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
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
|
/**
* \file layout_example1_L3.java
* \brief SBML Layout example
* \author Ralph Gauges
* \author Akiya Jouraku
* \author Frank Bergmann (adapted to use libsbml-5 package version)
*
/* Copyright 2004 European Media Laboratories Research gGmbH
*
* This library is free software; you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published
* by the Free Software Foundation; either version 2.1 of the License, or
* any later version.
*
* This library 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. The software and
* documentation provided hereunder is on an "as is" basis, and the
* European Media Laboratories Research gGmbH have no obligations to
* provide maintenance, support, updates, enhancements or modifications.
* In no event shall the European Media Laboratories Research gGmbH be
* liable to any party for direct, indirect, special, incidental or
* consequential damages, including lost profits, arising out of the use of
* this software and its documentation, even if the European Media
* Laboratories Research gGmbH have been advised of the possibility of such
* damage. See the GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this library; if not, write to the Free Software Foundation,
* Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*
* The original code contained here was initially developed by:
*
* Ralph Gaugess
* Bioinformatics Group
* European Media Laboratories Research gGmbH
* Schloss-Wolfsbrunnenweg 31c
* 69118 Heidelberg
* Germany
*
* http://www.eml-research.de/english/Research/BCB/
* mailto:ralph.gauges@eml-r.villa-bosch.de
*
* Contributor(s):
*/
import org.sbml.libsbml.*;
public class layout_example1_L3 {
/**
* @param args
*/
public static void main(String[] args) {
System.loadLibrary("sbmlj");
//
// Creates an SBMLNamespaces object with the given SBML level, version
// package name, package version.
//
// (NOTE) By defualt, the name of package (i.e. "layout") will be used
// if the arugment for the prefix is missing or empty. Thus the argument
// for the prefix can be added as follows:
//
// SBMLNamespaces sbmlns(3,1,"layout",1,"LAYOUT");
//
SBMLNamespaces sbmlns = new SBMLNamespaces (3, 1, "layout", 1);
//
// (NOTES) The above code creating an SBMLNamespaces object can be replaced
// with one of the following other styles.
//
// (1) Creates an SBMLNamespace object with a SBML core namespace and then
// adds a layout package namespace to the object.
//
// SBMLNamespaces sbmlns(3,1);
// sbmlns.addPkgNamespace("layout",1);
//
// OR
//
// SBMLNamespaces sbmlns(3,1);
// sbmlns.addNamespace(LayoutExtension::XmlnsL3V1V1,"layout");
//
// (2) Creates a LayoutPkgNamespaces object (SBMLNamespace derived class for
// layout package. The class is basically used for createing an SBase derived
// objects belonging to the layout package) with the given SBML level, version,
// and package version
//
// LayoutPkgNamespaces sbmlns(3,1,1);
//
// create the document
SBMLDocument document = new SBMLDocument (sbmlns);
// set the "required" attribute of layout package to "true"
document.setPkgRequired ("layout", true);
// create the Model
Model model = document.createModel ();
model.setId ("TestModel");
document.setModel (model);
// create the Compartment
Compartment compartment = model.createCompartment ();
compartment.setId ("Compartment_1");
compartment.setConstant (true);
// create the Species
Species species1 = model.createSpecies ();
species1.setId ("Species_1");
species1.setCompartment (compartment.getId ());
species1.setHasOnlySubstanceUnits (false);
species1.setBoundaryCondition (false);
species1.setConstant (false);
Species species2 = model.createSpecies ();
species2.setId ("Species_2");
species2.setCompartment (compartment.getId ());
species2.setHasOnlySubstanceUnits (false);
species2.setBoundaryCondition (false);
species2.setConstant (false);
// create the Reactions
Reaction reaction1 = model.createReaction ();
reaction1.setId ("Reaction_1");
reaction1.setReversible (false);
reaction1.setFast (false);
SpeciesReference reference1 = reaction1.createReactant ();
reference1.setSpecies (species1.getId ());
reference1.setId ("SpeciesReference_1");
reference1.setConstant (false);
SpeciesReference reference2 = reaction1.createProduct ();
reference2.setSpecies (species2.getId ());
reference2.setId ("SpeciesReference_2");
reference2.setConstant (false);
Reaction reaction2 = model.createReaction ();
reaction2.setId ("Reaction_2");
reaction2.setReversible (false);
reaction2.setFast (false);
SpeciesReference reference3 = reaction2.createReactant ();
reference3.setSpecies (species2.getId ());
reference3.setId ("SpeciesReference_3");
reference3.setConstant (false);
SpeciesReference reference4 = reaction2.createProduct ();
reference4.setSpecies (species1.getId ());
reference4.setId ("SpeciesReference_4");
reference4.setConstant (false);
// create the Layout
//
// set the LayoutPkgNamespaces for Level 3 Version1 Layout Version 1
//
LayoutPkgNamespaces layoutns = new LayoutPkgNamespaces (3, 1, 1);
//
// Get a LayoutModelPlugin object plugged in the model object.
//
// The type of the returned value of SBase::getPlugin() function is SBasePlugin, and
// thus the value needs to be casted for the corresponding derived class.
//
SBasePlugin basePlugin = (model.getPlugin ("layout"));
LayoutModelPlugin mplugin = (LayoutModelPlugin)basePlugin;
if (mplugin == null) {
System.err.println("[Fatal Error] Layout Extension Level "
+ layoutns.getLevel () + " Version "
+ layoutns.getVersion () + " package version "
+ layoutns.getPackageVersion () + " is not registered.");
System.exit(1);
}
//
// Creates a Layout object via LayoutModelPlugin object.
//
Layout layout = mplugin.createLayout ();
layout.setId ("Layout_1");
Dimensions dim = new Dimensions (layoutns, 400.0, 220.0);
layout.setDimensions (dim);
// create the CompartmentGlyph
CompartmentGlyph compartmentGlyph = layout.createCompartmentGlyph ();
compartmentGlyph.setId ("CompartmentGlyph_1");
compartmentGlyph.setCompartmentId (compartment.getId ());
BoundingBox bb = new BoundingBox (layoutns, "bb1", 5, 5, 390, 210);
compartmentGlyph.setBoundingBox (bb);
// create the SpeciesGlyphs
SpeciesGlyph speciesGlyph1 = layout.createSpeciesGlyph ();
speciesGlyph1.setId ("SpeciesGlyph_1");
speciesGlyph1.setSpeciesId (species1.getId ());
bb = new BoundingBox (layoutns, "bb2", 80, 26, 240, 24);
speciesGlyph1.setBoundingBox (bb);
TextGlyph textGlyph1 = layout.createTextGlyph ();
textGlyph1.setId ("TextGlyph_01");
bb = new BoundingBox (layoutns, "bbA", 92, 26, 228, 24);
textGlyph1.setBoundingBox (bb);
textGlyph1.setOriginOfTextId (speciesGlyph1.getId ());
textGlyph1.setGraphicalObjectId (speciesGlyph1.getId ());
SpeciesGlyph speciesGlyph2 = layout.createSpeciesGlyph ();
speciesGlyph2.setId ("SpeciesGlyph_2");
speciesGlyph2.setSpeciesId (species2.getId ());
bb = new BoundingBox (layoutns, "bb3", 80, 170, 240, 24);
speciesGlyph2.setBoundingBox (bb);
TextGlyph textGlyph2 = layout.createTextGlyph ();
textGlyph2.setId ("TextGlyph_02");
bb = new BoundingBox (layoutns, "bbB", 92, 170, 228, 24);
textGlyph2.setBoundingBox (bb);
textGlyph2.setOriginOfTextId (speciesGlyph2.getId ());
textGlyph2.setGraphicalObjectId (speciesGlyph2.getId ());
// create the ReactionGlyphs
ReactionGlyph reactionGlyph1 = layout.createReactionGlyph ();
reactionGlyph1.setId ("ReactionGlyph_1");
reactionGlyph1.setReactionId (reaction1.getId ());
Curve reactionCurve1 = reactionGlyph1.getCurve ();
LineSegment ls = reactionCurve1.createLineSegment ();
Point p = new Point (layoutns, 165, 105);
ls.setStart (p);
p = new Point (layoutns, 165, 115);
ls.setEnd (p);
ReactionGlyph reactionGlyph2 = layout.createReactionGlyph ();
reactionGlyph2.setId ("ReactionGlyph_1");
reactionGlyph2.setReactionId (reaction2.getId ());
Curve reactionCurve2 = reactionGlyph2.getCurve ();
ls = reactionCurve2.createLineSegment ();
p = new Point (layoutns, 235, 105);
ls.setStart (p);
p = new Point (layoutns, 235, 115);
ls.setEnd (p);
// add the SpeciesReferenceGlyphs
SpeciesReferenceGlyph speciesReferenceGlyph1 = reactionGlyph1.createSpeciesReferenceGlyph ();
speciesReferenceGlyph1.setId ("SpeciesReferenceGlyph_1");
speciesReferenceGlyph1.setSpeciesGlyphId (speciesGlyph1.getId ());
speciesReferenceGlyph1.setSpeciesReferenceId (reference1.getId ());
speciesReferenceGlyph1.setRole (libsbml.SPECIES_ROLE_SUBSTRATE);
Curve speciesReferenceCurve1 = speciesReferenceGlyph1.getCurve ();
CubicBezier cb = speciesReferenceCurve1.createCubicBezier ();
p = new Point (layoutns, 165, 105);
cb.setStart (p);
p = new Point (layoutns, 165, 90);
cb.setBasePoint1 (p);
p = new Point (layoutns, 165, 90);
cb.setBasePoint2 (p);
p = new Point (layoutns, 195, 60);
cb.setEnd (p);
SpeciesReferenceGlyph speciesReferenceGlyph2 = reactionGlyph1.createSpeciesReferenceGlyph ();
speciesReferenceGlyph2.setId ("SpeciesReferenceGlyph_2");
speciesReferenceGlyph2.setSpeciesGlyphId (speciesGlyph2.getId ());
speciesReferenceGlyph2.setSpeciesReferenceId (reference2.getId ());
speciesReferenceGlyph2.setRole (libsbml.SPECIES_ROLE_PRODUCT);
Curve speciesReferenceCurve2 = speciesReferenceGlyph2.getCurve ();
cb = speciesReferenceCurve2.createCubicBezier ();
p = new Point (layoutns, 165, 115);
cb.setStart (p);
p = new Point (layoutns, 165, 130);
cb.setBasePoint1 (p);
p = new Point (layoutns, 165, 130);
cb.setBasePoint2 (p);
p = new Point (layoutns, 195, 160);
cb.setEnd (p);
SpeciesReferenceGlyph speciesReferenceGlyph3 = reactionGlyph2.createSpeciesReferenceGlyph ();
speciesReferenceGlyph3.setId ("SpeciesReferenceGlyph_3");
speciesReferenceGlyph3.setSpeciesGlyphId (speciesGlyph2.getId ());
speciesReferenceGlyph3.setSpeciesReferenceId (reference3.getId ());
speciesReferenceGlyph3.setRole (libsbml.SPECIES_ROLE_SUBSTRATE);
Curve speciesReferenceCurve3 = speciesReferenceGlyph3.getCurve ();
cb = speciesReferenceCurve3.createCubicBezier ();
p = new Point (layoutns, 235, 115);
cb.setStart (p);
p = new Point (layoutns, 235, 130);
cb.setBasePoint1 (p);
p = new Point (layoutns, 235, 130);
cb.setBasePoint2 (p);
p = new Point (layoutns, 205, 160);
cb.setEnd (p);
SpeciesReferenceGlyph speciesReferenceGlyph4 = reactionGlyph2.createSpeciesReferenceGlyph ();
speciesReferenceGlyph4.setId ("SpeciesReferenceGlyph_4");
speciesReferenceGlyph4.setSpeciesGlyphId (speciesGlyph1.getId ());
speciesReferenceGlyph4.setSpeciesReferenceId (reference4.getId ());
speciesReferenceGlyph4.setRole (libsbml.SPECIES_ROLE_PRODUCT);
Curve speciesReferenceCurve4 = speciesReferenceGlyph4.getCurve ();
cb = speciesReferenceCurve4.createCubicBezier ();
p = new Point (layoutns, 235, 105);
cb.setStart (p);
p = new Point (layoutns, 235, 90);
cb.setBasePoint1 (p);
p = new Point (layoutns, 235, 90);
cb.setBasePoint2 (p);
p = new Point (layoutns, 205, 60);
cb.setEnd (p);
libsbml.writeSBML (document, "layout_example1_L3-java.xml");
}
}
|
