1 /* massXpert - the true massist's program. 2 -------------------------------------- 3 Copyright(C) 2006,2007 Filippo Rusconi 4 5 http://www.massxpert.org/massXpert 6 7 This file is part of the massXpert project. 8 9 The massxpert project is the successor to the "GNU polyxmass" 10 project that is an official GNU project package(see 11 www.gnu.org). The massXpert project is not endorsed by the GNU 12 project, although it is released ---in its entirety--- under the 13 GNU General Public License. A huge part of the code in massXpert 14 is actually a C++ rewrite of code in GNU polyxmass. As such 15 massXpert was started at the Centre National de la Recherche 16 Scientifique(FRANCE), that granted me the formal authorization to 17 publish it under this Free Software License. 18 19 This software is free software; you can redistribute it and/or 20 modify it under the terms of the GNU General Public 21 License version 3, as published by the Free Software Foundation. 22 23 24 This software is distributed in the hope that it will be useful, 25 but WITHOUT ANY WARRANTY; without even the implied warranty of 26 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 27 General Public License for more details. 28 29 You should have received a copy of the GNU General Public License 30 along with this software; if not, write to the 31 32 Free Software Foundation, Inc., 33 34 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA. 35 */ 36 37 38 #ifndef FRAGMENTER_HPP 39 #define FRAGMENTER_HPP 40 41 42 /////////////////////// Local includes 43 #include "fragSpec.hpp" 44 #include "fragOptions.hpp" 45 #include "calcOptions.hpp" 46 #include "polymer.hpp" 47 #include "ionizeRule.hpp" 48 #include "oligomerList.hpp" 49 #include "crossLinkedRegion.hpp" 50 51 namespace massXpert 52 { 53 54 class Fragmenter 55 { 56 private: 57 const QPointer<Polymer> mp_polymer; 58 const PolChemDef *mp_polChemDef; 59 QList<FragOptions *> m_fragOptionList; 60 CalcOptions m_calcOptions; 61 IonizeRule m_ionizeRule; 62 63 // Pointer to an oligomer list which WE DO NOT OWN. 64 OligomerList *mp_oligomerList; 65 66 // A list of CrossLinkedRegion instances that we compute in case 67 // there are cross-links in the fragmented sequence. 68 QList<CrossLinkedRegion *> m_crossLinkedRegionList; 69 70 71 public: 72 Fragmenter(Polymer *, const PolChemDef *, 73 const QList<FragOptions *> &fragOptionList, 74 const CalcOptions &, const IonizeRule &); 75 76 Fragmenter(const Fragmenter &); 77 ~Fragmenter(); 78 79 void addFragOptions(FragOptions *); 80 81 void setOligomerList(OligomerList *); 82 OligomerList * oligomerList(); 83 84 bool fragment(); 85 int fragmentEndNone(FragOptions &); 86 int fragmentEndLeft(FragOptions &); 87 int fragmentEndRight(FragOptions &); 88 89 bool accountFragRule(FragRule *, bool, int, int, Ponderable *); 90 int accountFormulas(OligomerList *, FragOptions &, QString, int); 91 OligomerList *accountIonizationLevels(OligomerList *, FragOptions &); 92 93 void emptyOligomerList(); 94 }; 95 96 } // namespace massXpert 97 98 99 #endif // FRAGMENTER_HPP 100