) |
| 503 |
|
|
return *this; |
| 504 |
|
|
|
| 505 |
|
1 |
mcsp_polChemDef = other.mcsp_polChemDef; |
| 506 |
|
1 |
m_name = other.m_name; |
| 507 |
|
1 |
m_prevCode = other.m_prevCode; |
| 508 |
|
1 |
m_currCode = other.m_currCode; |
| 509 |
|
1 |
m_nextCode = other.m_nextCode; |
| 510 |
|
1 |
m_comment = other.m_comment; |
| 511 |
|
1 |
m_formula = other.m_formula; |
| 512 |
|
|
|
| 513 |
|
1 |
ErrorList error_list; |
| 514 |
1/2
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|
1 |
m_isValid = validate(&error_list); |
| 515 |
|
|
|
| 516 |
1/2
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✓ Branch 1 taken 1 times.
|
1 |
if(!m_isValid) |
| 517 |
|
✗ |
qCritical() |
| 518 |
|
|
<< "Upon assignment of FragmentationRule, the instance failed to " |
| 519 |
|
✗ |
"validate with errors:" |
| 520 |
|
✗ |
<< Utils::joinErrorList(error_list, ", "); |
| 521 |
|
|
|
| 522 |
|
1 |
return *this; |
| 523 |
|
1 |
} |
| 524 |
|
|
|
| 525 |
|
|
/*! |
| 526 |
|
|
\brief Returns true if \c this instance and \a other are identical. |
| 527 |
|
|
*/ |
| 528 |
|
|
bool |
| 529 |
|
4 |
FragmentationRule::operator==(const FragmentationRule &other) const |
| 530 |
|
|
{ |
| 531 |
1/2
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|
4 |
if(&other == this) |
| 532 |
|
|
return true; |
| 533 |
|
|
|
| 534 |
3/6
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✓ Branch 5 taken 4 times.
|
4 |
return mcsp_polChemDef == other.mcsp_polChemDef && m_name == other.m_name && |
| 535 |
3/6
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✓ Branch 5 taken 4 times.
|
4 |
m_prevCode == other.m_prevCode && m_currCode == other.m_currCode && |
| 536 |
4/8
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✓ Branch 7 taken 4 times.
|
12 |
m_nextCode == other.m_nextCode && m_comment == other.m_comment && |
| 537 |
|
4 |
m_formula == other.m_formula; |
| 538 |
|
|
} |
| 539 |
|
|
|
| 540 |
|
|
/*! |
| 541 |
|
|
\brief Returns true if \c this and \a other are different. |
| 542 |
|
|
|
| 543 |
|
|
Returns the negated result of operator==(). |
| 544 |
|
|
*/ |
| 545 |
|
|
bool |
| 546 |
|
9 |
FragmentationRule::operator!=(const FragmentationRule &other) const |
| 547 |
|
|
{ |
| 548 |
2/2
✓ Branch 0 taken 2 times.
✓ Branch 1 taken 7 times.
|
9 |
if(&other == this) |
| 549 |
|
|
return false; |
| 550 |
|
|
|
| 551 |
|
2 |
return !operator==(other); |
| 552 |
|
|
} |
| 553 |
|
|
|
| 554 |
|
|
|
| 555 |
|
|
//////////////// VALIDATIONS ///////////////////// |
| 556 |
|
|
/*! |
| 557 |
|
|
\brief Validates the FragmentationRule, recording any error as a message in \a error_list_p. |
| 558 |
|
|
|
| 559 |
|
|
The validation involves checking that: |
| 560 |
|
|
|
| 561 |
|
|
\list |
| 562 |
|
|
\li The member PolChemDef cannot be nullptr. |
| 563 |
|
|
|
| 564 |
|
|
\li The name is not empty. |
| 565 |
|
|
|
| 566 |
|
|
\li The previous code is valid if non empty. |
| 567 |
|
|
|
| 568 |
|
|
\li The current code is valid if non empty. |
| 569 |
|
|
|
| 570 |
|
|
\li The next code is valid if non empty. |
| 571 |
|
|
|
| 572 |
|
|
\li The formula validates successfully if non empty. |
| 573 |
|
|
\endlist |
| 574 |
|
|
|
| 575 |
|
|
The m_isValid member is set to true upon success, false otherwise and returned. |
| 576 |
|
|
*/ |
| 577 |
|
|
bool |
| 578 |
|
102 |
FragmentationRule::validate(ErrorList *error_list_p) const |
| 579 |
|
|
{ |
| 580 |
2/2
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|
102 |
qsizetype error_count = error_list_p->size(); |
| 581 |
|
|
|
| 582 |
2/2
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✓ Branch 1 taken 98 times.
|
102 |
if(mcsp_polChemDef == nullptr || mcsp_polChemDef.get() == nullptr) |
| 583 |
|
|
{ |
| 584 |
|
8 |
qCritical() << "A FragmentationRule with no PolChemDef available cannot " |
| 585 |
1/2
✓ Branch 1 taken 4 times.
✗ Branch 2 not taken.
|
4 |
"validate successfully."; |
| 586 |
|
8 |
error_list_p->push_back( |
| 587 |
|
|
"A FragmentationRule with no PolChemDef available cannot validate " |
| 588 |
|
|
"successfully"); |
| 589 |
|
|
} |
| 590 |
|
|
|
| 591 |
2/2
✓ Branch 0 taken 7 times.
✓ Branch 1 taken 95 times.
|
102 |
if(m_name.isEmpty()) |
| 592 |
|
|
{ |
| 593 |
|
14 |
qCritical() |
| 594 |
1/2
✓ Branch 1 taken 7 times.
✗ Branch 2 not taken.
|
7 |
<< "A FragmentationRule with no name cannot validate successfully."; |
| 595 |
|
14 |
error_list_p->push_back( |
| 596 |
|
|
"A FragmentationRule with no name cannot validate successfully"); |
| 597 |
|
|
} |
| 598 |
|
|
|
| 599 |
4/6
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|
102 |
if(m_prevCode.isEmpty() && m_currCode.isEmpty() && m_nextCode.isEmpty()) |
| 600 |
|
|
{ |
| 601 |
|
16 |
qCritical() << "A FragmentationRule with not a single Monomer code " |
| 602 |
1/2
✓ Branch 1 taken 8 times.
✗ Branch 2 not taken.
|
8 |
"cannot validate successfully."; |
| 603 |
|
16 |
error_list_p->push_back( |
| 604 |
|
|
"A FragmentationRule with not a single Monomer code cannot validate " |
| 605 |
|
|
"successfully"); |
| 606 |
|
|
} |
| 607 |
|
|
|
| 608 |
2/2
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✓ Branch 1 taken 4 times.
|
102 |
if(mcsp_polChemDef != nullptr && mcsp_polChemDef.get() != nullptr && |
| 609 |
2/2
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✓ Branch 1 taken 4 times.
|
98 |
!m_prevCode.isEmpty()) |
| 610 |
|
|
{ |
| 611 |
2/4
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✗ Branch 2 not taken.
✗ Branch 3 not taken.
✓ Branch 4 taken 94 times.
|
188 |
if(mcsp_polChemDef->getMonomerCstSPtrByCode(m_prevCode) == nullptr) |
| 612 |
|
|
{ |
| 613 |
|
✗ |
qCritical() |
| 614 |
|
|
<< "A FragmentationRule with an unknown previous monomer code " |
| 615 |
|
✗ |
"cannot validate successfully."; |
| 616 |
|
✗ |
error_list_p->push_back( |
| 617 |
|
|
"A FragmentationRule with an unknown previous monomer code cannot " |
| 618 |
|
|
"validate " |
| 619 |
|
|
"successfully"); |
| 620 |
|
|
} |
| 621 |
|
|
} |
| 622 |
|
|
|
| 623 |
2/2
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✓ Branch 1 taken 4 times.
|
102 |
if(mcsp_polChemDef != nullptr && mcsp_polChemDef.get() != nullptr && |
| 624 |
2/2
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✓ Branch 1 taken 5 times.
|
98 |
!m_currCode.isEmpty()) |
| 625 |
|
|
{ |
| 626 |
2/4
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✗ Branch 2 not taken.
✗ Branch 3 not taken.
✓ Branch 4 taken 93 times.
|
186 |
if(mcsp_polChemDef->getMonomerCstSPtrByCode(m_currCode) == nullptr) |
| 627 |
|
|
{ |
| 628 |
|
✗ |
qCritical() |
| 629 |
|
|
<< "A FragmentationRule with an unknown current monomer code " |
| 630 |
|
✗ |
"cannot validate successfully."; |
| 631 |
|
✗ |
error_list_p->push_back( |
| 632 |
|
|
"A FragmentationRule with an unknown current monomer code cannot " |
| 633 |
|
|
"validate " |
| 634 |
|
|
"successfully"); |
| 635 |
|
|
} |
| 636 |
|
|
} |
| 637 |
|
|
|
| 638 |
2/2
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✓ Branch 1 taken 4 times.
|
102 |
if(mcsp_polChemDef != nullptr && mcsp_polChemDef.get() != nullptr && |
| 639 |
2/2
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✓ Branch 1 taken 6 times.
|
98 |
!m_nextCode.isEmpty()) |
| 640 |
|
|
{ |
| 641 |
2/4
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✗ Branch 2 not taken.
✗ Branch 3 not taken.
✓ Branch 4 taken 92 times.
|
184 |
if(mcsp_polChemDef->getMonomerCstSPtrByCode(m_nextCode) == nullptr) |
| 642 |
|
|
{ |
| 643 |
|
✗ |
qCritical() |
| 644 |
|
|
<< "A FragmentationRule with an unknown next monomer code " |
| 645 |
|
✗ |
"cannot validate successfully."; |
| 646 |
|
✗ |
error_list_p->push_back( |
| 647 |
|
|
"A FragmentationRule with an unknown next monomer code cannot " |
| 648 |
|
|
"validate " |
| 649 |
|
|
"successfully"); |
| 650 |
|
|
} |
| 651 |
|
|
} |
| 652 |
|
|
|
| 653 |
2/2
✓ Branch 2 taken 11 times.
✓ Branch 3 taken 91 times.
|
102 |
if(m_formula.getActionFormula().isEmpty()) |
| 654 |
|
|
{ |
| 655 |
|
22 |
qCritical() |
| 656 |
|
|
<< "A FragmentationRule with no Formula does not make sense and " |
| 657 |
1/2
✓ Branch 1 taken 11 times.
✗ Branch 2 not taken.
|
11 |
"cannot validate successfully."; |
| 658 |
|
22 |
error_list_p->push_back( |
| 659 |
|
|
"A FragmentationRule with no Formula does not make sense and cannot " |
| 660 |
|
|
"validate " |
| 661 |
|
|
"successfully"); |
| 662 |
|
|
} |
| 663 |
|
|
|
| 664 |
4/4
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✓ Branch 1 taken 4 times.
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✓ Branch 3 taken 91 times.
|
200 |
if(mcsp_polChemDef != nullptr && mcsp_polChemDef.get() != nullptr && |
| 665 |
3/4
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|
200 |
!m_formula.validate(mcsp_polChemDef->getIsotopicDataCstSPtr(), error_list_p)) |
| 666 |
|
|
{ |
| 667 |
|
14 |
qCritical() << "A FragmentationRule with a non-empty invalid Formula " |
| 668 |
1/2
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|
7 |
"cannot validate successfully."; |
| 669 |
|
14 |
error_list_p->push_back( |
| 670 |
|
|
"A FragmentationRule with a non-empty invalid Formula cannot validate " |
| 671 |
|
|
"successfully"); |
| 672 |
|
|
} |
| 673 |
|
|
|
| 674 |
|
102 |
m_isValid = error_list_p->size() > error_count ? false : true; |
| 675 |
|
|
|
| 676 |
|
102 |
return m_isValid; |
| 677 |
|
|
} |
| 678 |
|
|
|
| 679 |
|
|
|
| 680 |
|
|
/*! |
| 681 |
|
|
\brief Returns the validity status of this FragmentationRule. |
| 682 |
|
|
*/ |
| 683 |
|
|
bool |
| 684 |
|
11 |
FragmentationRule::isValid() const |
| 685 |
|
|
{ |
| 686 |
|
11 |
return m_isValid; |
| 687 |
|
|
} |
| 688 |
|
|
|
| 689 |
|
|
//////////////// UTILITIES ///////////////////// |
| 690 |
|
|
/*! |
| 691 |
|
|
\brief Returns a string with the textual representation of this |
| 692 |
|
|
FragmentationRule instance. |
| 693 |
|
|
*/ |
| 694 |
|
|
QString |
| 695 |
|
✗ |
FragmentationRule::toString() const |
| 696 |
|
|
{ |
| 697 |
|
✗ |
QString text = "Fragmentation rule:\n"; |
| 698 |
|
|
|
| 699 |
|
✗ |
text += QString("name: %1 - prev code: %2 - curr code: %3 - next code: %4 - formula: %5 - comment: %6 - is valid? %7\n").arg(m_name).arg(m_prevCode).arg(m_currCode).arg(m_nextCode).arg(m_formula.getActionFormula(/*with_title*/ true)).arg(m_comment).arg(m_isValid ? "true" : "false"); |
| 700 |
|
|
|
| 701 |
|
✗ |
return text; |
| 702 |
|
✗ |
} |
| 703 |
|
|
|
| 704 |
|
|
|
| 705 |
|
|
/*! |
| 706 |
|
|
\brief Parses the FragmentationRule XML \a element. |
| 707 |
|
|
|
| 708 |
|
|
Upon parsing and validation of the parsed data, the member data are updated, |
| 709 |
|
|
thus essentially initializing this FragmentationRule instance. |
| 710 |
|
|
|
| 711 |
|
|
Returns true if parsing and formula validation were successful, false otherwise. |
| 712 |
|
|
*/ |
| 713 |
|
|
bool |
| 714 |
|
6 |
FragmentationRule::renderXmlFgrElement(const QDomElement &element) |
| 715 |
|
|
{ |
| 716 |
|
6 |
QDomElement child; |
| 717 |
|
|
|
| 718 |
|
6 |
bool prevSet = false; |
| 719 |
|
6 |
bool currSet = false; |
| 720 |
|
6 |
bool nextSet = false; |
| 721 |
|
6 |
bool commentSet = false; |
| 722 |
|
|
|
| 723 |
|
|
/* The xml node we are in is structured this way: |
| 724 |
|
|
* |
| 725 |
|
|
* <fgr> |
| 726 |
|
|
* <name>one_rule</name> |
| 727 |
|
|
* <formula>+H2O</formula> |
| 728 |
|
|
* <prev-mnm-code>M</prev-mnm-code> |
| 729 |
|
|
* <this-mnm-code>Y</this-mnm-code> |
| 730 |
|
|
* <next-mnm-code>T</next-mnm-code> |
| 731 |
|
|
* <comment>opt_comment</comment> |
| 732 |
|
|
* </fgr> |
| 733 |
|
|
* |
| 734 |
|
|
* And the element parameter points to the |
| 735 |
|
|
* |
| 736 |
|
|
* <fgr> element tag: |
| 737 |
|
|
* ^ |
| 738 |
|
|
* | |
| 739 |
|
|
* +----- here we are right now. |
| 740 |
|
|
* |
| 741 |
|
|
* Which means that element.tagName() == "fgr" and that |
| 742 |
|
|
* we'll have to go one step down to the first child of the |
| 743 |
|
|
* current node in order to get to the <name> element. |
| 744 |
|
|
* |
| 745 |
|
|
* The DTD: |
| 746 |
|
|
* <!ELEMENT fgr(name, formula, prev-mnm-code?, |
| 747 |
|
|
* this-mnm-code?, next-mnm-code?, comment?)> |
| 748 |
|
|
*/ |
| 749 |
|
|
|
| 750 |
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|
12 |
if(element.tagName() != "fgr") |
| 751 |
|
|
return false; |
| 752 |
|
|
|
| 753 |
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|
12 |
child = element.firstChildElement(); |
| 754 |
|
|
|
| 755 |
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|
12 |
if(child.isNull() || child.tagName() != "name") |
| 756 |
|
|
return false; |
| 757 |
|
|
|
| 758 |
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|
6 |
m_name = child.text(); |
| 759 |
|
|
|
| 760 |
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|
12 |
child = child.nextSiblingElement(); |
| 761 |
|
|
|
| 762 |
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|
12 |
if(child.isNull() || child.tagName() != "formula") |
| 763 |
|
|
return false; |
| 764 |
|
|
|
| 765 |
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|
6 |
if(!m_formula.renderXmlFormulaElement(child)) |
| 766 |
|
|
return false; |
| 767 |
|
|
|
| 768 |
|
|
// Since the following items are not obligatory, we have to while() |
| 769 |
|
|
// until we have no more items... |
| 770 |
|
|
|
| 771 |
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|
12 |
child = child.nextSiblingElement(); |
| 772 |
|
|
|
| 773 |
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|
30 |
while(!child.isNull()) |
| 774 |
|
|
{ |
| 775 |
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|
48 |
if(child.tagName() == "prev-mnm-code") |
| 776 |
|
|
{ |
| 777 |
1/2
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|
6 |
if(prevSet) |
| 778 |
|
|
return false; |
| 779 |
|
|
else |
| 780 |
|
|
{ |
| 781 |
1/2
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|
6 |
m_prevCode = child.text(); |
| 782 |
|
6 |
prevSet = true; |
| 783 |
|
|
} |
| 784 |
|
|
} |
| 785 |
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|
36 |
else if(child.tagName() == "curr-mnm-code") |
| 786 |
|
|
{ |
| 787 |
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|
6 |
if(currSet) |
| 788 |
|
|
return false; |
| 789 |
|
|
else |
| 790 |
|
|
{ |
| 791 |
1/2
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|
6 |
m_currCode = child.text(); |
| 792 |
|
6 |
currSet = true; |
| 793 |
|
|
} |
| 794 |
|
|
} |
| 795 |
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|
24 |
else if(child.tagName() == "next-mnm-code") |
| 796 |
|
|
{ |
| 797 |
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|
6 |
if(nextSet) |
| 798 |
|
|
return false; |
| 799 |
|
|
else |
| 800 |
|
|
{ |
| 801 |
1/2
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|
6 |
m_nextCode = child.text(); |
| 802 |
|
6 |
nextSet = true; |
| 803 |
|
|
} |
| 804 |
|
|
} |
| 805 |
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|
12 |
else if(child.tagName() == "comment") |
| 806 |
|
|
{ |
| 807 |
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|
6 |
if(commentSet) |
| 808 |
|
|
return false; |
| 809 |
|
|
else |
| 810 |
|
|
{ |
| 811 |
1/2
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|
6 |
m_comment = child.text(); |
| 812 |
|
6 |
commentSet = true; |
| 813 |
|
|
} |
| 814 |
|
|
} |
| 815 |
|
|
|
| 816 |
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|
48 |
child = child.nextSiblingElement(); |
| 817 |
|
|
} |
| 818 |
|
|
|
| 819 |
|
6 |
ErrorList error_list; |
| 820 |
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|
6 |
m_isValid = validate(&error_list); |
| 821 |
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|
6 |
if(!m_isValid) |
| 822 |
|
|
{ |
| 823 |
|
✗ |
qCritical() |
| 824 |
|
✗ |
<< "The FragmentationRule rendered from <clr> element is invalid."; |
| 825 |
|
|
} |
| 826 |
|
|
|
| 827 |
|
6 |
return m_isValid; |
| 828 |
|
12 |
} |
| 829 |
|
|
|
| 830 |
|
|
|
| 831 |
|
|
/*! |
| 832 |
|
|
\brief Formats a string suitable to use as an XML element. |
| 833 |
|
|
|
| 834 |
|
|
|
| 835 |
|
|
The string is suitable to be used as an XML element in a polymer chemistry |
| 836 |
|
|
definition file. The typical fragmentation rule element that is generated in |
| 837 |
|
|
this function looks like this: |
| 838 |
|
|
|
| 839 |
|
|
\code |
| 840 |
|
|
<fgr> |
| 841 |
|
|
<name>a-fgr-2</name> |
| 842 |
|
|
<formula>+H100</formula> |
| 843 |
|
|
<prev-mnm-code>F</prev-mnm-code> |
| 844 |
|
|
<curr-mnm-code>D</curr-mnm-code> |
| 845 |
|
|
<next-mnm-code>E</next-mnm-code> |
| 846 |
|
|
<comment>comment here!</comment> |
| 847 |
|
|
</fgr> |
| 848 |
|
|
\endcode |
| 849 |
|
|
|
| 850 |
|
|
The formatting of the XML element takes into account \a offset and \a |
| 851 |
|
|
indent by prepending the string with \a offset * \a indent character substring. |
| 852 |
|
|
|
| 853 |
|
|
\a indent defaults to two spaces. |
| 854 |
|
|
|
| 855 |
|
|
Returns a dynamically allocated string that needs to be freed after use. |
| 856 |
|
|
*/ |
| 857 |
|
|
QString |
| 858 |
|
2 |
FragmentationRule::formatXmlFgrElement(int offset, const QString &indent) |
| 859 |
|
|
{ |
| 860 |
|
|
|
| 861 |
|
2 |
int newOffset; |
| 862 |
|
2 |
int iter = 0; |
| 863 |
|
|
|
| 864 |
|
2 |
QString lead(""); |
| 865 |
|
2 |
QString text; |
| 866 |
|
|
|
| 867 |
|
|
|
| 868 |
|
|
// Prepare the lead. |
| 869 |
|
2 |
newOffset = offset; |
| 870 |
2/2
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|
5 |
while(iter < newOffset) |
| 871 |
|
|
{ |
| 872 |
1/2
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✗ Branch 2 not taken.
|
3 |
lead += indent; |
| 873 |
|
3 |
++iter; |
| 874 |
|
|
} |
| 875 |
|
|
|
| 876 |
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|
4 |
text += QString("%1<fgr>\n").arg(lead); |
| 877 |
|
|
|
| 878 |
|
|
// Prepare the lead. |
| 879 |
|
2 |
++newOffset; |
| 880 |
|
2 |
lead.clear(); |
| 881 |
|
2 |
iter = 0; |
| 882 |
2/2
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|
9 |
while(iter < newOffset) |
| 883 |
|
|
{ |
| 884 |
1/2
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|
5 |
lead += indent; |
| 885 |
|
5 |
++iter; |
| 886 |
|
|
} |
| 887 |
|
|
|
| 888 |
|
|
// Continue with indented elements. |
| 889 |
|
|
|
| 890 |
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|
4 |
text += QString("%1<name>%2</name>\n").arg(lead).arg(m_name); |
| 891 |
|
|
|
| 892 |
1/2
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|
2 |
text += QString("%1<formula>%2</formula>\n") |
| 893 |
1/2
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|
4 |
.arg(lead) |
| 894 |
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|
4 |
.arg(m_formula.getActionFormula()); |
| 895 |
|
|
|
| 896 |
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|
2 |
if(!m_prevCode.isEmpty()) |
| 897 |
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|
2 |
text += QString("%1<prev-mnm-code>%2</prev-mnm-code>\n") |
| 898 |
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|
4 |
.arg(lead) |
| 899 |
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|
6 |
.arg(m_prevCode); |
| 900 |
|
|
|
| 901 |
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|
2 |
if(!m_currCode.isEmpty()) |
| 902 |
1/2
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|
2 |
text += QString("%1<curr-mnm-code>%2</curr-mnm-code>\n") |
| 903 |
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|
4 |
.arg(lead) |
| 904 |
1/2
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|
6 |
.arg(m_currCode); |
| 905 |
|
|
|
| 906 |
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|
2 |
if(!m_nextCode.isEmpty()) |
| 907 |
1/2
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|
2 |
text += QString("%1<next-mnm-code>%2</next-mnm-code>\n") |
| 908 |
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|
4 |
.arg(lead) |
| 909 |
1/2
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|
6 |
.arg(m_nextCode); |
| 910 |
|
|
|
| 911 |
1/2
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|
2 |
if(!m_comment.isEmpty()) |
| 912 |
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|
4 |
text += QString("%1<comment>%2</comment>\n").arg(lead).arg(m_comment); |
| 913 |
|
|
|
| 914 |
|
|
// Prepare the lead. |
| 915 |
|
2 |
--newOffset; |
| 916 |
|
2 |
lead.clear(); |
| 917 |
|
2 |
iter = 0; |
| 918 |
2/2
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✓ Branch 2 taken 2 times.
|
7 |
while(iter < newOffset) |
| 919 |
|
|
{ |
| 920 |
1/2
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✗ Branch 2 not taken.
|
3 |
lead += indent; |
| 921 |
|
3 |
++iter; |
| 922 |
|
|
} |
| 923 |
|
|
|
| 924 |
2/4
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✗ Branch 2 not taken.
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|
4 |
text += QString("%1</fgr>\n").arg(lead); |
| 925 |
|
|
|
| 926 |
|
2 |
return text; |
| 927 |
|
2 |
} |
| 928 |
|
|
|
| 929 |
|
|
} // namespace libXpertMassCore |
| 930 |
|
|
|
| 931 |
|
|
} // namespace MsXpS |
| 932 |
|
|
|