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
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
|
/* Copyright (C) 2006-2010 Joan Queralt Molina
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* This program 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 program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*
*/
package biogenesis;
import java.awt.Color;
import java.io.File;
import java.io.IOException;
import java.io.PrintStream;
import java.util.ArrayList;
import java.util.List;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.xml.sax.ErrorHandler;
import org.xml.sax.SAXException;
import org.xml.sax.SAXParseException;
public class BioXMLParser implements ErrorHandler {
protected DocumentBuilder builder = null;
protected Document doc = null;
public BioXMLParser() {
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
factory.setValidating(true);
try {
builder = factory.newDocumentBuilder();
builder.setErrorHandler(this);
} catch (ParserConfigurationException e) {
e.printStackTrace();
}
}
public static void writeGeneticCode(PrintStream ps, GeneticCode geneticCode) {
ps.println("<?xml version=\"1.0\" encoding=\"UTF-8\"?>"); //$NON-NLS-1$
ps.println("<!DOCTYPE genetic_code ["); //$NON-NLS-1$
ps.println("<!ELEMENT genetic_code (gene+)>"); //$NON-NLS-1$
ps.println("<!ATTLIST genetic_code symmetry (1|2|3|4|5|6|7|8) #REQUIRED>"); //$NON-NLS-1$
ps.println("<!ATTLIST genetic_code mirror (yes|no) #REQUIRED>"); //$NON-NLS-1$
ps.println("<!ATTLIST genetic_code disperse (yes|no) #REQUIRED>"); //$NON-NLS-1$
ps.println("<!ELEMENT gene EMPTY>"); //$NON-NLS-1$
ps.println("<!ATTLIST gene length CDATA #REQUIRED>"); //$NON-NLS-1$
ps.println("<!ATTLIST gene theta CDATA #REQUIRED>"); //$NON-NLS-1$
ps.println("<!ATTLIST gene color (red|green|blue|cyan|yellow|gray|white) #REQUIRED>"); //$NON-NLS-1$
ps.println("]>"); //$NON-NLS-1$
ps.println("<genetic_code symmetry=\""+Integer.toString(geneticCode.getSymmetry())+ //$NON-NLS-1$
"\" mirror=\""+(geneticCode.getMirror()==0?"no":"yes")+ //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
"\" disperse=\""+(geneticCode.getDisperseChildren()?"yes":"no")+ //$NON-NLS-1$//$NON-NLS-2$ //$NON-NLS-3$
"\">"); //$NON-NLS-1$
for (int i=0; i<geneticCode.getNGenes(); i++)
writeGene(ps,geneticCode.getGene(i));
ps.println("</genetic_code>"); //$NON-NLS-1$
}
public static void writeGene(PrintStream ps, Gene gene) {
ps.println("\t<gene length=\""+Double.toString(gene.getLength())+"\" theta=\""+ //$NON-NLS-1$ //$NON-NLS-2$
Double.toString(gene.getTheta())+"\" color=\""+ //$NON-NLS-1$
colorToString(gene.getColor())+"\" />"); //$NON-NLS-1$
}
public GeneticCode parseGeneticCode(File f) throws SAXException, IOException {
int symmetry, mirror;
boolean disperse;
List<Gene> genes = new ArrayList<Gene>();
String s;
doc = builder.parse(f);
Element geneticCode = doc.getDocumentElement();
if (geneticCode.getNodeName().equals("genetic_code")) { //$NON-NLS-1$
s = geneticCode.getAttribute("symmetry"); //$NON-NLS-1$
try {
symmetry = Integer.parseInt(s); //$NON-NLS-1$
} catch (NumberFormatException e) {
throw new SAXException("Symmetry has not an allowed value."); //$NON-NLS-1$
}
if (symmetry<1 || symmetry>8)
throw new SAXException("Symmetry has not an allowed value."); //$NON-NLS-1$
s = geneticCode.getAttribute("mirror"); //$NON-NLS-1$
if (s.equals("yes")) //$NON-NLS-1$
mirror = 1;
else
if (s.equals("no")) //$NON-NLS-1$
mirror = 0;
else
throw new SAXException("Mirror has not an allowed value."); //$NON-NLS-1$
s = geneticCode.getAttribute("disperse"); //$NON-NLS-1$
if (s.equals("yes")) //$NON-NLS-1$
disperse = true;
else
if (s.equals("no")) //$NON-NLS-1$
disperse = false;
else
throw new SAXException("Disperse has not an allowed value."); //$NON-NLS-1$
Node gene = geneticCode.getFirstChild();
gene = getNextElement(gene);
while (gene != null) {
genes.add(parseGene((Element)gene));
gene = getNextElement(gene.getNextSibling());
}
return new GeneticCode(genes, symmetry, mirror, disperse);
}
throw new SAXException("This file does not contain a genetic_code."); //$NON-NLS-1$
}
private static Node getNextElement(Node n) {
while (n != null && n.getNodeType() != Node.ELEMENT_NODE)
n = n.getNextSibling();
return n;
}
public Gene parseGene(Element gene) throws SAXException {
double length, theta;
Color color;
if (gene.getNodeName().equals("gene")) { //$NON-NLS-1$
try {
length = Double.parseDouble(gene.getAttribute("length")); //$NON-NLS-1$
theta = Double.parseDouble(gene.getAttribute("theta")); //$NON-NLS-1$
} catch (NumberFormatException e) {
throw new SAXException("Attributes length and theta do not exist or have not an allowed value."); //$NON-NLS-1$
}
try {
color = stringToColor(gene.getAttribute("color")); //$NON-NLS-1$
} catch (IllegalArgumentException e) {
throw new SAXException("Attribute color does not exist or has not an allowed value."); //$NON-NLS-1$
}
return new Gene(length,theta,color);
}
throw new SAXException("Parse error. "+gene.getNodeName()+" found but gene expected."); //$NON-NLS-1$//$NON-NLS-2$
}
private static Color stringToColor(String s) throws IllegalArgumentException {
if (s.equals("green")) return Color.GREEN; //$NON-NLS-1$
if (s.equals("red")) return Color.RED; //$NON-NLS-1$
if (s.equals("blue")) return Color.BLUE; //$NON-NLS-1$
if (s.equals("cyan")) return Color.CYAN; //$NON-NLS-1$
if (s.equals("gray")) return Color.GRAY; //$NON-NLS-1$
if (s.equals("white")) return Color.WHITE; //$NON-NLS-1$
if (s.equals("yellow")) return Color.YELLOW; //$NON-NLS-1$
throw new IllegalArgumentException();
}
private static String colorToString(Color c) {
if (c.equals(Color.RED)) return "red"; //$NON-NLS-1$
if (c.equals(Color.GREEN)) return "green"; //$NON-NLS-1$
if (c.equals(Color.BLUE)) return "blue"; //$NON-NLS-1$
if (c.equals(Color.CYAN)) return "cyan"; //$NON-NLS-1$
if (c.equals(Color.WHITE)) return "white"; //$NON-NLS-1$
if (c.equals(Color.GRAY)) return "gray"; //$NON-NLS-1$
if (c.equals(Color.YELLOW)) return "yellow"; //$NON-NLS-1$
return ""; //$NON-NLS-1$
}
public void warning(SAXParseException arg0) throws SAXException {
throw new SAXException(arg0.getMessage());
}
public void error(SAXParseException arg0) throws SAXException {
throw new SAXException(arg0.getMessage());
}
public void fatalError(SAXParseException arg0) throws SAXException {
throw new SAXException(arg0.getMessage());
}
}
|
