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 CROSS_LINK_HPP
39 #define CROSS_LINK_HPP
40 //#warning "Entering CROSS_LINK_HPP"
41 
42 
43 /////////////////////// Local includes
44 #include "crossLinker.hpp"
45 #include "monomer.hpp"
46 
47 namespace massXpert
48 {
49 
50   class Polymer;
51 
52 
53   enum CrossLinkEncompassed
54     {
55       MXP_CROSS_LINK_ENCOMPASSED_NO = 0,
56       MXP_CROSS_LINK_ENCOMPASSED_PARTIAL = 1,
57       MXP_CROSS_LINK_ENCOMPASSED_FULL = 2,
58     };
59 
60   class CrossLink : public CrossLinker
61   {
62   protected:
63     // We do not own these two monomers and polymer.
64     QPointer<Polymer> mp_polymer;
65     QList<const Monomer *> m_monomerList;
66 
67     QString m_comment;
68 
69   public:
70     CrossLink(const PolChemDef *,
71 	       Polymer *,
72 	       const QString &,
73 	       const QString &,
74 	       const QString & = QString());
75 
76     CrossLink(const CrossLink &);
77 
78     CrossLink(const CrossLinker &,
79 	       Polymer *,
80 	       const QString & = QString());
81 
82     ~CrossLink();
83 
84     bool setMonomerAt(Monomer *, int);
85     bool appendMonomer(const Monomer *);
86     const Monomer *monomerAt(int);
87     bool removeMonomerAt(int);
88 
89     void setPolymer(Polymer *);
90     Polymer *polymer();
91 
92     void setComment(const QString &);
93     const QString &comment()const;
94 
95     virtual bool operator ==(const CrossLink &) const;
96 
97     int populateMonomerList(QString);
98     QList<const Monomer *> *monomerList();
99     int monomerIndexList(QList<int> *);
100     QString monomerIndexText();
101     QString monomerPosText();
102 
103     int involvesMonomer(const Monomer *) const;
104     const Monomer *firstMonomer() const;
105     int encompassedBy(int, int, int *in = 0, int * = 0);
106     int encompassedBy(const CoordinateList &, int *in = 0, int * = 0);
107 
108     int involvedMonomers(QList<Monomer *> *);
109 
110 
111     bool validate();
112 
113     virtual bool calculateMasses();
114 
115     virtual bool accountMasses(double * = 0, double * = 0, int = 1);
116     virtual bool accountMasses(Ponderable *, int = 1);
117 
118     QString *prepareResultsTxtString();
119   };
120 
121 } // namespace massXpert
122 
123 
124 #endif // CROSS_LINK_HPP
125