1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
|
/* massXpert - the true massist's program.
--------------------------------------
Copyright(C) 2006,2007 Filippo Rusconi
http://www.massxpert.org/massXpert
This file is part of the massXpert project.
The massxpert project is the successor to the "GNU polyxmass"
project that is an official GNU project package(see
www.gnu.org). The massXpert project is not endorsed by the GNU
project, although it is released ---in its entirety--- under the
GNU General Public License. A huge part of the code in massXpert
is actually a C++ rewrite of code in GNU polyxmass. As such
massXpert was started at the Centre National de la Recherche
Scientifique(FRANCE), that granted me the formal authorization to
publish it under this Free Software License.
This software is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public
License version 3, as published by the Free Software Foundation.
This software is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
General Public License for more details.
You should have received a copy of the GNU General Public License
along with this software; if not, write to the
Free Software Foundation, Inc.,
51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA.
*/
/////////////////////// Local includes
#include "chemicalGroupRule.hpp"
namespace massXpert
{
ChemicalGroupRule::ChemicalGroupRule(QString entity, QString name,
int outcome)
: m_entity(entity), m_name(name), m_outcome(outcome)
{
Q_ASSERT(m_outcome == MXP_CHEMGROUP_RULE_LOST ||
m_outcome == MXP_CHEMGROUP_RULE_PRESERVED);
}
void
ChemicalGroupRule::setEntity(QString entity)
{
m_entity = entity;
}
QString
ChemicalGroupRule::entity()
{
return m_entity;
}
void
ChemicalGroupRule::setName(QString name)
{
m_name = name;
}
QString
ChemicalGroupRule::name()
{
return m_name;
}
void
ChemicalGroupRule::setOutcome(int outcome)
{
m_outcome = outcome;
}
int
ChemicalGroupRule::outcome()
{
return m_outcome;
}
bool
ChemicalGroupRule::renderXmlElement(const QDomElement &element)
{
QDomElement child;
// In an acidobasic definition file, the following xml structure
// is encountered:
//
//
// <mnmchemgroup>
// <name>N-term NH2</name>
// <pka>9.6</pka>
// <acidcharged>TRUE</acidcharged>
// <polrule>left_trapped</polrule>
// <chemgrouprule>
// <entity>LE_PLM_MODIF</entity>
// <name>Acetylation</name>
// <outcome>LOST</outcome>
// </chemgrouprule>
//
// The relevant DTD line is:
// <!ELEMENT chemgrouprule(entity,name,outcome)>
// And the element the parameter points to is:
// <chemgrouprule>
// Which means that element.tagName() == "chemgrouprule" and that we'll
// have to go one step down to the first child of the current node
// in order to get to the <entity> element.
if (element.tagName() != "chemgrouprule")
return false;
child = element.firstChildElement("entity");
if (child.isNull())
return false;
m_entity = child.text();
child = child.nextSiblingElement();
if (child.isNull() || child.tagName() != "name")
return false;
m_name = child.text();
child = child.nextSiblingElement();
if (child.isNull() || child.tagName() != "outcome")
return false;
if (child.text() == "LOST")
m_outcome = MXP_CHEMGROUP_RULE_LOST;
else if (child.text() == "PRESERVED")
m_outcome = MXP_CHEMGROUP_RULE_PRESERVED;
else
return false;
return true;
}
} // namespace massXpert
|
