1 /**
2 * Filename : TestRenderWriting.cpp
3 * Description : Unit tests for writing render information in the
4 * context of a complete model with layout.
5 * Organization: University of Heidelberg
6 * Created : 2008-10-24
7 *
8 * Copyright 2008 University of Heidelberg
9 *
10 * This library is free software; you can redistribute it and/or modify it
11 * under the terms of the GNU Lesser General Public License as published
12 * by the Free Software Foundation; either version 2.1 of the License, or
13 * any later version.
14 *
15 * This library is distributed in the hope that it will be useful, but
16 * WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
17 * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
18 * documentation provided hereunder is on an "as is" basis, and the
19 * European Media Laboratories Research gGmbH have no obligations to
20 * provide maintenance, support, updates, enhancements or modifications.
21 * In no event shall the European Media Laboratories Research gGmbH be
22 * liable to any party for direct, indirect, special, incidental or
23 * consequential damages, including lost profits, arising out of the use of
24 * this software and its documentation, even if the European Media
25 * Laboratories Research gGmbH have been advised of the possibility of such
26 * damage. See the GNU Lesser General Public License for more details.
27 *
28 * You should have received a copy of the GNU Lesser General Public License
29 * along with this library; if not, write to the Free Software Foundation,
30 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
31 *
32 * The original code contained here was initially developed by:
33 *
34 * Ralph Gauges
35 * Group for Modelling of Biological Systems
36 * University of Heidelberg
37 * Im Neuenheimer Feld 267
38 * 69120 Heidelberg
39 * Germany
40 *
41 * http://otto.bioquant.uni-heidelberg.de
42 * mailto:ralph.gauges@bioquant.uni-heidelberg.de
43 *
44 * Contributor(s):
45 */
46
47 #include <sbml/common/common.h>
48 #include <sbml/common/extern.h>
49
50 #include <sbml/SBMLReader.h>
51 #include <sbml/SBMLWriter.h>
52 #include <sbml/SBMLDocument.h>
53 #include <sbml/Model.h>
54 #include <sbml/packages/layout/sbml/test/utility.h>
55 #include <sbml/packages/layout/extension/LayoutModelPlugin.h>
56 #include <sbml/packages/layout/sbml/Layout.h>
57 #include <sbml/packages/layout/sbml/Point.h>
58 #include <sbml/packages/layout/sbml/LineSegment.h>
59 #include <sbml/packages/layout/sbml/CubicBezier.h>
60 #include <sbml/packages/layout/sbml/Curve.h>
61
62 #include <sbml/packages/render/extension/RenderLayoutPlugin.h>
63 #include <sbml/packages/render/extension/RenderListOfLayoutsPlugin.h>
64 #include <sbml/packages/render/extension/RenderGraphicalObjectPlugin.h>
65 #include <sbml/packages/render/sbml/GlobalRenderInformation.h>
66 #include <sbml/packages/render/sbml/LocalRenderInformation.h>
67 #include <sbml/packages/render/sbml/ColorDefinition.h>
68 #include <sbml/packages/render/sbml/LocalStyle.h>
69 #include <sbml/packages/render/sbml/GlobalStyle.h>
70 #include <sbml/packages/render/sbml/Rectangle.h>
71 #include <sbml/packages/render/sbml/Polygon.h>
72 #include <sbml/packages/render/sbml/Text.h>
73 #include <sbml/packages/render/sbml/RenderPoint.h>
74 #include <sbml/packages/render/sbml/RenderCubicBezier.h>
75
76 #include <check.h>
77 #include <limits>
78
79 #include <string>
80
81 LIBSBML_CPP_NAMESPACE_USE
82
83 BEGIN_C_DECLS
84
85 static RenderPkgNamespaces* renderns;
86 static LayoutPkgNamespaces* layoutns;
87
88 void
RenderWriting_setup(void)89 RenderWriting_setup (void)
90 {
91 renderns = new (std::nothrow) RenderPkgNamespaces();
92 layoutns = new (std::nothrow) LayoutPkgNamespaces();
93 }
94
95 void
RenderWriting_teardown(void)96 RenderWriting_teardown (void)
97 {
98 delete renderns;
99 delete layoutns;
100 }
101
102
START_TEST(test_RenderWriting_write_l2_ojectrole)103 START_TEST (test_RenderWriting_write_l2_ojectrole)
104 {
105 SBMLDocument doc(2, 4);
106 doc.getSBMLNamespaces()->addPackageNamespace("layout", 1);
107 doc.getSBMLNamespaces()->addPackageNamespace("render", 1);
108 Model* model = doc.createModel();
109 model->setId("test");
110 Compartment *comp = model->createCompartment();
111 comp->initDefaults();
112 comp->setId("c1");
113 Species* species = model->createSpecies();
114 species->initDefaults();
115 species->setId("s1");
116 species->setCompartment("c1");
117 LayoutModelPlugin* layoutPlugin = (LayoutModelPlugin*)model->getPlugin("layout");
118 Layout* layout= layoutPlugin ->createLayout();
119 layout->setId("l1");
120 SpeciesGlyph* glyph = layout->createSpeciesGlyph();
121 glyph->initDefaults();
122 glyph->setId("g1");
123
124 RenderGraphicalObjectPlugin* goPlugin = (RenderGraphicalObjectPlugin*)glyph->getPlugin("render");
125 goPlugin->setObjectRole("myRole");
126
127 std::string modelString = writeSBMLToStdString(&doc);
128
129
130 std::string::size_type index = modelString.find("objectRole=\"myRole");
131 fail_unless(index != std::string::npos);
132
133 }
134 END_TEST
135
136
START_TEST(test_RenderWriting_write_model_1)137 START_TEST (test_RenderWriting_write_model_1)
138 {
139 const char* s =
140 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
141 "<sbml xmlns=\"http://www.sbml.org/sbml/level2\" level=\"2\" version=\"1\">\n"
142 " <model id=\"TestModel\">\n"
143 " <annotation>\n"
144 " <listOfLayouts xmlns=\"http://projects.eml.org/bcb/sbml/level2\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\">\n"
145 " <annotation xmlns=\"http://www.sbml.org/sbml/level2\">\n"
146 " <listOfGlobalRenderInformation xmlns=\"http://projects.eml.org/bcb/sbml/render/level2\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\">\n"
147 " <renderInformation id=\"wireFrame\" name=\"wireframe style\" \n"
148 " programName=\"Ralph Gauges\" programVersion=\"1.0\" backgroundColor='#FFFFFFFF'>\n"
149 " <listOfColorDefinitions>\n"
150 " <colorDefinition id=\"white\" value=\"#ffffff\"/>\n"
151 " <colorDefinition id=\"black\" value=\"#000000\"/>\n"
152 " </listOfColorDefinitions>\n"
153 " <listOfStyles>\n"
154 " <style id=\"compartmentGlyphStyle\" typeList=\"COMPARTMENTGLYPH\">\n"
155 " <g stroke=\"black\" stroke-width=\"1\">\n"
156 " <rectangle x=\"0\" y=\"0\" width=\"100%\" height=\"100%\"/>\n"
157 " </g>\n"
158 " </style> \n"
159 " <style id=\"speciesGlyphStyle\" typeList=\"SPECIESGLYPH\">\n"
160 " <g stroke=\"black\" stroke-width=\"1\">\n"
161 " <rectangle x=\"0\" y=\"0\" width=\"100%\" height=\"100%\"/>\n"
162 " </g>\n"
163 " </style>\n"
164 " <style id=\"reactionGlyphStyle\" typeList=\"REACTIONGLYPH SPECIESREFERENCEGLYPH TEXTGLYPH\">\n"
165 " <g stroke=\"black\" stroke-width=\"1\" font-size=\"12\" text-anchor=\"middle\" />\n"
166 " </style>\n"
167 " </listOfStyles>\n"
168 " </renderInformation>\n"
169 " <renderInformation id=\"defaultGrayStyle\" name=\"grayscale style\" \n"
170 " programName=\"Ralph Gauges\" programVersion=\"1.0\" backgroundColor='#FFFFFFFF'>\n"
171 " <listOfColorDefinitions>\n"
172 " <colorDefinition id=\"lightGray\" value=\"#cecece\"/>\n"
173 " <colorDefinition id=\"white\" value=\"#ffffff\"/>\n"
174 " <colorDefinition id=\"black\" value=\"#000000\"/>\n"
175 " <colorDefinition id=\"lightGray2\" value=\"#f0f0f0\" />\n"
176 " <colorDefinition id=\"gray\" value=\"#0b0b0b\" />\n"
177 " </listOfColorDefinitions>\n"
178 " <listOfGradientDefinitions>\n"
179 " <radialGradient id=\"speciesGlyphGradient\">\n"
180 " <stop offset=\"0\" stop-color=\"white\" />\n"
181 " <stop offset=\"100%\" stop-color=\"lightGray\" />\n"
182 " </radialGradient>\n"
183 " </listOfGradientDefinitions>\n"
184 " <listOfLineEndings>\n"
185 " <lineEnding id=\"simpleHead_black\">\n"
186 " <boundingBox xmlns=\"http://projects.eml.org/bcb/sbml/level2\" >\n"
187 " <position x=\"-8\" y=\"-3\" />\n"
188 " <dimensions width=\"10\" height=\"6\" />\n"
189 " </boundingBox>\n"
190 " <g stroke=\"black\" stroke-width=\"1\" fill=\"black\">\n"
191 " <polygon>\n"
192 " <listOfElements>\n"
193 " <element xsi:type=\"RenderPoint\" x=\"0\" y=\"0\"/>\n"
194 " <element xsi:type=\"RenderPoint\" x=\"10\" y=\"3\"/>\n"
195 " <element xsi:type=\"RenderPoint\" x=\"0\" y=\"6\"/>\n"
196 " </listOfElements>\n"
197 " </polygon>\n"
198 " </g>\n"
199 " </lineEnding>\n"
200 " </listOfLineEndings>\n"
201 " <listOfStyles>\n"
202 " <style id=\"compartmentGlyphStyle\" typeList=\"COMPARTMENTGLYPH\">\n"
203 " <g stroke=\"gray\" stroke-width=\"1\">\n"
204 " <rectangle fill=\"lightGray2\" x=\"0\" y=\"0\" width=\"100%\" height=\"100%\" rx=\"5%\" />\n"
205 " </g>\n"
206 " </style> \n"
207 " <style id=\"speciesGlyphStyle\" typeList=\"SPECIESGLYPH\">\n"
208 " <g stroke=\"black\" stroke-width=\"1\">\n"
209 " <rectangle fill=\"speciesGlyphGradient\" x=\"0\" y=\"0\" width=\"100%\" height=\"100%\" rx=\"5%\" />\n"
210 " </g>\n"
211 " </style>\n"
212 " <style id=\"reactionGlyphStyle\" typeList=\"REACTIONGLYPH TEXTGLYPH\">\n"
213 " <g stroke=\"black\" stroke-width=\"1\" font-size=\"12\" text-anchor=\"middle\" />\n"
214 " </style>\n"
215 " <style id=\"reactantSpeciesReferenceGlyphStyle\" roleList=\"product sideproduct sidesubstrate substrate\">\n"
216 " <g stroke=\"#000000\" stroke-width=\"1\" />\n"
217 " </style>\n"
218 " <style id=\"activatorSpeciesReferenceGlyphStyle\" roleList=\"activator\">\n"
219 " <g stroke=\"#000000\" stroke-width=\"1\" />\n"
220 " </style>\n"
221 " <style id=\"modifierSpeciesReferenceGlyphStyle\" roleList=\"modifier\">\n"
222 " <g stroke=\"#000000\" stroke-width=\"1\" />\n"
223 " </style>\n"
224 " <style id=\"inhibitorSpeciesReferenceGlyphStyle\" roleList=\"inhibitor\">\n"
225 " <g stroke=\"#000000\" stroke-width=\"1\" />\n"
226 " </style>\n"
227 " </listOfStyles>\n"
228 " </renderInformation>\n"
229 " <renderInformation id=\"shortGrayStyle\" name=\"modified default style to grayscale\" referenceRenderInformation=\"defaultStyle\" \n"
230 " programName=\"Ralph Gauges\" programVersion=\"1.0\" backgroundColor='#FFFFFFFF'>\n"
231 " <listOfColorDefinitions>\n"
232 " <colorDefinition id=\"lightBlue\" value=\"#cecece\"/>\n"
233 " <colorDefinition id=\"white\" value=\"#ffffff\"/>\n"
234 " <colorDefinition id=\"black\" value=\"#000000\"/>\n"
235 " <colorDefinition id=\"red\" value=\"#000000\"/>\n"
236 " <colorDefinition id=\"green\" value=\"#000000\"/>\n"
237 " <colorDefinition id=\"blue\" value=\"#000000\"/>\n"
238 " <colorDefinition id=\"lightYellow\" value=\"#f0f0f0\" />\n"
239 " <colorDefinition id=\"darkGreen\" value=\"#0b0b0b\" />\n"
240 " </listOfColorDefinitions>\n"
241 " </renderInformation>\n"
242 " <renderInformation id=\"defaultStyle\" name=\"default style\" \n"
243 " programName=\"Ralph Gauges\" programVersion=\"1.0\" backgroundColor='#FFFFFFFF'>\n"
244 " <listOfColorDefinitions>\n"
245 " <colorDefinition id=\"lightBlue\" value=\"#add8e6\"/>\n"
246 " <colorDefinition id=\"white\" value=\"#ffffff\"/>\n"
247 " <colorDefinition id=\"black\" value=\"#000000\"/>\n"
248 " <colorDefinition id=\"red\" value=\"#ff0000\"/>\n"
249 " <colorDefinition id=\"green\" value=\"#00ff00\"/>\n"
250 " <colorDefinition id=\"blue\" value=\"#0000ff\"/>\n"
251 " <colorDefinition id=\"lightYellow\" value=\"#ffffd1\" />\n"
252 " <colorDefinition id=\"darkGreen\" value=\"#002000\" />\n"
253 " </listOfColorDefinitions>\n"
254 " <listOfGradientDefinitions>\n"
255 " <radialGradient id=\"speciesGlyphGradient\">\n"
256 " <stop offset=\"0\" stop-color=\"white\" />\n"
257 " <stop offset=\"100%\" stop-color=\"lightBlue\" />\n"
258 " </radialGradient>\n"
259 " </listOfGradientDefinitions>\n"
260 " <listOfLineEndings>\n"
261 " <lineEnding id=\"simpleHead_black\">\n"
262 " <boundingBox xmlns=\"http://projects.eml.org/bcb/sbml/level2\" >\n"
263 " <position x=\"-8\" y=\"-3\" />\n"
264 " <dimensions width=\"10\" height=\"6\" />\n"
265 " </boundingBox>\n"
266 " <g stroke=\"black\" stroke-width=\"1\" fill=\"black\">\n"
267 " <polygon>\n"
268 " <listOfElements>\n"
269 " <element xsi:type=\"RenderPoint\" x=\"0\" y=\"0\"/>\n"
270 " <element xsi:type=\"RenderPoint\" x=\"10\" y=\"3\"/>\n"
271 " <element xsi:type=\"RenderPoint\" x=\"0\" y=\"6\"/>\n"
272 " </listOfElements>\n"
273 " </polygon>\n"
274 " </g>\n"
275 " </lineEnding>\n"
276 " <lineEnding id=\"simpleHead_red\">\n"
277 " <boundingBox xmlns=\"http://projects.eml.org/bcb/sbml/level2\" >\n"
278 " <position x=\"-8\" y=\"-3\" />\n"
279 " <dimensions width=\"10\" height=\"6\" />\n"
280 " </boundingBox>\n"
281 " <g stroke=\"red\" stroke-width=\"1\" fill=\"red\">\n"
282 " <polygon>\n"
283 " <listOfElements>\n"
284 " <element xsi:type=\"RenderPoint\" x=\"0\" y=\"0\"/>\n"
285 " <element xsi:type=\"RenderPoint\" x=\"10\" y=\"3\"/>\n"
286 " <element xsi:type=\"RenderPoint\" x=\"0\" y=\"6\"/>\n"
287 " </listOfElements>\n"
288 " </polygon>\n"
289 " </g>\n"
290 " </lineEnding>\n"
291 " <lineEnding id=\"simpleHead_green\">\n"
292 " <boundingBox xmlns=\"http://projects.eml.org/bcb/sbml/level2\" >\n"
293 " <position x=\"-8\" y=\"-3\" />\n"
294 " <dimensions width=\"10\" height=\"6\" />\n"
295 " </boundingBox>\n"
296 " <g stroke=\"green\" stroke-width=\"1\" fill=\"green\">\n"
297 " <polygon>\n"
298 " <listOfElements>\n"
299 " <element xsi:type=\"RenderPoint\" x=\"0\" y=\"0\"/>\n"
300 " <element xsi:type=\"RenderPoint\" x=\"10\" y=\"3\"/>\n"
301 " <element xsi:type=\"RenderPoint\" x=\"0\" y=\"6\"/>\n"
302 " </listOfElements>\n"
303 " </polygon>\n"
304 " </g>\n"
305 " </lineEnding>\n"
306 " <lineEnding id=\"simpleHead_blue\">\n"
307 " <boundingBox xmlns=\"http://projects.eml.org/bcb/sbml/level2\" >\n"
308 " <position x=\"-8\" y=\"-3\" />\n"
309 " <dimensions width=\"10\" height=\"6\" />\n"
310 " </boundingBox>\n"
311 " <g stroke=\"blue\" stroke-width=\"1\" fill=\"blue\">\n"
312 " <polygon>\n"
313 " <listOfElements>\n"
314 " <element xsi:type=\"RenderPoint\" x=\"0\" y=\"0\"/>\n"
315 " <element xsi:type=\"RenderPoint\" x=\"10\" y=\"3\"/>\n"
316 " <element xsi:type=\"RenderPoint\" x=\"0\" y=\"6\"/>\n"
317 " </listOfElements>\n"
318 " </polygon>\n"
319 " </g>\n"
320 " </lineEnding>\n"
321 " </listOfLineEndings>\n"
322 " <listOfStyles>\n"
323 " <style id=\"compartmentGlyphStyle\" typeList=\"COMPARTMENTGLYPH\">\n"
324 " <g stroke=\"darkGreen\" stroke-width=\"1\">\n"
325 " <rectangle fill=\"lightYellow\" x=\"0\" y=\"0\" width=\"100%\" height=\"100%\" rx=\"10%\" ry=\"10%\" />\n"
326 " </g>\n"
327 " </style> \n"
328 " <style id=\"speciesGlyphStyle\" typeList=\"SPECIESGLYPH\">\n"
329 " <g stroke=\"black\" stroke-width=\"1\">\n"
330 " <rectangle fill=\"speciesGlyphGradient\" x=\"0\" y=\"0\" width=\"100%\" height=\"100%\" rx=\"5\" ry=\"50%\" />\n"
331 " </g>\n"
332 " </style>\n"
333 " <style id=\"reactionGlyphStyle\" typeList=\"REACTIONGLYPH TEXTGLYPH\">\n"
334 " <g stroke=\"black\" stroke-width=\"1\" font-size=\"12\" text-anchor=\"middle\" />\n"
335 " </style>\n"
336 " <style id=\"reactantSpeciesReferenceGlyphStyle\" roleList=\"product sideproduct sidesubstrate substrate\">\n"
337 " <g stroke=\"#000000\" stroke-width=\"1\" endHead=\"simpleHead_black\" />\n"
338 " </style>\n"
339 " <style id=\"activatorSpeciesReferenceGlyphStyle\" roleList=\"activator\">\n"
340 " <g stroke=\"green\" stroke-width=\"1\" endHead=\"simpleHead_green\" />\n"
341 " </style>\n"
342 " <style id=\"modifierSpeciesReferenceGlyphStyle\" roleList=\"modifier\">\n"
343 " <g stroke=\"blue\" stroke-width=\"1\" endHead=\"simpleHead_blue\" />\n"
344 " </style>\n"
345 " <style id=\"inhibitorSpeciesReferenceGlyphStyle\" roleList=\"inhibitor\">\n"
346 " <g stroke=\"red\" stroke-width=\"1\" endHead=\"simpleHead_red\" />\n"
347 " </style>\n"
348 " </listOfStyles>\n"
349 " </renderInformation>\n"
350 " </listOfGlobalRenderInformation>\n"
351 " </annotation>\n"
352 " <layout id=\"Layout_1\">\n"
353 " <annotation xmlns=\"http://www.sbml.org/sbml/level2\">\n"
354 " <listOfRenderInformation xmlns=\"http://projects.eml.org/bcb/sbml/render/level2\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" versionMajor='2' versionMinor='1' >\n"
355 " <renderInformation id=\"highlightGlucose\" referenceRenderInformation=\"defaultStyle\"\n"
356 " programName=\"Ralph Gauges\" programVersion=\"1.0\" backgroundColor='#FFFFFFFF'>\n"
357 " <listOfColorDefinitions>\n"
358 " <colorDefinition id=\"lightRed\" value=\"#e6add8\"/>\n"
359 " <colorDefinition id=\"white\" value=\"#ffffff\"/>\n"
360 " </listOfColorDefinitions>\n"
361 " <listOfGradientDefinitions>\n"
362 " <radialGradient id=\"highlightedSpeciesGlyphGradient\">\n"
363 " <stop offset=\"0\" stop-color=\"white\" />\n"
364 " <stop offset=\"100%\" stop-color=\"lightRed\" />\n"
365 " </radialGradient>\n"
366 " </listOfGradientDefinitions>\n"
367 " <listOfStyles>\n"
368 " <style id=\"highlightedGlucose\" idList=\"SpeciesGlyph_Glucose\" >\n"
369 " <g stroke=\"black\" stroke-width=\"1\">\n"
370 " <rectangle fill=\"highlightedSpeciesGlyphGradient\" x=\"0\" y=\"0\" width=\"100%\" height=\"100%\" rx=\"5\" ry=\"50%\" />\n"
371 " </g>\n"
372 " </style>\n"
373 " </listOfStyles>\n"
374 " </renderInformation>\n"
375 " </listOfRenderInformation>\n"
376 " </annotation>\n"
377 " <dimensions width=\"2320\" height=\"1000\"/>\n"
378 " <listOfCompartmentGlyphs>\n"
379 " <compartmentGlyph id=\"CompartmentGlyph_1\" compartment=\"Hepatocyte\">\n"
380 " <boundingBox id=\"bb_compartment\">\n"
381 " <position x=\"10\" y=\"10\"/>\n"
382 " <dimensions width=\"2300\" height=\"980\"/>\n"
383 " </boundingBox>\n"
384 " </compartmentGlyph>\n"
385 " <compartmentGlyph id=\"Mito1_Glyph\" compartment=\"Mito_1\">\n"
386 " <boundingBox id=\"bb_mito1\">\n"
387 " <position x=\"100\" y=\"100\"/>\n"
388 " <dimensions width=\"300\" height=\"100\"/>\n"
389 " </boundingBox>\n"
390 " </compartmentGlyph>\n"
391 " <compartmentGlyph id=\"Mito2_Glyph\" compartment=\"Mito_2\">\n"
392 " <boundingBox id=\"bb_mito2\">\n"
393 " <position x=\"200\" y=\"650\"/>\n"
394 " <dimensions width=\"300\" height=\"100\"/>\n"
395 " </boundingBox>\n"
396 " </compartmentGlyph>\n"
397 " <compartmentGlyph id=\"Mito3_Glyph_2\" compartment=\"Mito_3\">\n"
398 " <boundingBox id=\"bb_mito3_2\">\n"
399 " <position x=\"1470\" y=\"30\"/>\n"
400 " <dimensions width=\"820\" height=\"536\"/>\n"
401 " </boundingBox>\n"
402 " </compartmentGlyph>\n"
403 " </listOfCompartmentGlyphs>\n"
404 " <listOfSpeciesGlyphs>\n"
405 " <speciesGlyph id=\"SpeciesGlyph_malate_cyt\" species=\"malate_cyt\">\n"
406 " <boundingBox id=\"bb_sg_malate_cyt\">\n"
407 " <position x=\"580\" y=\"280\"/>\n"
408 " <dimensions width=\"240\" height=\"36\"/>\n"
409 " </boundingBox>\n"
410 " </speciesGlyph>\n"
411 " <speciesGlyph id=\"SpeciesGlyph_oxaloacetate_cyt\" species=\"oxaloacetate_cyt\">\n"
412 " <boundingBox id=\"bb_sg_oxaloacetate_cyt\">\n"
413 " <position x=\"580\" y=\"480\"/>\n"
414 " <dimensions width=\"240\" height=\"36\"/>\n"
415 " </boundingBox>\n"
416 " </speciesGlyph>\n"
417 " <speciesGlyph id=\"SpeciesGlyph_aspartate_cyt\" species=\"aspartate_cyt\">\n"
418 " <boundingBox id=\"bb_sg_aspartate_cyt\">\n"
419 " <position x=\"580\" y=\"680\"/>\n"
420 " <dimensions width=\"240\" height=\"36\"/>\n"
421 " </boundingBox>\n"
422 " </speciesGlyph>\n"
423 " <speciesGlyph id=\"SpeciesGlyph_glutamate_cyt\" species=\"glutamate_cyt\">\n"
424 " <boundingBox id=\"bb_sg_glutamate_cyt\">\n"
425 " <position x=\"800\" y=\"610\"/>\n"
426 " <dimensions width=\"240\" height=\"36\"/>\n"
427 " </boundingBox>\n"
428 " </speciesGlyph>\n"
429 " <speciesGlyph id=\"SpeciesGlyph_aKetoglutarate_cyt\" species=\"aKetoglutarate_cyt\">\n"
430 " <boundingBox id=\"bb_sg_aKetoglutarate_cyt\">\n"
431 " <position x=\"860\" y=\"500\"/>\n"
432 " <dimensions width=\"280\" height=\"36\"/>\n"
433 " </boundingBox>\n"
434 " </speciesGlyph>\n"
435 " <speciesGlyph id=\"SpeciesGlyph_nad_cyt\" species=\"nad_cyt\">\n"
436 " <boundingBox id=\"bb_sg_nad_cyt\">\n"
437 " <position x=\"520\" y=\"350\"/>\n"
438 " <dimensions width=\"100\" height=\"24\"/>\n"
439 " </boundingBox>\n"
440 " </speciesGlyph>\n"
441 " <speciesGlyph id=\"SpeciesGlyph_nadh_cyt\" species=\"nadh_cyt\">\n"
442 " <boundingBox id=\"bb_sg_nadh_cyt\">\n"
443 " <position x=\"520\" y=\"430\"/>\n"
444 " <dimensions width=\"100\" height=\"24\"/>\n"
445 " </boundingBox>\n"
446 " </speciesGlyph>\n"
447 " <speciesGlyph id=\"SpeciesGlyph_h_cyt\" species=\"h_cyt\">\n"
448 " <boundingBox id=\"bb_sg_h_cyt\">\n"
449 " <position x=\"430\" y=\"430\"/>\n"
450 " <dimensions width=\"40\" height=\"24\"/>\n"
451 " </boundingBox>\n"
452 " </speciesGlyph>\n"
453 " <speciesGlyph id=\"SpeciesGlyph_malate_mito3\" species=\"malate_mito3\">\n"
454 " <boundingBox id=\"bb_sg_malate_mito3\">\n"
455 " <position x=\"1850\" y=\"80\"/>\n"
456 " <dimensions width=\"240\" height=\"36\"/>\n"
457 " </boundingBox>\n"
458 " </speciesGlyph>\n"
459 " <speciesGlyph id=\"SpeciesGlyph_oxaloacetate_mito3\" species=\"oxaloacetate_mito3\">\n"
460 " <boundingBox id=\"bb_sg_oxaloacetate_mito3\">\n"
461 " <position x=\"1850\" y=\"280\"/>\n"
462 " <dimensions width=\"240\" height=\"36\"/>\n"
463 " </boundingBox>\n"
464 " </speciesGlyph>\n"
465 " <speciesGlyph id=\"SpeciesGlyph_aspartate_mito3\" species=\"aspartate_mito3\">\n"
466 " <boundingBox id=\"bb_sg_aspartate_mito3\">\n"
467 " <position x=\"1850\" y=\"480\"/>\n"
468 " <dimensions width=\"240\" height=\"36\"/>\n"
469 " </boundingBox>\n"
470 " </speciesGlyph>\n"
471 " <speciesGlyph id=\"SpeciesGlyph_glutamate_mito3\" species=\"glutamate_mito3\">\n"
472 " <boundingBox id=\"bb_sg_glutamate_mito3\">\n"
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909 " <textGlyph id=\"TextGlyph_glutamate_cyt\" graphicalObject=\"SpeciesGlyph_glutamate_cyt\" originOfText=\"glutamate_cyt\">\n"
910 " <boundingBox id=\"bb_tg_glutamate_cyt\">\n"
911 " <position x=\"810\" y=\"610\"/>\n"
912 " <dimensions width=\"220\" height=\"36\"/>\n"
913 " </boundingBox>\n"
914 " </textGlyph>\n"
915 " <textGlyph id=\"TextGlyph_aKetoglutarate_cyt\" graphicalObject=\"SpeciesGlyph_aKetoglutarate_cyt\" originOfText=\"aKetoglutarate_cyt\">\n"
916 " <boundingBox id=\"bb_tg_aKetoglutarate_cyt\">\n"
917 " <position x=\"870\" y=\"500\"/>\n"
918 " <dimensions width=\"260\" height=\"36\"/>\n"
919 " </boundingBox>\n"
920 " </textGlyph>\n"
921 " <textGlyph id=\"TextGlyph_nad_cyt\" graphicalObject=\"SpeciesGlyph_nad_cyt\" originOfText=\"nad_cyt\">\n"
922 " <boundingBox id=\"bb_tg_nad_cyt\">\n"
923 " <position x=\"525\" y=\"350\"/>\n"
924 " <dimensions width=\"80\" height=\"24\"/>\n"
925 " </boundingBox>\n"
926 " </textGlyph>\n"
927 " <textGlyph id=\"TextGlyph_nadh_cyt\" graphicalObject=\"SpeciesGlyph_nadh_cyt\" originOfText=\"nadh_cyt\">\n"
928 " <boundingBox id=\"bb_tg_nadh_cyt\">\n"
929 " <position x=\"525\" y=\"430\"/>\n"
930 " <dimensions width=\"80\" height=\"24\"/>\n"
931 " </boundingBox>\n"
932 " </textGlyph>\n"
933 " <textGlyph id=\"TextGlyph_h_cyt\" graphicalObject=\"SpeciesGlyph_h_cyt\" originOfText=\"h_cyt\">\n"
934 " <boundingBox id=\"bb_tg_h_cyt\">\n"
935 " <position x=\"435\" y=\"430\"/>\n"
936 " <dimensions width=\"30\" height=\"24\"/>\n"
937 " </boundingBox>\n"
938 " </textGlyph>\n"
939 " <textGlyph id=\"tg_rg_malaltedh_cyt\" graphicalObject=\"rg_malatedh_cyt\" originOfText=\"reaction_malatedh_cyt\">\n"
940 " <boundingBox id=\"bb_tg_rg_malaltedh_cyt\">\n"
941 " <position x=\"700\" y=\"385\"/>\n"
942 " <dimensions width=\"210\" height=\"24\"/>\n"
943 " </boundingBox>\n"
944 " </textGlyph>\n"
945 " <textGlyph id=\"tg_rg_aspartateat_cyt\" graphicalObject=\"rg_aspartateat_cyt\" originOfText=\"reaction_aspartateat_cyt\">\n"
946 " <boundingBox id=\"bb_tg_rg_aspartateat_cyt\">\n"
947 " <position x=\"440\" y=\"585\"/>\n"
948 " <dimensions width=\"260\" height=\"24\"/>\n"
949 " </boundingBox>\n"
950 " </textGlyph>\n"
951 " <textGlyph id=\"TextGlyph_malate_mito3\" graphicalObject=\"SpeciesGlyph_malate_mito3\" originOfText=\"malate_mito3\">\n"
952 " <boundingBox id=\"bb_tg_malatate_mito3\">\n"
953 " <position x=\"1860\" y=\"80\"/>\n"
954 " <dimensions width=\"220\" height=\"36\"/>\n"
955 " </boundingBox>\n"
956 " </textGlyph>\n"
957 " <textGlyph id=\"TextGlyph_oxaloacetate_mito3\" graphicalObject=\"SpeciesGlyph_oxaloacetate_mito3\" originOfText=\"oxaloacetate_mito3\">\n"
958 " <boundingBox id=\"bb_tg_oxaloacetate_mito3\">\n"
959 " <position x=\"1860\" y=\"280\"/>\n"
960 " <dimensions width=\"220\" height=\"36\"/>\n"
961 " </boundingBox>\n"
962 " </textGlyph>\n"
963 " <textGlyph id=\"TextGlyph_aspartate_mito3\" graphicalObject=\"SpeciesGlyph_aspartate_mito3\" originOfText=\"aspartate_mito3\">\n"
964 " <boundingBox id=\"bb_tg_aspartate_mito3\">\n"
965 " <position x=\"1860\" y=\"480\"/>\n"
966 " <dimensions width=\"220\" height=\"36\"/>\n"
967 " </boundingBox>\n"
968 " </textGlyph>\n"
969 " <textGlyph id=\"TextGlyph_glutamate_mito3\" graphicalObject=\"SpeciesGlyph_glutamate_mito3\" originOfText=\"glutamate_mito3\">\n"
970 " <boundingBox id=\"bb_tg_glutamate_mito3\">\n"
971 " <position x=\"1560\" y=\"430\"/>\n"
972 " <dimensions width=\"220\" height=\"36\"/>\n"
973 " </boundingBox>\n"
974 " </textGlyph>\n"
975 " <textGlyph id=\"TextGlyph_aKetoglutarate_mito3\" graphicalObject=\"SpeciesGlyph_aKetoglutarate_mito3\" originOfText=\"aKetoglutarate_mito3\">\n"
976 " <boundingBox id=\"bb_tg_aKetoglutarate_mito3\">\n"
977 " <position x=\"1540\" y=\"300\"/>\n"
978 " <dimensions width=\"260\" height=\"36\"/>\n"
979 " </boundingBox>\n"
980 " </textGlyph>\n"
981 " <textGlyph id=\"TextGlyph_nad_mito3\" graphicalObject=\"SpeciesGlyph_nad_mito3\" originOfText=\"nad_mito3\">\n"
982 " <boundingBox id=\"bb_tg_nad_mito3\">\n"
983 " <position x=\"2055\" y=\"150\"/>\n"
984 " <dimensions width=\"80\" height=\"24\"/>\n"
985 " </boundingBox>\n"
986 " </textGlyph>\n"
987 " <textGlyph id=\"TextGlyph_nadh_mito3\" graphicalObject=\"SpeciesGlyph_nadh_mito3\" originOfText=\"nadh_mito3\">\n"
988 " <boundingBox id=\"bb_tg_nadh_mito3\">\n"
989 " <position x=\"2055\" y=\"230\"/>\n"
990 " <dimensions width=\"80\" height=\"24\"/>\n"
991 " </boundingBox>\n"
992 " </textGlyph>\n"
993 " <textGlyph id=\"TextGlyph_h_mito3\" graphicalObject=\"SpeciesGlyph_h_mito3\" originOfText=\"h_mito3\">\n"
994 " <boundingBox id=\"bb_tg_h_mito3\">\n"
995 " <position x=\"2205\" y=\"230\"/>\n"
996 " <dimensions width=\"30\" height=\"24\"/>\n"
997 " </boundingBox>\n"
998 " </textGlyph>\n"
999 " <textGlyph id=\"tg_rg_malatedh_mito3\" graphicalObject=\"rg_malatedh_mito3\" originOfText=\"reaction_malatedh_mito3\">\n"
1000 " <boundingBox id=\"bb_tg_rg_malatedh_mito3\">\n"
1001 " <position x=\"1740\" y=\"185\"/>\n"
1002 " <dimensions width=\"220\" height=\"24\"/>\n"
1003 " </boundingBox>\n"
1004 " </textGlyph>\n"
1005 " <textGlyph id=\"tg_rg_aspartateat_mito3\" graphicalObject=\"rg_aspartateat_mito3\" originOfText=\"reaction_aspartateat_mito3\">\n"
1006 " <boundingBox id=\"bb_tg_rg_aspartateat_mito3\">\n"
1007 " <position x=\"1970\" y=\"385\"/>\n"
1008 " <dimensions width=\"260\" height=\"24\"/>\n"
1009 " </boundingBox>\n"
1010 " </textGlyph>\n"
1011 " <textGlyph id=\"tg_rg_aspartateCarrier\" graphicalObject=\"rg_aspartateCarrier\" originOfText=\"aspartateCarrier\">\n"
1012 " <boundingBox id=\"bb_tg_rg_aspartateCarrier\">\n"
1013 " <position x=\"1380\" y=\"500\"/>\n"
1014 " <dimensions width=\"160\" height=\"24\"/>\n"
1015 " </boundingBox>\n"
1016 " </textGlyph>\n"
1017 " <textGlyph id=\"tg_rg_malateCarrier\" graphicalObject=\"rg_malateCarrier\" originOfText=\"malateCarrier\">\n"
1018 " <boundingBox id=\"bb_tg_rg_malateCarrier\">\n"
1019 " <position x=\"1360\" y=\"330\"/>\n"
1020 " <dimensions width=\"140\" height=\"24\"/>\n"
1021 " </boundingBox>\n"
1022 " </textGlyph>\n"
1023 " </listOfTextGlyphs>\n"
1024 " </layout>\n"
1025 " </listOfLayouts>\n"
1026 " </annotation>\n"
1027 " <listOfCompartments>\n"
1028 " <compartment id=\"Hepatocyte\" name=\"Hepatocyte\"/>\n"
1029 " <compartment id=\"Mito_1\" name=\"Mito 1\" outside=\"Hepatocyte\"/>\n"
1030 " <compartment id=\"Mito_2\" name=\"Mito 2\" outside=\"Hepatocyte\"/>\n"
1031 " <compartment id=\"Mito_3\" name=\"Mito 3\" outside=\"Hepatocyte\"/>\n"
1032 " </listOfCompartments>\n"
1033 " <listOfSpecies>\n"
1034 " <species id=\"malate_cyt\" name=\"Malate\" compartment=\"Hepatocyte\"/>\n"
1035 " <species id=\"malate_mito1\" name=\"Malate\" compartment=\"Mito_1\"/>\n"
1036 " <species id=\"malate_mito2\" name=\"Malate\" compartment=\"Mito_2\"/>\n"
1037 " <species id=\"malate_mito3\" name=\"Malate\" compartment=\"Mito_3\"/>\n"
1038 " <species id=\"oxaloacetate_cyt\" name=\"Oxaloacetate\" compartment=\"Hepatocyte\"/>\n"
1039 " <species id=\"oxaloacetate_mito1\" name=\"Oxaloacetate\" compartment=\"Mito_1\"/>\n"
1040 " <species id=\"oxaloacetate_mito2\" name=\"Oxaloacetate\" compartment=\"Mito_2\"/>\n"
1041 " <species id=\"oxaloacetate_mito3\" name=\"Oxaloacetate\" compartment=\"Mito_3\"/>\n"
1042 " <species id=\"aspartate_cyt\" name=\"Aspartate\" compartment=\"Hepatocyte\"/>\n"
1043 " <species id=\"aspartate_mito1\" name=\"Aspartate\" compartment=\"Mito_1\"/>\n"
1044 " <species id=\"aspartate_mito2\" name=\"Aspartate\" compartment=\"Mito_2\"/>\n"
1045 " <species id=\"aspartate_mito3\" name=\"Aspartate\" compartment=\"Mito_3\"/>\n"
1046 " <species id=\"glutamate_cyt\" name=\"Glutamate\" compartment=\"Hepatocyte\"/>\n"
1047 " <species id=\"glutamate_mito1\" name=\"Glutamate\" compartment=\"Mito_1\"/>\n"
1048 " <species id=\"glutamate_mito2\" name=\"Glutamate\" compartment=\"Mito_2\"/>\n"
1049 " <species id=\"glutamate_mito3\" name=\"Glutamate\" compartment=\"Mito_3\"/>\n"
1050 " <species id=\"aKetoglutarate_cyt\" name=\"alpha-Ketoglutarate\" compartment=\"Hepatocyte\"/>\n"
1051 " <species id=\"aKetoglutarate_mito1\" name=\"alpha-Ketoglutarate\" compartment=\"Mito_1\"/>\n"
1052 " <species id=\"aKetoglutarate_mito2\" name=\"alpha-Ketoglutarate\" compartment=\"Mito_2\"/>\n"
1053 " <species id=\"aKetoglutarate_mito3\" name=\"alpha-Ketoglutarate\" compartment=\"Mito_3\"/>\n"
1054 " <species id=\"h_cyt\" name=\"H+\" compartment=\"Hepatocyte\"/>\n"
1055 " <species id=\"h_mito1\" name=\"H+\" compartment=\"Mito_1\"/>\n"
1056 " <species id=\"h_mito2\" name=\"H+\" compartment=\"Mito_2\"/>\n"
1057 " <species id=\"h_mito3\" name=\"H+\" compartment=\"Mito_3\"/>\n"
1058 " <species id=\"nad_cyt\" name=\"NAD+\" compartment=\"Hepatocyte\"/>\n"
1059 " <species id=\"nad_mito1\" name=\"NAD+\" compartment=\"Mito_1\"/>\n"
1060 " <species id=\"nad_mito2\" name=\"NAD+\" compartment=\"Mito_2\"/>\n"
1061 " <species id=\"nad_mito3\" name=\"NAD+\" compartment=\"Mito_3\"/>\n"
1062 " <species id=\"nadh_cyt\" name=\"NADH\" compartment=\"Hepatocyte\"/>\n"
1063 " <species id=\"nadh_mito1\" name=\"NADH\" compartment=\"Mito_1\"/>\n"
1064 " <species id=\"nadh_mito2\" name=\"NADH\" compartment=\"Mito_2\"/>\n"
1065 " <species id=\"nadh_mito3\" name=\"NADH\" compartment=\"Mito_3\"/>\n"
1066 " </listOfSpecies>\n"
1067 " <listOfReactions>\n"
1068 " <reaction id=\"reaction_malatedh_cyt\" name=\"malate dehydrogenase\" reversible=\"false\">\n"
1069 " <listOfReactants>\n"
1070 " <speciesReference species=\"malate_cyt\">\n"
1071 " <annotation>\n"
1072 " <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_malate_cyt\"/>\n"
1073 "</annotation>\n"
1074 " </speciesReference>\n"
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1078 "</annotation>\n"
1079 " </speciesReference>\n"
1080 " </listOfReactants>\n"
1081 " <listOfProducts>\n"
1082 " <speciesReference species=\"nadh_cyt\">\n"
1083 " <annotation>\n"
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1085 "</annotation>\n"
1086 " </speciesReference>\n"
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1091 " </speciesReference>\n"
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1095 "</annotation>\n"
1096 " </speciesReference>\n"
1097 " </listOfProducts>\n"
1098 " </reaction>\n"
1099 " <reaction id=\"reaction_aspartateat_cyt\" name=\"aspartate aminotransferase\" reversible=\"false\">\n"
1100 " <listOfReactants>\n"
1101 " <speciesReference species=\"oxaloacetate_cyt\">\n"
1102 " <annotation>\n"
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1104 "</annotation>\n"
1105 " </speciesReference>\n"
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1110 " </speciesReference>\n"
1111 " </listOfReactants>\n"
1112 " <listOfProducts>\n"
1113 " <speciesReference species=\"aspartate_cyt\">\n"
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1117 " </speciesReference>\n"
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1121 "</annotation>\n"
1122 " </speciesReference>\n"
1123 " </listOfProducts>\n"
1124 " </reaction>\n"
1125 " <reaction id=\"reaction_malatedh_mito1\" name=\"malate dehydrogenase\" reversible=\"false\">\n"
1126 " <listOfReactants>\n"
1127 " <speciesReference species=\"malate_mito1\">\n"
1128 " <annotation>\n"
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1131 " </speciesReference>\n"
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1143 " </speciesReference>\n"
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1152 "</annotation>\n"
1153 " </speciesReference>\n"
1154 " </listOfProducts>\n"
1155 " </reaction>\n"
1156 " <reaction id=\"reaction_aspartateat_mito1\" name=\"aspartate aminotransferase\" reversible=\"false\">\n"
1157 " <listOfReactants>\n"
1158 " <speciesReference species=\"oxaloacetate_mito1\">\n"
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1164 " <annotation>\n"
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1178 "</annotation>\n"
1179 " </speciesReference>\n"
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1181 " </reaction>\n"
1182 " <reaction id=\"reaction_malatedh_mito2\" name=\"malate dehydrogenase\" reversible=\"false\">\n"
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1184 " <speciesReference species=\"malate_mito2\">\n"
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1195 " <listOfProducts>\n"
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1199 "</annotation>\n"
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1209 "</annotation>\n"
1210 " </speciesReference>\n"
1211 " </listOfProducts>\n"
1212 " </reaction>\n"
1213 " <reaction id=\"reaction_aspartateat_mito2\" name=\"aspartate aminotransferase\" reversible=\"false\">\n"
1214 " <listOfReactants>\n"
1215 " <speciesReference species=\"oxaloacetate_mito2\">\n"
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1221 " <annotation>\n"
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1224 " </speciesReference>\n"
1225 " </listOfReactants>\n"
1226 " <listOfProducts>\n"
1227 " <speciesReference species=\"aspartate_mito2\">\n"
1228 " <annotation>\n"
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1230 "</annotation>\n"
1231 " </speciesReference>\n"
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1235 "</annotation>\n"
1236 " </speciesReference>\n"
1237 " </listOfProducts>\n"
1238 " </reaction>\n"
1239 " <reaction id=\"reaction_malatedh_mito3\" name=\"malate dehydrogenase\" reversible=\"false\">\n"
1240 " <listOfReactants>\n"
1241 " <speciesReference species=\"malate_mito3\">\n"
1242 " <annotation>\n"
1243 " <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_malate_mito3\"/>\n"
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1245 " </speciesReference>\n"
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1247 " <annotation>\n"
1248 " <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_nad_mito3\"/>\n"
1249 "</annotation>\n"
1250 " </speciesReference>\n"
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1252 " <listOfProducts>\n"
1253 " <speciesReference species=\"nadh_mito3\">\n"
1254 " <annotation>\n"
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1256 "</annotation>\n"
1257 " </speciesReference>\n"
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1262 " </speciesReference>\n"
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1266 "</annotation>\n"
1267 " </speciesReference>\n"
1268 " </listOfProducts>\n"
1269 " </reaction>\n"
1270 " <reaction id=\"reaction_aspartateat_mito3\" name=\"aspartate aminotransferase\" reversible=\"false\">\n"
1271 " <listOfReactants>\n"
1272 " <speciesReference species=\"oxaloacetate_mito3\">\n"
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1284 " <speciesReference species=\"aspartate_mito3\">\n"
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1287 "</annotation>\n"
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1292 "</annotation>\n"
1293 " </speciesReference>\n"
1294 " </listOfProducts>\n"
1295 " </reaction>\n"
1296 " <reaction id=\"aspartateCarrier\" name=\"aspartate carrier\">\n"
1297 " <listOfReactants>\n"
1298 " <speciesReference species=\"glutamate_mito3\">\n"
1299 " <annotation>\n"
1300 " <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_glutamate_mito3_2\"/>\n"
1301 "</annotation>\n"
1302 " </speciesReference>\n"
1303 " <speciesReference species=\"aspartate_cyt\">\n"
1304 " <annotation>\n"
1305 " <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_aspartate_cyt_2\"/>\n"
1306 "</annotation>\n"
1307 " </speciesReference>\n"
1308 " </listOfReactants>\n"
1309 " <listOfProducts>\n"
1310 " <speciesReference species=\"glutamate_cyt\">\n"
1311 " <annotation>\n"
1312 " <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_glutamate_cyt_2\"/>\n"
1313 "</annotation>\n"
1314 " </speciesReference>\n"
1315 " <speciesReference species=\"aspartate_mito3\">\n"
1316 " <annotation>\n"
1317 " <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_aspartate_mito3_2\"/>\n"
1318 "</annotation>\n"
1319 " </speciesReference>\n"
1320 " </listOfProducts>\n"
1321 " </reaction>\n"
1322 " <reaction id=\"malateCarrier\" name=\"malate carrier\">\n"
1323 " <listOfReactants>\n"
1324 " <speciesReference species=\"aKetoglutarate_mito3\">\n"
1325 " <annotation>\n"
1326 " <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_aKetoglutarate_mito3_2\"/>\n"
1327 "</annotation>\n"
1328 " </speciesReference>\n"
1329 " <speciesReference species=\"malate_cyt\">\n"
1330 " <annotation>\n"
1331 " <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_malate_cyt_2\"/>\n"
1332 "</annotation>\n"
1333 " </speciesReference>\n"
1334 " </listOfReactants>\n"
1335 " <listOfProducts>\n"
1336 " <speciesReference species=\"aKetoglutarate_cyt\">\n"
1337 " <annotation>\n"
1338 " <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_aKetoglutarate_cyt_2\"/>\n"
1339 "</annotation>\n"
1340 " </speciesReference>\n"
1341 " <speciesReference species=\"malate_mito3\">\n"
1342 " <annotation>\n"
1343 " <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_malate_mito3_2\"/>\n"
1344 "</annotation>\n"
1345 " </speciesReference>\n"
1346 " </listOfProducts>\n"
1347 " </reaction>\n"
1348 " </listOfReactions>\n"
1349 " </model>\n"
1350 "</sbml> \n"
1351 ;
1352
1353 XMLInputStream stream(s,false);
1354 XMLNode node(stream);
1355 // create the document
1356
1357 SBMLDocument *document=new SBMLDocument(2,1);
1358
1359 document->enablePackage(LayoutExtension::getXmlnsL2(), "layout", true);
1360 document->enablePackage(RenderExtension::getXmlnsL2(), "render", true);
1361
1362 LayoutPkgNamespaces layoutns(2);
1363
1364 // create the Model
1365
1366 Model* model=document->createModel();
1367 model->setId("TestModel");
1368 document->setModel(model);
1369
1370 // create the Compartment
1371
1372 Compartment* compartment=model->createCompartment();
1373 compartment->setId("Hepatocyte");
1374 compartment->setName("Hepatocyte");
1375
1376 Compartment* mito1=model->createCompartment();
1377 mito1->setId("Mito_1");
1378 mito1->setName("Mito 1");
1379 mito1->setOutside(compartment->getId());
1380
1381 Compartment* mito2=model->createCompartment();
1382 mito2->setId("Mito_2");
1383 mito2->setName("Mito 2");
1384 mito2->setOutside(compartment->getId());
1385
1386 Compartment* mito3=model->createCompartment();
1387 mito3->setId("Mito_3");
1388 mito3->setName("Mito 3");
1389 mito3->setOutside(compartment->getId());
1390
1391
1392 // create the Species
1393
1394 // Malate
1395 Species* malate_cyt=model->createSpecies();
1396 malate_cyt->setId("malate_cyt");
1397 malate_cyt->setName("Malate");
1398 malate_cyt->setCompartment(compartment->getId());
1399
1400 Species* malate_mito1=model->createSpecies();
1401 malate_mito1->setId("malate_mito1");
1402 malate_mito1->setCompartment(mito1->getId());
1403 malate_mito1->setName("Malate");
1404
1405 Species* malate_mito2=model->createSpecies();
1406 malate_mito2->setId("malate_mito2");
1407 malate_mito2->setCompartment(mito2->getId());
1408 malate_mito2->setName("Malate");
1409
1410 Species* malate_mito3=model->createSpecies();
1411 malate_mito3->setId("malate_mito3");
1412 malate_mito3->setCompartment(mito3->getId());
1413 malate_mito3->setName("Malate");
1414
1415
1416 // Oxaloacetate
1417 Species* oxaloacetate_cyt=model->createSpecies();
1418 oxaloacetate_cyt->setId("oxaloacetate_cyt");
1419 oxaloacetate_cyt->setName("Oxaloacetate");
1420 oxaloacetate_cyt->setCompartment(compartment->getId());
1421
1422 Species* oxaloacetate_mito1=model->createSpecies();
1423 oxaloacetate_mito1->setId("oxaloacetate_mito1");
1424 oxaloacetate_mito1->setCompartment(mito1->getId());
1425 oxaloacetate_mito1->setName("Oxaloacetate");
1426
1427 Species* oxaloacetate_mito2=model->createSpecies();
1428 oxaloacetate_mito2->setId("oxaloacetate_mito2");
1429 oxaloacetate_mito2->setCompartment(mito2->getId());
1430 oxaloacetate_mito2->setName("Oxaloacetate");
1431
1432 Species* oxaloacetate_mito3=model->createSpecies();
1433 oxaloacetate_mito3->setId("oxaloacetate_mito3");
1434 oxaloacetate_mito3->setCompartment(mito3->getId());
1435 oxaloacetate_mito3->setName("Oxaloacetate");
1436
1437
1438 // Aspartate
1439 Species* aspartate_cyt=model->createSpecies();
1440 aspartate_cyt->setId("aspartate_cyt");
1441 aspartate_cyt->setName("Aspartate");
1442 aspartate_cyt->setCompartment(compartment->getId());
1443
1444 Species* aspartate_mito1=model->createSpecies();
1445 aspartate_mito1->setId("aspartate_mito1");
1446 aspartate_mito1->setCompartment(mito1->getId());
1447 aspartate_mito1->setName("Aspartate");
1448
1449 Species* aspartate_mito2=model->createSpecies();
1450 aspartate_mito2->setId("aspartate_mito2");
1451 aspartate_mito2->setCompartment(mito2->getId());
1452 aspartate_mito2->setName("Aspartate");
1453
1454 Species* aspartate_mito3=model->createSpecies();
1455 aspartate_mito3->setId("aspartate_mito3");
1456 aspartate_mito3->setCompartment(mito3->getId());
1457 aspartate_mito3->setName("Aspartate");
1458
1459
1460 // Glutamate
1461 Species* glutamate_cyt=model->createSpecies();
1462 glutamate_cyt->setId("glutamate_cyt");
1463 glutamate_cyt->setName("Glutamate");
1464 glutamate_cyt->setCompartment(compartment->getId());
1465
1466 Species* glutamate_mito1=model->createSpecies();
1467 glutamate_mito1->setId("glutamate_mito1");
1468 glutamate_mito1->setCompartment(mito1->getId());
1469 glutamate_mito1->setName("Glutamate");
1470
1471 Species* glutamate_mito2=model->createSpecies();
1472 glutamate_mito2->setId("glutamate_mito2");
1473 glutamate_mito2->setCompartment(mito2->getId());
1474 glutamate_mito2->setName("Glutamate");
1475
1476 Species* glutamate_mito3=model->createSpecies();
1477 glutamate_mito3->setId("glutamate_mito3");
1478 glutamate_mito3->setCompartment(mito3->getId());
1479 glutamate_mito3->setName("Glutamate");
1480
1481
1482 // alpha-Ketoglutarate
1483 Species* aKetoglutarate_cyt=model->createSpecies();
1484 aKetoglutarate_cyt->setId("aKetoglutarate_cyt");
1485 aKetoglutarate_cyt->setName("alpha-Ketoglutarate");
1486 aKetoglutarate_cyt->setCompartment(compartment->getId());
1487
1488 Species* aKetoglutarate_mito1=model->createSpecies();
1489 aKetoglutarate_mito1->setId("aKetoglutarate_mito1");
1490 aKetoglutarate_mito1->setCompartment(mito1->getId());
1491 aKetoglutarate_mito1->setName("alpha-Ketoglutarate");
1492
1493 Species* aKetoglutarate_mito2=model->createSpecies();
1494 aKetoglutarate_mito2->setId("aKetoglutarate_mito2");
1495 aKetoglutarate_mito2->setCompartment(mito2->getId());
1496 aKetoglutarate_mito2->setName("alpha-Ketoglutarate");
1497
1498 Species* aKetoglutarate_mito3=model->createSpecies();
1499 aKetoglutarate_mito3->setId("aKetoglutarate_mito3");
1500 aKetoglutarate_mito3->setCompartment(mito3->getId());
1501 aKetoglutarate_mito3->setName("alpha-Ketoglutarate");
1502
1503
1504 // protons
1505 Species* h_cyt=model->createSpecies();
1506 h_cyt->setId("h_cyt");
1507 h_cyt->setName("H+");
1508 h_cyt->setCompartment(compartment->getId());
1509
1510 Species* h_mito1=model->createSpecies();
1511 h_mito1->setId("h_mito1");
1512 h_mito1->setCompartment(mito1->getId());
1513 h_mito1->setName("H+");
1514
1515 Species* h_mito2=model->createSpecies();
1516 h_mito2->setId("h_mito2");
1517 h_mito2->setCompartment(mito2->getId());
1518 h_mito2->setName("H+");
1519
1520 Species* h_mito3=model->createSpecies();
1521 h_mito3->setId("h_mito3");
1522 h_mito3->setCompartment(mito3->getId());
1523 h_mito3->setName("H+");
1524
1525
1526 // NAD+
1527 Species* nad_cyt=model->createSpecies();
1528 nad_cyt->setId("nad_cyt");
1529 nad_cyt->setName("NAD+");
1530 nad_cyt->setCompartment(compartment->getId());
1531
1532 Species* nad_mito1=model->createSpecies();
1533 nad_mito1->setId("nad_mito1");
1534 nad_mito1->setCompartment(mito1->getId());
1535 nad_mito1->setName("NAD+");
1536
1537 Species* nad_mito2=model->createSpecies();
1538 nad_mito2->setId("nad_mito2");
1539 nad_mito2->setCompartment(mito2->getId());
1540 nad_mito2->setName("NAD+");
1541
1542 Species* nad_mito3=model->createSpecies();
1543 nad_mito3->setId("nad_mito3");
1544 nad_mito3->setCompartment(mito3->getId());
1545 nad_mito3->setName("NAD+");
1546
1547
1548 // NADH
1549 Species* nadh_cyt=model->createSpecies();
1550 nadh_cyt->setId("nadh_cyt");
1551 nadh_cyt->setName("NADH");
1552 nadh_cyt->setCompartment(compartment->getId());
1553
1554 Species* nadh_mito1=model->createSpecies();
1555 nadh_mito1->setId("nadh_mito1");
1556 nadh_mito1->setCompartment(mito1->getId());
1557 nadh_mito1->setName("NADH");
1558
1559 Species* nadh_mito2=model->createSpecies();
1560 nadh_mito2->setId("nadh_mito2");
1561 nadh_mito2->setCompartment(mito2->getId());
1562 nadh_mito2->setName("NADH");
1563
1564 Species* nadh_mito3=model->createSpecies();
1565 nadh_mito3->setId("nadh_mito3");
1566 nadh_mito3->setCompartment(mito3->getId());
1567 nadh_mito3->setName("NADH");
1568
1569
1570
1571
1572 // create the Reactions
1573
1574 // Cytosol
1575
1576 // Malate Dehydrogenase
1577 Reaction* malatedh_cyt=model->createReaction();
1578 malatedh_cyt->setId("reaction_malatedh_cyt");
1579 malatedh_cyt->setName("malate dehydrogenase");
1580 malatedh_cyt->setReversible(false);
1581
1582 SpeciesReference* sr_malate_cyt=malatedh_cyt->createReactant();
1583 sr_malate_cyt->setSpecies(malate_cyt->getId());
1584 sr_malate_cyt->setId("sr_malate_cyt");
1585
1586 SpeciesReference* sr_nad_cyt=malatedh_cyt->createReactant();
1587 sr_nad_cyt->setSpecies(nad_cyt->getId());
1588 sr_nad_cyt->setId("sr_nad_cyt");
1589
1590 SpeciesReference* sr_nadh_cyt=malatedh_cyt->createProduct();
1591 sr_nadh_cyt->setSpecies(nadh_cyt->getId());
1592 sr_nadh_cyt->setId("sr_nadh_cyt");
1593
1594 SpeciesReference* sr_h_cyt=malatedh_cyt->createProduct();
1595 sr_h_cyt->setSpecies(h_cyt->getId());
1596 sr_h_cyt->setId("sr_h_cyt");
1597
1598 SpeciesReference* sr_oxaloacetate_cyt_1=malatedh_cyt->createProduct();
1599 sr_oxaloacetate_cyt_1->setSpecies(oxaloacetate_cyt->getId());
1600 sr_oxaloacetate_cyt_1->setId("sr_oxaloacetate_cyt_1");
1601
1602 //Aspartate Aminotransferase
1603 Reaction* aspartateat_cyt=model->createReaction();
1604 aspartateat_cyt->setId("reaction_aspartateat_cyt");
1605 aspartateat_cyt->setName("aspartate aminotransferase");
1606 aspartateat_cyt->setReversible(false);
1607
1608 SpeciesReference* sr_oxaloacetate_cyt_2=aspartateat_cyt->createReactant();
1609 sr_oxaloacetate_cyt_2->setSpecies(oxaloacetate_cyt->getId());
1610 sr_oxaloacetate_cyt_2->setId("sr_oxaloacetate_cyt_2");
1611
1612 SpeciesReference* sr_glutamate_cyt_1=aspartateat_cyt->createReactant();
1613 sr_glutamate_cyt_1->setSpecies(glutamate_cyt->getId());
1614 sr_glutamate_cyt_1->setId("sr_glutamate_cyt_1");
1615
1616 SpeciesReference* sr_aspartate_cyt_1=aspartateat_cyt->createProduct();
1617 sr_aspartate_cyt_1->setSpecies(aspartate_cyt->getId());
1618 sr_aspartate_cyt_1->setId("sr_aspartate_cyt_1");
1619
1620 SpeciesReference* sr_aKetoglutarate_cyt_1=aspartateat_cyt->createProduct();
1621 sr_aKetoglutarate_cyt_1->setSpecies(aKetoglutarate_cyt->getId());
1622 sr_aKetoglutarate_cyt_1->setId("sr_aKetoglutarate_cyt_1");
1623
1624
1625 // Mito 1
1626
1627 // Malate Dehydrogenase
1628 Reaction* malatedh_mito1=model->createReaction();
1629 malatedh_mito1->setId("reaction_malatedh_mito1");
1630 malatedh_mito1->setName("malate dehydrogenase");
1631 malatedh_mito1->setReversible(false);
1632
1633 SpeciesReference* sr_malate_mito1=malatedh_mito1->createReactant();
1634 sr_malate_mito1->setSpecies(malate_mito1->getId());
1635 sr_malate_mito1->setId("sr_malate_mito1");
1636
1637 SpeciesReference* sr_nad_mito1=malatedh_mito1->createReactant();
1638 sr_nad_mito1->setSpecies(nad_mito1->getId());
1639 sr_nad_mito1->setId("sr_nad_mito1");
1640
1641 SpeciesReference* sr_nadh_mito1=malatedh_mito1->createProduct();
1642 sr_nadh_mito1->setSpecies(nadh_mito1->getId());
1643 sr_nadh_mito1->setId("sr_nadh_mito1");
1644
1645 SpeciesReference* sr_h_mito1=malatedh_mito1->createProduct();
1646 sr_h_mito1->setSpecies(h_mito1->getId());
1647 sr_h_mito1->setId("sr_h_mito1");
1648
1649 SpeciesReference* sr_oxaloacetate_mito1_1=malatedh_mito1->createProduct();
1650 sr_oxaloacetate_mito1_1->setSpecies(oxaloacetate_mito1->getId());
1651 sr_oxaloacetate_mito1_1->setId("sr_oxaloacetate_mito1_1");
1652
1653 //Aspartate Aminotransferase
1654 Reaction* aspartateat_mito1=model->createReaction();
1655 aspartateat_mito1->setId("reaction_aspartateat_mito1");
1656 aspartateat_mito1->setName("aspartate aminotransferase");
1657 aspartateat_mito1->setReversible(false);
1658
1659 SpeciesReference* sr_oxaloacetate_mito1_2=aspartateat_mito1->createReactant();
1660 sr_oxaloacetate_mito1_2->setSpecies(oxaloacetate_mito1->getId());
1661 sr_oxaloacetate_mito1_2->setId("sr_oxaloacetate_mito1_2");
1662
1663 SpeciesReference* sr_glutamate_mito1=aspartateat_mito1->createReactant();
1664 sr_glutamate_mito1->setSpecies(glutamate_mito1->getId());
1665 sr_glutamate_mito1->setId("sr_glutamate_mito1");
1666
1667 SpeciesReference* sr_aspartate_mito1=aspartateat_mito1->createProduct();
1668 sr_aspartate_mito1->setSpecies(aspartate_mito1->getId());
1669 sr_aspartate_mito1->setId("sr_aspartate_mito1");
1670
1671 SpeciesReference* sr_aKetoglutarate_mito1=aspartateat_mito1->createProduct();
1672 sr_aKetoglutarate_mito1->setSpecies(aKetoglutarate_mito1->getId());
1673 sr_aKetoglutarate_mito1->setId("sr_aKetoglutarate_mito1");
1674
1675
1676 // Mito 2
1677
1678 // Malate Dehydrogenase
1679 Reaction* malatedh_mito2=model->createReaction();
1680 malatedh_mito2->setId("reaction_malatedh_mito2");
1681 malatedh_mito2->setName("malate dehydrogenase");
1682 malatedh_mito2->setReversible(false);
1683
1684 SpeciesReference* sr_malate_mito2=malatedh_mito2->createReactant();
1685 sr_malate_mito2->setSpecies(malate_mito2->getId());
1686 sr_malate_mito2->setId("sr_malate_mito2");
1687
1688 SpeciesReference* sr_nad_mito2=malatedh_mito2->createReactant();
1689 sr_nad_mito2->setSpecies(nad_mito2->getId());
1690 sr_nad_mito2->setId("sr_nad_mito2");
1691
1692 SpeciesReference* sr_nadh_mito2=malatedh_mito2->createProduct();
1693 sr_nadh_mito2->setSpecies(nadh_mito2->getId());
1694 sr_nadh_mito2->setId("sr_nadh_mito2");
1695
1696 SpeciesReference* sr_h_mito2=malatedh_mito2->createProduct();
1697 sr_h_mito2->setSpecies(h_mito2->getId());
1698 sr_h_mito2->setId("sr_h_mito2");
1699
1700 SpeciesReference* sr_oxaloacetate_mito2_1=malatedh_mito2->createProduct();
1701 sr_oxaloacetate_mito2_1->setSpecies(oxaloacetate_mito2->getId());
1702 sr_oxaloacetate_mito2_1->setId("sr_oxaloacetate_mito2_1");
1703
1704 //Aspartate Aminotransferase
1705 Reaction* aspartateat_mito2=model->createReaction();
1706 aspartateat_mito2->setId("reaction_aspartateat_mito2");
1707 aspartateat_mito2->setName("aspartate aminotransferase");
1708 aspartateat_mito2->setReversible(false);
1709
1710 SpeciesReference* sr_oxaloacetate_mito2_2=aspartateat_mito2->createReactant();
1711 sr_oxaloacetate_mito2_2->setSpecies(oxaloacetate_mito2->getId());
1712 sr_oxaloacetate_mito2_2->setId("sr_oxaloacetate_mito2_2");
1713
1714 SpeciesReference* sr_glutamate_mito2=aspartateat_mito2->createReactant();
1715 sr_glutamate_mito2->setSpecies(glutamate_mito2->getId());
1716 sr_glutamate_mito2->setId("sr_glutamate_mito2");
1717
1718 SpeciesReference* sr_aspartate_mito2=aspartateat_mito2->createProduct();
1719 sr_aspartate_mito2->setSpecies(aspartate_mito2->getId());
1720 sr_aspartate_mito2->setId("sr_aspartate_mito2");
1721
1722 SpeciesReference* sr_aKetoglutarate_mito2=aspartateat_mito2->createProduct();
1723 sr_aKetoglutarate_mito2->setSpecies(aKetoglutarate_mito2->getId());
1724 sr_aKetoglutarate_mito2->setId("sr_aKetoglutarate_mito2");
1725
1726
1727 // Mito 3
1728
1729 // Malate Dehydrogenase
1730 Reaction* malatedh_mito3=model->createReaction();
1731 malatedh_mito3->setId("reaction_malatedh_mito3");
1732 malatedh_mito3->setName("malate dehydrogenase");
1733 malatedh_mito3->setReversible(false);
1734
1735 SpeciesReference* sr_malate_mito3=malatedh_mito3->createReactant();
1736 sr_malate_mito3->setSpecies(malate_mito3->getId());
1737 sr_malate_mito3->setId("sr_malate_mito3");
1738
1739 SpeciesReference* sr_nad_mito3=malatedh_mito3->createReactant();
1740 sr_nad_mito3->setSpecies(nad_mito3->getId());
1741 sr_nad_mito3->setId("sr_nad_mito3");
1742
1743 SpeciesReference* sr_nadh_mito3=malatedh_mito3->createProduct();
1744 sr_nadh_mito3->setSpecies(nadh_mito3->getId());
1745 sr_nadh_mito3->setId("sr_nadh_mito3");
1746
1747 SpeciesReference* sr_h_mito3=malatedh_mito3->createProduct();
1748 sr_h_mito3->setSpecies(h_mito3->getId());
1749 sr_h_mito3->setId("sr_h_mito3");
1750
1751 SpeciesReference* sr_oxaloacetate_mito3_1=malatedh_mito3->createProduct();
1752 sr_oxaloacetate_mito3_1->setSpecies(oxaloacetate_mito3->getId());
1753 sr_oxaloacetate_mito3_1->setId("sr_oxaloacetate_mito3_1");
1754
1755 //Aspartate Aminotransferase
1756 Reaction* aspartateat_mito3=model->createReaction();
1757 aspartateat_mito3->setId("reaction_aspartateat_mito3");
1758 aspartateat_mito3->setName("aspartate aminotransferase");
1759 aspartateat_mito3->setReversible(false);
1760
1761 SpeciesReference* sr_oxaloacetate_mito3_2=aspartateat_mito3->createReactant();
1762 sr_oxaloacetate_mito3_2->setSpecies(oxaloacetate_mito3->getId());
1763 sr_oxaloacetate_mito3_2->setId("sr_oxaloacetate_mito3_2");
1764
1765
1766 SpeciesReference* sr_glutamate_mito3_1=aspartateat_mito3->createReactant();
1767 sr_glutamate_mito3_1->setSpecies(glutamate_mito3->getId());
1768 sr_glutamate_mito3_1->setId("sr_glutamate_mito3_1");
1769
1770
1771 SpeciesReference* sr_aspartate_mito3_1=aspartateat_mito3->createProduct();
1772 sr_aspartate_mito3_1->setSpecies(aspartate_mito3->getId());
1773 sr_aspartate_mito3_1->setId("sr_aspartate_mito3_1");
1774
1775
1776 SpeciesReference* sr_aKetoglutarate_mito3_1=aspartateat_mito3->createProduct();
1777 sr_aKetoglutarate_mito3_1->setSpecies(aKetoglutarate_mito3->getId());
1778 sr_aKetoglutarate_mito3_1->setId("sr_aKetoglutarate_mito3_1");
1779
1780
1781 // aspartate carrier
1782
1783 Reaction* aspartateCarrier=model->createReaction();
1784 aspartateCarrier->setId("aspartateCarrier");
1785 aspartateCarrier->setName("aspartate carrier");
1786 aspartateCarrier->setReversible(true);
1787
1788 SpeciesReference* sr_glutamate_mito3_2=aspartateCarrier->createReactant();
1789 sr_glutamate_mito3_2->setSpecies(glutamate_mito3->getId());
1790 sr_glutamate_mito3_2->setId("sr_glutamate_mito3_2");
1791
1792 SpeciesReference* sr_aspartate_cyt_2=aspartateCarrier->createReactant();
1793 sr_aspartate_cyt_2->setSpecies(aspartate_cyt->getId());
1794 sr_aspartate_cyt_2->setId("sr_aspartate_cyt_2");
1795
1796 SpeciesReference* sr_glutamate_cyt_2=aspartateCarrier->createProduct();
1797 sr_glutamate_cyt_2->setSpecies(glutamate_cyt->getId());
1798 sr_glutamate_cyt_2->setId("sr_glutamate_cyt_2");
1799
1800 SpeciesReference* sr_aspartate_mito3_2=aspartateCarrier->createProduct();
1801 sr_aspartate_mito3_2->setSpecies(aspartate_mito3->getId());
1802 sr_aspartate_mito3_2->setId("sr_aspartate_mito3_2");
1803
1804 // malate carrier
1805
1806 Reaction* malateCarrier=model->createReaction();
1807 malateCarrier->setId("malateCarrier");
1808 malateCarrier->setName("malate carrier");
1809 malateCarrier->setReversible(true);
1810
1811 SpeciesReference* sr_aKetoglutarate_mito3_2=malateCarrier->createReactant();
1812 sr_aKetoglutarate_mito3_2->setSpecies(aKetoglutarate_mito3->getId());
1813 sr_aKetoglutarate_mito3_2->setId("sr_aKetoglutarate_mito3_2");
1814
1815 SpeciesReference* sr_malate_cyt_2=malateCarrier->createReactant();
1816 sr_malate_cyt_2->setSpecies(malate_cyt->getId());
1817 sr_malate_cyt_2->setId("sr_malate_cyt_2");
1818
1819 SpeciesReference* sr_aKetoglutarate_cyt_2=malateCarrier->createProduct();
1820 sr_aKetoglutarate_cyt_2->setSpecies(aKetoglutarate_cyt->getId());
1821 sr_aKetoglutarate_cyt_2->setId("sr_aKetoglutarate_cyt_2");
1822
1823 SpeciesReference* sr_malate_mito3_2=malateCarrier->createProduct();
1824 sr_malate_mito3_2->setSpecies(malate_mito3->getId());
1825 sr_malate_mito3_2->setId("sr_malate_mito3_2");
1826
1827
1828 /////////// create the Layout
1829 LayoutModelPlugin *plugin = (LayoutModelPlugin*)model->getPlugin("layout");
1830 fail_unless(plugin != NULL);
1831 if (plugin == NULL) return;
1832
1833 Layout* layout=plugin->createLayout();
1834
1835 layout->setId("Layout_1");
1836 Dimensions dim(&layoutns, 2320.0,1000.0);
1837 layout->setDimensions(&dim);
1838
1839
1840 // create the CompartmentGlyph
1841
1842 CompartmentGlyph* compartmentGlyph=layout->createCompartmentGlyph();
1843 compartmentGlyph->setId("CompartmentGlyph_1");
1844 compartmentGlyph->setCompartmentId(compartment->getId());
1845 BoundingBox bb=BoundingBox(&layoutns, "bb_compartment",10,10,2300,980);
1846 compartmentGlyph->setBoundingBox(&bb);
1847
1848 TextGlyph* tg=layout->createTextGlyph();
1849 tg->setId("TextGlyph_Hepatocyte");
1850 tg->setOriginOfTextId(compartment->getId());
1851 bb=BoundingBox(&layoutns, "bb_tg_compartment",50,870,300,72);
1852 tg->setBoundingBox(&bb);
1853 tg->setGraphicalObjectId(compartmentGlyph->getId());
1854
1855 CompartmentGlyph* mito1Glyph=layout->createCompartmentGlyph();
1856 mito1Glyph->setId("Mito1_Glyph");
1857 mito1Glyph->setCompartmentId(mito1->getId());
1858 bb=BoundingBox(&layoutns, "bb_mito1",100,100,300,100);
1859 mito1Glyph->setBoundingBox(&bb);
1860
1861 tg=layout->createTextGlyph();
1862 tg->setId("TextGlyph_mito1");
1863 tg->setOriginOfTextId(mito1->getId());
1864 bb=BoundingBox(&layoutns, "bb_tg_mito1",110,110,280,72);
1865 tg->setBoundingBox(&bb);
1866 tg->setGraphicalObjectId(mito1Glyph->getId());
1867
1868
1869 CompartmentGlyph* mito2Glyph=layout->createCompartmentGlyph();
1870 mito2Glyph->setId("Mito2_Glyph");
1871 mito2Glyph->setCompartmentId(mito2->getId());
1872 bb=BoundingBox(&layoutns, "bb_mito2",200,650,300,100);
1873 mito2Glyph->setBoundingBox(&bb);
1874
1875 tg=layout->createTextGlyph();
1876 tg->setId("TextGlyph_mito2");
1877 tg->setOriginOfTextId(mito2->getId());
1878 bb=BoundingBox(&layoutns, "bb_tg_mito2",210,660,280,72);
1879 tg->setBoundingBox(&bb);
1880 tg->setGraphicalObjectId(mito2Glyph->getId());
1881
1882 CompartmentGlyph* mito3Glyph_2=layout->createCompartmentGlyph();
1883 mito3Glyph_2->setId("Mito3_Glyph_2");
1884 mito3Glyph_2->setCompartmentId(mito3->getId());
1885 bb=BoundingBox(&layoutns, "bb_mito3_2",1470,30,820,536);
1886 mito3Glyph_2->setBoundingBox(&bb);
1887
1888 tg=layout->createTextGlyph();
1889 tg->setId("TextGlyph_mito3_2");
1890 tg->setOriginOfTextId(mito3->getId());
1891 bb=BoundingBox(&layoutns, "bb_tg_mito3_2",1475,35,200,72);
1892 tg->setBoundingBox(&bb);
1893 tg->setGraphicalObjectId(mito3Glyph_2->getId());
1894
1895
1896
1897
1898 // create the SpeciesGlyphs
1899
1900 // Cytosol
1901
1902 // Malate cyt
1903 SpeciesGlyph* speciesGlyph_malate_cyt=layout->createSpeciesGlyph();
1904 speciesGlyph_malate_cyt->setId("SpeciesGlyph_malate_cyt");
1905 speciesGlyph_malate_cyt->setSpeciesId(malate_cyt->getId());
1906 bb=BoundingBox(&layoutns, "bb_sg_malate_cyt",580,280,240,36);
1907 speciesGlyph_malate_cyt->setBoundingBox(&bb);
1908
1909 tg=layout->createTextGlyph();
1910 tg->setId("TextGlyph_malate_cyt");
1911 bb=BoundingBox(&layoutns, "bb_tg_malatate_cyt",590,280,220,36);
1912 tg->setBoundingBox(&bb);
1913 tg->setOriginOfTextId(malate_cyt->getId());
1914 tg->setGraphicalObjectId(speciesGlyph_malate_cyt->getId());
1915
1916 // Oxaloacetate cyt
1917 SpeciesGlyph* speciesGlyph_oxaloacetate_cyt=layout->createSpeciesGlyph();
1918 speciesGlyph_oxaloacetate_cyt->setId("SpeciesGlyph_oxaloacetate_cyt");
1919 speciesGlyph_oxaloacetate_cyt->setSpeciesId(oxaloacetate_cyt->getId());
1920 bb=BoundingBox(&layoutns, "bb_sg_oxaloacetate_cyt",580,480,240,36);
1921 speciesGlyph_oxaloacetate_cyt->setBoundingBox(&bb);
1922
1923 tg=layout->createTextGlyph();
1924 tg->setId("TextGlyph_oxaloacetate_cyt");
1925 bb=BoundingBox(&layoutns, "bb_tg_oxaloacetate_cyt",590,480,220,36);
1926 tg->setBoundingBox(&bb);
1927 tg->setOriginOfTextId(oxaloacetate_cyt->getId());
1928 tg->setGraphicalObjectId(speciesGlyph_oxaloacetate_cyt->getId());
1929
1930 // Aspartate cyt
1931 SpeciesGlyph* speciesGlyph_aspartate_cyt=layout->createSpeciesGlyph();
1932 speciesGlyph_aspartate_cyt->setId("SpeciesGlyph_aspartate_cyt");
1933 speciesGlyph_aspartate_cyt->setSpeciesId(aspartate_cyt->getId());
1934 bb=BoundingBox(&layoutns, "bb_sg_aspartate_cyt",580,680,240,36);
1935 speciesGlyph_aspartate_cyt->setBoundingBox(&bb);
1936
1937 tg=layout->createTextGlyph();
1938 tg->setId("TextGlyph_aspartate_cyt");
1939 bb=BoundingBox(&layoutns, "bb_tg_aspartate_cyt",590,680,220,36);
1940 tg->setBoundingBox(&bb);
1941 tg->setOriginOfTextId(aspartate_cyt->getId());
1942 tg->setGraphicalObjectId(speciesGlyph_aspartate_cyt->getId());
1943
1944 // Glutamate cyt
1945 SpeciesGlyph* speciesGlyph_glutamate_cyt=layout->createSpeciesGlyph();
1946 speciesGlyph_glutamate_cyt->setId("SpeciesGlyph_glutamate_cyt");
1947 speciesGlyph_glutamate_cyt->setSpeciesId(glutamate_cyt->getId());
1948 bb=BoundingBox(&layoutns, "bb_sg_glutamate_cyt",800,610,240,36);
1949 speciesGlyph_glutamate_cyt->setBoundingBox(&bb);
1950
1951 tg=layout->createTextGlyph();
1952 tg->setId("TextGlyph_glutamate_cyt");
1953 bb=BoundingBox(&layoutns, "bb_tg_glutamate_cyt",810,610,220,36);
1954 tg->setBoundingBox(&bb);
1955 tg->setOriginOfTextId(glutamate_cyt->getId());
1956 tg->setGraphicalObjectId(speciesGlyph_glutamate_cyt->getId());
1957
1958 // alpha-Ketoglutarate cyt
1959 SpeciesGlyph* speciesGlyph_aKetoglutarate_cyt=layout->createSpeciesGlyph();
1960 speciesGlyph_aKetoglutarate_cyt->setId("SpeciesGlyph_aKetoglutarate_cyt");
1961 speciesGlyph_aKetoglutarate_cyt->setSpeciesId(aKetoglutarate_cyt->getId());
1962 bb=BoundingBox(&layoutns, "bb_sg_aKetoglutarate_cyt",860,500,280,36);
1963 speciesGlyph_aKetoglutarate_cyt->setBoundingBox(&bb);
1964
1965 tg=layout->createTextGlyph();
1966 tg->setId("TextGlyph_aKetoglutarate_cyt");
1967 bb=BoundingBox(&layoutns, "bb_tg_aKetoglutarate_cyt",870,500,260,36);
1968 tg->setBoundingBox(&bb);
1969 tg->setOriginOfTextId(aKetoglutarate_cyt->getId());
1970 tg->setGraphicalObjectId(speciesGlyph_aKetoglutarate_cyt->getId());
1971
1972 // NAD+ cyt
1973 SpeciesGlyph* speciesGlyph_nad_cyt=layout->createSpeciesGlyph();
1974 speciesGlyph_nad_cyt->setId("SpeciesGlyph_nad_cyt");
1975 speciesGlyph_nad_cyt->setSpeciesId(nad_cyt->getId());
1976 bb=BoundingBox(&layoutns, "bb_sg_nad_cyt",520,350,100,24);
1977 speciesGlyph_nad_cyt->setBoundingBox(&bb);
1978
1979 tg=layout->createTextGlyph();
1980 tg->setId("TextGlyph_nad_cyt");
1981 bb=BoundingBox(&layoutns, "bb_tg_nad_cyt",525,350,80,24);
1982 tg->setBoundingBox(&bb);
1983 tg->setOriginOfTextId(nad_cyt->getId());
1984 tg->setGraphicalObjectId(speciesGlyph_nad_cyt->getId());
1985
1986 // NADH cyt
1987 SpeciesGlyph* speciesGlyph_nadh_cyt=layout->createSpeciesGlyph();
1988 speciesGlyph_nadh_cyt->setId("SpeciesGlyph_nadh_cyt");
1989 speciesGlyph_nadh_cyt->setSpeciesId(nadh_cyt->getId());
1990 bb=BoundingBox(&layoutns, "bb_sg_nadh_cyt",520,430,100,24);
1991 speciesGlyph_nadh_cyt->setBoundingBox(&bb);
1992
1993 tg=layout->createTextGlyph();
1994 tg->setId("TextGlyph_nadh_cyt");
1995 bb=BoundingBox(&layoutns, "bb_tg_nadh_cyt",525,430,80,24);
1996 tg->setBoundingBox(&bb);
1997 tg->setOriginOfTextId(nadh_cyt->getId());
1998 tg->setGraphicalObjectId(speciesGlyph_nadh_cyt->getId());
1999
2000 // H+ cyt
2001 SpeciesGlyph* speciesGlyph_h_cyt=layout->createSpeciesGlyph();
2002 speciesGlyph_h_cyt->setId("SpeciesGlyph_h_cyt");
2003 speciesGlyph_h_cyt->setSpeciesId(h_cyt->getId());
2004 bb=BoundingBox(&layoutns, "bb_sg_h_cyt",430,430,40,24);
2005 speciesGlyph_h_cyt->setBoundingBox(&bb);
2006
2007 tg=layout->createTextGlyph();
2008 tg->setId("TextGlyph_h_cyt");
2009 bb=BoundingBox(&layoutns, "bb_tg_h_cyt",435,430,30,24);
2010 tg->setBoundingBox(&bb);
2011 tg->setOriginOfTextId(h_cyt->getId());
2012 tg->setGraphicalObjectId(speciesGlyph_h_cyt->getId());
2013
2014
2015 // create the ReactionGlyphs
2016
2017 ReactionGlyph* rg_malatedh_cyt=layout->createReactionGlyph();
2018 rg_malatedh_cyt->setId("rg_malatedh_cyt");
2019 rg_malatedh_cyt->setReactionId(malatedh_cyt->getId());
2020
2021 Curve* curve=rg_malatedh_cyt->getCurve();
2022 LineSegment* ls=curve->createLineSegment();
2023 Point p(&layoutns, 700,381);
2024 ls->setStart(&p);
2025 p=Point(&layoutns, 700,415);
2026 ls->setEnd(&p);
2027
2028 tg=layout->createTextGlyph();
2029 tg->setId("tg_rg_malaltedh_cyt");
2030 bb=BoundingBox(&layoutns, "bb_tg_rg_malaltedh_cyt",700,385,210,24);
2031 tg->setBoundingBox(&bb);
2032 tg->setOriginOfTextId(malatedh_cyt->getId());
2033 tg->setGraphicalObjectId(rg_malatedh_cyt->getId());
2034
2035
2036 ReactionGlyph* rg_aspartateat_cyt=layout->createReactionGlyph();
2037 rg_aspartateat_cyt->setId("rg_aspartateat_cyt");
2038 rg_aspartateat_cyt->setReactionId(aspartateat_cyt->getId());
2039
2040 curve=rg_aspartateat_cyt->getCurve();
2041 ls=curve->createLineSegment();
2042 p=Point(&layoutns, 700,581);
2043 ls->setStart(&p);
2044 p=Point(&layoutns, 700,615);
2045 ls->setEnd(&p);
2046
2047 tg=layout->createTextGlyph();
2048 tg->setId("tg_rg_aspartateat_cyt");
2049 bb=BoundingBox(&layoutns, "bb_tg_rg_aspartateat_cyt",440,585,260,24);
2050 tg->setBoundingBox(&bb);
2051 tg->setOriginOfTextId(aspartateat_cyt->getId());
2052 tg->setGraphicalObjectId(rg_aspartateat_cyt->getId());
2053
2054
2055
2056 // add the SpeciesReferenceGlyphs
2057
2058 SpeciesReferenceGlyph* srg_malate_cyt_1=rg_malatedh_cyt->createSpeciesReferenceGlyph();
2059 srg_malate_cyt_1->setId("srg_malate_cyt_1");
2060 srg_malate_cyt_1->setSpeciesGlyphId(speciesGlyph_malate_cyt->getId());
2061 srg_malate_cyt_1->setSpeciesReferenceId(sr_malate_cyt->getId());
2062 srg_malate_cyt_1->setRole(SPECIES_ROLE_SUBSTRATE);
2063
2064 ls=srg_malate_cyt_1->createLineSegment();
2065 p=Point(&layoutns, 700,381);
2066 ls->setStart(&p);
2067 p=Point(&layoutns, 700,316);
2068 ls->setEnd(&p);
2069
2070 SpeciesReferenceGlyph* srg_nad_cyt=rg_malatedh_cyt->createSpeciesReferenceGlyph();
2071 srg_nad_cyt->setId("srg_nad_cyt");
2072 srg_nad_cyt->setSpeciesGlyphId(speciesGlyph_nad_cyt->getId());
2073 srg_nad_cyt->setSpeciesReferenceId(sr_nad_cyt->getId());
2074 srg_nad_cyt->setRole(SPECIES_ROLE_SUBSTRATE);
2075
2076 CubicBezier* cb=srg_nad_cyt->createCubicBezier();
2077 p=Point(&layoutns, 700,381);
2078 cb->setStart(&p);
2079 p=Point(&layoutns, 700,362);
2080 cb->setBasePoint1(&p);
2081 p=Point(&layoutns, 700,362);
2082 cb->setBasePoint2(&p);
2083 p=Point(&layoutns, 620,362);
2084 cb->setEnd(&p);
2085
2086 SpeciesReferenceGlyph* srg_oxaloacetate_cyt_1=rg_malatedh_cyt->createSpeciesReferenceGlyph();
2087 srg_oxaloacetate_cyt_1->setId("srg_oxaloacetate_cyt_1");
2088 srg_oxaloacetate_cyt_1->setSpeciesGlyphId(speciesGlyph_oxaloacetate_cyt->getId());
2089 srg_oxaloacetate_cyt_1->setSpeciesReferenceId(sr_oxaloacetate_cyt_1->getId());
2090 srg_oxaloacetate_cyt_1->setRole(SPECIES_ROLE_PRODUCT);
2091
2092 curve=srg_oxaloacetate_cyt_1->getCurve();
2093 ls=curve->createLineSegment();
2094 p=Point(&layoutns, 700,415);
2095 ls->setStart(&p);
2096 p=Point(&layoutns, 700,480);
2097 ls->setEnd(&p);
2098
2099 SpeciesReferenceGlyph* srg_nadh_cyt=rg_malatedh_cyt->createSpeciesReferenceGlyph();
2100 srg_nadh_cyt->setId("srg_nadh_cyt");
2101 srg_nadh_cyt->setSpeciesGlyphId(speciesGlyph_nadh_cyt->getId());
2102 srg_nadh_cyt->setSpeciesReferenceId(sr_nadh_cyt->getId());
2103 srg_nadh_cyt->setRole(SPECIES_ROLE_PRODUCT);
2104
2105 cb=srg_nadh_cyt->createCubicBezier();
2106 p=Point(&layoutns, 700,415);
2107 cb->setStart(&p);
2108 p=Point(&layoutns, 700,442);
2109 cb->setBasePoint1(&p);
2110 p=Point(&layoutns, 700,442);
2111 cb->setBasePoint2(&p);
2112 p=Point(&layoutns, 620,442);
2113 cb->setEnd(&p);
2114
2115 SpeciesReferenceGlyph* srg_h_cyt=rg_malatedh_cyt->createSpeciesReferenceGlyph();
2116 srg_h_cyt->setId("srg_h_cyt");
2117 srg_h_cyt->setSpeciesGlyphId(speciesGlyph_h_cyt->getId());
2118 srg_h_cyt->setSpeciesReferenceId(sr_h_cyt->getId());
2119 srg_h_cyt->setRole(SPECIES_ROLE_PRODUCT);
2120
2121 cb=srg_h_cyt->createCubicBezier();
2122 p=Point(&layoutns, 700,415);
2123 cb->setStart(&p);
2124 p=Point(&layoutns, 570,415);
2125 cb->setBasePoint1(&p);
2126 p=Point(&layoutns, 570,415);
2127 cb->setBasePoint2(&p);
2128 p=Point(&layoutns, 470,430);
2129 cb->setEnd(&p);
2130
2131 SpeciesReferenceGlyph* srg_oxaloacetate_cyt_2=rg_aspartateat_cyt->createSpeciesReferenceGlyph();
2132 srg_oxaloacetate_cyt_2->setId("srg_oxaloacetate_cyt_2");
2133 srg_oxaloacetate_cyt_2->setSpeciesGlyphId(speciesGlyph_oxaloacetate_cyt->getId());
2134 srg_oxaloacetate_cyt_2->setSpeciesReferenceId(sr_oxaloacetate_cyt_2->getId());
2135 srg_oxaloacetate_cyt_2->setRole(SPECIES_ROLE_SUBSTRATE);
2136
2137 curve=srg_oxaloacetate_cyt_2->getCurve();
2138 ls=curve->createLineSegment();
2139 p=Point(&layoutns, 700,581);
2140 ls->setStart(&p);
2141 p=Point(&layoutns, 700,516);
2142 ls->setEnd(&p);
2143
2144 SpeciesReferenceGlyph* srg_glutamate_cyt_1=rg_aspartateat_cyt->createSpeciesReferenceGlyph();
2145 srg_glutamate_cyt_1->setId("srg_glutamate_cyt_1");
2146 srg_glutamate_cyt_1->setSpeciesGlyphId(speciesGlyph_glutamate_cyt->getId());
2147 srg_glutamate_cyt_1->setSpeciesReferenceId(sr_glutamate_cyt_1->getId());
2148 srg_glutamate_cyt_1->setRole(SPECIES_ROLE_SUBSTRATE);
2149
2150 curve=srg_glutamate_cyt_1->getCurve();
2151 cb=curve->createCubicBezier();
2152 p=Point(&layoutns, 700,581);
2153 cb->setStart(&p);
2154 p=Point(&layoutns, 750,581);
2155 cb->setBasePoint1(&p);
2156 p=Point(&layoutns, 750,628);
2157 cb->setBasePoint2(&p);
2158 p=Point(&layoutns, 800,628);
2159 cb->setEnd(&p);
2160
2161 SpeciesReferenceGlyph* srg_aspartate_cyt_1=rg_aspartateat_cyt->createSpeciesReferenceGlyph();
2162 srg_aspartate_cyt_1->setId("srg_aspartate_cyt_1");
2163 srg_aspartate_cyt_1->setSpeciesGlyphId(speciesGlyph_aspartate_cyt->getId());
2164 srg_aspartate_cyt_1->setSpeciesReferenceId(sr_aspartate_cyt_1->getId());
2165 srg_aspartate_cyt_1->setRole(SPECIES_ROLE_PRODUCT);
2166
2167 curve=srg_aspartate_cyt_1->getCurve();
2168 ls=curve->createLineSegment();
2169 p=Point(&layoutns, 700,615);
2170 ls->setStart(&p);
2171 p=Point(&layoutns, 700,680);
2172 ls->setEnd(&p);
2173
2174 SpeciesReferenceGlyph* srg_aKetoglutarate_cyt_1=rg_aspartateat_cyt->createSpeciesReferenceGlyph();
2175 srg_aKetoglutarate_cyt_1->setId("srg_aKetoglutaratecyt_1");
2176 srg_aKetoglutarate_cyt_1->setSpeciesGlyphId(speciesGlyph_aKetoglutarate_cyt->getId());
2177 srg_aKetoglutarate_cyt_1->setSpeciesReferenceId(sr_aKetoglutarate_cyt_1->getId());
2178 srg_aKetoglutarate_cyt_1->setRole(SPECIES_ROLE_PRODUCT);
2179
2180 curve=srg_aKetoglutarate_cyt_1->getCurve();
2181 cb=curve->createCubicBezier();
2182 p=Point(&layoutns, 700,615);
2183 cb->setStart(&p);
2184 p=Point(&layoutns, 790,615);
2185 cb->setBasePoint1(&p);
2186 p=Point(&layoutns, 790,515);
2187 cb->setBasePoint2(&p);
2188 p=Point(&layoutns, 860,515);
2189 cb->setEnd(&p);
2190
2191
2192 // Malate mito3
2193 SpeciesGlyph* speciesGlyph_malate_mito3=layout->createSpeciesGlyph();
2194 speciesGlyph_malate_mito3->setId("SpeciesGlyph_malate_mito3");
2195 speciesGlyph_malate_mito3->setSpeciesId(malate_mito3->getId());
2196 bb=BoundingBox(&layoutns, "bb_sg_malate_mito3",1850,80,240,36);
2197 speciesGlyph_malate_mito3->setBoundingBox(&bb);
2198
2199 tg=layout->createTextGlyph();
2200 tg->setId("TextGlyph_malate_mito3");
2201 bb=BoundingBox(&layoutns, "bb_tg_malatate_mito3",1860,80,220,36);
2202 tg->setBoundingBox(&bb);
2203 tg->setOriginOfTextId(malate_mito3->getId());
2204 tg->setGraphicalObjectId(speciesGlyph_malate_mito3->getId());
2205
2206 // Oxaloacetate mito3
2207 SpeciesGlyph* speciesGlyph_oxaloacetate_mito3=layout->createSpeciesGlyph();
2208 speciesGlyph_oxaloacetate_mito3->setId("SpeciesGlyph_oxaloacetate_mito3");
2209 speciesGlyph_oxaloacetate_mito3->setSpeciesId(oxaloacetate_mito3->getId());
2210 bb=BoundingBox(&layoutns, "bb_sg_oxaloacetate_mito3",1850,280,240,36);
2211 speciesGlyph_oxaloacetate_mito3->setBoundingBox(&bb);
2212
2213 tg=layout->createTextGlyph();
2214 tg->setId("TextGlyph_oxaloacetate_mito3");
2215 bb=BoundingBox(&layoutns, "bb_tg_oxaloacetate_mito3",1860,280,220,36);
2216 tg->setBoundingBox(&bb);
2217 tg->setOriginOfTextId(oxaloacetate_mito3->getId());
2218 tg->setGraphicalObjectId(speciesGlyph_oxaloacetate_mito3->getId());
2219
2220 // Aspartate mito3
2221 SpeciesGlyph* speciesGlyph_aspartate_mito3=layout->createSpeciesGlyph();
2222 speciesGlyph_aspartate_mito3->setId("SpeciesGlyph_aspartate_mito3");
2223 speciesGlyph_aspartate_mito3->setSpeciesId(aspartate_mito3->getId());
2224 bb=BoundingBox(&layoutns, "bb_sg_aspartate_mito3",1850,480,240,36);
2225 speciesGlyph_aspartate_mito3->setBoundingBox(&bb);
2226
2227 tg=layout->createTextGlyph();
2228 tg->setId("TextGlyph_aspartate_mito3");
2229 bb=BoundingBox(&layoutns, "bb_tg_aspartate_mito3",1860,480,220,36);
2230 tg->setBoundingBox(&bb);
2231 tg->setOriginOfTextId(aspartate_mito3->getId());
2232 tg->setGraphicalObjectId(speciesGlyph_aspartate_mito3->getId());
2233
2234 // Glutamate mito3
2235 SpeciesGlyph* speciesGlyph_glutamate_mito3=layout->createSpeciesGlyph();
2236 speciesGlyph_glutamate_mito3->setId("SpeciesGlyph_glutamate_mito3");
2237 speciesGlyph_glutamate_mito3->setSpeciesId(glutamate_mito3->getId());
2238 bb=BoundingBox(&layoutns, "bb_sg_glutamate_mito3",1550,430,240,36);
2239 speciesGlyph_glutamate_mito3->setBoundingBox(&bb);
2240
2241 tg=layout->createTextGlyph();
2242 tg->setId("TextGlyph_glutamate_mito3");
2243 bb=BoundingBox(&layoutns, "bb_tg_glutamate_mito3",1560,430,220,36);
2244 tg->setBoundingBox(&bb);
2245 tg->setOriginOfTextId(glutamate_mito3->getId());
2246 tg->setGraphicalObjectId(speciesGlyph_glutamate_mito3->getId());
2247
2248 // alpha-Ketoglutarate mito3
2249 SpeciesGlyph* speciesGlyph_aKetoglutarate_mito3=layout->createSpeciesGlyph();
2250 speciesGlyph_aKetoglutarate_mito3->setId("SpeciesGlyph_aKetoglutarate_mito3");
2251 speciesGlyph_aKetoglutarate_mito3->setSpeciesId(aKetoglutarate_mito3->getId());
2252 bb=BoundingBox(&layoutns, "bb_sg_aKetoglutarate_mito3",1530,300,280,36);
2253 speciesGlyph_aKetoglutarate_mito3->setBoundingBox(&bb);
2254
2255 tg=layout->createTextGlyph();
2256 tg->setId("TextGlyph_aKetoglutarate_mito3");
2257 bb=BoundingBox(&layoutns, "bb_tg_aKetoglutarate_mito3",1540,300,260,36);
2258 tg->setBoundingBox(&bb);
2259 tg->setOriginOfTextId(aKetoglutarate_mito3->getId());
2260 tg->setGraphicalObjectId(speciesGlyph_aKetoglutarate_mito3->getId());
2261
2262 // NAD+ mito3
2263 SpeciesGlyph* speciesGlyph_nad_mito3=layout->createSpeciesGlyph();
2264 speciesGlyph_nad_mito3->setId("SpeciesGlyph_nad_mito3");
2265 speciesGlyph_nad_mito3->setSpeciesId(nad_mito3->getId());
2266 bb=BoundingBox(&layoutns, "bb_sg_nad_mito3",2050,150,100,24);
2267 speciesGlyph_nad_mito3->setBoundingBox(&bb);
2268
2269 tg=layout->createTextGlyph();
2270 tg->setId("TextGlyph_nad_mito3");
2271 bb=BoundingBox(&layoutns, "bb_tg_nad_mito3",2055,150,80,24);
2272 tg->setBoundingBox(&bb);
2273 tg->setOriginOfTextId(nad_mito3->getId());
2274 tg->setGraphicalObjectId(speciesGlyph_nad_mito3->getId());
2275
2276 // NADH mito3
2277 SpeciesGlyph* speciesGlyph_nadh_mito3=layout->createSpeciesGlyph();
2278 speciesGlyph_nadh_mito3->setId("SpeciesGlyph_nadh_mito3");
2279 speciesGlyph_nadh_mito3->setSpeciesId(nadh_mito3->getId());
2280 bb=BoundingBox(&layoutns, "bb_sg_nadh_mito3",2050,230,100,24);
2281 speciesGlyph_nadh_mito3->setBoundingBox(&bb);
2282
2283 tg=layout->createTextGlyph();
2284 tg->setId("TextGlyph_nadh_mito3");
2285 bb=BoundingBox(&layoutns, "bb_tg_nadh_mito3",2055,230,80,24);
2286 tg->setBoundingBox(&bb);
2287 tg->setOriginOfTextId(nadh_mito3->getId());
2288 tg->setGraphicalObjectId(speciesGlyph_nadh_mito3->getId());
2289
2290 // H+ mito3
2291 SpeciesGlyph* speciesGlyph_h_mito3=layout->createSpeciesGlyph();
2292 speciesGlyph_h_mito3->setId("SpeciesGlyph_h_mito3");
2293 speciesGlyph_h_mito3->setSpeciesId(h_mito3->getId());
2294 bb=BoundingBox(&layoutns, "bb_sg_h_mito3",2200,230,40,24);
2295 speciesGlyph_h_mito3->setBoundingBox(&bb);
2296
2297 tg=layout->createTextGlyph();
2298 tg->setId("TextGlyph_h_mito3");
2299 bb=BoundingBox(&layoutns, "bb_tg_h_mito3",2205,230,30,24);
2300 tg->setBoundingBox(&bb);
2301 tg->setOriginOfTextId(h_mito3->getId());
2302 tg->setGraphicalObjectId(speciesGlyph_h_mito3->getId());
2303
2304
2305 // create the ReactionGlyphs
2306
2307 ReactionGlyph* rg_malatedh_mito3=layout->createReactionGlyph();
2308 rg_malatedh_mito3->setId("rg_malatedh_mito3");
2309 rg_malatedh_mito3->setReactionId(malatedh_mito3->getId());
2310
2311 curve=rg_malatedh_mito3->getCurve();
2312 ls=curve->createLineSegment();
2313 p=Point(&layoutns, 1970,181);
2314 ls->setStart(&p);
2315 p=Point(&layoutns, 1970,215);
2316 ls->setEnd(&p);
2317
2318 tg=layout->createTextGlyph();
2319 tg->setId("tg_rg_malatedh_mito3");
2320 bb=BoundingBox(&layoutns, "bb_tg_rg_malatedh_mito3",1740,185,220,24);
2321 tg->setBoundingBox(&bb);
2322 tg->setOriginOfTextId(malatedh_mito3->getId());
2323 tg->setGraphicalObjectId(rg_malatedh_mito3->getId());
2324
2325 ReactionGlyph* rg_aspartateat_mito3=layout->createReactionGlyph();
2326 rg_aspartateat_mito3->setId("rg_aspartateat_mito3");
2327 rg_aspartateat_mito3->setReactionId(aspartateat_mito3->getId());
2328
2329 curve=rg_aspartateat_mito3->getCurve();
2330 ls=curve->createLineSegment();
2331 p=Point(&layoutns, 1970,381);
2332 ls->setStart(&p);
2333 p=Point(&layoutns, 1970,415);
2334 ls->setEnd(&p);
2335
2336 tg=layout->createTextGlyph();
2337 tg->setId("tg_rg_aspartateat_mito3");
2338 bb=BoundingBox(&layoutns, "bb_tg_rg_aspartateat_mito3",1970,385,260,24);
2339 tg->setBoundingBox(&bb);
2340 tg->setOriginOfTextId(aspartateat_mito3->getId());
2341 tg->setGraphicalObjectId(rg_aspartateat_mito3->getId());
2342
2343
2344 // add the SpeciesReferenceGlyphs
2345
2346 SpeciesReferenceGlyph* srg_malate_mito3_1=rg_malatedh_mito3->createSpeciesReferenceGlyph();
2347 srg_malate_mito3_1->setId("srg_malate_mito3_1");
2348 srg_malate_mito3_1->setSpeciesGlyphId(speciesGlyph_malate_mito3->getId());
2349 srg_malate_mito3_1->setSpeciesReferenceId(sr_malate_mito3->getId());
2350 srg_malate_mito3_1->setRole(SPECIES_ROLE_SUBSTRATE);
2351
2352 ls=srg_malate_mito3_1->createLineSegment();
2353 p=Point(&layoutns, 1970,181);
2354 ls->setStart(&p);
2355 p=Point(&layoutns, 1970,116);
2356 ls->setEnd(&p);
2357
2358 SpeciesReferenceGlyph* srg_nad_mito3=rg_malatedh_mito3->createSpeciesReferenceGlyph();
2359 srg_nad_mito3->setId("srg_nad_mito3");
2360 srg_nad_mito3->setSpeciesGlyphId(speciesGlyph_nad_mito3->getId());
2361 srg_nad_mito3->setSpeciesReferenceId(sr_nad_mito3->getId());
2362 srg_nad_mito3->setRole(SPECIES_ROLE_SUBSTRATE);
2363
2364 cb=srg_nad_mito3->createCubicBezier();
2365 p=Point(&layoutns, 1970,181);
2366 cb->setStart(&p);
2367 p=Point(&layoutns, 1970,162);
2368 cb->setBasePoint1(&p);
2369 p=Point(&layoutns, 1970,162);
2370 cb->setBasePoint2(&p);
2371 p=Point(&layoutns, 2050,162);
2372 cb->setEnd(&p);
2373
2374 SpeciesReferenceGlyph* srg_oxaloacetate_mito3_1=rg_malatedh_mito3->createSpeciesReferenceGlyph();
2375 srg_oxaloacetate_mito3_1->setId("srg_oxaloacetate_mito3_1");
2376 srg_oxaloacetate_mito3_1->setSpeciesGlyphId(speciesGlyph_oxaloacetate_mito3->getId());
2377 srg_oxaloacetate_mito3_1->setSpeciesReferenceId(sr_oxaloacetate_mito3_1->getId());
2378 srg_oxaloacetate_mito3_1->setRole(SPECIES_ROLE_PRODUCT);
2379
2380 curve=srg_oxaloacetate_mito3_1->getCurve();
2381 ls=curve->createLineSegment();
2382 p=Point(&layoutns, 1970,215);
2383 ls->setStart(&p);
2384 p=Point(&layoutns, 1970,280);
2385 ls->setEnd(&p);
2386
2387 SpeciesReferenceGlyph* srg_nadh_mito3=rg_malatedh_mito3->createSpeciesReferenceGlyph();
2388 srg_nadh_mito3->setId("srg_nadh_mito3");
2389 srg_nadh_mito3->setSpeciesGlyphId(speciesGlyph_nadh_mito3->getId());
2390 srg_nadh_mito3->setSpeciesReferenceId(sr_nadh_mito3->getId());
2391 srg_nadh_mito3->setRole(SPECIES_ROLE_PRODUCT);
2392
2393 cb=srg_nadh_mito3->createCubicBezier();
2394 p=Point(&layoutns, 1970,215);
2395 cb->setStart(&p);
2396 p=Point(&layoutns, 1970,242);
2397 cb->setBasePoint1(&p);
2398 p=Point(&layoutns, 1970,242);
2399 cb->setBasePoint2(&p);
2400 p=Point(&layoutns, 2050,242);
2401 cb->setEnd(&p);
2402
2403 SpeciesReferenceGlyph* srg_h_mito3=rg_malatedh_mito3->createSpeciesReferenceGlyph();
2404 srg_h_mito3->setId("srg_h_mito3");
2405 srg_h_mito3->setSpeciesGlyphId(speciesGlyph_h_mito3->getId());
2406 srg_h_mito3->setSpeciesReferenceId(sr_h_mito3->getId());
2407 srg_h_mito3->setRole(SPECIES_ROLE_PRODUCT);
2408
2409 cb=srg_h_mito3->createCubicBezier();
2410 p=Point(&layoutns, 1970,215);
2411 cb->setStart(&p);
2412 p=Point(&layoutns, 2100,215);
2413 cb->setBasePoint1(&p);
2414 p=Point(&layoutns, 2100,215);
2415 cb->setBasePoint2(&p);
2416 p=Point(&layoutns, 2200,230);
2417 cb->setEnd(&p);
2418
2419 SpeciesReferenceGlyph* srg_oxaloacetate_mito3_2=rg_aspartateat_mito3->createSpeciesReferenceGlyph();
2420 srg_oxaloacetate_mito3_2->setId("srg_oxaloacetate_mito3_2");
2421 srg_oxaloacetate_mito3_2->setSpeciesGlyphId(speciesGlyph_oxaloacetate_mito3->getId());
2422 srg_oxaloacetate_mito3_2->setSpeciesReferenceId(sr_oxaloacetate_mito3_2->getId());
2423 srg_oxaloacetate_mito3_2->setRole(SPECIES_ROLE_SUBSTRATE);
2424
2425 curve=srg_oxaloacetate_mito3_2->getCurve();
2426 ls=curve->createLineSegment();
2427 p=Point(&layoutns, 1970,381);
2428 ls->setStart(&p);
2429 p=Point(&layoutns, 1970,316);
2430 ls->setEnd(&p);
2431
2432 SpeciesReferenceGlyph* srg_glutamate_mito3_1=rg_aspartateat_mito3->createSpeciesReferenceGlyph();
2433 srg_glutamate_mito3_1->setId("srg_glutamate_mito3_1");
2434 srg_glutamate_mito3_1->setSpeciesGlyphId(speciesGlyph_glutamate_mito3->getId());
2435 srg_glutamate_mito3_1->setSpeciesReferenceId(sr_glutamate_mito3_1->getId());
2436 srg_glutamate_mito3_1->setRole(SPECIES_ROLE_SUBSTRATE);
2437
2438 curve=srg_glutamate_mito3_1->getCurve();
2439 cb=curve->createCubicBezier();
2440 p=Point(&layoutns, 1970,381);
2441 cb->setStart(&p);
2442 p=Point(&layoutns, 1880,381);
2443 cb->setBasePoint1(&p);
2444 p=Point(&layoutns, 1880,448);
2445 cb->setBasePoint2(&p);
2446 p=Point(&layoutns, 1790,448);
2447 cb->setEnd(&p);
2448
2449 SpeciesReferenceGlyph* srg_aspartate_mito3_1=rg_aspartateat_mito3->createSpeciesReferenceGlyph();
2450 srg_aspartate_mito3_1->setId("srg_aspartate_mito3_1");
2451 srg_aspartate_mito3_1->setSpeciesGlyphId(speciesGlyph_aspartate_mito3->getId());
2452 srg_aspartate_mito3_1->setSpeciesReferenceId(sr_aspartate_mito3_1->getId());
2453 srg_aspartate_mito3_1->setRole(SPECIES_ROLE_PRODUCT);
2454
2455 curve=srg_aspartate_mito3_1->getCurve();
2456 ls=curve->createLineSegment();
2457 p=Point(&layoutns, 1970,415);
2458 ls->setStart(&p);
2459 p=Point(&layoutns, 1970,480);
2460 ls->setEnd(&p);
2461
2462 SpeciesReferenceGlyph* srg_aKetoglutarate_mito3_1=rg_aspartateat_mito3->createSpeciesReferenceGlyph();
2463 srg_aKetoglutarate_mito3_1->setId("srg_aKetoglutaratemito3_1");
2464 srg_aKetoglutarate_mito3_1->setSpeciesGlyphId(speciesGlyph_aKetoglutarate_mito3->getId());
2465 srg_aKetoglutarate_mito3_1->setSpeciesReferenceId(sr_aKetoglutarate_mito3_1->getId());
2466 srg_aKetoglutarate_mito3_1->setRole(SPECIES_ROLE_PRODUCT);
2467
2468 curve=srg_aKetoglutarate_mito3_1->getCurve();
2469 cb=curve->createCubicBezier();
2470 p=Point(&layoutns, 1970,415);
2471 cb->setStart(&p);
2472 p=Point(&layoutns, 1880,415);
2473 cb->setBasePoint1(&p);
2474 p=Point(&layoutns, 1880,315);
2475 cb->setBasePoint2(&p);
2476 p=Point(&layoutns, 1810,315);
2477 cb->setEnd(&p);
2478
2479 // add the transport reaction glyphs
2480
2481 ReactionGlyph* rg_aspartateCarrier=layout->createReactionGlyph();
2482 rg_aspartateCarrier->setId("rg_aspartateCarrier");
2483 rg_aspartateCarrier->setReactionId(aspartateCarrier->getId());
2484
2485 curve=rg_aspartateCarrier->getCurve();
2486 ls=curve->createLineSegment();
2487 p=Point(&layoutns, 1420,530);
2488 ls->setStart(&p);
2489 p=Point(&layoutns, 1360,550);
2490 ls->setEnd(&p);
2491
2492 tg=layout->createTextGlyph();
2493 tg->setId("tg_rg_aspartateCarrier");
2494 bb=BoundingBox(&layoutns, "bb_tg_rg_aspartateCarrier",1380,500,160,24);
2495 tg->setBoundingBox(&bb);
2496 tg->setOriginOfTextId(aspartateCarrier->getId());
2497 tg->setGraphicalObjectId(rg_aspartateCarrier->getId());
2498
2499
2500 ReactionGlyph* rg_malateCarrier=layout->createReactionGlyph();
2501 rg_malateCarrier->setId("rg_malateCarrier");
2502 rg_malateCarrier->setReactionId(malateCarrier->getId());
2503
2504 curve=rg_malateCarrier->getCurve();
2505 ls=curve->createLineSegment();
2506 p=Point(&layoutns, 1420,320);
2507 ls->setStart(&p);
2508 p=Point(&layoutns, 1360,340);
2509 ls->setEnd(&p);
2510
2511 tg=layout->createTextGlyph();
2512 tg->setId("tg_rg_malateCarrier");
2513 bb=BoundingBox(&layoutns, "bb_tg_rg_malateCarrier",1360,330,140,24);
2514 tg->setBoundingBox(&bb);
2515 tg->setOriginOfTextId(malateCarrier->getId());
2516 tg->setGraphicalObjectId(rg_malateCarrier->getId());
2517
2518
2519
2520 // add the SpeciesReferenceGlyphs for the transporters
2521
2522 SpeciesReferenceGlyph* srg_aKetoglutarate_mito3_2=rg_malateCarrier->createSpeciesReferenceGlyph();
2523 srg_aKetoglutarate_mito3_2->setId("srg_aKetoglutarate_mito3_2");
2524 srg_aKetoglutarate_mito3_2->setSpeciesGlyphId(speciesGlyph_aKetoglutarate_mito3->getId());
2525 srg_aKetoglutarate_mito3_2->setSpeciesReferenceId(sr_aKetoglutarate_mito3_2->getId());
2526 srg_aKetoglutarate_mito3_2->setRole(SPECIES_ROLE_SUBSTRATE);
2527
2528 curve=srg_aKetoglutarate_mito3_2->getCurve();
2529 ls=curve->createLineSegment();
2530 p=Point(&layoutns, 1420,320);
2531 ls->setStart(&p);
2532 p=Point(&layoutns, 1530,318);
2533 ls->setEnd(&p);
2534
2535
2536 SpeciesReferenceGlyph* srg_aKetoglutarate_cyt_2=rg_malateCarrier->createSpeciesReferenceGlyph();
2537 srg_aKetoglutarate_cyt_2->setId("srg_aKetoglutarate_cyt_2");
2538 srg_aKetoglutarate_cyt_2->setSpeciesGlyphId(speciesGlyph_aKetoglutarate_cyt->getId());
2539 srg_aKetoglutarate_cyt_2->setSpeciesReferenceId(sr_aKetoglutarate_cyt_2->getId());
2540 srg_aKetoglutarate_cyt_2->setRole(SPECIES_ROLE_PRODUCT);
2541
2542 curve=srg_aKetoglutarate_cyt_2->getCurve();
2543 ls=curve->createLineSegment();
2544 p=Point(&layoutns, 1360,340);
2545 ls->setStart(&p);
2546 p=Point(&layoutns, 1140,518);
2547 ls->setEnd(&p);
2548
2549
2550 SpeciesReferenceGlyph* srg_malate_cyt_2=rg_malateCarrier->createSpeciesReferenceGlyph();
2551 srg_malate_cyt_2->setId("srg_malate_cyt_2");
2552 srg_malate_cyt_2->setSpeciesGlyphId(speciesGlyph_malate_cyt->getId());
2553 srg_malate_cyt_2->setSpeciesReferenceId(sr_malate_cyt_2->getId());
2554 srg_malate_cyt_2->setRole(SPECIES_ROLE_SUBSTRATE);
2555
2556 curve=srg_malate_cyt_2->getCurve();
2557 cb=curve->createCubicBezier();
2558 p=Point(&layoutns, 1420,320);
2559 cb->setStart(&p);
2560 p=Point(&layoutns, 1390,250);
2561 cb->setBasePoint1(&p);
2562 p=Point(&layoutns, 1390,250);
2563 cb->setBasePoint2(&p);
2564 p=Point(&layoutns, 820,298);
2565 cb->setEnd(&p);
2566
2567
2568 SpeciesReferenceGlyph* srg_malate_mito3_2=rg_malateCarrier->createSpeciesReferenceGlyph();
2569 srg_malate_mito3_2->setId("srg_malate_mito3_2");
2570 srg_malate_mito3_2->setSpeciesGlyphId(speciesGlyph_malate_mito3->getId());
2571 srg_malate_mito3_2->setSpeciesReferenceId(sr_malate_mito3_2->getId());
2572 srg_malate_mito3_2->setRole(SPECIES_ROLE_PRODUCT);
2573
2574 curve=srg_malate_mito3_2->getCurve();
2575 cb=curve->createCubicBezier();
2576 p=Point(&layoutns, 1360,340);
2577 cb->setStart(&p);
2578 p=Point(&layoutns, 1390,150);
2579 cb->setBasePoint1(&p);
2580 p=Point(&layoutns, 1390,150);
2581 cb->setBasePoint2(&p);
2582 p=Point(&layoutns, 1850,98);
2583 cb->setEnd(&p);
2584
2585
2586
2587
2588
2589
2590 SpeciesReferenceGlyph* srg_aspartate_mito3_2=rg_aspartateCarrier->createSpeciesReferenceGlyph();
2591 srg_aspartate_mito3_2->setId("srg_aspartate_mito3_2");
2592 srg_aspartate_mito3_2->setSpeciesGlyphId(speciesGlyph_aspartate_mito3->getId());
2593 srg_aspartate_mito3_2->setSpeciesReferenceId(sr_aspartate_mito3_2->getId());
2594 srg_aspartate_mito3_2->setRole(SPECIES_ROLE_SUBSTRATE);
2595
2596 curve=srg_aspartate_mito3_2->getCurve();
2597 ls=curve->createLineSegment();
2598 p=Point(&layoutns, 1420,530);
2599 ls->setStart(&p);
2600 p=Point(&layoutns, 1850,498);
2601 ls->setEnd(&p);
2602
2603
2604 SpeciesReferenceGlyph* srg_aspartate_cyt_2=rg_aspartateCarrier->createSpeciesReferenceGlyph();
2605 srg_aspartate_cyt_2->setId("srg_aspartate_cyt_2");
2606 srg_aspartate_cyt_2->setSpeciesGlyphId(speciesGlyph_aspartate_cyt->getId());
2607 srg_aspartate_cyt_2->setSpeciesReferenceId(sr_aspartate_cyt_2->getId());
2608 srg_aspartate_cyt_2->setRole(SPECIES_ROLE_PRODUCT);
2609
2610 curve=srg_aspartate_cyt_2->getCurve();
2611 cb=curve->createCubicBezier();
2612 p=Point(&layoutns, 1360,550);
2613 cb->setStart(&p);
2614 p=Point(&layoutns, 1390,698);
2615 cb->setBasePoint1(&p);
2616 p=Point(&layoutns, 1390,698);
2617 cb->setBasePoint2(&p);
2618 p=Point(&layoutns, 820,698);
2619 cb->setEnd(&p);
2620
2621
2622 SpeciesReferenceGlyph* srg_glutamate_cyt_2=rg_aspartateCarrier->createSpeciesReferenceGlyph();
2623 srg_glutamate_cyt_2->setId("srg_glutamate_cyt_2");
2624 srg_glutamate_cyt_2->setSpeciesGlyphId(speciesGlyph_glutamate_cyt->getId());
2625 srg_glutamate_cyt_2->setSpeciesReferenceId(sr_glutamate_cyt_2->getId());
2626 srg_glutamate_cyt_2->setRole(SPECIES_ROLE_SUBSTRATE);
2627
2628 curve=srg_glutamate_cyt_2->getCurve();
2629 cb=curve->createCubicBezier();
2630 p=Point(&layoutns, 1420,530);
2631 cb->setStart(&p);
2632 p=Point(&layoutns, 1390,648);
2633 cb->setBasePoint1(&p);
2634 p=Point(&layoutns, 1390,648);
2635 cb->setBasePoint2(&p);
2636 p=Point(&layoutns, 1050,628);
2637 cb->setEnd(&p);
2638
2639
2640 SpeciesReferenceGlyph* srg_glutamate_mito3_2=rg_aspartateCarrier->createSpeciesReferenceGlyph();
2641 srg_glutamate_mito3_2->setId("srg_glutamate_mito3_2");
2642 srg_glutamate_mito3_2->setSpeciesGlyphId(speciesGlyph_glutamate_mito3->getId());
2643 srg_glutamate_mito3_2->setSpeciesReferenceId(sr_glutamate_mito3_2->getId());
2644 srg_glutamate_mito3_2->setRole(SPECIES_ROLE_PRODUCT);
2645
2646 curve=srg_glutamate_mito3_2->getCurve();
2647 cb=curve->createCubicBezier();
2648 p=Point(&layoutns, 1360,550);
2649 cb->setStart(&p);
2650 p=Point(&layoutns, 1390,448);
2651 cb->setBasePoint1(&p);
2652 p=Point(&layoutns, 1390,448);
2653 cb->setBasePoint2(&p);
2654 p=Point(&layoutns, 1550,448);
2655 cb->setEnd(&p);
2656
2657 // now we add some global render information
2658 ListOfLayouts* pListOfLayouts=plugin->getListOfLayouts();
2659 fail_unless(pListOfLayouts!=NULL);
2660
2661 RenderListOfLayoutsPlugin* lolPlugin = (RenderListOfLayoutsPlugin*)pListOfLayouts->getPlugin("render");
2662 GlobalRenderInformation* pGlobalRender=lolPlugin->createGlobalRenderInformation();
2663 pGlobalRender->setId("wireFrame");
2664 pGlobalRender->setName("wireframe style");
2665 pGlobalRender->setProgramName("Ralph Gauges");
2666 pGlobalRender->setProgramVersion("1.0");
2667 pGlobalRender->setBackgroundColor("#FFFFFFFF");
2668 // color definitions
2669 ColorDefinition* pColorDefinition=pGlobalRender->createColorDefinition();
2670 pColorDefinition->setId("white");
2671 pColorDefinition->setColorValue("#FFFFFF");
2672 pColorDefinition=pGlobalRender->createColorDefinition();
2673 pColorDefinition->setId("black");
2674 pColorDefinition->setColorValue("#000000");
2675 // styles
2676 // style for compartment glyphs
2677 GlobalStyle* pGlobalStyle=pGlobalRender->createStyle("compartmentGlyphStyle");
2678 pGlobalStyle->addType("COMPARTMENTGLYPH");
2679 RenderGroup* pGroup=pGlobalStyle->getGroup();
2680 pGroup->setStroke("black");
2681 pGroup->setStrokeWidth(1.0);
2682 Rectangle* pRectangle=pGroup->createRectangle();
2683 pRectangle->setCoordinatesAndSize(RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0),RelAbsVector(0.0,100.0),RelAbsVector(0.0,100.0));
2684 pRectangle->setRadiusX(RelAbsVector(0.0,0.0));
2685
2686 // style for species glyphs
2687 pGlobalStyle=pGlobalRender->createStyle("speciesGlyphStyle");
2688 pGlobalStyle->addType("SPECIESGLYPH");
2689 pGroup=pGlobalStyle->getGroup();
2690 pGroup->setStroke("black");
2691 pGroup->setStrokeWidth(1.0);
2692 pRectangle=pGroup->createRectangle();
2693 pRectangle->setCoordinatesAndSize(RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0),RelAbsVector(0.0,100.0),RelAbsVector(0.0,100.0));
2694 pRectangle->setRadiusX(RelAbsVector(0.0,0.0));
2695
2696 // style for all other glyphs
2697 pGlobalStyle=pGlobalRender->createStyle("reactionGlyphStyle");
2698 pGlobalStyle->addType("SPECIESREFERENCEGLYPH");
2699 pGlobalStyle->addType("REACTIONGLYPH");
2700 pGlobalStyle->addType("TEXTGLYPH");
2701 pGroup=pGlobalStyle->getGroup();
2702 pGroup->setStroke("black");
2703 pGroup->setStrokeWidth(1.0);
2704 pGroup->setFontSize(RelAbsVector(12.0,0.0));
2705 pGroup->setTextAnchor(Text::ANCHOR_MIDDLE);
2706
2707 // second render information
2708 lolPlugin = (RenderListOfLayoutsPlugin*)pListOfLayouts->getPlugin("render");
2709 pGlobalRender=lolPlugin->createGlobalRenderInformation();
2710 pGlobalRender->setId("defaultGrayStyle");
2711 pGlobalRender->setName("grayscale style");
2712 pGlobalRender->setProgramName("Ralph Gauges");
2713 pGlobalRender->setProgramVersion("1.0");
2714 pGlobalRender->setBackgroundColor("#FFFFFFFF");
2715 // color definitions
2716 pColorDefinition=pGlobalRender->createColorDefinition();
2717 pColorDefinition->setId("lightGray");
2718 pColorDefinition->setColorValue("#CECECE");
2719 pColorDefinition=pGlobalRender->createColorDefinition();
2720 pColorDefinition->setId("white");
2721 pColorDefinition->setColorValue("#FFFFFF");
2722 pColorDefinition=pGlobalRender->createColorDefinition();
2723 pColorDefinition->setId("black");
2724 pColorDefinition->setColorValue("#000000");
2725 pColorDefinition=pGlobalRender->createColorDefinition();
2726 pColorDefinition->setId("lightGray2");
2727 pColorDefinition->setColorValue("#F0F0F0");
2728 pColorDefinition=pGlobalRender->createColorDefinition();
2729 pColorDefinition->setId("gray");
2730 pColorDefinition->setColorValue("#0B0B0B");
2731 // gradient definitions
2732 RadialGradient* pRadialGradient=pGlobalRender->createRadialGradientDefinition();
2733 pRadialGradient->setId("speciesGlyphGradient");
2734 GradientStop* pStop=pRadialGradient->createGradientStop();
2735 pStop->setOffset(RelAbsVector(0.0,0.0));
2736 pStop->setStopColor("white");
2737 pStop=pRadialGradient->createGradientStop();
2738 pStop->setOffset(RelAbsVector(0.0,100.0));
2739 pStop->setStopColor("lightGray");
2740 // line endings
2741 LineEnding* pLineEnding=pGlobalRender->createLineEnding();
2742 pLineEnding->setId("simpleHead_black");
2743 p=Point(&layoutns, -8,-3);
2744 Dimensions d(&layoutns, 10,6);
2745 pLineEnding->getBoundingBox()->setPosition(&p);
2746 pLineEnding->getBoundingBox()->setDimensions(&d);
2747 pGroup=pLineEnding->getGroup();
2748 pGroup->setStroke("black");
2749 pGroup->setStrokeWidth(1.0);
2750 pGroup->setFillColor("black");
2751 Polygon* pPolygon=pGroup->createPolygon();
2752 RenderPoint* pR=pPolygon->createPoint();
2753 pR->setCoordinates(RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0));
2754 pR=pPolygon->createPoint();
2755 pR->setCoordinates(RelAbsVector(10.0,0.0),RelAbsVector(3.0,0.0));
2756 pR=pPolygon->createPoint();
2757 pR->setCoordinates(RelAbsVector(0.0,0.0),RelAbsVector(6.0,0.0));
2758
2759 // styles
2760 // style for compartment glyphs
2761 pGlobalStyle=pGlobalRender->createStyle("compartmentGlyphStyle");
2762 pGlobalStyle->addType("COMPARTMENTGLYPH");
2763 pGroup=pGlobalStyle->getGroup();
2764 pGroup->setStroke("gray");
2765 pGroup->setStrokeWidth(1.0);
2766 pRectangle=pGroup->createRectangle();
2767 pRectangle->setCoordinatesAndSize(RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0),RelAbsVector(0.0,100.0),RelAbsVector(0.0,100.0));
2768 pRectangle->setRadiusX(RelAbsVector(0.0,5.0));
2769 pRectangle->setFillColor("lightGray2");
2770
2771 // style for species glyphs
2772 pGlobalStyle=pGlobalRender->createStyle("speciesGlyphStyle");
2773 pGlobalStyle->addType("SPECIESGLYPH");
2774 pGroup=pGlobalStyle->getGroup();
2775 pGroup->setStroke("black");
2776 pGroup->setStrokeWidth(1.0);
2777 pRectangle=pGroup->createRectangle();
2778 pRectangle->setCoordinatesAndSize(RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0),RelAbsVector(0.0,100.0),RelAbsVector(0.0,100.0));
2779 pRectangle->setRadiusX(RelAbsVector(0.0,5.0));
2780 pRectangle->setFillColor("speciesGlyphGradient");
2781
2782 // style for reaction and text glyphs
2783 pGlobalStyle=pGlobalRender->createStyle("reactionGlyphStyle");
2784 pGlobalStyle->addType("REACTIONGLYPH");
2785 pGlobalStyle->addType("TEXTGLYPH");
2786 pGroup=pGlobalStyle->getGroup();
2787 pGroup->setStroke("black");
2788 pGroup->setStrokeWidth(1.0);
2789 pGroup->setFontSize(RelAbsVector(12.0,0.0));
2790 pGroup->setTextAnchor(Text::ANCHOR_MIDDLE);
2791
2792 // style for substrate and product species reference glyphs
2793 pGlobalStyle=pGlobalRender->createStyle("reactantSpeciesReferenceGlyphStyle");
2794 pGlobalStyle->addRole("substrate");
2795 pGlobalStyle->addRole("sidesubstrate");
2796 pGlobalStyle->addRole("product");
2797 pGlobalStyle->addRole("sideproduct");
2798 pGroup=pGlobalStyle->getGroup();
2799 pGroup->setStroke("#000000");
2800 pGroup->setStrokeWidth(1.0);
2801
2802 // style for activator species reference glyphs
2803 pGlobalStyle=pGlobalRender->createStyle("activatorSpeciesReferenceGlyphStyle");
2804 pGlobalStyle->addRole("activator");
2805 pGroup=pGlobalStyle->getGroup();
2806 pGroup->setStroke("#000000");
2807 pGroup->setStrokeWidth(1.0);
2808
2809 // style for modifier species reference glyphs
2810 pGlobalStyle=pGlobalRender->createStyle("modifierSpeciesReferenceGlyphStyle");
2811 pGlobalStyle->addRole("modifier");
2812 pGroup=pGlobalStyle->getGroup();
2813 pGroup->setStroke("#000000");
2814 pGroup->setStrokeWidth(1.0);
2815
2816 // style for inhibitor species reference glyphs
2817 pGlobalStyle=pGlobalRender->createStyle("inhibitorSpeciesReferenceGlyphStyle");
2818 pGlobalStyle->addRole("inhibitor");
2819 pGroup=pGlobalStyle->getGroup();
2820 pGroup->setStroke("#000000");
2821 pGroup->setStrokeWidth(1.0);
2822
2823 // short gray style which uses the default style and just redefines some colors
2824 // second render information
2825 lolPlugin = (RenderListOfLayoutsPlugin*)pListOfLayouts->getPlugin("render");
2826 pGlobalRender=lolPlugin->createGlobalRenderInformation();
2827 pGlobalRender->setId("shortGrayStyle");
2828 pGlobalRender->setName("modified default style to grayscale");
2829 pGlobalRender->setReferenceRenderInformationId("defaultStyle");
2830 pGlobalRender->setProgramName("Ralph Gauges");
2831 pGlobalRender->setProgramVersion("1.0");
2832 pGlobalRender->setBackgroundColor("#FFFFFFFF");
2833 // color definitions
2834 pColorDefinition=pGlobalRender->createColorDefinition();
2835 pColorDefinition->setId("lightBlue");
2836 pColorDefinition->setColorValue("#CECECE");
2837 pColorDefinition=pGlobalRender->createColorDefinition();
2838 pColorDefinition->setId("white");
2839 pColorDefinition->setColorValue("#FFFFFF");
2840 pColorDefinition=pGlobalRender->createColorDefinition();
2841 pColorDefinition->setId("black");
2842 pColorDefinition->setColorValue("#000000");
2843 pColorDefinition=pGlobalRender->createColorDefinition();
2844 pColorDefinition->setId("red");
2845 pColorDefinition->setColorValue("#000000");
2846 pColorDefinition=pGlobalRender->createColorDefinition();
2847 pColorDefinition->setId("green");
2848 pColorDefinition->setColorValue("#000000");
2849 pColorDefinition=pGlobalRender->createColorDefinition();
2850 pColorDefinition->setId("blue");
2851 pColorDefinition->setColorValue("#000000");
2852 pColorDefinition=pGlobalRender->createColorDefinition();
2853 pColorDefinition->setId("lightYellow");
2854 pColorDefinition->setColorValue("#F0F0F0");
2855 pColorDefinition=pGlobalRender->createColorDefinition();
2856 pColorDefinition->setId("darkGreen");
2857 pColorDefinition->setColorValue("#0B0B0B");
2858
2859 // render information for the default color style
2860 lolPlugin = (RenderListOfLayoutsPlugin*)pListOfLayouts->getPlugin("render");
2861 pGlobalRender=lolPlugin->createGlobalRenderInformation();
2862 pGlobalRender->setId("defaultStyle");
2863 pGlobalRender->setName("default style");
2864 pGlobalRender->setProgramName("Ralph Gauges");
2865 pGlobalRender->setProgramVersion("1.0");
2866 pGlobalRender->setBackgroundColor("#FFFFFFFF");
2867 // color definitions
2868 pColorDefinition=pGlobalRender->createColorDefinition();
2869 pColorDefinition->setId("lightBlue");
2870 pColorDefinition->setColorValue("#ADD8E6");
2871 pColorDefinition=pGlobalRender->createColorDefinition();
2872 pColorDefinition->setId("white");
2873 pColorDefinition->setColorValue("#FFFFFF");
2874 pColorDefinition=pGlobalRender->createColorDefinition();
2875 pColorDefinition->setId("black");
2876 pColorDefinition->setColorValue("#000000");
2877 pColorDefinition=pGlobalRender->createColorDefinition();
2878 pColorDefinition->setId("red");
2879 pColorDefinition->setColorValue("#FF0000");
2880 pColorDefinition=pGlobalRender->createColorDefinition();
2881 pColorDefinition->setId("green");
2882 pColorDefinition->setColorValue("#00FF00");
2883 pColorDefinition=pGlobalRender->createColorDefinition();
2884 pColorDefinition->setId("blue");
2885 pColorDefinition->setColorValue("#0000FF");
2886 pColorDefinition=pGlobalRender->createColorDefinition();
2887 pColorDefinition->setId("lightYellow");
2888 pColorDefinition->setColorValue("#FFFFD1");
2889 pColorDefinition=pGlobalRender->createColorDefinition();
2890 pColorDefinition->setId("darkGreen");
2891 pColorDefinition->setColorValue("#002000");
2892 // gradient definitions
2893 pRadialGradient=pGlobalRender->createRadialGradientDefinition();
2894 pRadialGradient->setId("speciesGlyphGradient");
2895 pStop=pRadialGradient->createGradientStop();
2896 pStop->setOffset(RelAbsVector(0.0,0.0));
2897 pStop->setStopColor("white");
2898 pStop=pRadialGradient->createGradientStop();
2899 pStop->setOffset(RelAbsVector(0.0,100.0));
2900 pStop->setStopColor("lightBlue");
2901 // line endings
2902 pLineEnding=pGlobalRender->createLineEnding();
2903 pLineEnding->setId("simpleHead_black");
2904 pLineEnding->getBoundingBox()->setPosition(&p);
2905 pLineEnding->getBoundingBox()->setDimensions(&d);
2906 pGroup=pLineEnding->getGroup();
2907 pGroup->setStroke("black");
2908 pGroup->setStrokeWidth(1.0);
2909 pGroup->setFillColor("black");
2910 pPolygon=pGroup->createPolygon();
2911 pR=pPolygon->createPoint();
2912 pR->setCoordinates(RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0));
2913 pR=pPolygon->createPoint();
2914 pR->setCoordinates(RelAbsVector(10.0,0.0),RelAbsVector(3.0,0.0));
2915 pR=pPolygon->createPoint();
2916 pR->setCoordinates(RelAbsVector(0.0,0.0),RelAbsVector(6.0,0.0));
2917 pLineEnding=pGlobalRender->createLineEnding();
2918 pLineEnding->setId("simpleHead_red");
2919 pLineEnding->getBoundingBox()->setPosition(&p);
2920 pLineEnding->getBoundingBox()->setDimensions(&d);
2921 pGroup=pLineEnding->getGroup();
2922 pGroup->setStroke("red");
2923 pGroup->setStrokeWidth(1.0);
2924 pGroup->setFillColor("red");
2925 pPolygon=pGroup->createPolygon();
2926 pR=pPolygon->createPoint();
2927 pR->setCoordinates(RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0));
2928 pR=pPolygon->createPoint();
2929 pR->setCoordinates(RelAbsVector(10.0,0.0),RelAbsVector(3.0,0.0));
2930 pR=pPolygon->createPoint();
2931 pR->setCoordinates(RelAbsVector(0.0,0.0),RelAbsVector(6.0,0.0));
2932 pLineEnding=pGlobalRender->createLineEnding();
2933 pLineEnding->setId("simpleHead_green");
2934 pLineEnding->getBoundingBox()->setPosition(&p);
2935 pLineEnding->getBoundingBox()->setDimensions(&d);
2936 pGroup=pLineEnding->getGroup();
2937 pGroup->setStroke("green");
2938 pGroup->setStrokeWidth(1.0);
2939 pGroup->setFillColor("green");
2940 pPolygon=pGroup->createPolygon();
2941 pR=pPolygon->createPoint();
2942 pR->setCoordinates(RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0));
2943 pR=pPolygon->createPoint();
2944 pR->setCoordinates(RelAbsVector(10.0,0.0),RelAbsVector(3.0,0.0));
2945 pR=pPolygon->createPoint();
2946 pR->setCoordinates(RelAbsVector(0.0,0.0),RelAbsVector(6.0,0.0));
2947 pLineEnding=pGlobalRender->createLineEnding();
2948 pLineEnding->setId("simpleHead_blue");
2949 pLineEnding->getBoundingBox()->setPosition(&p);
2950 pLineEnding->getBoundingBox()->setDimensions(&d);
2951 pGroup=pLineEnding->getGroup();
2952 pGroup->setStroke("blue");
2953 pGroup->setStrokeWidth(1.0);
2954 pGroup->setFillColor("blue");
2955 pPolygon=pGroup->createPolygon();
2956 pR=pPolygon->createPoint();
2957 pR->setCoordinates(RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0));
2958 pR=pPolygon->createPoint();
2959 pR->setCoordinates(RelAbsVector(10.0,0.0),RelAbsVector(3.0,0.0));
2960 pR=pPolygon->createPoint();
2961 pR->setCoordinates(RelAbsVector(0.0,0.0),RelAbsVector(6.0,0.0));
2962
2963 // styles
2964 // style for compartment glyphs
2965 pGlobalStyle=pGlobalRender->createStyle("compartmentGlyphStyle");
2966 pGlobalStyle->addType("COMPARTMENTGLYPH");
2967 pGroup=pGlobalStyle->getGroup();
2968 pGroup->setStroke("darkGreen");
2969 pGroup->setStrokeWidth(1.0);
2970 pRectangle=pGroup->createRectangle();
2971 pRectangle->setCoordinatesAndSize(RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0),RelAbsVector(0.0,100.0),RelAbsVector(0.0,100.0));
2972 pRectangle->setRadiusX(RelAbsVector(0.0,10.0));
2973 pRectangle->setRadiusY(RelAbsVector(0.0,10.0));
2974 pRectangle->setFillColor("lightYellow");
2975
2976 // style for species glyphs
2977 pGlobalStyle=pGlobalRender->createStyle("speciesGlyphStyle");
2978 pGlobalStyle->addType("SPECIESGLYPH");
2979 pGroup=pGlobalStyle->getGroup();
2980 pGroup->setStroke("black");
2981 pGroup->setStrokeWidth(1.0);
2982 pRectangle=pGroup->createRectangle();
2983 pRectangle->setCoordinatesAndSize(RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0),RelAbsVector(0.0,100.0),RelAbsVector(0.0,100.0));
2984 pRectangle->setRadiusX(RelAbsVector(5.0,0.0));
2985 pRectangle->setRadiusY(RelAbsVector(0.0,50.0));
2986 pRectangle->setFillColor("speciesGlyphGradient");
2987
2988 // style for reaction and text glyphs
2989 pGlobalStyle=pGlobalRender->createStyle("reactionGlyphStyle");
2990 pGlobalStyle->addType("REACTIONGLYPH");
2991 pGlobalStyle->addType("TEXTGLYPH");
2992 pGroup=pGlobalStyle->getGroup();
2993 pGroup->setStroke("black");
2994 pGroup->setStrokeWidth(1.0);
2995 pGroup->setFontSize(RelAbsVector(12.0,0.0));
2996 pGroup->setTextAnchor(Text::ANCHOR_MIDDLE);
2997
2998 // style for substrate and product species reference glyphs
2999 pGlobalStyle=pGlobalRender->createStyle("reactantSpeciesReferenceGlyphStyle");
3000 pGlobalStyle->addRole("substrate");
3001 pGlobalStyle->addRole("sidesubstrate");
3002 pGlobalStyle->addRole("product");
3003 pGlobalStyle->addRole("sideproduct");
3004 pGroup=pGlobalStyle->getGroup();
3005 pGroup->setStroke("#000000");
3006 pGroup->setStrokeWidth(1.0);
3007 pGroup->setEndHead("simpleHead_black");
3008
3009 // style for activator species reference glyphs
3010 pGlobalStyle=pGlobalRender->createStyle("activatorSpeciesReferenceGlyphStyle");
3011 pGlobalStyle->addRole("activator");
3012 pGroup=pGlobalStyle->getGroup();
3013 pGroup->setStroke("green");
3014 pGroup->setStrokeWidth(1.0);
3015 pGroup->setEndHead("simpleHead_green");
3016
3017 // style for modifier species reference glyphs
3018 pGlobalStyle=pGlobalRender->createStyle("modifierSpeciesReferenceGlyphStyle");
3019 pGlobalStyle->addRole("modifier");
3020 pGroup=pGlobalStyle->getGroup();
3021 pGroup->setStroke("blue");
3022 pGroup->setStrokeWidth(1.0);
3023 pGroup->setEndHead("simpleHead_blue");
3024
3025 // style for inhibitor species reference glyphs
3026 pGlobalStyle=pGlobalRender->createStyle("inhibitorSpeciesReferenceGlyphStyle");
3027 pGlobalStyle->addRole("inhibitor");
3028 pGroup=pGlobalStyle->getGroup();
3029 pGroup->setStroke("red");
3030 pGroup->setStrokeWidth(1.0);
3031 pGroup->setEndHead("simpleHead_red");
3032
3033
3034 // local style that references a global style and redefines some things
3035 RenderLayoutPlugin* lPlugin = (RenderLayoutPlugin*)layout->getPlugin("render");
3036 lPlugin->getListOfLocalRenderInformation()->setVersion(2, 1);
3037 LocalRenderInformation* pLocalRender=lPlugin->createLocalRenderInformation();
3038 pLocalRender->setId("highlightGlucose");
3039 pLocalRender->setReferenceRenderInformationId("defaultStyle");
3040 pLocalRender->setProgramName("Ralph Gauges");
3041 pLocalRender->setProgramVersion("1.0");
3042 pLocalRender->setBackgroundColor("#FFFFFFFF");
3043 // color definitions
3044 pColorDefinition=pLocalRender->createColorDefinition();
3045 pColorDefinition->setId("lightRed");
3046 pColorDefinition->setColorValue("#E6ADD8");
3047 pColorDefinition=pLocalRender->createColorDefinition();
3048 pColorDefinition->setId("white");
3049 pColorDefinition->setColorValue("#FFFFFF");
3050 // gradient definitions
3051 pRadialGradient=pLocalRender->createRadialGradientDefinition();
3052 pRadialGradient->setId("highlightedSpeciesGlyphGradient");
3053 pStop=pRadialGradient->createGradientStop();
3054 pStop->setOffset(RelAbsVector(0.0,0.0));
3055 pStop->setStopColor("white");
3056 pStop=pRadialGradient->createGradientStop();
3057 pStop->setOffset(RelAbsVector(0.0,100.0));
3058 pStop->setStopColor("lightRed");
3059
3060 // style for highligted species glyph
3061 LocalStyle* pLocalStyle=pLocalRender->createStyle("highlightedGlucose");
3062 pLocalStyle->addId("SpeciesGlyph_Glucose");
3063 pGroup=pLocalStyle->getGroup();
3064 pGroup->setStroke("black");
3065 pGroup->setStrokeWidth(1.0);
3066 pRectangle=pGroup->createRectangle();
3067 pRectangle->setCoordinatesAndSize(RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0),RelAbsVector(0.0,100.0),RelAbsVector(0.0,100.0));
3068 pRectangle->setRadiusX(RelAbsVector(5.0,0.0));
3069 pRectangle->setRadiusY(RelAbsVector(0.0,50.0));
3070 pRectangle->setFillColor("highlightedSpeciesGlyphGradient");
3071
3072 SBMLWriter writer;
3073
3074 //bool result=writeSBML(document,"example6.xml");
3075 char* writtenContent=writer.writeToString(document);
3076
3077 XMLInputStream stream2(writtenContent,false);
3078 XMLNode node2(stream2);
3079
3080 const XMLNode* listOfLayouts1,*listOfLayouts2;
3081 listOfLayouts1=&node;
3082 fail_unless(listOfLayouts1->getName()=="sbml");
3083 unsigned int i,iMax=listOfLayouts1->getNumChildren();
3084 for(i=0;i<iMax;++i)
3085 {
3086 if(listOfLayouts1->getChild(i).getName()=="model")
3087 {
3088 listOfLayouts1=&listOfLayouts1->getChild(i);
3089 break;
3090 }
3091 }
3092 fail_unless(listOfLayouts1->getName()=="model");
3093 iMax=listOfLayouts1->getNumChildren();
3094 for(i=0;i<iMax;++i)
3095 {
3096 if(listOfLayouts1->getChild(i).getName()=="annotation")
3097 {
3098 listOfLayouts1=&listOfLayouts1->getChild(i);
3099 break;
3100 }
3101 }
3102 fail_unless(listOfLayouts1->getName()=="annotation");
3103 iMax=listOfLayouts1->getNumChildren();
3104 for(i=0;i<iMax;++i)
3105 {
3106 if(listOfLayouts1->getChild(i).getName()=="listOfLayouts")
3107 {
3108 listOfLayouts1=&listOfLayouts1->getChild(i);
3109 break;
3110 }
3111 }
3112 fail_unless(listOfLayouts1->getName()=="listOfLayouts");
3113
3114 listOfLayouts2=&node2;
3115 fail_unless(listOfLayouts2->getName()=="sbml");
3116 iMax=listOfLayouts2->getNumChildren();
3117 for(i=0;i<iMax;++i)
3118 {
3119 if(listOfLayouts2->getChild(i).getName()=="model")
3120 {
3121 listOfLayouts2=&listOfLayouts2->getChild(i);
3122 break;
3123 }
3124 }
3125 fail_unless(listOfLayouts2->getName()=="model");
3126 iMax=listOfLayouts2->getNumChildren();
3127 for(i=0;i<iMax;++i)
3128 {
3129 if(listOfLayouts2->getChild(i).getName()=="annotation")
3130 {
3131 listOfLayouts2=&listOfLayouts2->getChild(i);
3132 break;
3133 }
3134 }
3135 fail_unless(listOfLayouts2->getName()=="annotation");
3136 iMax=listOfLayouts2->getNumChildren();
3137 for(i=0;i<iMax;++i)
3138 {
3139 if(listOfLayouts2->getChild(i).getName()=="listOfLayouts")
3140 {
3141 listOfLayouts2=&listOfLayouts2->getChild(i);
3142 break;
3143 }
3144 }
3145 fail_unless(listOfLayouts2->getName()=="listOfLayouts");
3146
3147 std::string l1 = listOfLayouts1->toXMLString();
3148 std::string l2 = listOfLayouts2->toXMLString();
3149 //fail_unless(l1 == l2);
3150
3151 // until the sbml element gets a namespace, we only compare the listOfLayouts element and all its children.
3152 fail_unless(listOfLayouts1->equals(*listOfLayouts2));
3153
3154 free(writtenContent);
3155 delete document;
3156 }
3157 END_TEST
3158
START_TEST(test_RenderWriting_write_L3_model_1)3159 START_TEST (test_RenderWriting_write_L3_model_1)
3160 {
3161 const char* s = \
3162 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>"
3163 "<sbml xmlns=\"http://www.sbml.org/sbml/level3/version1/core\" xmlns:layout=\"http://www.sbml.org/sbml/level3/version1/layout/version1\" xmlns:render=\"http://www.sbml.org/sbml/level3/version1/render/version1\" level=\"3\" version=\"1\" layout:required=\"false\" render:required=\"false\">"
3164 " <model id=\"TestModel\">"
3165 " <listOfCompartments>"
3166 " <compartment id=\"Hepatocyte\" name=\"Hepatocyte\"/>"
3167 " <compartment id=\"Mito_1\" name=\"Mito 1\"/>"
3168 " <compartment id=\"Mito_2\" name=\"Mito 2\"/>"
3169 " <compartment id=\"Mito_3\" name=\"Mito 3\"/>"
3170 " </listOfCompartments>"
3171 " <listOfSpecies>"
3172 " <species id=\"malate_cyt\" name=\"Malate\" compartment=\"Hepatocyte\"/>"
3173 " <species id=\"malate_mito1\" name=\"Malate\" compartment=\"Mito_1\"/>"
3174 " <species id=\"malate_mito2\" name=\"Malate\" compartment=\"Mito_2\"/>"
3175 " <species id=\"malate_mito3\" name=\"Malate\" compartment=\"Mito_3\"/>"
3176 " <species id=\"oxaloacetate_cyt\" name=\"Oxaloacetate\" compartment=\"Hepatocyte\"/>"
3177 " <species id=\"oxaloacetate_mito1\" name=\"Oxaloacetate\" compartment=\"Mito_1\"/>"
3178 " <species id=\"oxaloacetate_mito2\" name=\"Oxaloacetate\" compartment=\"Mito_2\"/>"
3179 " <species id=\"oxaloacetate_mito3\" name=\"Oxaloacetate\" compartment=\"Mito_3\"/>"
3180 " <species id=\"aspartate_cyt\" name=\"Aspartate\" compartment=\"Hepatocyte\"/>"
3181 " <species id=\"aspartate_mito1\" name=\"Aspartate\" compartment=\"Mito_1\"/>"
3182 " <species id=\"aspartate_mito2\" name=\"Aspartate\" compartment=\"Mito_2\"/>"
3183 " <species id=\"aspartate_mito3\" name=\"Aspartate\" compartment=\"Mito_3\"/>"
3184 " <species id=\"glutamate_cyt\" name=\"Glutamate\" compartment=\"Hepatocyte\"/>"
3185 " <species id=\"glutamate_mito1\" name=\"Glutamate\" compartment=\"Mito_1\"/>"
3186 " <species id=\"glutamate_mito2\" name=\"Glutamate\" compartment=\"Mito_2\"/>"
3187 " <species id=\"glutamate_mito3\" name=\"Glutamate\" compartment=\"Mito_3\"/>"
3188 " <species id=\"aKetoglutarate_cyt\" name=\"alpha-Ketoglutarate\" compartment=\"Hepatocyte\"/>"
3189 " <species id=\"aKetoglutarate_mito1\" name=\"alpha-Ketoglutarate\" compartment=\"Mito_1\"/>"
3190 " <species id=\"aKetoglutarate_mito2\" name=\"alpha-Ketoglutarate\" compartment=\"Mito_2\"/>"
3191 " <species id=\"aKetoglutarate_mito3\" name=\"alpha-Ketoglutarate\" compartment=\"Mito_3\"/>"
3192 " <species id=\"h_cyt\" name=\"H+\" compartment=\"Hepatocyte\"/>"
3193 " <species id=\"h_mito1\" name=\"H+\" compartment=\"Mito_1\"/>"
3194 " <species id=\"h_mito2\" name=\"H+\" compartment=\"Mito_2\"/>"
3195 " <species id=\"h_mito3\" name=\"H+\" compartment=\"Mito_3\"/>"
3196 " <species id=\"nad_cyt\" name=\"NAD+\" compartment=\"Hepatocyte\"/>"
3197 " <species id=\"nad_mito1\" name=\"NAD+\" compartment=\"Mito_1\"/>"
3198 " <species id=\"nad_mito2\" name=\"NAD+\" compartment=\"Mito_2\"/>"
3199 " <species id=\"nad_mito3\" name=\"NAD+\" compartment=\"Mito_3\"/>"
3200 " <species id=\"nadh_cyt\" name=\"NADH\" compartment=\"Hepatocyte\"/>"
3201 " <species id=\"nadh_mito1\" name=\"NADH\" compartment=\"Mito_1\"/>"
3202 " <species id=\"nadh_mito2\" name=\"NADH\" compartment=\"Mito_2\"/>"
3203 " <species id=\"nadh_mito3\" name=\"NADH\" compartment=\"Mito_3\"/>"
3204 " </listOfSpecies>"
3205 " <listOfReactions>"
3206 " <reaction id=\"reaction_malatedh_cyt\" name=\"malate dehydrogenase\" reversible=\"false\">"
3207 " <listOfReactants>"
3208 " <speciesReference id=\"sr_malate_cyt\" species=\"malate_cyt\"/>"
3209 " <speciesReference id=\"sr_nad_cyt\" species=\"nad_cyt\"/>"
3210 " </listOfReactants>"
3211 " <listOfProducts>"
3212 " <speciesReference id=\"sr_nadh_cyt\" species=\"nadh_cyt\"/>"
3213 " <speciesReference id=\"sr_h_cyt\" species=\"h_cyt\"/>"
3214 " <speciesReference id=\"sr_oxaloacetate_cyt_1\" species=\"oxaloacetate_cyt\"/>"
3215 " </listOfProducts>"
3216 " </reaction>"
3217 " <reaction id=\"reaction_aspartateat_cyt\" name=\"aspartate aminotransferase\" reversible=\"false\">"
3218 " <listOfReactants>"
3219 " <speciesReference id=\"sr_oxaloacetate_cyt_2\" species=\"oxaloacetate_cyt\"/>"
3220 " <speciesReference id=\"sr_glutamate_cyt_1\" species=\"glutamate_cyt\"/>"
3221 " </listOfReactants>"
3222 " <listOfProducts>"
3223 " <speciesReference id=\"sr_aspartate_cyt_1\" species=\"aspartate_cyt\"/>"
3224 " <speciesReference id=\"sr_aKetoglutarate_cyt_1\" species=\"aKetoglutarate_cyt\"/>"
3225 " </listOfProducts>"
3226 " </reaction>"
3227 " <reaction id=\"reaction_malatedh_mito1\" name=\"malate dehydrogenase\" reversible=\"false\">"
3228 " <listOfReactants>"
3229 " <speciesReference id=\"sr_malate_mito1\" species=\"malate_mito1\"/>"
3230 " <speciesReference id=\"sr_nad_mito1\" species=\"nad_mito1\"/>"
3231 " </listOfReactants>"
3232 " <listOfProducts>"
3233 " <speciesReference id=\"sr_nadh_mito1\" species=\"nadh_mito1\"/>"
3234 " <speciesReference id=\"sr_h_mito1\" species=\"h_mito1\"/>"
3235 " <speciesReference id=\"sr_oxaloacetate_mito1_1\" species=\"oxaloacetate_mito1\"/>"
3236 " </listOfProducts>"
3237 " </reaction>"
3238 " <reaction id=\"reaction_aspartateat_mito1\" name=\"aspartate aminotransferase\" reversible=\"false\">"
3239 " <listOfReactants>"
3240 " <speciesReference id=\"sr_oxaloacetate_mito1_2\" species=\"oxaloacetate_mito1\"/>"
3241 " <speciesReference id=\"sr_glutamate_mito1\" species=\"glutamate_mito1\"/>"
3242 " </listOfReactants>"
3243 " <listOfProducts>"
3244 " <speciesReference id=\"sr_aspartate_mito1\" species=\"aspartate_mito1\"/>"
3245 " <speciesReference id=\"sr_aKetoglutarate_mito1\" species=\"aKetoglutarate_mito1\"/>"
3246 " </listOfProducts>"
3247 " </reaction>"
3248 " <reaction id=\"reaction_malatedh_mito2\" name=\"malate dehydrogenase\" reversible=\"false\">"
3249 " <listOfReactants>"
3250 " <speciesReference id=\"sr_malate_mito2\" species=\"malate_mito2\"/>"
3251 " <speciesReference id=\"sr_nad_mito2\" species=\"nad_mito2\"/>"
3252 " </listOfReactants>"
3253 " <listOfProducts>"
3254 " <speciesReference id=\"sr_nadh_mito2\" species=\"nadh_mito2\"/>"
3255 " <speciesReference id=\"sr_h_mito2\" species=\"h_mito2\"/>"
3256 " <speciesReference id=\"sr_oxaloacetate_mito2_1\" species=\"oxaloacetate_mito2\"/>"
3257 " </listOfProducts>"
3258 " </reaction>"
3259 " <reaction id=\"reaction_aspartateat_mito2\" name=\"aspartate aminotransferase\" reversible=\"false\">"
3260 " <listOfReactants>"
3261 " <speciesReference id=\"sr_oxaloacetate_mito2_2\" species=\"oxaloacetate_mito2\"/>"
3262 " <speciesReference id=\"sr_glutamate_mito2\" species=\"glutamate_mito2\"/>"
3263 " </listOfReactants>"
3264 " <listOfProducts>"
3265 " <speciesReference id=\"sr_aspartate_mito2\" species=\"aspartate_mito2\"/>"
3266 " <speciesReference id=\"sr_aKetoglutarate_mito2\" species=\"aKetoglutarate_mito2\"/>"
3267 " </listOfProducts>"
3268 " </reaction>"
3269 " <reaction id=\"reaction_malatedh_mito3\" name=\"malate dehydrogenase\" reversible=\"false\">"
3270 " <listOfReactants>"
3271 " <speciesReference id=\"sr_malate_mito3\" species=\"malate_mito3\"/>"
3272 " <speciesReference id=\"sr_nad_mito3\" species=\"nad_mito3\"/>"
3273 " </listOfReactants>"
3274 " <listOfProducts>"
3275 " <speciesReference id=\"sr_nadh_mito3\" species=\"nadh_mito3\"/>"
3276 " <speciesReference id=\"sr_h_mito3\" species=\"h_mito3\"/>"
3277 " <speciesReference id=\"sr_oxaloacetate_mito3_1\" species=\"oxaloacetate_mito3\"/>"
3278 " </listOfProducts>"
3279 " </reaction>"
3280 " <reaction id=\"reaction_aspartateat_mito3\" name=\"aspartate aminotransferase\" reversible=\"false\">"
3281 " <listOfReactants>"
3282 " <speciesReference id=\"sr_oxaloacetate_mito3_2\" species=\"oxaloacetate_mito3\"/>"
3283 " <speciesReference id=\"sr_glutamate_mito3_1\" species=\"glutamate_mito3\"/>"
3284 " </listOfReactants>"
3285 " <listOfProducts>"
3286 " <speciesReference id=\"sr_aspartate_mito3_1\" species=\"aspartate_mito3\"/>"
3287 " <speciesReference id=\"sr_aKetoglutarate_mito3_1\" species=\"aKetoglutarate_mito3\"/>"
3288 " </listOfProducts>"
3289 " </reaction>"
3290 " <reaction id=\"aspartateCarrier\" name=\"aspartate carrier\" reversible=\"true\">"
3291 " <listOfReactants>"
3292 " <speciesReference id=\"sr_glutamate_mito3_2\" species=\"glutamate_mito3\"/>"
3293 " <speciesReference id=\"sr_aspartate_cyt_2\" species=\"aspartate_cyt\"/>"
3294 " </listOfReactants>"
3295 " <listOfProducts>"
3296 " <speciesReference id=\"sr_glutamate_cyt_2\" species=\"glutamate_cyt\"/>"
3297 " <speciesReference id=\"sr_aspartate_mito3_2\" species=\"aspartate_mito3\"/>"
3298 " </listOfProducts>"
3299 " </reaction>"
3300 " <reaction id=\"malateCarrier\" name=\"malate carrier\" reversible=\"true\">"
3301 " <listOfReactants>"
3302 " <speciesReference id=\"sr_aKetoglutarate_mito3_2\" species=\"aKetoglutarate_mito3\"/>"
3303 " <speciesReference id=\"sr_malate_cyt_2\" species=\"malate_cyt\"/>"
3304 " </listOfReactants>"
3305 " <listOfProducts>"
3306 " <speciesReference id=\"sr_aKetoglutarate_cyt_2\" species=\"aKetoglutarate_cyt\"/>"
3307 " <speciesReference id=\"sr_malate_mito3_2\" species=\"malate_mito3\"/>"
3308 " </listOfProducts>"
3309 " </reaction>"
3310 " </listOfReactions>"
3311 " <layout:listOfLayouts xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\">"
3312 " <layout:layout layout:id=\"Layout_1\">"
3313 " <layout:dimensions layout:width=\"2320\" layout:height=\"1000\"/>"
3314 " <layout:listOfCompartmentGlyphs>"
3315 " <layout:compartmentGlyph layout:id=\"CompartmentGlyph_1\" layout:compartment=\"Hepatocyte\">"
3316 " <layout:boundingBox layout:id=\"bb_compartment\">"
3317 " <layout:position layout:x=\"10\" layout:y=\"10\"/>"
3318 " <layout:dimensions layout:width=\"2300\" layout:height=\"980\"/>"
3319 " </layout:boundingBox>"
3320 " </layout:compartmentGlyph>"
3321 " <layout:compartmentGlyph layout:id=\"Mito1_Glyph\" layout:compartment=\"Mito_1\">"
3322 " <layout:boundingBox layout:id=\"bb_mito1\">"
3323 " <layout:position layout:x=\"100\" layout:y=\"100\"/>"
3324 " <layout:dimensions layout:width=\"300\" layout:height=\"100\"/>"
3325 " </layout:boundingBox>"
3326 " </layout:compartmentGlyph>"
3327 " <layout:compartmentGlyph layout:id=\"Mito2_Glyph\" layout:compartment=\"Mito_2\">"
3328 " <layout:boundingBox layout:id=\"bb_mito2\">"
3329 " <layout:position layout:x=\"200\" layout:y=\"650\"/>"
3330 " <layout:dimensions layout:width=\"300\" layout:height=\"100\"/>"
3331 " </layout:boundingBox>"
3332 " </layout:compartmentGlyph>"
3333 " <layout:compartmentGlyph layout:id=\"Mito3_Glyph_2\" layout:compartment=\"Mito_3\">"
3334 " <layout:boundingBox layout:id=\"bb_mito3_2\">"
3335 " <layout:position layout:x=\"1470\" layout:y=\"30\"/>"
3336 " <layout:dimensions layout:width=\"820\" layout:height=\"536\"/>"
3337 " </layout:boundingBox>"
3338 " </layout:compartmentGlyph>"
3339 " </layout:listOfCompartmentGlyphs>"
3340 " <layout:listOfSpeciesGlyphs>"
3341 " <layout:speciesGlyph layout:id=\"SpeciesGlyph_malate_cyt\" layout:species=\"malate_cyt\">"
3342 " <layout:boundingBox layout:id=\"bb_sg_malate_cyt\">"
3343 " <layout:position layout:x=\"580\" layout:y=\"280\"/>"
3344 " <layout:dimensions layout:width=\"240\" layout:height=\"36\"/>"
3345 " </layout:boundingBox>"
3346 " </layout:speciesGlyph>"
3347 " <layout:speciesGlyph layout:id=\"SpeciesGlyph_oxaloacetate_cyt\" layout:species=\"oxaloacetate_cyt\">"
3348 " <layout:boundingBox layout:id=\"bb_sg_oxaloacetate_cyt\">"
3349 " <layout:position layout:x=\"580\" layout:y=\"480\"/>"
3350 " <layout:dimensions layout:width=\"240\" layout:height=\"36\"/>"
3351 " </layout:boundingBox>"
3352 " </layout:speciesGlyph>"
3353 " <layout:speciesGlyph layout:id=\"SpeciesGlyph_aspartate_cyt\" layout:species=\"aspartate_cyt\">"
3354 " <layout:boundingBox layout:id=\"bb_sg_aspartate_cyt\">"
3355 " <layout:position layout:x=\"580\" layout:y=\"680\"/>"
3356 " <layout:dimensions layout:width=\"240\" layout:height=\"36\"/>"
3357 " </layout:boundingBox>"
3358 " </layout:speciesGlyph>"
3359 " <layout:speciesGlyph layout:id=\"SpeciesGlyph_glutamate_cyt\" layout:species=\"glutamate_cyt\">"
3360 " <layout:boundingBox layout:id=\"bb_sg_glutamate_cyt\">"
3361 " <layout:position layout:x=\"800\" layout:y=\"610\"/>"
3362 " <layout:dimensions layout:width=\"240\" layout:height=\"36\"/>"
3363 " </layout:boundingBox>"
3364 " </layout:speciesGlyph>"
3365 " <layout:speciesGlyph layout:id=\"SpeciesGlyph_aKetoglutarate_cyt\" layout:species=\"aKetoglutarate_cyt\">"
3366 " <layout:boundingBox layout:id=\"bb_sg_aKetoglutarate_cyt\">"
3367 " <layout:position layout:x=\"860\" layout:y=\"500\"/>"
3368 " <layout:dimensions layout:width=\"280\" layout:height=\"36\"/>"
3369 " </layout:boundingBox>"
3370 " </layout:speciesGlyph>"
3371 " <layout:speciesGlyph layout:id=\"SpeciesGlyph_nad_cyt\" layout:species=\"nad_cyt\">"
3372 " <layout:boundingBox layout:id=\"bb_sg_nad_cyt\">"
3373 " <layout:position layout:x=\"520\" layout:y=\"350\"/>"
3374 " <layout:dimensions layout:width=\"100\" layout:height=\"24\"/>"
3375 " </layout:boundingBox>"
3376 " </layout:speciesGlyph>"
3377 " <layout:speciesGlyph layout:id=\"SpeciesGlyph_nadh_cyt\" layout:species=\"nadh_cyt\">"
3378 " <layout:boundingBox layout:id=\"bb_sg_nadh_cyt\">"
3379 " <layout:position layout:x=\"520\" layout:y=\"430\"/>"
3380 " <layout:dimensions layout:width=\"100\" layout:height=\"24\"/>"
3381 " </layout:boundingBox>"
3382 " </layout:speciesGlyph>"
3383 " <layout:speciesGlyph layout:id=\"SpeciesGlyph_h_cyt\" layout:species=\"h_cyt\">"
3384 " <layout:boundingBox layout:id=\"bb_sg_h_cyt\">"
3385 " <layout:position layout:x=\"430\" layout:y=\"430\"/>"
3386 " <layout:dimensions layout:width=\"40\" layout:height=\"24\"/>"
3387 " </layout:boundingBox>"
3388 " </layout:speciesGlyph>"
3389 " <layout:speciesGlyph layout:id=\"SpeciesGlyph_malate_mito3\" layout:species=\"malate_mito3\">"
3390 " <layout:boundingBox layout:id=\"bb_sg_malate_mito3\">"
3391 " <layout:position layout:x=\"1850\" layout:y=\"80\"/>"
3392 " <layout:dimensions layout:width=\"240\" layout:height=\"36\"/>"
3393 " </layout:boundingBox>"
3394 " </layout:speciesGlyph>"
3395 " <layout:speciesGlyph layout:id=\"SpeciesGlyph_oxaloacetate_mito3\" layout:species=\"oxaloacetate_mito3\">"
3396 " <layout:boundingBox layout:id=\"bb_sg_oxaloacetate_mito3\">"
3397 " <layout:position layout:x=\"1850\" layout:y=\"280\"/>"
3398 " <layout:dimensions layout:width=\"240\" layout:height=\"36\"/>"
3399 " </layout:boundingBox>"
3400 " </layout:speciesGlyph>"
3401 " <layout:speciesGlyph layout:id=\"SpeciesGlyph_aspartate_mito3\" layout:species=\"aspartate_mito3\">"
3402 " <layout:boundingBox layout:id=\"bb_sg_aspartate_mito3\">"
3403 " <layout:position layout:x=\"1850\" layout:y=\"480\"/>"
3404 " <layout:dimensions layout:width=\"240\" layout:height=\"36\"/>"
3405 " </layout:boundingBox>"
3406 " </layout:speciesGlyph>"
3407 " <layout:speciesGlyph layout:id=\"SpeciesGlyph_glutamate_mito3\" layout:species=\"glutamate_mito3\">"
3408 " <layout:boundingBox layout:id=\"bb_sg_glutamate_mito3\">"
3409 " <layout:position layout:x=\"1550\" layout:y=\"430\"/>"
3410 " <layout:dimensions layout:width=\"240\" layout:height=\"36\"/>"
3411 " </layout:boundingBox>"
3412 " </layout:speciesGlyph>"
3413 " <layout:speciesGlyph layout:id=\"SpeciesGlyph_aKetoglutarate_mito3\" layout:species=\"aKetoglutarate_mito3\">"
3414 " <layout:boundingBox layout:id=\"bb_sg_aKetoglutarate_mito3\">"
3415 " <layout:position layout:x=\"1530\" layout:y=\"300\"/>"
3416 " <layout:dimensions layout:width=\"280\" layout:height=\"36\"/>"
3417 " </layout:boundingBox>"
3418 " </layout:speciesGlyph>"
3419 " <layout:speciesGlyph layout:id=\"SpeciesGlyph_nad_mito3\" layout:species=\"nad_mito3\">"
3420 " <layout:boundingBox layout:id=\"bb_sg_nad_mito3\">"
3421 " <layout:position layout:x=\"2050\" layout:y=\"150\"/>"
3422 " <layout:dimensions layout:width=\"100\" layout:height=\"24\"/>"
3423 " </layout:boundingBox>"
3424 " </layout:speciesGlyph>"
3425 " <layout:speciesGlyph layout:id=\"SpeciesGlyph_nadh_mito3\" layout:species=\"nadh_mito3\">"
3426 " <layout:boundingBox layout:id=\"bb_sg_nadh_mito3\">"
3427 " <layout:position layout:x=\"2050\" layout:y=\"230\"/>"
3428 " <layout:dimensions layout:width=\"100\" layout:height=\"24\"/>"
3429 " </layout:boundingBox>"
3430 " </layout:speciesGlyph>"
3431 " <layout:speciesGlyph layout:id=\"SpeciesGlyph_h_mito3\" layout:species=\"h_mito3\">"
3432 " <layout:boundingBox layout:id=\"bb_sg_h_mito3\">"
3433 " <layout:position layout:x=\"2200\" layout:y=\"230\"/>"
3434 " <layout:dimensions layout:width=\"40\" layout:height=\"24\"/>"
3435 " </layout:boundingBox>"
3436 " </layout:speciesGlyph>"
3437 " </layout:listOfSpeciesGlyphs>"
3438 " <layout:listOfReactionGlyphs>"
3439 " <layout:reactionGlyph layout:id=\"rg_malatedh_cyt\" layout:reaction=\"reaction_malatedh_cyt\">"
3440 " <layout:curve>"
3441 " <layout:listOfCurveSegments>"
3442 " <layout:curveSegment xsi:type=\"LineSegment\">"
3443 " <layout:start layout:x=\"700\" layout:y=\"381\"/>"
3444 " <layout:end layout:x=\"700\" layout:y=\"415\"/>"
3445 " </layout:curveSegment>"
3446 " </layout:listOfCurveSegments>"
3447 " </layout:curve>"
3448 " <layout:listOfSpeciesReferenceGlyphs>"
3449 " <layout:speciesReferenceGlyph layout:id=\"srg_malate_cyt_1\" layout:speciesReference=\"sr_malate_cyt\" layout:speciesGlyph=\"SpeciesGlyph_malate_cyt\" layout:role=\"substrate\">"
3450 " <layout:curve>"
3451 " <layout:listOfCurveSegments>"
3452 " <layout:curveSegment xsi:type=\"LineSegment\">"
3453 " <layout:start layout:x=\"700\" layout:y=\"381\"/>"
3454 " <layout:end layout:x=\"700\" layout:y=\"316\"/>"
3455 " </layout:curveSegment>"
3456 " </layout:listOfCurveSegments>"
3457 " </layout:curve>"
3458 " </layout:speciesReferenceGlyph>"
3459 " <layout:speciesReferenceGlyph layout:id=\"srg_nad_cyt\" layout:speciesReference=\"sr_nad_cyt\" layout:speciesGlyph=\"SpeciesGlyph_nad_cyt\" layout:role=\"substrate\">"
3460 " <layout:curve>"
3461 " <layout:listOfCurveSegments>"
3462 " <layout:curveSegment xsi:type=\"CubicBezier\">"
3463 " <layout:start layout:x=\"700\" layout:y=\"381\"/>"
3464 " <layout:end layout:x=\"620\" layout:y=\"362\"/>"
3465 " <layout:basePoint1 layout:x=\"700\" layout:y=\"362\"/>"
3466 " <layout:basePoint2 layout:x=\"700\" layout:y=\"362\"/>"
3467 " </layout:curveSegment>"
3468 " </layout:listOfCurveSegments>"
3469 " </layout:curve>"
3470 " </layout:speciesReferenceGlyph>"
3471 " <layout:speciesReferenceGlyph layout:id=\"srg_oxaloacetate_cyt_1\" layout:speciesReference=\"sr_oxaloacetate_cyt_1\" layout:speciesGlyph=\"SpeciesGlyph_oxaloacetate_cyt\" layout:role=\"product\">"
3472 " <layout:curve>"
3473 " <layout:listOfCurveSegments>"
3474 " <layout:curveSegment xsi:type=\"LineSegment\">"
3475 " <layout:start layout:x=\"700\" layout:y=\"415\"/>"
3476 " <layout:end layout:x=\"700\" layout:y=\"480\"/>"
3477 " </layout:curveSegment>"
3478 " </layout:listOfCurveSegments>"
3479 " </layout:curve>"
3480 " </layout:speciesReferenceGlyph>"
3481 " <layout:speciesReferenceGlyph layout:id=\"srg_nadh_cyt\" layout:speciesReference=\"sr_nadh_cyt\" layout:speciesGlyph=\"SpeciesGlyph_nadh_cyt\" layout:role=\"product\">"
3482 " <layout:curve>"
3483 " <layout:listOfCurveSegments>"
3484 " <layout:curveSegment xsi:type=\"CubicBezier\">"
3485 " <layout:start layout:x=\"700\" layout:y=\"415\"/>"
3486 " <layout:end layout:x=\"620\" layout:y=\"442\"/>"
3487 " <layout:basePoint1 layout:x=\"700\" layout:y=\"442\"/>"
3488 " <layout:basePoint2 layout:x=\"700\" layout:y=\"442\"/>"
3489 " </layout:curveSegment>"
3490 " </layout:listOfCurveSegments>"
3491 " </layout:curve>"
3492 " </layout:speciesReferenceGlyph>"
3493 " <layout:speciesReferenceGlyph layout:id=\"srg_h_cyt\" layout:speciesReference=\"sr_h_cyt\" layout:speciesGlyph=\"SpeciesGlyph_h_cyt\" layout:role=\"product\">"
3494 " <layout:curve>"
3495 " <layout:listOfCurveSegments>"
3496 " <layout:curveSegment xsi:type=\"CubicBezier\">"
3497 " <layout:start layout:x=\"700\" layout:y=\"415\"/>"
3498 " <layout:end layout:x=\"470\" layout:y=\"430\"/>"
3499 " <layout:basePoint1 layout:x=\"570\" layout:y=\"415\"/>"
3500 " <layout:basePoint2 layout:x=\"570\" layout:y=\"415\"/>"
3501 " </layout:curveSegment>"
3502 " </layout:listOfCurveSegments>"
3503 " </layout:curve>"
3504 " </layout:speciesReferenceGlyph>"
3505 " </layout:listOfSpeciesReferenceGlyphs>"
3506 " </layout:reactionGlyph>"
3507 " <layout:reactionGlyph layout:id=\"rg_aspartateat_cyt\" layout:reaction=\"reaction_aspartateat_cyt\">"
3508 " <layout:curve>"
3509 " <layout:listOfCurveSegments>"
3510 " <layout:curveSegment xsi:type=\"LineSegment\">"
3511 " <layout:start layout:x=\"700\" layout:y=\"581\"/>"
3512 " <layout:end layout:x=\"700\" layout:y=\"615\"/>"
3513 " </layout:curveSegment>"
3514 " </layout:listOfCurveSegments>"
3515 " </layout:curve>"
3516 " <layout:listOfSpeciesReferenceGlyphs>"
3517 " <layout:speciesReferenceGlyph layout:id=\"srg_oxaloacetate_cyt_2\" layout:speciesReference=\"sr_oxaloacetate_cyt_2\" layout:speciesGlyph=\"SpeciesGlyph_oxaloacetate_cyt\" layout:role=\"substrate\">"
3518 " <layout:curve>"
3519 " <layout:listOfCurveSegments>"
3520 " <layout:curveSegment xsi:type=\"LineSegment\">"
3521 " <layout:start layout:x=\"700\" layout:y=\"581\"/>"
3522 " <layout:end layout:x=\"700\" layout:y=\"516\"/>"
3523 " </layout:curveSegment>"
3524 " </layout:listOfCurveSegments>"
3525 " </layout:curve>"
3526 " </layout:speciesReferenceGlyph>"
3527 " <layout:speciesReferenceGlyph layout:id=\"srg_glutamate_cyt_1\" layout:speciesReference=\"sr_glutamate_cyt_1\" layout:speciesGlyph=\"SpeciesGlyph_glutamate_cyt\" layout:role=\"substrate\">"
3528 " <layout:curve>"
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3535 " </layout:curveSegment>"
3536 " </layout:listOfCurveSegments>"
3537 " </layout:curve>"
3538 " </layout:speciesReferenceGlyph>"
3539 " <layout:speciesReferenceGlyph layout:id=\"srg_aspartate_cyt_1\" layout:speciesReference=\"sr_aspartate_cyt_1\" layout:speciesGlyph=\"SpeciesGlyph_aspartate_cyt\" layout:role=\"product\">"
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3545 " </layout:curveSegment>"
3546 " </layout:listOfCurveSegments>"
3547 " </layout:curve>"
3548 " </layout:speciesReferenceGlyph>"
3549 " <layout:speciesReferenceGlyph layout:id=\"srg_aKetoglutaratecyt_1\" layout:speciesReference=\"sr_aKetoglutarate_cyt_1\" layout:speciesGlyph=\"SpeciesGlyph_aKetoglutarate_cyt\" layout:role=\"product\">"
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3556 " <layout:basePoint2 layout:x=\"790\" layout:y=\"515\"/>"
3557 " </layout:curveSegment>"
3558 " </layout:listOfCurveSegments>"
3559 " </layout:curve>"
3560 " </layout:speciesReferenceGlyph>"
3561 " </layout:listOfSpeciesReferenceGlyphs>"
3562 " </layout:reactionGlyph>"
3563 " <layout:reactionGlyph layout:id=\"rg_malatedh_mito3\" layout:reaction=\"reaction_malatedh_mito3\">"
3564 " <layout:curve>"
3565 " <layout:listOfCurveSegments>"
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3570 " </layout:listOfCurveSegments>"
3571 " </layout:curve>"
3572 " <layout:listOfSpeciesReferenceGlyphs>"
3573 " <layout:speciesReferenceGlyph layout:id=\"srg_malate_mito3_1\" layout:speciesReference=\"sr_malate_mito3\" layout:speciesGlyph=\"SpeciesGlyph_malate_mito3\" layout:role=\"substrate\">"
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3578 " <layout:end layout:x=\"1970\" layout:y=\"116\"/>"
3579 " </layout:curveSegment>"
3580 " </layout:listOfCurveSegments>"
3581 " </layout:curve>"
3582 " </layout:speciesReferenceGlyph>"
3583 " <layout:speciesReferenceGlyph layout:id=\"srg_nad_mito3\" layout:speciesReference=\"sr_nad_mito3\" layout:speciesGlyph=\"SpeciesGlyph_nad_mito3\" layout:role=\"substrate\">"
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3592 " </layout:listOfCurveSegments>"
3593 " </layout:curve>"
3594 " </layout:speciesReferenceGlyph>"
3595 " <layout:speciesReferenceGlyph layout:id=\"srg_oxaloacetate_mito3_1\" layout:speciesReference=\"sr_oxaloacetate_mito3_1\" layout:speciesGlyph=\"SpeciesGlyph_oxaloacetate_mito3\" layout:role=\"product\">"
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3597 " <layout:listOfCurveSegments>"
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3600 " <layout:end layout:x=\"1970\" layout:y=\"280\"/>"
3601 " </layout:curveSegment>"
3602 " </layout:listOfCurveSegments>"
3603 " </layout:curve>"
3604 " </layout:speciesReferenceGlyph>"
3605 " <layout:speciesReferenceGlyph layout:id=\"srg_nadh_mito3\" layout:speciesReference=\"sr_nadh_mito3\" layout:speciesGlyph=\"SpeciesGlyph_nadh_mito3\" layout:role=\"product\">"
3606 " <layout:curve>"
3607 " <layout:listOfCurveSegments>"
3608 " <layout:curveSegment xsi:type=\"CubicBezier\">"
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3611 " <layout:basePoint1 layout:x=\"1970\" layout:y=\"242\"/>"
3612 " <layout:basePoint2 layout:x=\"1970\" layout:y=\"242\"/>"
3613 " </layout:curveSegment>"
3614 " </layout:listOfCurveSegments>"
3615 " </layout:curve>"
3616 " </layout:speciesReferenceGlyph>"
3617 " <layout:speciesReferenceGlyph layout:id=\"srg_h_mito3\" layout:speciesReference=\"sr_h_mito3\" layout:speciesGlyph=\"SpeciesGlyph_h_mito3\" layout:role=\"product\">"
3618 " <layout:curve>"
3619 " <layout:listOfCurveSegments>"
3620 " <layout:curveSegment xsi:type=\"CubicBezier\">"
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3624 " <layout:basePoint2 layout:x=\"2100\" layout:y=\"215\"/>"
3625 " </layout:curveSegment>"
3626 " </layout:listOfCurveSegments>"
3627 " </layout:curve>"
3628 " </layout:speciesReferenceGlyph>"
3629 " </layout:listOfSpeciesReferenceGlyphs>"
3630 " </layout:reactionGlyph>"
3631 " <layout:reactionGlyph layout:id=\"rg_aspartateat_mito3\" layout:reaction=\"reaction_aspartateat_mito3\">"
3632 " <layout:curve>"
3633 " <layout:listOfCurveSegments>"
3634 " <layout:curveSegment xsi:type=\"LineSegment\">"
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3636 " <layout:end layout:x=\"1970\" layout:y=\"415\"/>"
3637 " </layout:curveSegment>"
3638 " </layout:listOfCurveSegments>"
3639 " </layout:curve>"
3640 " <layout:listOfSpeciesReferenceGlyphs>"
3641 " <layout:speciesReferenceGlyph layout:id=\"srg_oxaloacetate_mito3_2\" layout:speciesReference=\"sr_oxaloacetate_mito3_2\" layout:speciesGlyph=\"SpeciesGlyph_oxaloacetate_mito3\" layout:role=\"substrate\">"
3642 " <layout:curve>"
3643 " <layout:listOfCurveSegments>"
3644 " <layout:curveSegment xsi:type=\"LineSegment\">"
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3646 " <layout:end layout:x=\"1970\" layout:y=\"316\"/>"
3647 " </layout:curveSegment>"
3648 " </layout:listOfCurveSegments>"
3649 " </layout:curve>"
3650 " </layout:speciesReferenceGlyph>"
3651 " <layout:speciesReferenceGlyph layout:id=\"srg_glutamate_mito3_1\" layout:speciesReference=\"sr_glutamate_mito3_1\" layout:speciesGlyph=\"SpeciesGlyph_glutamate_mito3\" layout:role=\"substrate\">"
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3653 " <layout:listOfCurveSegments>"
3654 " <layout:curveSegment xsi:type=\"CubicBezier\">"
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3658 " <layout:basePoint2 layout:x=\"1880\" layout:y=\"448\"/>"
3659 " </layout:curveSegment>"
3660 " </layout:listOfCurveSegments>"
3661 " </layout:curve>"
3662 " </layout:speciesReferenceGlyph>"
3663 " <layout:speciesReferenceGlyph layout:id=\"srg_aspartate_mito3_1\" layout:speciesReference=\"sr_aspartate_mito3_1\" layout:speciesGlyph=\"SpeciesGlyph_aspartate_mito3\" layout:role=\"product\">"
3664 " <layout:curve>"
3665 " <layout:listOfCurveSegments>"
3666 " <layout:curveSegment xsi:type=\"LineSegment\">"
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3668 " <layout:end layout:x=\"1970\" layout:y=\"480\"/>"
3669 " </layout:curveSegment>"
3670 " </layout:listOfCurveSegments>"
3671 " </layout:curve>"
3672 " </layout:speciesReferenceGlyph>"
3673 " <layout:speciesReferenceGlyph layout:id=\"srg_aKetoglutaratemito3_1\" layout:speciesReference=\"sr_aKetoglutarate_mito3_1\" layout:speciesGlyph=\"SpeciesGlyph_aKetoglutarate_mito3\" layout:role=\"product\">"
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3675 " <layout:listOfCurveSegments>"
3676 " <layout:curveSegment xsi:type=\"CubicBezier\">"
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3680 " <layout:basePoint2 layout:x=\"1880\" layout:y=\"315\"/>"
3681 " </layout:curveSegment>"
3682 " </layout:listOfCurveSegments>"
3683 " </layout:curve>"
3684 " </layout:speciesReferenceGlyph>"
3685 " </layout:listOfSpeciesReferenceGlyphs>"
3686 " </layout:reactionGlyph>"
3687 " <layout:reactionGlyph layout:id=\"rg_aspartateCarrier\" layout:reaction=\"aspartateCarrier\">"
3688 " <layout:curve>"
3689 " <layout:listOfCurveSegments>"
3690 " <layout:curveSegment xsi:type=\"LineSegment\">"
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3692 " <layout:end layout:x=\"1360\" layout:y=\"550\"/>"
3693 " </layout:curveSegment>"
3694 " </layout:listOfCurveSegments>"
3695 " </layout:curve>"
3696 " <layout:listOfSpeciesReferenceGlyphs>"
3697 " <layout:speciesReferenceGlyph layout:id=\"srg_aspartate_mito3_2\" layout:speciesReference=\"sr_aspartate_mito3_2\" layout:speciesGlyph=\"SpeciesGlyph_aspartate_mito3\" layout:role=\"substrate\">"
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3699 " <layout:listOfCurveSegments>"
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3703 " </layout:curveSegment>"
3704 " </layout:listOfCurveSegments>"
3705 " </layout:curve>"
3706 " </layout:speciesReferenceGlyph>"
3707 " <layout:speciesReferenceGlyph layout:id=\"srg_aspartate_cyt_2\" layout:speciesReference=\"sr_aspartate_cyt_2\" layout:speciesGlyph=\"SpeciesGlyph_aspartate_cyt\" layout:role=\"product\">"
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3709 " <layout:listOfCurveSegments>"
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3714 " <layout:basePoint2 layout:x=\"1390\" layout:y=\"698\"/>"
3715 " </layout:curveSegment>"
3716 " </layout:listOfCurveSegments>"
3717 " </layout:curve>"
3718 " </layout:speciesReferenceGlyph>"
3719 " <layout:speciesReferenceGlyph layout:id=\"srg_glutamate_cyt_2\" layout:speciesReference=\"sr_glutamate_cyt_2\" layout:speciesGlyph=\"SpeciesGlyph_glutamate_cyt\" layout:role=\"substrate\">"
3720 " <layout:curve>"
3721 " <layout:listOfCurveSegments>"
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3725 " <layout:basePoint1 layout:x=\"1390\" layout:y=\"648\"/>"
3726 " <layout:basePoint2 layout:x=\"1390\" layout:y=\"648\"/>"
3727 " </layout:curveSegment>"
3728 " </layout:listOfCurveSegments>"
3729 " </layout:curve>"
3730 " </layout:speciesReferenceGlyph>"
3731 " <layout:speciesReferenceGlyph layout:id=\"srg_glutamate_mito3_2\" layout:speciesReference=\"sr_glutamate_mito3_2\" layout:speciesGlyph=\"SpeciesGlyph_glutamate_mito3\" layout:role=\"product\">"
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3733 " <layout:listOfCurveSegments>"
3734 " <layout:curveSegment xsi:type=\"CubicBezier\">"
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3737 " <layout:basePoint1 layout:x=\"1390\" layout:y=\"448\"/>"
3738 " <layout:basePoint2 layout:x=\"1390\" layout:y=\"448\"/>"
3739 " </layout:curveSegment>"
3740 " </layout:listOfCurveSegments>"
3741 " </layout:curve>"
3742 " </layout:speciesReferenceGlyph>"
3743 " </layout:listOfSpeciesReferenceGlyphs>"
3744 " </layout:reactionGlyph>"
3745 " <layout:reactionGlyph layout:id=\"rg_malateCarrier\" layout:reaction=\"malateCarrier\">"
3746 " <layout:curve>"
3747 " <layout:listOfCurveSegments>"
3748 " <layout:curveSegment xsi:type=\"LineSegment\">"
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3750 " <layout:end layout:x=\"1360\" layout:y=\"340\"/>"
3751 " </layout:curveSegment>"
3752 " </layout:listOfCurveSegments>"
3753 " </layout:curve>"
3754 " <layout:listOfSpeciesReferenceGlyphs>"
3755 " <layout:speciesReferenceGlyph layout:id=\"srg_aKetoglutarate_mito3_2\" layout:speciesReference=\"sr_aKetoglutarate_mito3_2\" layout:speciesGlyph=\"SpeciesGlyph_aKetoglutarate_mito3\" layout:role=\"substrate\">"
3756 " <layout:curve>"
3757 " <layout:listOfCurveSegments>"
3758 " <layout:curveSegment xsi:type=\"LineSegment\">"
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3761 " </layout:curveSegment>"
3762 " </layout:listOfCurveSegments>"
3763 " </layout:curve>"
3764 " </layout:speciesReferenceGlyph>"
3765 " <layout:speciesReferenceGlyph layout:id=\"srg_aKetoglutarate_cyt_2\" layout:speciesReference=\"sr_aKetoglutarate_cyt_2\" layout:speciesGlyph=\"SpeciesGlyph_aKetoglutarate_cyt\" layout:role=\"product\">"
3766 " <layout:curve>"
3767 " <layout:listOfCurveSegments>"
3768 " <layout:curveSegment xsi:type=\"LineSegment\">"
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3770 " <layout:end layout:x=\"1140\" layout:y=\"518\"/>"
3771 " </layout:curveSegment>"
3772 " </layout:listOfCurveSegments>"
3773 " </layout:curve>"
3774 " </layout:speciesReferenceGlyph>"
3775 " <layout:speciesReferenceGlyph layout:id=\"srg_malate_cyt_2\" layout:speciesReference=\"sr_malate_cyt_2\" layout:speciesGlyph=\"SpeciesGlyph_malate_cyt\" layout:role=\"substrate\">"
3776 " <layout:curve>"
3777 " <layout:listOfCurveSegments>"
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3782 " <layout:basePoint2 layout:x=\"1390\" layout:y=\"250\"/>"
3783 " </layout:curveSegment>"
3784 " </layout:listOfCurveSegments>"
3785 " </layout:curve>"
3786 " </layout:speciesReferenceGlyph>"
3787 " <layout:speciesReferenceGlyph layout:id=\"srg_malate_mito3_2\" layout:speciesReference=\"sr_malate_mito3_2\" layout:speciesGlyph=\"SpeciesGlyph_malate_mito3\" layout:role=\"product\">"
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3789 " <layout:listOfCurveSegments>"
3790 " <layout:curveSegment xsi:type=\"CubicBezier\">"
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3794 " <layout:basePoint2 layout:x=\"1390\" layout:y=\"150\"/>"
3795 " </layout:curveSegment>"
3796 " </layout:listOfCurveSegments>"
3797 " </layout:curve>"
3798 " </layout:speciesReferenceGlyph>"
3799 " </layout:listOfSpeciesReferenceGlyphs>"
3800 " </layout:reactionGlyph>"
3801 " </layout:listOfReactionGlyphs>"
3802 " <layout:listOfTextGlyphs>"
3803 " <layout:textGlyph layout:id=\"TextGlyph_Hepatocyte\" layout:originOfText=\"Hepatocyte\" layout:graphicalObject=\"CompartmentGlyph_1\">"
3804 " <layout:boundingBox layout:id=\"bb_tg_compartment\">"
3805 " <layout:position layout:x=\"50\" layout:y=\"870\"/>"
3806 " <layout:dimensions layout:width=\"300\" layout:height=\"72\"/>"
3807 " </layout:boundingBox>"
3808 " </layout:textGlyph>"
3809 " <layout:textGlyph layout:id=\"TextGlyph_mito1\" layout:originOfText=\"Mito_1\" layout:graphicalObject=\"Mito1_Glyph\">"
3810 " <layout:boundingBox layout:id=\"bb_tg_mito1\">"
3811 " <layout:position layout:x=\"110\" layout:y=\"110\"/>"
3812 " <layout:dimensions layout:width=\"280\" layout:height=\"72\"/>"
3813 " </layout:boundingBox>"
3814 " </layout:textGlyph>"
3815 " <layout:textGlyph layout:id=\"TextGlyph_mito2\" layout:originOfText=\"Mito_2\" layout:graphicalObject=\"Mito2_Glyph\">"
3816 " <layout:boundingBox layout:id=\"bb_tg_mito2\">"
3817 " <layout:position layout:x=\"210\" layout:y=\"660\"/>"
3818 " <layout:dimensions layout:width=\"280\" layout:height=\"72\"/>"
3819 " </layout:boundingBox>"
3820 " </layout:textGlyph>"
3821 " <layout:textGlyph layout:id=\"TextGlyph_mito3_2\" layout:originOfText=\"Mito_3\" layout:graphicalObject=\"Mito3_Glyph_2\">"
3822 " <layout:boundingBox layout:id=\"bb_tg_mito3_2\">"
3823 " <layout:position layout:x=\"1475\" layout:y=\"35\"/>"
3824 " <layout:dimensions layout:width=\"200\" layout:height=\"72\"/>"
3825 " </layout:boundingBox>"
3826 " </layout:textGlyph>"
3827 " <layout:textGlyph layout:id=\"TextGlyph_malate_cyt\" layout:originOfText=\"malate_cyt\" layout:graphicalObject=\"SpeciesGlyph_malate_cyt\">"
3828 " <layout:boundingBox layout:id=\"bb_tg_malatate_cyt\">"
3829 " <layout:position layout:x=\"590\" layout:y=\"280\"/>"
3830 " <layout:dimensions layout:width=\"220\" layout:height=\"36\"/>"
3831 " </layout:boundingBox>"
3832 " </layout:textGlyph>"
3833 " <layout:textGlyph layout:id=\"TextGlyph_oxaloacetate_cyt\" layout:originOfText=\"oxaloacetate_cyt\" layout:graphicalObject=\"SpeciesGlyph_oxaloacetate_cyt\">"
3834 " <layout:boundingBox layout:id=\"bb_tg_oxaloacetate_cyt\">"
3835 " <layout:position layout:x=\"590\" layout:y=\"480\"/>"
3836 " <layout:dimensions layout:width=\"220\" layout:height=\"36\"/>"
3837 " </layout:boundingBox>"
3838 " </layout:textGlyph>"
3839 " <layout:textGlyph layout:id=\"TextGlyph_aspartate_cyt\" layout:originOfText=\"aspartate_cyt\" layout:graphicalObject=\"SpeciesGlyph_aspartate_cyt\">"
3840 " <layout:boundingBox layout:id=\"bb_tg_aspartate_cyt\">"
3841 " <layout:position layout:x=\"590\" layout:y=\"680\"/>"
3842 " <layout:dimensions layout:width=\"220\" layout:height=\"36\"/>"
3843 " </layout:boundingBox>"
3844 " </layout:textGlyph>"
3845 " <layout:textGlyph layout:id=\"TextGlyph_glutamate_cyt\" layout:originOfText=\"glutamate_cyt\" layout:graphicalObject=\"SpeciesGlyph_glutamate_cyt\">"
3846 " <layout:boundingBox layout:id=\"bb_tg_glutamate_cyt\">"
3847 " <layout:position layout:x=\"810\" layout:y=\"610\"/>"
3848 " <layout:dimensions layout:width=\"220\" layout:height=\"36\"/>"
3849 " </layout:boundingBox>"
3850 " </layout:textGlyph>"
3851 " <layout:textGlyph layout:id=\"TextGlyph_aKetoglutarate_cyt\" layout:originOfText=\"aKetoglutarate_cyt\" layout:graphicalObject=\"SpeciesGlyph_aKetoglutarate_cyt\">"
3852 " <layout:boundingBox layout:id=\"bb_tg_aKetoglutarate_cyt\">"
3853 " <layout:position layout:x=\"870\" layout:y=\"500\"/>"
3854 " <layout:dimensions layout:width=\"260\" layout:height=\"36\"/>"
3855 " </layout:boundingBox>"
3856 " </layout:textGlyph>"
3857 " <layout:textGlyph layout:id=\"TextGlyph_nad_cyt\" layout:originOfText=\"nad_cyt\" layout:graphicalObject=\"SpeciesGlyph_nad_cyt\">"
3858 " <layout:boundingBox layout:id=\"bb_tg_nad_cyt\">"
3859 " <layout:position layout:x=\"525\" layout:y=\"350\"/>"
3860 " <layout:dimensions layout:width=\"80\" layout:height=\"24\"/>"
3861 " </layout:boundingBox>"
3862 " </layout:textGlyph>"
3863 " <layout:textGlyph layout:id=\"TextGlyph_nadh_cyt\" layout:originOfText=\"nadh_cyt\" layout:graphicalObject=\"SpeciesGlyph_nadh_cyt\">"
3864 " <layout:boundingBox layout:id=\"bb_tg_nadh_cyt\">"
3865 " <layout:position layout:x=\"525\" layout:y=\"430\"/>"
3866 " <layout:dimensions layout:width=\"80\" layout:height=\"24\"/>"
3867 " </layout:boundingBox>"
3868 " </layout:textGlyph>"
3869 " <layout:textGlyph layout:id=\"TextGlyph_h_cyt\" layout:originOfText=\"h_cyt\" layout:graphicalObject=\"SpeciesGlyph_h_cyt\">"
3870 " <layout:boundingBox layout:id=\"bb_tg_h_cyt\">"
3871 " <layout:position layout:x=\"435\" layout:y=\"430\"/>"
3872 " <layout:dimensions layout:width=\"30\" layout:height=\"24\"/>"
3873 " </layout:boundingBox>"
3874 " </layout:textGlyph>"
3875 " <layout:textGlyph layout:id=\"tg_rg_malaltedh_cyt\" layout:originOfText=\"reaction_malatedh_cyt\" layout:graphicalObject=\"rg_malatedh_cyt\">"
3876 " <layout:boundingBox layout:id=\"bb_tg_rg_malaltedh_cyt\">"
3877 " <layout:position layout:x=\"700\" layout:y=\"385\"/>"
3878 " <layout:dimensions layout:width=\"210\" layout:height=\"24\"/>"
3879 " </layout:boundingBox>"
3880 " </layout:textGlyph>"
3881 " <layout:textGlyph layout:id=\"tg_rg_aspartateat_cyt\" layout:originOfText=\"reaction_aspartateat_cyt\" layout:graphicalObject=\"rg_aspartateat_cyt\">"
3882 " <layout:boundingBox layout:id=\"bb_tg_rg_aspartateat_cyt\">"
3883 " <layout:position layout:x=\"440\" layout:y=\"585\"/>"
3884 " <layout:dimensions layout:width=\"260\" layout:height=\"24\"/>"
3885 " </layout:boundingBox>"
3886 " </layout:textGlyph>"
3887 " <layout:textGlyph layout:id=\"TextGlyph_malate_mito3\" layout:originOfText=\"malate_mito3\" layout:graphicalObject=\"SpeciesGlyph_malate_mito3\">"
3888 " <layout:boundingBox layout:id=\"bb_tg_malatate_mito3\">"
3889 " <layout:position layout:x=\"1860\" layout:y=\"80\"/>"
3890 " <layout:dimensions layout:width=\"220\" layout:height=\"36\"/>"
3891 " </layout:boundingBox>"
3892 " </layout:textGlyph>"
3893 " <layout:textGlyph layout:id=\"TextGlyph_oxaloacetate_mito3\" layout:originOfText=\"oxaloacetate_mito3\" layout:graphicalObject=\"SpeciesGlyph_oxaloacetate_mito3\">"
3894 " <layout:boundingBox layout:id=\"bb_tg_oxaloacetate_mito3\">"
3895 " <layout:position layout:x=\"1860\" layout:y=\"280\"/>"
3896 " <layout:dimensions layout:width=\"220\" layout:height=\"36\"/>"
3897 " </layout:boundingBox>"
3898 " </layout:textGlyph>"
3899 " <layout:textGlyph layout:id=\"TextGlyph_aspartate_mito3\" layout:originOfText=\"aspartate_mito3\" layout:graphicalObject=\"SpeciesGlyph_aspartate_mito3\">"
3900 " <layout:boundingBox layout:id=\"bb_tg_aspartate_mito3\">"
3901 " <layout:position layout:x=\"1860\" layout:y=\"480\"/>"
3902 " <layout:dimensions layout:width=\"220\" layout:height=\"36\"/>"
3903 " </layout:boundingBox>"
3904 " </layout:textGlyph>"
3905 " <layout:textGlyph layout:id=\"TextGlyph_glutamate_mito3\" layout:originOfText=\"glutamate_mito3\" layout:graphicalObject=\"SpeciesGlyph_glutamate_mito3\">"
3906 " <layout:boundingBox layout:id=\"bb_tg_glutamate_mito3\">"
3907 " <layout:position layout:x=\"1560\" layout:y=\"430\"/>"
3908 " <layout:dimensions layout:width=\"220\" layout:height=\"36\"/>"
3909 " </layout:boundingBox>"
3910 " </layout:textGlyph>"
3911 " <layout:textGlyph layout:id=\"TextGlyph_aKetoglutarate_mito3\" layout:originOfText=\"aKetoglutarate_mito3\" layout:graphicalObject=\"SpeciesGlyph_aKetoglutarate_mito3\">"
3912 " <layout:boundingBox layout:id=\"bb_tg_aKetoglutarate_mito3\">"
3913 " <layout:position layout:x=\"1540\" layout:y=\"300\"/>"
3914 " <layout:dimensions layout:width=\"260\" layout:height=\"36\"/>"
3915 " </layout:boundingBox>"
3916 " </layout:textGlyph>"
3917 " <layout:textGlyph layout:id=\"TextGlyph_nad_mito3\" layout:originOfText=\"nad_mito3\" layout:graphicalObject=\"SpeciesGlyph_nad_mito3\">"
3918 " <layout:boundingBox layout:id=\"bb_tg_nad_mito3\">"
3919 " <layout:position layout:x=\"2055\" layout:y=\"150\"/>"
3920 " <layout:dimensions layout:width=\"80\" layout:height=\"24\"/>"
3921 " </layout:boundingBox>"
3922 " </layout:textGlyph>"
3923 " <layout:textGlyph layout:id=\"TextGlyph_nadh_mito3\" layout:originOfText=\"nadh_mito3\" layout:graphicalObject=\"SpeciesGlyph_nadh_mito3\">"
3924 " <layout:boundingBox layout:id=\"bb_tg_nadh_mito3\">"
3925 " <layout:position layout:x=\"2055\" layout:y=\"230\"/>"
3926 " <layout:dimensions layout:width=\"80\" layout:height=\"24\"/>"
3927 " </layout:boundingBox>"
3928 " </layout:textGlyph>"
3929 " <layout:textGlyph layout:id=\"TextGlyph_h_mito3\" layout:originOfText=\"h_mito3\" layout:graphicalObject=\"SpeciesGlyph_h_mito3\">"
3930 " <layout:boundingBox layout:id=\"bb_tg_h_mito3\">"
3931 " <layout:position layout:x=\"2205\" layout:y=\"230\"/>"
3932 " <layout:dimensions layout:width=\"30\" layout:height=\"24\"/>"
3933 " </layout:boundingBox>"
3934 " </layout:textGlyph>"
3935 " <layout:textGlyph layout:id=\"tg_rg_malatedh_mito3\" layout:originOfText=\"reaction_malatedh_mito3\" layout:graphicalObject=\"rg_malatedh_mito3\">"
3936 " <layout:boundingBox layout:id=\"bb_tg_rg_malatedh_mito3\">"
3937 " <layout:position layout:x=\"1740\" layout:y=\"185\"/>"
3938 " <layout:dimensions layout:width=\"220\" layout:height=\"24\"/>"
3939 " </layout:boundingBox>"
3940 " </layout:textGlyph>"
3941 " <layout:textGlyph layout:id=\"tg_rg_aspartateat_mito3\" layout:originOfText=\"reaction_aspartateat_mito3\" layout:graphicalObject=\"rg_aspartateat_mito3\">"
3942 " <layout:boundingBox layout:id=\"bb_tg_rg_aspartateat_mito3\">"
3943 " <layout:position layout:x=\"1970\" layout:y=\"385\"/>"
3944 " <layout:dimensions layout:width=\"260\" layout:height=\"24\"/>"
3945 " </layout:boundingBox>"
3946 " </layout:textGlyph>"
3947 " <layout:textGlyph layout:id=\"tg_rg_aspartateCarrier\" layout:originOfText=\"aspartateCarrier\" layout:graphicalObject=\"rg_aspartateCarrier\">"
3948 " <layout:boundingBox layout:id=\"bb_tg_rg_aspartateCarrier\">"
3949 " <layout:position layout:x=\"1380\" layout:y=\"500\"/>"
3950 " <layout:dimensions layout:width=\"160\" layout:height=\"24\"/>"
3951 " </layout:boundingBox>"
3952 " </layout:textGlyph>"
3953 " <layout:textGlyph layout:id=\"tg_rg_malateCarrier\" layout:originOfText=\"malateCarrier\" layout:graphicalObject=\"rg_malateCarrier\">"
3954 " <layout:boundingBox layout:id=\"bb_tg_rg_malateCarrier\">"
3955 " <layout:position layout:x=\"1360\" layout:y=\"330\"/>"
3956 " <layout:dimensions layout:width=\"140\" layout:height=\"24\"/>"
3957 " </layout:boundingBox>"
3958 " </layout:textGlyph>"
3959 " </layout:listOfTextGlyphs>"
3960 " <render:listOfRenderInformation>"
3961 " <render:renderInformation render:id=\"highlightGlucose\" render:referenceRenderInformation=\"defaultStyle\" render:programName=\"Ralph Gauges\" render:programVersion=\"1.0\" render:backgroundColor='#FFFFFFFF'>"
3962 " <render:listOfColorDefinitions>"
3963 " <render:colorDefinition render:id=\"lightRed\" render:value=\"#e6add8\"/>"
3964 " <render:colorDefinition render:id=\"white\" render:value=\"#ffffff\"/>"
3965 " </render:listOfColorDefinitions>"
3966 " <render:listOfGradientDefinitions>"
3967 " <render:radialGradient render:id=\"highlightedSpeciesGlyphGradient\">"
3968 " <render:stop render:offset=\"0\" render:stop-color=\"white\"/>"
3969 " <render:stop render:offset=\"100%\" render:stop-color=\"lightRed\"/>"
3970 " </render:radialGradient>"
3971 " </render:listOfGradientDefinitions>"
3972 " <render:listOfStyles>"
3973 " <render:style render:id=\"highlightedGlucose\" render:idList=\"SpeciesGlyph_Glucose\">"
3974 " <render:g render:stroke=\"black\" render:stroke-width=\"1\">"
3975 " <render:rectangle render:fill=\"highlightedSpeciesGlyphGradient\" render:x=\"0\" render:y=\"0\" render:width=\"100%\" render:height=\"100%\" render:rx=\"5\" render:ry=\"50%\"/>"
3976 " </render:g>"
3977 " </render:style>"
3978 " </render:listOfStyles>"
3979 " </render:renderInformation>"
3980 " </render:listOfRenderInformation>"
3981 " </layout:layout>"
3982 " <render:listOfGlobalRenderInformation>"
3983 " <render:renderInformation render:id=\"wireFrame\" render:name=\"wireframe style\" render:programName=\"Ralph Gauges\" render:programVersion=\"1.0\" render:backgroundColor='#FFFFFFFF'>"
3984 " <render:listOfColorDefinitions>"
3985 " <render:colorDefinition render:id=\"white\" render:value=\"#ffffff\"/>"
3986 " <render:colorDefinition render:id=\"black\" render:value=\"#000000\"/>"
3987 " </render:listOfColorDefinitions>"
3988 " <render:listOfStyles>"
3989 " <render:style render:id=\"compartmentGlyphStyle\" render:typeList=\"COMPARTMENTGLYPH\">"
3990 " <render:g render:stroke=\"black\" render:stroke-width=\"1\">"
3991 " <render:rectangle render:x=\"0\" render:y=\"0\" render:width=\"100%\" render:height=\"100%\"/>"
3992 " </render:g>"
3993 " </render:style>"
3994 " <render:style render:id=\"speciesGlyphStyle\" render:typeList=\"SPECIESGLYPH\">"
3995 " <render:g render:stroke=\"black\" render:stroke-width=\"1\">"
3996 " <render:rectangle render:x=\"0\" render:y=\"0\" render:width=\"100%\" render:height=\"100%\"/>"
3997 " </render:g>"
3998 " </render:style>"
3999 " <render:style render:id=\"reactionGlyphStyle\" render:typeList=\"REACTIONGLYPH SPECIESREFERENCEGLYPH TEXTGLYPH\">"
4000 " <render:g render:stroke=\"black\" render:stroke-width=\"1\" render:font-size=\"12\" render:text-anchor=\"middle\"/>"
4001 " </render:style>"
4002 " </render:listOfStyles>"
4003 " </render:renderInformation>"
4004 " <render:renderInformation render:id=\"defaultGrayStyle\" render:name=\"grayscale style\" render:programName=\"Ralph Gauges\" render:programVersion=\"1.0\" render:backgroundColor='#FFFFFFFF'>"
4005 " <render:listOfColorDefinitions>"
4006 " <render:colorDefinition render:id=\"lightGray\" render:value=\"#cecece\"/>"
4007 " <render:colorDefinition render:id=\"white\" render:value=\"#ffffff\"/>"
4008 " <render:colorDefinition render:id=\"black\" render:value=\"#000000\"/>"
4009 " <render:colorDefinition render:id=\"lightGray2\" render:value=\"#f0f0f0\"/>"
4010 " <render:colorDefinition render:id=\"gray\" render:value=\"#0b0b0b\"/>"
4011 " </render:listOfColorDefinitions>"
4012 " <render:listOfGradientDefinitions>"
4013 " <render:radialGradient render:id=\"speciesGlyphGradient\">"
4014 " <render:stop render:offset=\"0\" render:stop-color=\"white\"/>"
4015 " <render:stop render:offset=\"100%\" render:stop-color=\"lightGray\"/>"
4016 " </render:radialGradient>"
4017 " </render:listOfGradientDefinitions>"
4018 " <render:listOfLineEndings>"
4019 " <render:lineEnding render:id=\"simpleHead_black\">"
4020 " <layout:boundingBox>"
4021 " <layout:position layout:x=\"-8\" layout:y=\"-3\"/>"
4022 " <layout:dimensions layout:width=\"10\" layout:height=\"6\"/>"
4023 " </layout:boundingBox>"
4024 " <render:g render:stroke=\"black\" render:stroke-width=\"1\" render:fill=\"black\">"
4025 " <render:polygon>"
4026 " <render:listOfElements>"
4027 " <render:element xsi:type=\"RenderPoint\" render:x=\"0\" render:y=\"0\"/>"
4028 " <render:element xsi:type=\"RenderPoint\" render:x=\"10\" render:y=\"3\"/>"
4029 " <render:element xsi:type=\"RenderPoint\" render:x=\"0\" render:y=\"6\"/>"
4030 " </render:listOfElements>"
4031 " </render:polygon>"
4032 " </render:g>"
4033 " </render:lineEnding>"
4034 " </render:listOfLineEndings>"
4035 " <render:listOfStyles>"
4036 " <render:style render:id=\"compartmentGlyphStyle\" render:typeList=\"COMPARTMENTGLYPH\">"
4037 " <render:g render:stroke=\"gray\" render:stroke-width=\"1\">"
4038 " <render:rectangle render:fill=\"lightGray2\" render:x=\"0\" render:y=\"0\" render:width=\"100%\" render:height=\"100%\" render:rx=\"5%\"/>"
4039 " </render:g>"
4040 " </render:style>"
4041 " <render:style render:id=\"speciesGlyphStyle\" render:typeList=\"SPECIESGLYPH\">"
4042 " <render:g render:stroke=\"black\" render:stroke-width=\"1\">"
4043 " <render:rectangle render:fill=\"speciesGlyphGradient\" render:x=\"0\" render:y=\"0\" render:width=\"100%\" render:height=\"100%\" render:rx=\"5%\"/>"
4044 " </render:g>"
4045 " </render:style>"
4046 " <render:style render:id=\"reactionGlyphStyle\" render:typeList=\"REACTIONGLYPH TEXTGLYPH\">"
4047 " <render:g render:stroke=\"black\" render:stroke-width=\"1\" render:font-size=\"12\" render:text-anchor=\"middle\"/>"
4048 " </render:style>"
4049 " <render:style render:id=\"reactantSpeciesReferenceGlyphStyle\" render:roleList=\"product sideproduct sidesubstrate substrate\">"
4050 " <render:g render:stroke=\"#000000\" render:stroke-width=\"1\"/>"
4051 " </render:style>"
4052 " <render:style render:id=\"activatorSpeciesReferenceGlyphStyle\" render:roleList=\"activator\">"
4053 " <render:g render:stroke=\"#000000\" render:stroke-width=\"1\"/>"
4054 " </render:style>"
4055 " <render:style render:id=\"modifierSpeciesReferenceGlyphStyle\" render:roleList=\"modifier\">"
4056 " <render:g render:stroke=\"#000000\" render:stroke-width=\"1\"/>"
4057 " </render:style>"
4058 " <render:style render:id=\"inhibitorSpeciesReferenceGlyphStyle\" render:roleList=\"inhibitor\">"
4059 " <render:g render:stroke=\"#000000\" render:stroke-width=\"1\"/>"
4060 " </render:style>"
4061 " </render:listOfStyles>"
4062 " </render:renderInformation>"
4063 " <render:renderInformation render:id=\"shortGrayStyle\" render:name=\"modified default style to grayscale\" render:referenceRenderInformation=\"defaultStyle\" render:programName=\"Ralph Gauges\" render:programVersion=\"1.0\" render:backgroundColor='#FFFFFFFF'>"
4064 " <render:listOfColorDefinitions>"
4065 " <render:colorDefinition render:id=\"lightBlue\" render:value=\"#cecece\"/>"
4066 " <render:colorDefinition render:id=\"white\" render:value=\"#ffffff\"/>"
4067 " <render:colorDefinition render:id=\"black\" render:value=\"#000000\"/>"
4068 " <render:colorDefinition render:id=\"red\" render:value=\"#000000\"/>"
4069 " <render:colorDefinition render:id=\"green\" render:value=\"#000000\"/>"
4070 " <render:colorDefinition render:id=\"blue\" render:value=\"#000000\"/>"
4071 " <render:colorDefinition render:id=\"lightYellow\" render:value=\"#f0f0f0\"/>"
4072 " <render:colorDefinition render:id=\"darkGreen\" render:value=\"#0b0b0b\"/>"
4073 " </render:listOfColorDefinitions>"
4074 " </render:renderInformation>"
4075 " <render:renderInformation render:id=\"defaultStyle\" render:name=\"default style\" render:programName=\"Ralph Gauges\" render:programVersion=\"1.0\" render:backgroundColor='#FFFFFFFF'>"
4076 " <render:listOfColorDefinitions>"
4077 " <render:colorDefinition render:id=\"lightBlue\" render:value=\"#add8e6\"/>"
4078 " <render:colorDefinition render:id=\"white\" render:value=\"#ffffff\"/>"
4079 " <render:colorDefinition render:id=\"black\" render:value=\"#000000\"/>"
4080 " <render:colorDefinition render:id=\"red\" render:value=\"#ff0000\"/>"
4081 " <render:colorDefinition render:id=\"green\" render:value=\"#00ff00\"/>"
4082 " <render:colorDefinition render:id=\"blue\" render:value=\"#0000ff\"/>"
4083 " <render:colorDefinition render:id=\"lightYellow\" render:value=\"#ffffd1\"/>"
4084 " <render:colorDefinition render:id=\"darkGreen\" render:value=\"#002000\"/>"
4085 " </render:listOfColorDefinitions>"
4086 " <render:listOfGradientDefinitions>"
4087 " <render:radialGradient render:id=\"speciesGlyphGradient\">"
4088 " <render:stop render:offset=\"0\" render:stop-color=\"white\"/>"
4089 " <render:stop render:offset=\"100%\" render:stop-color=\"lightBlue\"/>"
4090 " </render:radialGradient>"
4091 " </render:listOfGradientDefinitions>"
4092 " <render:listOfLineEndings>"
4093 " <render:lineEnding render:id=\"simpleHead_black\">"
4094 " <layout:boundingBox>"
4095 " <layout:position layout:x=\"-8\" layout:y=\"-3\"/>"
4096 " <layout:dimensions layout:width=\"10\" layout:height=\"6\"/>"
4097 " </layout:boundingBox>"
4098 " <render:g render:stroke=\"black\" render:stroke-width=\"1\" render:fill=\"black\">"
4099 " <render:polygon>"
4100 " <render:listOfElements>"
4101 " <render:element xsi:type=\"RenderPoint\" render:x=\"0\" render:y=\"0\"/>"
4102 " <render:element xsi:type=\"RenderPoint\" render:x=\"10\" render:y=\"3\"/>"
4103 " <render:element xsi:type=\"RenderPoint\" render:x=\"0\" render:y=\"6\"/>"
4104 " </render:listOfElements>"
4105 " </render:polygon>"
4106 " </render:g>"
4107 " </render:lineEnding>"
4108 " <render:lineEnding render:id=\"simpleHead_red\">"
4109 " <layout:boundingBox>"
4110 " <layout:position layout:x=\"-8\" layout:y=\"-3\"/>"
4111 " <layout:dimensions layout:width=\"10\" layout:height=\"6\"/>"
4112 " </layout:boundingBox>"
4113 " <render:g render:stroke=\"red\" render:stroke-width=\"1\" render:fill=\"red\">"
4114 " <render:polygon>"
4115 " <render:listOfElements>"
4116 " <render:element xsi:type=\"RenderPoint\" render:x=\"0\" render:y=\"0\"/>"
4117 " <render:element xsi:type=\"RenderPoint\" render:x=\"10\" render:y=\"3\"/>"
4118 " <render:element xsi:type=\"RenderPoint\" render:x=\"0\" render:y=\"6\"/>"
4119 " </render:listOfElements>"
4120 " </render:polygon>"
4121 " </render:g>"
4122 " </render:lineEnding>"
4123 " <render:lineEnding render:id=\"simpleHead_green\">"
4124 " <layout:boundingBox>"
4125 " <layout:position layout:x=\"-8\" layout:y=\"-3\"/>"
4126 " <layout:dimensions layout:width=\"10\" layout:height=\"6\"/>"
4127 " </layout:boundingBox>"
4128 " <render:g render:stroke=\"green\" render:stroke-width=\"1\" render:fill=\"green\">"
4129 " <render:polygon>"
4130 " <render:listOfElements>"
4131 " <render:element xsi:type=\"RenderPoint\" render:x=\"0\" render:y=\"0\"/>"
4132 " <render:element xsi:type=\"RenderPoint\" render:x=\"10\" render:y=\"3\"/>"
4133 " <render:element xsi:type=\"RenderPoint\" render:x=\"0\" render:y=\"6\"/>"
4134 " </render:listOfElements>"
4135 " </render:polygon>"
4136 " </render:g>"
4137 " </render:lineEnding>"
4138 " <render:lineEnding render:id=\"simpleHead_blue\">"
4139 " <layout:boundingBox>"
4140 " <layout:position layout:x=\"-8\" layout:y=\"-3\"/>"
4141 " <layout:dimensions layout:width=\"10\" layout:height=\"6\"/>"
4142 " </layout:boundingBox>"
4143 " <render:g render:stroke=\"blue\" render:stroke-width=\"1\" render:fill=\"blue\">"
4144 " <render:polygon>"
4145 " <render:listOfElements>"
4146 " <render:element xsi:type=\"RenderPoint\" render:x=\"0\" render:y=\"0\"/>"
4147 " <render:element xsi:type=\"RenderPoint\" render:x=\"10\" render:y=\"3\"/>"
4148 " <render:element xsi:type=\"RenderPoint\" render:x=\"0\" render:y=\"6\"/>"
4149 " </render:listOfElements>"
4150 " </render:polygon>"
4151 " </render:g>"
4152 " </render:lineEnding>"
4153 " </render:listOfLineEndings>"
4154 " <render:listOfStyles>"
4155 " <render:style render:id=\"compartmentGlyphStyle\" render:typeList=\"COMPARTMENTGLYPH\">"
4156 " <render:g render:stroke=\"darkGreen\" render:stroke-width=\"1\">"
4157 " <render:rectangle render:fill=\"lightYellow\" render:x=\"0\" render:y=\"0\" render:width=\"100%\" render:height=\"100%\" render:rx=\"10%\" render:ry=\"10%\"/>"
4158 " </render:g>"
4159 " </render:style>"
4160 " <render:style render:id=\"speciesGlyphStyle\" render:typeList=\"SPECIESGLYPH\">"
4161 " <render:g render:stroke=\"black\" render:stroke-width=\"1\">"
4162 " <render:rectangle render:fill=\"speciesGlyphGradient\" render:x=\"0\" render:y=\"0\" render:width=\"100%\" render:height=\"100%\" render:rx=\"5\" render:ry=\"50%\"/>"
4163 " </render:g>"
4164 " </render:style>"
4165 " <render:style render:id=\"reactionGlyphStyle\" render:typeList=\"REACTIONGLYPH TEXTGLYPH\">"
4166 " <render:g render:stroke=\"black\" render:stroke-width=\"1\" render:font-size=\"12\" render:text-anchor=\"middle\"/>"
4167 " </render:style>"
4168 " <render:style render:id=\"reactantSpeciesReferenceGlyphStyle\" render:roleList=\"product sideproduct sidesubstrate substrate\">"
4169 " <render:g render:stroke=\"#000000\" render:stroke-width=\"1\" render:endHead=\"simpleHead_black\"/>"
4170 " </render:style>"
4171 " <render:style render:id=\"activatorSpeciesReferenceGlyphStyle\" render:roleList=\"activator\">"
4172 " <render:g render:stroke=\"green\" render:stroke-width=\"1\" render:endHead=\"simpleHead_green\"/>"
4173 " </render:style>"
4174 " <render:style render:id=\"modifierSpeciesReferenceGlyphStyle\" render:roleList=\"modifier\">"
4175 " <render:g render:stroke=\"blue\" render:stroke-width=\"1\" render:endHead=\"simpleHead_blue\"/>"
4176 " </render:style>"
4177 " <render:style render:id=\"inhibitorSpeciesReferenceGlyphStyle\" render:roleList=\"inhibitor\">"
4178 " <render:g render:stroke=\"red\" render:stroke-width=\"1\" render:endHead=\"simpleHead_red\"/>"
4179 " </render:style>"
4180 " </render:listOfStyles>"
4181 " </render:renderInformation>"
4182 " </render:listOfGlobalRenderInformation>"
4183 " </layout:listOfLayouts>"
4184 " </model>"
4185 "</sbml>";
4186
4187
4188 XMLInputStream stream(s,false);
4189 XMLNode node(stream);
4190 // create the document
4191
4192 SBMLDocument *document=new SBMLDocument(3,1);
4193
4194 document->enablePackage(LayoutExtension::getXmlnsL3V1V1(), "layout", true);
4195 document->enablePackage(RenderExtension::getXmlnsL3V1V1(), "render", true);
4196
4197 LayoutPkgNamespaces layoutns;
4198
4199 document->setPackageRequired("layout", false);
4200 document->setPackageRequired("render", false);
4201
4202 // create the Model
4203
4204 Model* model=document->createModel();
4205 model->setId("TestModel");
4206 document->setModel(model);
4207
4208 // create the Compartment
4209
4210 Compartment* compartment=model->createCompartment();
4211 compartment->setId("Hepatocyte");
4212 compartment->setName("Hepatocyte");
4213
4214 Compartment* mito1=model->createCompartment();
4215 mito1->setId("Mito_1");
4216 mito1->setName("Mito 1");
4217 mito1->setOutside(compartment->getId());
4218
4219 Compartment* mito2=model->createCompartment();
4220 mito2->setId("Mito_2");
4221 mito2->setName("Mito 2");
4222 mito2->setOutside(compartment->getId());
4223
4224 Compartment* mito3=model->createCompartment();
4225 mito3->setId("Mito_3");
4226 mito3->setName("Mito 3");
4227 mito3->setOutside(compartment->getId());
4228
4229
4230 // create the Species
4231
4232 // Malate
4233 Species* malate_cyt=model->createSpecies();
4234 malate_cyt->setId("malate_cyt");
4235 malate_cyt->setName("Malate");
4236 malate_cyt->setCompartment(compartment->getId());
4237
4238 Species* malate_mito1=model->createSpecies();
4239 malate_mito1->setId("malate_mito1");
4240 malate_mito1->setCompartment(mito1->getId());
4241 malate_mito1->setName("Malate");
4242
4243 Species* malate_mito2=model->createSpecies();
4244 malate_mito2->setId("malate_mito2");
4245 malate_mito2->setCompartment(mito2->getId());
4246 malate_mito2->setName("Malate");
4247
4248 Species* malate_mito3=model->createSpecies();
4249 malate_mito3->setId("malate_mito3");
4250 malate_mito3->setCompartment(mito3->getId());
4251 malate_mito3->setName("Malate");
4252
4253
4254 // Oxaloacetate
4255 Species* oxaloacetate_cyt=model->createSpecies();
4256 oxaloacetate_cyt->setId("oxaloacetate_cyt");
4257 oxaloacetate_cyt->setName("Oxaloacetate");
4258 oxaloacetate_cyt->setCompartment(compartment->getId());
4259
4260 Species* oxaloacetate_mito1=model->createSpecies();
4261 oxaloacetate_mito1->setId("oxaloacetate_mito1");
4262 oxaloacetate_mito1->setCompartment(mito1->getId());
4263 oxaloacetate_mito1->setName("Oxaloacetate");
4264
4265 Species* oxaloacetate_mito2=model->createSpecies();
4266 oxaloacetate_mito2->setId("oxaloacetate_mito2");
4267 oxaloacetate_mito2->setCompartment(mito2->getId());
4268 oxaloacetate_mito2->setName("Oxaloacetate");
4269
4270 Species* oxaloacetate_mito3=model->createSpecies();
4271 oxaloacetate_mito3->setId("oxaloacetate_mito3");
4272 oxaloacetate_mito3->setCompartment(mito3->getId());
4273 oxaloacetate_mito3->setName("Oxaloacetate");
4274
4275
4276 // Aspartate
4277 Species* aspartate_cyt=model->createSpecies();
4278 aspartate_cyt->setId("aspartate_cyt");
4279 aspartate_cyt->setName("Aspartate");
4280 aspartate_cyt->setCompartment(compartment->getId());
4281
4282 Species* aspartate_mito1=model->createSpecies();
4283 aspartate_mito1->setId("aspartate_mito1");
4284 aspartate_mito1->setCompartment(mito1->getId());
4285 aspartate_mito1->setName("Aspartate");
4286
4287 Species* aspartate_mito2=model->createSpecies();
4288 aspartate_mito2->setId("aspartate_mito2");
4289 aspartate_mito2->setCompartment(mito2->getId());
4290 aspartate_mito2->setName("Aspartate");
4291
4292 Species* aspartate_mito3=model->createSpecies();
4293 aspartate_mito3->setId("aspartate_mito3");
4294 aspartate_mito3->setCompartment(mito3->getId());
4295 aspartate_mito3->setName("Aspartate");
4296
4297
4298 // Glutamate
4299 Species* glutamate_cyt=model->createSpecies();
4300 glutamate_cyt->setId("glutamate_cyt");
4301 glutamate_cyt->setName("Glutamate");
4302 glutamate_cyt->setCompartment(compartment->getId());
4303
4304 Species* glutamate_mito1=model->createSpecies();
4305 glutamate_mito1->setId("glutamate_mito1");
4306 glutamate_mito1->setCompartment(mito1->getId());
4307 glutamate_mito1->setName("Glutamate");
4308
4309 Species* glutamate_mito2=model->createSpecies();
4310 glutamate_mito2->setId("glutamate_mito2");
4311 glutamate_mito2->setCompartment(mito2->getId());
4312 glutamate_mito2->setName("Glutamate");
4313
4314 Species* glutamate_mito3=model->createSpecies();
4315 glutamate_mito3->setId("glutamate_mito3");
4316 glutamate_mito3->setCompartment(mito3->getId());
4317 glutamate_mito3->setName("Glutamate");
4318
4319
4320 // alpha-Ketoglutarate
4321 Species* aKetoglutarate_cyt=model->createSpecies();
4322 aKetoglutarate_cyt->setId("aKetoglutarate_cyt");
4323 aKetoglutarate_cyt->setName("alpha-Ketoglutarate");
4324 aKetoglutarate_cyt->setCompartment(compartment->getId());
4325
4326 Species* aKetoglutarate_mito1=model->createSpecies();
4327 aKetoglutarate_mito1->setId("aKetoglutarate_mito1");
4328 aKetoglutarate_mito1->setCompartment(mito1->getId());
4329 aKetoglutarate_mito1->setName("alpha-Ketoglutarate");
4330
4331 Species* aKetoglutarate_mito2=model->createSpecies();
4332 aKetoglutarate_mito2->setId("aKetoglutarate_mito2");
4333 aKetoglutarate_mito2->setCompartment(mito2->getId());
4334 aKetoglutarate_mito2->setName("alpha-Ketoglutarate");
4335
4336 Species* aKetoglutarate_mito3=model->createSpecies();
4337 aKetoglutarate_mito3->setId("aKetoglutarate_mito3");
4338 aKetoglutarate_mito3->setCompartment(mito3->getId());
4339 aKetoglutarate_mito3->setName("alpha-Ketoglutarate");
4340
4341
4342 // protons
4343 Species* h_cyt=model->createSpecies();
4344 h_cyt->setId("h_cyt");
4345 h_cyt->setName("H+");
4346 h_cyt->setCompartment(compartment->getId());
4347
4348 Species* h_mito1=model->createSpecies();
4349 h_mito1->setId("h_mito1");
4350 h_mito1->setCompartment(mito1->getId());
4351 h_mito1->setName("H+");
4352
4353 Species* h_mito2=model->createSpecies();
4354 h_mito2->setId("h_mito2");
4355 h_mito2->setCompartment(mito2->getId());
4356 h_mito2->setName("H+");
4357
4358 Species* h_mito3=model->createSpecies();
4359 h_mito3->setId("h_mito3");
4360 h_mito3->setCompartment(mito3->getId());
4361 h_mito3->setName("H+");
4362
4363
4364 // NAD+
4365 Species* nad_cyt=model->createSpecies();
4366 nad_cyt->setId("nad_cyt");
4367 nad_cyt->setName("NAD+");
4368 nad_cyt->setCompartment(compartment->getId());
4369
4370 Species* nad_mito1=model->createSpecies();
4371 nad_mito1->setId("nad_mito1");
4372 nad_mito1->setCompartment(mito1->getId());
4373 nad_mito1->setName("NAD+");
4374
4375 Species* nad_mito2=model->createSpecies();
4376 nad_mito2->setId("nad_mito2");
4377 nad_mito2->setCompartment(mito2->getId());
4378 nad_mito2->setName("NAD+");
4379
4380 Species* nad_mito3=model->createSpecies();
4381 nad_mito3->setId("nad_mito3");
4382 nad_mito3->setCompartment(mito3->getId());
4383 nad_mito3->setName("NAD+");
4384
4385
4386 // NADH
4387 Species* nadh_cyt=model->createSpecies();
4388 nadh_cyt->setId("nadh_cyt");
4389 nadh_cyt->setName("NADH");
4390 nadh_cyt->setCompartment(compartment->getId());
4391
4392 Species* nadh_mito1=model->createSpecies();
4393 nadh_mito1->setId("nadh_mito1");
4394 nadh_mito1->setCompartment(mito1->getId());
4395 nadh_mito1->setName("NADH");
4396
4397 Species* nadh_mito2=model->createSpecies();
4398 nadh_mito2->setId("nadh_mito2");
4399 nadh_mito2->setCompartment(mito2->getId());
4400 nadh_mito2->setName("NADH");
4401
4402 Species* nadh_mito3=model->createSpecies();
4403 nadh_mito3->setId("nadh_mito3");
4404 nadh_mito3->setCompartment(mito3->getId());
4405 nadh_mito3->setName("NADH");
4406
4407
4408
4409
4410 // create the Reactions
4411
4412 // Cytosol
4413
4414 // Malate Dehydrogenase
4415 Reaction* malatedh_cyt=model->createReaction();
4416 malatedh_cyt->setId("reaction_malatedh_cyt");
4417 malatedh_cyt->setName("malate dehydrogenase");
4418 malatedh_cyt->setReversible(false);
4419
4420 SpeciesReference* sr_malate_cyt=malatedh_cyt->createReactant();
4421 sr_malate_cyt->setSpecies(malate_cyt->getId());
4422 sr_malate_cyt->setId("sr_malate_cyt");
4423
4424 SpeciesReference* sr_nad_cyt=malatedh_cyt->createReactant();
4425 sr_nad_cyt->setSpecies(nad_cyt->getId());
4426 sr_nad_cyt->setId("sr_nad_cyt");
4427
4428 SpeciesReference* sr_nadh_cyt=malatedh_cyt->createProduct();
4429 sr_nadh_cyt->setSpecies(nadh_cyt->getId());
4430 sr_nadh_cyt->setId("sr_nadh_cyt");
4431
4432 SpeciesReference* sr_h_cyt=malatedh_cyt->createProduct();
4433 sr_h_cyt->setSpecies(h_cyt->getId());
4434 sr_h_cyt->setId("sr_h_cyt");
4435
4436 SpeciesReference* sr_oxaloacetate_cyt_1=malatedh_cyt->createProduct();
4437 sr_oxaloacetate_cyt_1->setSpecies(oxaloacetate_cyt->getId());
4438 sr_oxaloacetate_cyt_1->setId("sr_oxaloacetate_cyt_1");
4439
4440 //Aspartate Aminotransferase
4441 Reaction* aspartateat_cyt=model->createReaction();
4442 aspartateat_cyt->setId("reaction_aspartateat_cyt");
4443 aspartateat_cyt->setName("aspartate aminotransferase");
4444 aspartateat_cyt->setReversible(false);
4445
4446 SpeciesReference* sr_oxaloacetate_cyt_2=aspartateat_cyt->createReactant();
4447 sr_oxaloacetate_cyt_2->setSpecies(oxaloacetate_cyt->getId());
4448 sr_oxaloacetate_cyt_2->setId("sr_oxaloacetate_cyt_2");
4449
4450 SpeciesReference* sr_glutamate_cyt_1=aspartateat_cyt->createReactant();
4451 sr_glutamate_cyt_1->setSpecies(glutamate_cyt->getId());
4452 sr_glutamate_cyt_1->setId("sr_glutamate_cyt_1");
4453
4454 SpeciesReference* sr_aspartate_cyt_1=aspartateat_cyt->createProduct();
4455 sr_aspartate_cyt_1->setSpecies(aspartate_cyt->getId());
4456 sr_aspartate_cyt_1->setId("sr_aspartate_cyt_1");
4457
4458 SpeciesReference* sr_aKetoglutarate_cyt_1=aspartateat_cyt->createProduct();
4459 sr_aKetoglutarate_cyt_1->setSpecies(aKetoglutarate_cyt->getId());
4460 sr_aKetoglutarate_cyt_1->setId("sr_aKetoglutarate_cyt_1");
4461
4462
4463 // Mito 1
4464
4465 // Malate Dehydrogenase
4466 Reaction* malatedh_mito1=model->createReaction();
4467 malatedh_mito1->setId("reaction_malatedh_mito1");
4468 malatedh_mito1->setName("malate dehydrogenase");
4469 malatedh_mito1->setReversible(false);
4470
4471 SpeciesReference* sr_malate_mito1=malatedh_mito1->createReactant();
4472 sr_malate_mito1->setSpecies(malate_mito1->getId());
4473 sr_malate_mito1->setId("sr_malate_mito1");
4474
4475 SpeciesReference* sr_nad_mito1=malatedh_mito1->createReactant();
4476 sr_nad_mito1->setSpecies(nad_mito1->getId());
4477 sr_nad_mito1->setId("sr_nad_mito1");
4478
4479 SpeciesReference* sr_nadh_mito1=malatedh_mito1->createProduct();
4480 sr_nadh_mito1->setSpecies(nadh_mito1->getId());
4481 sr_nadh_mito1->setId("sr_nadh_mito1");
4482
4483 SpeciesReference* sr_h_mito1=malatedh_mito1->createProduct();
4484 sr_h_mito1->setSpecies(h_mito1->getId());
4485 sr_h_mito1->setId("sr_h_mito1");
4486
4487 SpeciesReference* sr_oxaloacetate_mito1_1=malatedh_mito1->createProduct();
4488 sr_oxaloacetate_mito1_1->setSpecies(oxaloacetate_mito1->getId());
4489 sr_oxaloacetate_mito1_1->setId("sr_oxaloacetate_mito1_1");
4490
4491 //Aspartate Aminotransferase
4492 Reaction* aspartateat_mito1=model->createReaction();
4493 aspartateat_mito1->setId("reaction_aspartateat_mito1");
4494 aspartateat_mito1->setName("aspartate aminotransferase");
4495 aspartateat_mito1->setReversible(false);
4496
4497 SpeciesReference* sr_oxaloacetate_mito1_2=aspartateat_mito1->createReactant();
4498 sr_oxaloacetate_mito1_2->setSpecies(oxaloacetate_mito1->getId());
4499 sr_oxaloacetate_mito1_2->setId("sr_oxaloacetate_mito1_2");
4500
4501 SpeciesReference* sr_glutamate_mito1=aspartateat_mito1->createReactant();
4502 sr_glutamate_mito1->setSpecies(glutamate_mito1->getId());
4503 sr_glutamate_mito1->setId("sr_glutamate_mito1");
4504
4505 SpeciesReference* sr_aspartate_mito1=aspartateat_mito1->createProduct();
4506 sr_aspartate_mito1->setSpecies(aspartate_mito1->getId());
4507 sr_aspartate_mito1->setId("sr_aspartate_mito1");
4508
4509 SpeciesReference* sr_aKetoglutarate_mito1=aspartateat_mito1->createProduct();
4510 sr_aKetoglutarate_mito1->setSpecies(aKetoglutarate_mito1->getId());
4511 sr_aKetoglutarate_mito1->setId("sr_aKetoglutarate_mito1");
4512
4513
4514 // Mito 2
4515
4516 // Malate Dehydrogenase
4517 Reaction* malatedh_mito2=model->createReaction();
4518 malatedh_mito2->setId("reaction_malatedh_mito2");
4519 malatedh_mito2->setName("malate dehydrogenase");
4520 malatedh_mito2->setReversible(false);
4521
4522 SpeciesReference* sr_malate_mito2=malatedh_mito2->createReactant();
4523 sr_malate_mito2->setSpecies(malate_mito2->getId());
4524 sr_malate_mito2->setId("sr_malate_mito2");
4525
4526 SpeciesReference* sr_nad_mito2=malatedh_mito2->createReactant();
4527 sr_nad_mito2->setSpecies(nad_mito2->getId());
4528 sr_nad_mito2->setId("sr_nad_mito2");
4529
4530 SpeciesReference* sr_nadh_mito2=malatedh_mito2->createProduct();
4531 sr_nadh_mito2->setSpecies(nadh_mito2->getId());
4532 sr_nadh_mito2->setId("sr_nadh_mito2");
4533
4534 SpeciesReference* sr_h_mito2=malatedh_mito2->createProduct();
4535 sr_h_mito2->setSpecies(h_mito2->getId());
4536 sr_h_mito2->setId("sr_h_mito2");
4537
4538 SpeciesReference* sr_oxaloacetate_mito2_1=malatedh_mito2->createProduct();
4539 sr_oxaloacetate_mito2_1->setSpecies(oxaloacetate_mito2->getId());
4540 sr_oxaloacetate_mito2_1->setId("sr_oxaloacetate_mito2_1");
4541
4542 //Aspartate Aminotransferase
4543 Reaction* aspartateat_mito2=model->createReaction();
4544 aspartateat_mito2->setId("reaction_aspartateat_mito2");
4545 aspartateat_mito2->setName("aspartate aminotransferase");
4546 aspartateat_mito2->setReversible(false);
4547
4548 SpeciesReference* sr_oxaloacetate_mito2_2=aspartateat_mito2->createReactant();
4549 sr_oxaloacetate_mito2_2->setSpecies(oxaloacetate_mito2->getId());
4550 sr_oxaloacetate_mito2_2->setId("sr_oxaloacetate_mito2_2");
4551
4552 SpeciesReference* sr_glutamate_mito2=aspartateat_mito2->createReactant();
4553 sr_glutamate_mito2->setSpecies(glutamate_mito2->getId());
4554 sr_glutamate_mito2->setId("sr_glutamate_mito2");
4555
4556 SpeciesReference* sr_aspartate_mito2=aspartateat_mito2->createProduct();
4557 sr_aspartate_mito2->setSpecies(aspartate_mito2->getId());
4558 sr_aspartate_mito2->setId("sr_aspartate_mito2");
4559
4560 SpeciesReference* sr_aKetoglutarate_mito2=aspartateat_mito2->createProduct();
4561 sr_aKetoglutarate_mito2->setSpecies(aKetoglutarate_mito2->getId());
4562 sr_aKetoglutarate_mito2->setId("sr_aKetoglutarate_mito2");
4563
4564
4565 // Mito 3
4566
4567 // Malate Dehydrogenase
4568 Reaction* malatedh_mito3=model->createReaction();
4569 malatedh_mito3->setId("reaction_malatedh_mito3");
4570 malatedh_mito3->setName("malate dehydrogenase");
4571 malatedh_mito3->setReversible(false);
4572
4573 SpeciesReference* sr_malate_mito3=malatedh_mito3->createReactant();
4574 sr_malate_mito3->setSpecies(malate_mito3->getId());
4575 sr_malate_mito3->setId("sr_malate_mito3");
4576
4577 SpeciesReference* sr_nad_mito3=malatedh_mito3->createReactant();
4578 sr_nad_mito3->setSpecies(nad_mito3->getId());
4579 sr_nad_mito3->setId("sr_nad_mito3");
4580
4581 SpeciesReference* sr_nadh_mito3=malatedh_mito3->createProduct();
4582 sr_nadh_mito3->setSpecies(nadh_mito3->getId());
4583 sr_nadh_mito3->setId("sr_nadh_mito3");
4584
4585 SpeciesReference* sr_h_mito3=malatedh_mito3->createProduct();
4586 sr_h_mito3->setSpecies(h_mito3->getId());
4587 sr_h_mito3->setId("sr_h_mito3");
4588
4589 SpeciesReference* sr_oxaloacetate_mito3_1=malatedh_mito3->createProduct();
4590 sr_oxaloacetate_mito3_1->setSpecies(oxaloacetate_mito3->getId());
4591 sr_oxaloacetate_mito3_1->setId("sr_oxaloacetate_mito3_1");
4592
4593 //Aspartate Aminotransferase
4594 Reaction* aspartateat_mito3=model->createReaction();
4595 aspartateat_mito3->setId("reaction_aspartateat_mito3");
4596 aspartateat_mito3->setName("aspartate aminotransferase");
4597 aspartateat_mito3->setReversible(false);
4598
4599 SpeciesReference* sr_oxaloacetate_mito3_2=aspartateat_mito3->createReactant();
4600 sr_oxaloacetate_mito3_2->setSpecies(oxaloacetate_mito3->getId());
4601 sr_oxaloacetate_mito3_2->setId("sr_oxaloacetate_mito3_2");
4602
4603
4604 SpeciesReference* sr_glutamate_mito3_1=aspartateat_mito3->createReactant();
4605 sr_glutamate_mito3_1->setSpecies(glutamate_mito3->getId());
4606 sr_glutamate_mito3_1->setId("sr_glutamate_mito3_1");
4607
4608
4609 SpeciesReference* sr_aspartate_mito3_1=aspartateat_mito3->createProduct();
4610 sr_aspartate_mito3_1->setSpecies(aspartate_mito3->getId());
4611 sr_aspartate_mito3_1->setId("sr_aspartate_mito3_1");
4612
4613
4614 SpeciesReference* sr_aKetoglutarate_mito3_1=aspartateat_mito3->createProduct();
4615 sr_aKetoglutarate_mito3_1->setSpecies(aKetoglutarate_mito3->getId());
4616 sr_aKetoglutarate_mito3_1->setId("sr_aKetoglutarate_mito3_1");
4617
4618
4619 // aspartate carrier
4620
4621 Reaction* aspartateCarrier=model->createReaction();
4622 aspartateCarrier->setId("aspartateCarrier");
4623 aspartateCarrier->setName("aspartate carrier");
4624 aspartateCarrier->setReversible(true);
4625
4626 SpeciesReference* sr_glutamate_mito3_2=aspartateCarrier->createReactant();
4627 sr_glutamate_mito3_2->setSpecies(glutamate_mito3->getId());
4628 sr_glutamate_mito3_2->setId("sr_glutamate_mito3_2");
4629
4630 SpeciesReference* sr_aspartate_cyt_2=aspartateCarrier->createReactant();
4631 sr_aspartate_cyt_2->setSpecies(aspartate_cyt->getId());
4632 sr_aspartate_cyt_2->setId("sr_aspartate_cyt_2");
4633
4634 SpeciesReference* sr_glutamate_cyt_2=aspartateCarrier->createProduct();
4635 sr_glutamate_cyt_2->setSpecies(glutamate_cyt->getId());
4636 sr_glutamate_cyt_2->setId("sr_glutamate_cyt_2");
4637
4638 SpeciesReference* sr_aspartate_mito3_2=aspartateCarrier->createProduct();
4639 sr_aspartate_mito3_2->setSpecies(aspartate_mito3->getId());
4640 sr_aspartate_mito3_2->setId("sr_aspartate_mito3_2");
4641
4642 // malate carrier
4643
4644 Reaction* malateCarrier=model->createReaction();
4645 malateCarrier->setId("malateCarrier");
4646 malateCarrier->setName("malate carrier");
4647 malateCarrier->setReversible(true);
4648
4649 SpeciesReference* sr_aKetoglutarate_mito3_2=malateCarrier->createReactant();
4650 sr_aKetoglutarate_mito3_2->setSpecies(aKetoglutarate_mito3->getId());
4651 sr_aKetoglutarate_mito3_2->setId("sr_aKetoglutarate_mito3_2");
4652
4653 SpeciesReference* sr_malate_cyt_2=malateCarrier->createReactant();
4654 sr_malate_cyt_2->setSpecies(malate_cyt->getId());
4655 sr_malate_cyt_2->setId("sr_malate_cyt_2");
4656
4657 SpeciesReference* sr_aKetoglutarate_cyt_2=malateCarrier->createProduct();
4658 sr_aKetoglutarate_cyt_2->setSpecies(aKetoglutarate_cyt->getId());
4659 sr_aKetoglutarate_cyt_2->setId("sr_aKetoglutarate_cyt_2");
4660
4661 SpeciesReference* sr_malate_mito3_2=malateCarrier->createProduct();
4662 sr_malate_mito3_2->setSpecies(malate_mito3->getId());
4663 sr_malate_mito3_2->setId("sr_malate_mito3_2");
4664
4665
4666 /////////// create the Layout
4667 LayoutModelPlugin *plugin = (LayoutModelPlugin*)model->getPlugin("layout");
4668 fail_unless(plugin != NULL);
4669 if (plugin == NULL) return;
4670
4671 Layout* layout=plugin ->createLayout();
4672
4673 layout->setId("Layout_1");
4674 Dimensions dim(&layoutns,2320.0,1000.0);
4675 layout->setDimensions(&dim);
4676
4677
4678 // create the CompartmentGlyph
4679
4680 CompartmentGlyph* compartmentGlyph=layout->createCompartmentGlyph();
4681 compartmentGlyph->setId("CompartmentGlyph_1");
4682 compartmentGlyph->setCompartmentId(compartment->getId());
4683 BoundingBox bb=BoundingBox(&layoutns, "bb_compartment",10,10,2300,980);
4684 compartmentGlyph->setBoundingBox(&bb);
4685
4686 TextGlyph* tg=layout->createTextGlyph();
4687 tg->setId("TextGlyph_Hepatocyte");
4688 tg->setOriginOfTextId(compartment->getId());
4689 bb=BoundingBox(&layoutns, "bb_tg_compartment",50,870,300,72);
4690 tg->setBoundingBox(&bb);
4691 tg->setGraphicalObjectId(compartmentGlyph->getId());
4692
4693 CompartmentGlyph* mito1Glyph=layout->createCompartmentGlyph();
4694 mito1Glyph->setId("Mito1_Glyph");
4695 mito1Glyph->setCompartmentId(mito1->getId());
4696 bb=BoundingBox(&layoutns, "bb_mito1",100,100,300,100);
4697 mito1Glyph->setBoundingBox(&bb);
4698
4699 tg=layout->createTextGlyph();
4700 tg->setId("TextGlyph_mito1");
4701 tg->setOriginOfTextId(mito1->getId());
4702 bb=BoundingBox(&layoutns, "bb_tg_mito1",110,110,280,72);
4703 tg->setBoundingBox(&bb);
4704 tg->setGraphicalObjectId(mito1Glyph->getId());
4705
4706
4707 CompartmentGlyph* mito2Glyph=layout->createCompartmentGlyph();
4708 mito2Glyph->setId("Mito2_Glyph");
4709 mito2Glyph->setCompartmentId(mito2->getId());
4710 bb=BoundingBox(&layoutns, "bb_mito2",200,650,300,100);
4711 mito2Glyph->setBoundingBox(&bb);
4712
4713 tg=layout->createTextGlyph();
4714 tg->setId("TextGlyph_mito2");
4715 tg->setOriginOfTextId(mito2->getId());
4716 bb=BoundingBox(&layoutns, "bb_tg_mito2",210,660,280,72);
4717 tg->setBoundingBox(&bb);
4718 tg->setGraphicalObjectId(mito2Glyph->getId());
4719
4720 CompartmentGlyph* mito3Glyph_2=layout->createCompartmentGlyph();
4721 mito3Glyph_2->setId("Mito3_Glyph_2");
4722 mito3Glyph_2->setCompartmentId(mito3->getId());
4723 bb=BoundingBox(&layoutns, "bb_mito3_2",1470,30,820,536);
4724 mito3Glyph_2->setBoundingBox(&bb);
4725
4726 tg=layout->createTextGlyph();
4727 tg->setId("TextGlyph_mito3_2");
4728 tg->setOriginOfTextId(mito3->getId());
4729 bb=BoundingBox(&layoutns, "bb_tg_mito3_2",1475,35,200,72);
4730 tg->setBoundingBox(&bb);
4731 tg->setGraphicalObjectId(mito3Glyph_2->getId());
4732
4733
4734
4735
4736 // create the SpeciesGlyphs
4737
4738 // Cytosol
4739
4740 // Malate cyt
4741 SpeciesGlyph* speciesGlyph_malate_cyt=layout->createSpeciesGlyph();
4742 speciesGlyph_malate_cyt->setId("SpeciesGlyph_malate_cyt");
4743 speciesGlyph_malate_cyt->setSpeciesId(malate_cyt->getId());
4744 bb=BoundingBox(&layoutns, "bb_sg_malate_cyt",580,280,240,36);
4745 speciesGlyph_malate_cyt->setBoundingBox(&bb);
4746
4747 tg=layout->createTextGlyph();
4748 tg->setId("TextGlyph_malate_cyt");
4749 bb=BoundingBox(&layoutns, "bb_tg_malatate_cyt",590,280,220,36);
4750 tg->setBoundingBox(&bb);
4751 tg->setOriginOfTextId(malate_cyt->getId());
4752 tg->setGraphicalObjectId(speciesGlyph_malate_cyt->getId());
4753
4754 // Oxaloacetate cyt
4755 SpeciesGlyph* speciesGlyph_oxaloacetate_cyt=layout->createSpeciesGlyph();
4756 speciesGlyph_oxaloacetate_cyt->setId("SpeciesGlyph_oxaloacetate_cyt");
4757 speciesGlyph_oxaloacetate_cyt->setSpeciesId(oxaloacetate_cyt->getId());
4758 bb=BoundingBox(&layoutns, "bb_sg_oxaloacetate_cyt",580,480,240,36);
4759 speciesGlyph_oxaloacetate_cyt->setBoundingBox(&bb);
4760
4761 tg=layout->createTextGlyph();
4762 tg->setId("TextGlyph_oxaloacetate_cyt");
4763 bb=BoundingBox(&layoutns, "bb_tg_oxaloacetate_cyt",590,480,220,36);
4764 tg->setBoundingBox(&bb);
4765 tg->setOriginOfTextId(oxaloacetate_cyt->getId());
4766 tg->setGraphicalObjectId(speciesGlyph_oxaloacetate_cyt->getId());
4767
4768 // Aspartate cyt
4769 SpeciesGlyph* speciesGlyph_aspartate_cyt=layout->createSpeciesGlyph();
4770 speciesGlyph_aspartate_cyt->setId("SpeciesGlyph_aspartate_cyt");
4771 speciesGlyph_aspartate_cyt->setSpeciesId(aspartate_cyt->getId());
4772 bb=BoundingBox(&layoutns, "bb_sg_aspartate_cyt",580,680,240,36);
4773 speciesGlyph_aspartate_cyt->setBoundingBox(&bb);
4774
4775 tg=layout->createTextGlyph();
4776 tg->setId("TextGlyph_aspartate_cyt");
4777 bb=BoundingBox(&layoutns, "bb_tg_aspartate_cyt",590,680,220,36);
4778 tg->setBoundingBox(&bb);
4779 tg->setOriginOfTextId(aspartate_cyt->getId());
4780 tg->setGraphicalObjectId(speciesGlyph_aspartate_cyt->getId());
4781
4782 // Glutamate cyt
4783 SpeciesGlyph* speciesGlyph_glutamate_cyt=layout->createSpeciesGlyph();
4784 speciesGlyph_glutamate_cyt->setId("SpeciesGlyph_glutamate_cyt");
4785 speciesGlyph_glutamate_cyt->setSpeciesId(glutamate_cyt->getId());
4786 bb=BoundingBox(&layoutns, "bb_sg_glutamate_cyt",800,610,240,36);
4787 speciesGlyph_glutamate_cyt->setBoundingBox(&bb);
4788
4789 tg=layout->createTextGlyph();
4790 tg->setId("TextGlyph_glutamate_cyt");
4791 bb=BoundingBox(&layoutns, "bb_tg_glutamate_cyt",810,610,220,36);
4792 tg->setBoundingBox(&bb);
4793 tg->setOriginOfTextId(glutamate_cyt->getId());
4794 tg->setGraphicalObjectId(speciesGlyph_glutamate_cyt->getId());
4795
4796 // alpha-Ketoglutarate cyt
4797 SpeciesGlyph* speciesGlyph_aKetoglutarate_cyt=layout->createSpeciesGlyph();
4798 speciesGlyph_aKetoglutarate_cyt->setId("SpeciesGlyph_aKetoglutarate_cyt");
4799 speciesGlyph_aKetoglutarate_cyt->setSpeciesId(aKetoglutarate_cyt->getId());
4800 bb=BoundingBox(&layoutns, "bb_sg_aKetoglutarate_cyt",860,500,280,36);
4801 speciesGlyph_aKetoglutarate_cyt->setBoundingBox(&bb);
4802
4803 tg=layout->createTextGlyph();
4804 tg->setId("TextGlyph_aKetoglutarate_cyt");
4805 bb=BoundingBox(&layoutns, "bb_tg_aKetoglutarate_cyt",870,500,260,36);
4806 tg->setBoundingBox(&bb);
4807 tg->setOriginOfTextId(aKetoglutarate_cyt->getId());
4808 tg->setGraphicalObjectId(speciesGlyph_aKetoglutarate_cyt->getId());
4809
4810 // NAD+ cyt
4811 SpeciesGlyph* speciesGlyph_nad_cyt=layout->createSpeciesGlyph();
4812 speciesGlyph_nad_cyt->setId("SpeciesGlyph_nad_cyt");
4813 speciesGlyph_nad_cyt->setSpeciesId(nad_cyt->getId());
4814 bb=BoundingBox(&layoutns, "bb_sg_nad_cyt",520,350,100,24);
4815 speciesGlyph_nad_cyt->setBoundingBox(&bb);
4816
4817 tg=layout->createTextGlyph();
4818 tg->setId("TextGlyph_nad_cyt");
4819 bb=BoundingBox(&layoutns, "bb_tg_nad_cyt",525,350,80,24);
4820 tg->setBoundingBox(&bb);
4821 tg->setOriginOfTextId(nad_cyt->getId());
4822 tg->setGraphicalObjectId(speciesGlyph_nad_cyt->getId());
4823
4824 // NADH cyt
4825 SpeciesGlyph* speciesGlyph_nadh_cyt=layout->createSpeciesGlyph();
4826 speciesGlyph_nadh_cyt->setId("SpeciesGlyph_nadh_cyt");
4827 speciesGlyph_nadh_cyt->setSpeciesId(nadh_cyt->getId());
4828 bb=BoundingBox(&layoutns, "bb_sg_nadh_cyt",520,430,100,24);
4829 speciesGlyph_nadh_cyt->setBoundingBox(&bb);
4830
4831 tg=layout->createTextGlyph();
4832 tg->setId("TextGlyph_nadh_cyt");
4833 bb=BoundingBox(&layoutns, "bb_tg_nadh_cyt",525,430,80,24);
4834 tg->setBoundingBox(&bb);
4835 tg->setOriginOfTextId(nadh_cyt->getId());
4836 tg->setGraphicalObjectId(speciesGlyph_nadh_cyt->getId());
4837
4838 // H+ cyt
4839 SpeciesGlyph* speciesGlyph_h_cyt=layout->createSpeciesGlyph();
4840 speciesGlyph_h_cyt->setId("SpeciesGlyph_h_cyt");
4841 speciesGlyph_h_cyt->setSpeciesId(h_cyt->getId());
4842 bb=BoundingBox(&layoutns, "bb_sg_h_cyt",430,430,40,24);
4843 speciesGlyph_h_cyt->setBoundingBox(&bb);
4844
4845 tg=layout->createTextGlyph();
4846 tg->setId("TextGlyph_h_cyt");
4847 bb=BoundingBox(&layoutns, "bb_tg_h_cyt",435,430,30,24);
4848 tg->setBoundingBox(&bb);
4849 tg->setOriginOfTextId(h_cyt->getId());
4850 tg->setGraphicalObjectId(speciesGlyph_h_cyt->getId());
4851
4852
4853 // create the ReactionGlyphs
4854
4855 ReactionGlyph* rg_malatedh_cyt=layout->createReactionGlyph();
4856 rg_malatedh_cyt->setId("rg_malatedh_cyt");
4857 rg_malatedh_cyt->setReactionId(malatedh_cyt->getId());
4858
4859 Curve* curve=rg_malatedh_cyt->getCurve();
4860 LineSegment* ls=curve->createLineSegment();
4861 Point p(&layoutns, 700,381);
4862 ls->setStart(&p);
4863 p=Point(&layoutns, 700,415);
4864 ls->setEnd(&p);
4865
4866 tg=layout->createTextGlyph();
4867 tg->setId("tg_rg_malaltedh_cyt");
4868 bb=BoundingBox(&layoutns, "bb_tg_rg_malaltedh_cyt",700,385,210,24);
4869 tg->setBoundingBox(&bb);
4870 tg->setOriginOfTextId(malatedh_cyt->getId());
4871 tg->setGraphicalObjectId(rg_malatedh_cyt->getId());
4872
4873
4874 ReactionGlyph* rg_aspartateat_cyt=layout->createReactionGlyph();
4875 rg_aspartateat_cyt->setId("rg_aspartateat_cyt");
4876 rg_aspartateat_cyt->setReactionId(aspartateat_cyt->getId());
4877
4878 curve=rg_aspartateat_cyt->getCurve();
4879 ls=curve->createLineSegment();
4880 p=Point(&layoutns, 700,581);
4881 ls->setStart(&p);
4882 p=Point(&layoutns, 700,615);
4883 ls->setEnd(&p);
4884
4885 tg=layout->createTextGlyph();
4886 tg->setId("tg_rg_aspartateat_cyt");
4887 bb=BoundingBox(&layoutns, "bb_tg_rg_aspartateat_cyt",440,585,260,24);
4888 tg->setBoundingBox(&bb);
4889 tg->setOriginOfTextId(aspartateat_cyt->getId());
4890 tg->setGraphicalObjectId(rg_aspartateat_cyt->getId());
4891
4892
4893
4894 // add the SpeciesReferenceGlyphs
4895
4896 SpeciesReferenceGlyph* srg_malate_cyt_1=rg_malatedh_cyt->createSpeciesReferenceGlyph();
4897 srg_malate_cyt_1->setId("srg_malate_cyt_1");
4898 srg_malate_cyt_1->setSpeciesGlyphId(speciesGlyph_malate_cyt->getId());
4899 srg_malate_cyt_1->setSpeciesReferenceId(sr_malate_cyt->getId());
4900 srg_malate_cyt_1->setRole(SPECIES_ROLE_SUBSTRATE);
4901
4902 ls=srg_malate_cyt_1->createLineSegment();
4903 p=Point(&layoutns, 700,381);
4904 ls->setStart(&p);
4905 p=Point(&layoutns, 700,316);
4906 ls->setEnd(&p);
4907
4908 SpeciesReferenceGlyph* srg_nad_cyt=rg_malatedh_cyt->createSpeciesReferenceGlyph();
4909 srg_nad_cyt->setId("srg_nad_cyt");
4910 srg_nad_cyt->setSpeciesGlyphId(speciesGlyph_nad_cyt->getId());
4911 srg_nad_cyt->setSpeciesReferenceId(sr_nad_cyt->getId());
4912 srg_nad_cyt->setRole(SPECIES_ROLE_SUBSTRATE);
4913
4914 CubicBezier* cb=srg_nad_cyt->createCubicBezier();
4915 p=Point(&layoutns, 700,381);
4916 cb->setStart(&p);
4917 p=Point(&layoutns, 700,362);
4918 cb->setBasePoint1(&p);
4919 p=Point(&layoutns, 700,362);
4920 cb->setBasePoint2(&p);
4921 p=Point(&layoutns, 620,362);
4922 cb->setEnd(&p);
4923
4924 SpeciesReferenceGlyph* srg_oxaloacetate_cyt_1=rg_malatedh_cyt->createSpeciesReferenceGlyph();
4925 srg_oxaloacetate_cyt_1->setId("srg_oxaloacetate_cyt_1");
4926 srg_oxaloacetate_cyt_1->setSpeciesGlyphId(speciesGlyph_oxaloacetate_cyt->getId());
4927 srg_oxaloacetate_cyt_1->setSpeciesReferenceId(sr_oxaloacetate_cyt_1->getId());
4928 srg_oxaloacetate_cyt_1->setRole(SPECIES_ROLE_PRODUCT);
4929
4930 curve=srg_oxaloacetate_cyt_1->getCurve();
4931 ls=curve->createLineSegment();
4932 p=Point(&layoutns, 700,415);
4933 ls->setStart(&p);
4934 p=Point(&layoutns, 700,480);
4935 ls->setEnd(&p);
4936
4937 SpeciesReferenceGlyph* srg_nadh_cyt=rg_malatedh_cyt->createSpeciesReferenceGlyph();
4938 srg_nadh_cyt->setId("srg_nadh_cyt");
4939 srg_nadh_cyt->setSpeciesGlyphId(speciesGlyph_nadh_cyt->getId());
4940 srg_nadh_cyt->setSpeciesReferenceId(sr_nadh_cyt->getId());
4941 srg_nadh_cyt->setRole(SPECIES_ROLE_PRODUCT);
4942
4943 cb=srg_nadh_cyt->createCubicBezier();
4944 p=Point(&layoutns, 700,415);
4945 cb->setStart(&p);
4946 p=Point(&layoutns, 700,442);
4947 cb->setBasePoint1(&p);
4948 p=Point(&layoutns, 700,442);
4949 cb->setBasePoint2(&p);
4950 p=Point(&layoutns, 620,442);
4951 cb->setEnd(&p);
4952
4953 SpeciesReferenceGlyph* srg_h_cyt=rg_malatedh_cyt->createSpeciesReferenceGlyph();
4954 srg_h_cyt->setId("srg_h_cyt");
4955 srg_h_cyt->setSpeciesGlyphId(speciesGlyph_h_cyt->getId());
4956 srg_h_cyt->setSpeciesReferenceId(sr_h_cyt->getId());
4957 srg_h_cyt->setRole(SPECIES_ROLE_PRODUCT);
4958
4959 cb=srg_h_cyt->createCubicBezier();
4960 p=Point(&layoutns, 700,415);
4961 cb->setStart(&p);
4962 p=Point(&layoutns, 570,415);
4963 cb->setBasePoint1(&p);
4964 p=Point(&layoutns, 570,415);
4965 cb->setBasePoint2(&p);
4966 p=Point(&layoutns, 470,430);
4967 cb->setEnd(&p);
4968
4969 SpeciesReferenceGlyph* srg_oxaloacetate_cyt_2=rg_aspartateat_cyt->createSpeciesReferenceGlyph();
4970 srg_oxaloacetate_cyt_2->setId("srg_oxaloacetate_cyt_2");
4971 srg_oxaloacetate_cyt_2->setSpeciesGlyphId(speciesGlyph_oxaloacetate_cyt->getId());
4972 srg_oxaloacetate_cyt_2->setSpeciesReferenceId(sr_oxaloacetate_cyt_2->getId());
4973 srg_oxaloacetate_cyt_2->setRole(SPECIES_ROLE_SUBSTRATE);
4974
4975 curve=srg_oxaloacetate_cyt_2->getCurve();
4976 ls=curve->createLineSegment();
4977 p=Point(&layoutns, 700,581);
4978 ls->setStart(&p);
4979 p=Point(&layoutns, 700,516);
4980 ls->setEnd(&p);
4981
4982 SpeciesReferenceGlyph* srg_glutamate_cyt_1=rg_aspartateat_cyt->createSpeciesReferenceGlyph();
4983 srg_glutamate_cyt_1->setId("srg_glutamate_cyt_1");
4984 srg_glutamate_cyt_1->setSpeciesGlyphId(speciesGlyph_glutamate_cyt->getId());
4985 srg_glutamate_cyt_1->setSpeciesReferenceId(sr_glutamate_cyt_1->getId());
4986 srg_glutamate_cyt_1->setRole(SPECIES_ROLE_SUBSTRATE);
4987
4988 curve=srg_glutamate_cyt_1->getCurve();
4989 cb=curve->createCubicBezier();
4990 p=Point(&layoutns, 700,581);
4991 cb->setStart(&p);
4992 p=Point(&layoutns, 750,581);
4993 cb->setBasePoint1(&p);
4994 p=Point(&layoutns, 750,628);
4995 cb->setBasePoint2(&p);
4996 p=Point(&layoutns, 800,628);
4997 cb->setEnd(&p);
4998
4999 SpeciesReferenceGlyph* srg_aspartate_cyt_1=rg_aspartateat_cyt->createSpeciesReferenceGlyph();
5000 srg_aspartate_cyt_1->setId("srg_aspartate_cyt_1");
5001 srg_aspartate_cyt_1->setSpeciesGlyphId(speciesGlyph_aspartate_cyt->getId());
5002 srg_aspartate_cyt_1->setSpeciesReferenceId(sr_aspartate_cyt_1->getId());
5003 srg_aspartate_cyt_1->setRole(SPECIES_ROLE_PRODUCT);
5004
5005 curve=srg_aspartate_cyt_1->getCurve();
5006 ls=curve->createLineSegment();
5007 p=Point(&layoutns, 700,615);
5008 ls->setStart(&p);
5009 p=Point(&layoutns, 700,680);
5010 ls->setEnd(&p);
5011
5012 SpeciesReferenceGlyph* srg_aKetoglutarate_cyt_1=rg_aspartateat_cyt->createSpeciesReferenceGlyph();
5013 srg_aKetoglutarate_cyt_1->setId("srg_aKetoglutaratecyt_1");
5014 srg_aKetoglutarate_cyt_1->setSpeciesGlyphId(speciesGlyph_aKetoglutarate_cyt->getId());
5015 srg_aKetoglutarate_cyt_1->setSpeciesReferenceId(sr_aKetoglutarate_cyt_1->getId());
5016 srg_aKetoglutarate_cyt_1->setRole(SPECIES_ROLE_PRODUCT);
5017
5018 curve=srg_aKetoglutarate_cyt_1->getCurve();
5019 cb=curve->createCubicBezier();
5020 p=Point(&layoutns, 700,615);
5021 cb->setStart(&p);
5022 p=Point(&layoutns, 790,615);
5023 cb->setBasePoint1(&p);
5024 p=Point(&layoutns, 790,515);
5025 cb->setBasePoint2(&p);
5026 p=Point(&layoutns, 860,515);
5027 cb->setEnd(&p);
5028
5029
5030 // Malate mito3
5031 SpeciesGlyph* speciesGlyph_malate_mito3=layout->createSpeciesGlyph();
5032 speciesGlyph_malate_mito3->setId("SpeciesGlyph_malate_mito3");
5033 speciesGlyph_malate_mito3->setSpeciesId(malate_mito3->getId());
5034 bb=BoundingBox(&layoutns, "bb_sg_malate_mito3",1850,80,240,36);
5035 speciesGlyph_malate_mito3->setBoundingBox(&bb);
5036
5037 tg=layout->createTextGlyph();
5038 tg->setId("TextGlyph_malate_mito3");
5039 bb=BoundingBox(&layoutns, "bb_tg_malatate_mito3",1860,80,220,36);
5040 tg->setBoundingBox(&bb);
5041 tg->setOriginOfTextId(malate_mito3->getId());
5042 tg->setGraphicalObjectId(speciesGlyph_malate_mito3->getId());
5043
5044 // Oxaloacetate mito3
5045 SpeciesGlyph* speciesGlyph_oxaloacetate_mito3=layout->createSpeciesGlyph();
5046 speciesGlyph_oxaloacetate_mito3->setId("SpeciesGlyph_oxaloacetate_mito3");
5047 speciesGlyph_oxaloacetate_mito3->setSpeciesId(oxaloacetate_mito3->getId());
5048 bb=BoundingBox(&layoutns, "bb_sg_oxaloacetate_mito3",1850,280,240,36);
5049 speciesGlyph_oxaloacetate_mito3->setBoundingBox(&bb);
5050
5051 tg=layout->createTextGlyph();
5052 tg->setId("TextGlyph_oxaloacetate_mito3");
5053 bb=BoundingBox(&layoutns, "bb_tg_oxaloacetate_mito3",1860,280,220,36);
5054 tg->setBoundingBox(&bb);
5055 tg->setOriginOfTextId(oxaloacetate_mito3->getId());
5056 tg->setGraphicalObjectId(speciesGlyph_oxaloacetate_mito3->getId());
5057
5058 // Aspartate mito3
5059 SpeciesGlyph* speciesGlyph_aspartate_mito3=layout->createSpeciesGlyph();
5060 speciesGlyph_aspartate_mito3->setId("SpeciesGlyph_aspartate_mito3");
5061 speciesGlyph_aspartate_mito3->setSpeciesId(aspartate_mito3->getId());
5062 bb=BoundingBox(&layoutns, "bb_sg_aspartate_mito3",1850,480,240,36);
5063 speciesGlyph_aspartate_mito3->setBoundingBox(&bb);
5064
5065 tg=layout->createTextGlyph();
5066 tg->setId("TextGlyph_aspartate_mito3");
5067 bb=BoundingBox(&layoutns, "bb_tg_aspartate_mito3",1860,480,220,36);
5068 tg->setBoundingBox(&bb);
5069 tg->setOriginOfTextId(aspartate_mito3->getId());
5070 tg->setGraphicalObjectId(speciesGlyph_aspartate_mito3->getId());
5071
5072 // Glutamate mito3
5073 SpeciesGlyph* speciesGlyph_glutamate_mito3=layout->createSpeciesGlyph();
5074 speciesGlyph_glutamate_mito3->setId("SpeciesGlyph_glutamate_mito3");
5075 speciesGlyph_glutamate_mito3->setSpeciesId(glutamate_mito3->getId());
5076 bb=BoundingBox(&layoutns, "bb_sg_glutamate_mito3",1550,430,240,36);
5077 speciesGlyph_glutamate_mito3->setBoundingBox(&bb);
5078
5079 tg=layout->createTextGlyph();
5080 tg->setId("TextGlyph_glutamate_mito3");
5081 bb=BoundingBox(&layoutns, "bb_tg_glutamate_mito3",1560,430,220,36);
5082 tg->setBoundingBox(&bb);
5083 tg->setOriginOfTextId(glutamate_mito3->getId());
5084 tg->setGraphicalObjectId(speciesGlyph_glutamate_mito3->getId());
5085
5086 // alpha-Ketoglutarate mito3
5087 SpeciesGlyph* speciesGlyph_aKetoglutarate_mito3=layout->createSpeciesGlyph();
5088 speciesGlyph_aKetoglutarate_mito3->setId("SpeciesGlyph_aKetoglutarate_mito3");
5089 speciesGlyph_aKetoglutarate_mito3->setSpeciesId(aKetoglutarate_mito3->getId());
5090 bb=BoundingBox(&layoutns, "bb_sg_aKetoglutarate_mito3",1530,300,280,36);
5091 speciesGlyph_aKetoglutarate_mito3->setBoundingBox(&bb);
5092
5093 tg=layout->createTextGlyph();
5094 tg->setId("TextGlyph_aKetoglutarate_mito3");
5095 bb=BoundingBox(&layoutns, "bb_tg_aKetoglutarate_mito3",1540,300,260,36);
5096 tg->setBoundingBox(&bb);
5097 tg->setOriginOfTextId(aKetoglutarate_mito3->getId());
5098 tg->setGraphicalObjectId(speciesGlyph_aKetoglutarate_mito3->getId());
5099
5100 // NAD+ mito3
5101 SpeciesGlyph* speciesGlyph_nad_mito3=layout->createSpeciesGlyph();
5102 speciesGlyph_nad_mito3->setId("SpeciesGlyph_nad_mito3");
5103 speciesGlyph_nad_mito3->setSpeciesId(nad_mito3->getId());
5104 bb=BoundingBox(&layoutns, "bb_sg_nad_mito3",2050,150,100,24);
5105 speciesGlyph_nad_mito3->setBoundingBox(&bb);
5106
5107 tg=layout->createTextGlyph();
5108 tg->setId("TextGlyph_nad_mito3");
5109 bb=BoundingBox(&layoutns, "bb_tg_nad_mito3",2055,150,80,24);
5110 tg->setBoundingBox(&bb);
5111 tg->setOriginOfTextId(nad_mito3->getId());
5112 tg->setGraphicalObjectId(speciesGlyph_nad_mito3->getId());
5113
5114 // NADH mito3
5115 SpeciesGlyph* speciesGlyph_nadh_mito3=layout->createSpeciesGlyph();
5116 speciesGlyph_nadh_mito3->setId("SpeciesGlyph_nadh_mito3");
5117 speciesGlyph_nadh_mito3->setSpeciesId(nadh_mito3->getId());
5118 bb=BoundingBox(&layoutns, "bb_sg_nadh_mito3",2050,230,100,24);
5119 speciesGlyph_nadh_mito3->setBoundingBox(&bb);
5120
5121 tg=layout->createTextGlyph();
5122 tg->setId("TextGlyph_nadh_mito3");
5123 bb=BoundingBox(&layoutns, "bb_tg_nadh_mito3",2055,230,80,24);
5124 tg->setBoundingBox(&bb);
5125 tg->setOriginOfTextId(nadh_mito3->getId());
5126 tg->setGraphicalObjectId(speciesGlyph_nadh_mito3->getId());
5127
5128 // H+ mito3
5129 SpeciesGlyph* speciesGlyph_h_mito3=layout->createSpeciesGlyph();
5130 speciesGlyph_h_mito3->setId("SpeciesGlyph_h_mito3");
5131 speciesGlyph_h_mito3->setSpeciesId(h_mito3->getId());
5132 bb=BoundingBox(&layoutns, "bb_sg_h_mito3",2200,230,40,24);
5133 speciesGlyph_h_mito3->setBoundingBox(&bb);
5134
5135 tg=layout->createTextGlyph();
5136 tg->setId("TextGlyph_h_mito3");
5137 bb=BoundingBox(&layoutns, "bb_tg_h_mito3",2205,230,30,24);
5138 tg->setBoundingBox(&bb);
5139 tg->setOriginOfTextId(h_mito3->getId());
5140 tg->setGraphicalObjectId(speciesGlyph_h_mito3->getId());
5141
5142
5143 // create the ReactionGlyphs
5144
5145 ReactionGlyph* rg_malatedh_mito3=layout->createReactionGlyph();
5146 rg_malatedh_mito3->setId("rg_malatedh_mito3");
5147 rg_malatedh_mito3->setReactionId(malatedh_mito3->getId());
5148
5149 curve=rg_malatedh_mito3->getCurve();
5150 ls=curve->createLineSegment();
5151 p=Point(&layoutns, 1970,181);
5152 ls->setStart(&p);
5153 p=Point(&layoutns, 1970,215);
5154 ls->setEnd(&p);
5155
5156 tg=layout->createTextGlyph();
5157 tg->setId("tg_rg_malatedh_mito3");
5158 bb=BoundingBox(&layoutns, "bb_tg_rg_malatedh_mito3",1740,185,220,24);
5159 tg->setBoundingBox(&bb);
5160 tg->setOriginOfTextId(malatedh_mito3->getId());
5161 tg->setGraphicalObjectId(rg_malatedh_mito3->getId());
5162
5163 ReactionGlyph* rg_aspartateat_mito3=layout->createReactionGlyph();
5164 rg_aspartateat_mito3->setId("rg_aspartateat_mito3");
5165 rg_aspartateat_mito3->setReactionId(aspartateat_mito3->getId());
5166
5167 curve=rg_aspartateat_mito3->getCurve();
5168 ls=curve->createLineSegment();
5169 p=Point(&layoutns, 1970,381);
5170 ls->setStart(&p);
5171 p=Point(&layoutns, 1970,415);
5172 ls->setEnd(&p);
5173
5174 tg=layout->createTextGlyph();
5175 tg->setId("tg_rg_aspartateat_mito3");
5176 bb=BoundingBox(&layoutns, "bb_tg_rg_aspartateat_mito3",1970,385,260,24);
5177 tg->setBoundingBox(&bb);
5178 tg->setOriginOfTextId(aspartateat_mito3->getId());
5179 tg->setGraphicalObjectId(rg_aspartateat_mito3->getId());
5180
5181
5182 // add the SpeciesReferenceGlyphs
5183
5184 SpeciesReferenceGlyph* srg_malate_mito3_1=rg_malatedh_mito3->createSpeciesReferenceGlyph();
5185 srg_malate_mito3_1->setId("srg_malate_mito3_1");
5186 srg_malate_mito3_1->setSpeciesGlyphId(speciesGlyph_malate_mito3->getId());
5187 srg_malate_mito3_1->setSpeciesReferenceId(sr_malate_mito3->getId());
5188 srg_malate_mito3_1->setRole(SPECIES_ROLE_SUBSTRATE);
5189
5190 ls=srg_malate_mito3_1->createLineSegment();
5191 p=Point(&layoutns, 1970,181);
5192 ls->setStart(&p);
5193 p=Point(&layoutns, 1970,116);
5194 ls->setEnd(&p);
5195
5196 SpeciesReferenceGlyph* srg_nad_mito3=rg_malatedh_mito3->createSpeciesReferenceGlyph();
5197 srg_nad_mito3->setId("srg_nad_mito3");
5198 srg_nad_mito3->setSpeciesGlyphId(speciesGlyph_nad_mito3->getId());
5199 srg_nad_mito3->setSpeciesReferenceId(sr_nad_mito3->getId());
5200 srg_nad_mito3->setRole(SPECIES_ROLE_SUBSTRATE);
5201
5202 cb=srg_nad_mito3->createCubicBezier();
5203 p=Point(&layoutns, 1970,181);
5204 cb->setStart(&p);
5205 p=Point(&layoutns, 1970,162);
5206 cb->setBasePoint1(&p);
5207 p=Point(&layoutns, 1970,162);
5208 cb->setBasePoint2(&p);
5209 p=Point(&layoutns, 2050,162);
5210 cb->setEnd(&p);
5211
5212 SpeciesReferenceGlyph* srg_oxaloacetate_mito3_1=rg_malatedh_mito3->createSpeciesReferenceGlyph();
5213 srg_oxaloacetate_mito3_1->setId("srg_oxaloacetate_mito3_1");
5214 srg_oxaloacetate_mito3_1->setSpeciesGlyphId(speciesGlyph_oxaloacetate_mito3->getId());
5215 srg_oxaloacetate_mito3_1->setSpeciesReferenceId(sr_oxaloacetate_mito3_1->getId());
5216 srg_oxaloacetate_mito3_1->setRole(SPECIES_ROLE_PRODUCT);
5217
5218 curve=srg_oxaloacetate_mito3_1->getCurve();
5219 ls=curve->createLineSegment();
5220 p=Point(&layoutns, 1970,215);
5221 ls->setStart(&p);
5222 p=Point(&layoutns, 1970,280);
5223 ls->setEnd(&p);
5224
5225 SpeciesReferenceGlyph* srg_nadh_mito3=rg_malatedh_mito3->createSpeciesReferenceGlyph();
5226 srg_nadh_mito3->setId("srg_nadh_mito3");
5227 srg_nadh_mito3->setSpeciesGlyphId(speciesGlyph_nadh_mito3->getId());
5228 srg_nadh_mito3->setSpeciesReferenceId(sr_nadh_mito3->getId());
5229 srg_nadh_mito3->setRole(SPECIES_ROLE_PRODUCT);
5230
5231 cb=srg_nadh_mito3->createCubicBezier();
5232 p=Point(&layoutns, 1970,215);
5233 cb->setStart(&p);
5234 p=Point(&layoutns, 1970,242);
5235 cb->setBasePoint1(&p);
5236 p=Point(&layoutns, 1970,242);
5237 cb->setBasePoint2(&p);
5238 p=Point(&layoutns, 2050,242);
5239 cb->setEnd(&p);
5240
5241 SpeciesReferenceGlyph* srg_h_mito3=rg_malatedh_mito3->createSpeciesReferenceGlyph();
5242 srg_h_mito3->setId("srg_h_mito3");
5243 srg_h_mito3->setSpeciesGlyphId(speciesGlyph_h_mito3->getId());
5244 srg_h_mito3->setSpeciesReferenceId(sr_h_mito3->getId());
5245 srg_h_mito3->setRole(SPECIES_ROLE_PRODUCT);
5246
5247 cb=srg_h_mito3->createCubicBezier();
5248 p=Point(&layoutns, 1970,215);
5249 cb->setStart(&p);
5250 p=Point(&layoutns, 2100,215);
5251 cb->setBasePoint1(&p);
5252 p=Point(&layoutns, 2100,215);
5253 cb->setBasePoint2(&p);
5254 p=Point(&layoutns, 2200,230);
5255 cb->setEnd(&p);
5256
5257 SpeciesReferenceGlyph* srg_oxaloacetate_mito3_2=rg_aspartateat_mito3->createSpeciesReferenceGlyph();
5258 srg_oxaloacetate_mito3_2->setId("srg_oxaloacetate_mito3_2");
5259 srg_oxaloacetate_mito3_2->setSpeciesGlyphId(speciesGlyph_oxaloacetate_mito3->getId());
5260 srg_oxaloacetate_mito3_2->setSpeciesReferenceId(sr_oxaloacetate_mito3_2->getId());
5261 srg_oxaloacetate_mito3_2->setRole(SPECIES_ROLE_SUBSTRATE);
5262
5263 curve=srg_oxaloacetate_mito3_2->getCurve();
5264 ls=curve->createLineSegment();
5265 p=Point(&layoutns, 1970,381);
5266 ls->setStart(&p);
5267 p=Point(&layoutns, 1970,316);
5268 ls->setEnd(&p);
5269
5270 SpeciesReferenceGlyph* srg_glutamate_mito3_1=rg_aspartateat_mito3->createSpeciesReferenceGlyph();
5271 srg_glutamate_mito3_1->setId("srg_glutamate_mito3_1");
5272 srg_glutamate_mito3_1->setSpeciesGlyphId(speciesGlyph_glutamate_mito3->getId());
5273 srg_glutamate_mito3_1->setSpeciesReferenceId(sr_glutamate_mito3_1->getId());
5274 srg_glutamate_mito3_1->setRole(SPECIES_ROLE_SUBSTRATE);
5275
5276 curve=srg_glutamate_mito3_1->getCurve();
5277 cb=curve->createCubicBezier();
5278 p=Point(&layoutns, 1970,381);
5279 cb->setStart(&p);
5280 p=Point(&layoutns, 1880,381);
5281 cb->setBasePoint1(&p);
5282 p=Point(&layoutns, 1880,448);
5283 cb->setBasePoint2(&p);
5284 p=Point(&layoutns, 1790,448);
5285 cb->setEnd(&p);
5286
5287 SpeciesReferenceGlyph* srg_aspartate_mito3_1=rg_aspartateat_mito3->createSpeciesReferenceGlyph();
5288 srg_aspartate_mito3_1->setId("srg_aspartate_mito3_1");
5289 srg_aspartate_mito3_1->setSpeciesGlyphId(speciesGlyph_aspartate_mito3->getId());
5290 srg_aspartate_mito3_1->setSpeciesReferenceId(sr_aspartate_mito3_1->getId());
5291 srg_aspartate_mito3_1->setRole(SPECIES_ROLE_PRODUCT);
5292
5293 curve=srg_aspartate_mito3_1->getCurve();
5294 ls=curve->createLineSegment();
5295 p=Point(&layoutns, 1970,415);
5296 ls->setStart(&p);
5297 p=Point(&layoutns, 1970,480);
5298 ls->setEnd(&p);
5299
5300 SpeciesReferenceGlyph* srg_aKetoglutarate_mito3_1=rg_aspartateat_mito3->createSpeciesReferenceGlyph();
5301 srg_aKetoglutarate_mito3_1->setId("srg_aKetoglutaratemito3_1");
5302 srg_aKetoglutarate_mito3_1->setSpeciesGlyphId(speciesGlyph_aKetoglutarate_mito3->getId());
5303 srg_aKetoglutarate_mito3_1->setSpeciesReferenceId(sr_aKetoglutarate_mito3_1->getId());
5304 srg_aKetoglutarate_mito3_1->setRole(SPECIES_ROLE_PRODUCT);
5305
5306 curve=srg_aKetoglutarate_mito3_1->getCurve();
5307 cb=curve->createCubicBezier();
5308 p=Point(&layoutns, 1970,415);
5309 cb->setStart(&p);
5310 p=Point(&layoutns, 1880,415);
5311 cb->setBasePoint1(&p);
5312 p=Point(&layoutns, 1880,315);
5313 cb->setBasePoint2(&p);
5314 p=Point(&layoutns, 1810,315);
5315 cb->setEnd(&p);
5316
5317 // add the transport reaction glyphs
5318
5319 ReactionGlyph* rg_aspartateCarrier=layout->createReactionGlyph();
5320 rg_aspartateCarrier->setId("rg_aspartateCarrier");
5321 rg_aspartateCarrier->setReactionId(aspartateCarrier->getId());
5322
5323 curve=rg_aspartateCarrier->getCurve();
5324 ls=curve->createLineSegment();
5325 p=Point(&layoutns, 1420,530);
5326 ls->setStart(&p);
5327 p=Point(&layoutns, 1360,550);
5328 ls->setEnd(&p);
5329
5330 tg=layout->createTextGlyph();
5331 tg->setId("tg_rg_aspartateCarrier");
5332 bb=BoundingBox(&layoutns, "bb_tg_rg_aspartateCarrier",1380,500,160,24);
5333 tg->setBoundingBox(&bb);
5334 tg->setOriginOfTextId(aspartateCarrier->getId());
5335 tg->setGraphicalObjectId(rg_aspartateCarrier->getId());
5336
5337
5338 ReactionGlyph* rg_malateCarrier=layout->createReactionGlyph();
5339 rg_malateCarrier->setId("rg_malateCarrier");
5340 rg_malateCarrier->setReactionId(malateCarrier->getId());
5341
5342 curve=rg_malateCarrier->getCurve();
5343 ls=curve->createLineSegment();
5344 p=Point(&layoutns, 1420,320);
5345 ls->setStart(&p);
5346 p=Point(&layoutns, 1360,340);
5347 ls->setEnd(&p);
5348
5349 tg=layout->createTextGlyph();
5350 tg->setId("tg_rg_malateCarrier");
5351 bb=BoundingBox( &layoutns, "bb_tg_rg_malateCarrier",1360,330,140,24);
5352 tg->setBoundingBox(&bb);
5353 tg->setOriginOfTextId(malateCarrier->getId());
5354 tg->setGraphicalObjectId(rg_malateCarrier->getId());
5355
5356
5357
5358 // add the SpeciesReferenceGlyphs for the transporters
5359
5360 SpeciesReferenceGlyph* srg_aKetoglutarate_mito3_2=rg_malateCarrier->createSpeciesReferenceGlyph();
5361 srg_aKetoglutarate_mito3_2->setId("srg_aKetoglutarate_mito3_2");
5362 srg_aKetoglutarate_mito3_2->setSpeciesGlyphId(speciesGlyph_aKetoglutarate_mito3->getId());
5363 srg_aKetoglutarate_mito3_2->setSpeciesReferenceId(sr_aKetoglutarate_mito3_2->getId());
5364 srg_aKetoglutarate_mito3_2->setRole(SPECIES_ROLE_SUBSTRATE);
5365
5366 curve=srg_aKetoglutarate_mito3_2->getCurve();
5367 ls=curve->createLineSegment();
5368 p=Point(&layoutns, 1420,320);
5369 ls->setStart(&p);
5370 p=Point(&layoutns, 1530,318);
5371 ls->setEnd(&p);
5372
5373
5374 SpeciesReferenceGlyph* srg_aKetoglutarate_cyt_2=rg_malateCarrier->createSpeciesReferenceGlyph();
5375 srg_aKetoglutarate_cyt_2->setId("srg_aKetoglutarate_cyt_2");
5376 srg_aKetoglutarate_cyt_2->setSpeciesGlyphId(speciesGlyph_aKetoglutarate_cyt->getId());
5377 srg_aKetoglutarate_cyt_2->setSpeciesReferenceId(sr_aKetoglutarate_cyt_2->getId());
5378 srg_aKetoglutarate_cyt_2->setRole(SPECIES_ROLE_PRODUCT);
5379
5380 curve=srg_aKetoglutarate_cyt_2->getCurve();
5381 ls=curve->createLineSegment();
5382 p=Point(&layoutns, 1360,340);
5383 ls->setStart(&p);
5384 p=Point(&layoutns, 1140,518);
5385 ls->setEnd(&p);
5386
5387
5388 SpeciesReferenceGlyph* srg_malate_cyt_2=rg_malateCarrier->createSpeciesReferenceGlyph();
5389 srg_malate_cyt_2->setId("srg_malate_cyt_2");
5390 srg_malate_cyt_2->setSpeciesGlyphId(speciesGlyph_malate_cyt->getId());
5391 srg_malate_cyt_2->setSpeciesReferenceId(sr_malate_cyt_2->getId());
5392 srg_malate_cyt_2->setRole(SPECIES_ROLE_SUBSTRATE);
5393
5394 curve=srg_malate_cyt_2->getCurve();
5395 cb=curve->createCubicBezier();
5396 p=Point(&layoutns, 1420,320);
5397 cb->setStart(&p);
5398 p=Point(&layoutns, 1390,250);
5399 cb->setBasePoint1(&p);
5400 p=Point(&layoutns, 1390,250);
5401 cb->setBasePoint2(&p);
5402 p=Point(&layoutns, 820,298);
5403 cb->setEnd(&p);
5404
5405
5406 SpeciesReferenceGlyph* srg_malate_mito3_2=rg_malateCarrier->createSpeciesReferenceGlyph();
5407 srg_malate_mito3_2->setId("srg_malate_mito3_2");
5408 srg_malate_mito3_2->setSpeciesGlyphId(speciesGlyph_malate_mito3->getId());
5409 srg_malate_mito3_2->setSpeciesReferenceId(sr_malate_mito3_2->getId());
5410 srg_malate_mito3_2->setRole(SPECIES_ROLE_PRODUCT);
5411
5412 curve=srg_malate_mito3_2->getCurve();
5413 cb=curve->createCubicBezier();
5414 p=Point(&layoutns, 1360,340);
5415 cb->setStart(&p);
5416 p=Point(&layoutns, 1390,150);
5417 cb->setBasePoint1(&p);
5418 p=Point(&layoutns, 1390,150);
5419 cb->setBasePoint2(&p);
5420 p=Point(&layoutns, 1850,98);
5421 cb->setEnd(&p);
5422
5423
5424
5425
5426
5427
5428 SpeciesReferenceGlyph* srg_aspartate_mito3_2=rg_aspartateCarrier->createSpeciesReferenceGlyph();
5429 srg_aspartate_mito3_2->setId("srg_aspartate_mito3_2");
5430 srg_aspartate_mito3_2->setSpeciesGlyphId(speciesGlyph_aspartate_mito3->getId());
5431 srg_aspartate_mito3_2->setSpeciesReferenceId(sr_aspartate_mito3_2->getId());
5432 srg_aspartate_mito3_2->setRole(SPECIES_ROLE_SUBSTRATE);
5433
5434 curve=srg_aspartate_mito3_2->getCurve();
5435 ls=curve->createLineSegment();
5436 p=Point(&layoutns, 1420,530);
5437 ls->setStart(&p);
5438 p=Point(&layoutns, 1850,498);
5439 ls->setEnd(&p);
5440
5441
5442 SpeciesReferenceGlyph* srg_aspartate_cyt_2=rg_aspartateCarrier->createSpeciesReferenceGlyph();
5443 srg_aspartate_cyt_2->setId("srg_aspartate_cyt_2");
5444 srg_aspartate_cyt_2->setSpeciesGlyphId(speciesGlyph_aspartate_cyt->getId());
5445 srg_aspartate_cyt_2->setSpeciesReferenceId(sr_aspartate_cyt_2->getId());
5446 srg_aspartate_cyt_2->setRole(SPECIES_ROLE_PRODUCT);
5447
5448 curve=srg_aspartate_cyt_2->getCurve();
5449 cb=curve->createCubicBezier();
5450 p=Point(&layoutns, 1360,550);
5451 cb->setStart(&p);
5452 p=Point(&layoutns, 1390,698);
5453 cb->setBasePoint1(&p);
5454 p=Point(&layoutns, 1390,698);
5455 cb->setBasePoint2(&p);
5456 p=Point(&layoutns, 820,698);
5457 cb->setEnd(&p);
5458
5459
5460 SpeciesReferenceGlyph* srg_glutamate_cyt_2=rg_aspartateCarrier->createSpeciesReferenceGlyph();
5461 srg_glutamate_cyt_2->setId("srg_glutamate_cyt_2");
5462 srg_glutamate_cyt_2->setSpeciesGlyphId(speciesGlyph_glutamate_cyt->getId());
5463 srg_glutamate_cyt_2->setSpeciesReferenceId(sr_glutamate_cyt_2->getId());
5464 srg_glutamate_cyt_2->setRole(SPECIES_ROLE_SUBSTRATE);
5465
5466 curve=srg_glutamate_cyt_2->getCurve();
5467 cb=curve->createCubicBezier();
5468 p=Point(&layoutns, 1420,530);
5469 cb->setStart(&p);
5470 p=Point(&layoutns, 1390,648);
5471 cb->setBasePoint1(&p);
5472 p=Point(&layoutns, 1390,648);
5473 cb->setBasePoint2(&p);
5474 p=Point(&layoutns, 1050,628);
5475 cb->setEnd(&p);
5476
5477
5478 SpeciesReferenceGlyph* srg_glutamate_mito3_2=rg_aspartateCarrier->createSpeciesReferenceGlyph();
5479 srg_glutamate_mito3_2->setId("srg_glutamate_mito3_2");
5480 srg_glutamate_mito3_2->setSpeciesGlyphId(speciesGlyph_glutamate_mito3->getId());
5481 srg_glutamate_mito3_2->setSpeciesReferenceId(sr_glutamate_mito3_2->getId());
5482 srg_glutamate_mito3_2->setRole(SPECIES_ROLE_PRODUCT);
5483
5484 curve=srg_glutamate_mito3_2->getCurve();
5485 cb=curve->createCubicBezier();
5486 p=Point(&layoutns, 1360,550);
5487 cb->setStart(&p);
5488 p=Point(&layoutns, 1390,448);
5489 cb->setBasePoint1(&p);
5490 p=Point(&layoutns, 1390,448);
5491 cb->setBasePoint2(&p);
5492 p=Point(&layoutns, 1550,448);
5493 cb->setEnd(&p);
5494
5495 // now we add some global render information
5496 ListOfLayouts* pListOfLayouts=plugin->getListOfLayouts();
5497 fail_unless(pListOfLayouts!=NULL);
5498
5499 RenderListOfLayoutsPlugin* lolPlugin = (RenderListOfLayoutsPlugin* ) pListOfLayouts->getPlugin("render");
5500 GlobalRenderInformation* pGlobalRender=lolPlugin->createGlobalRenderInformation();
5501 pGlobalRender->setId("wireFrame");
5502 pGlobalRender->setName("wireframe style");
5503 pGlobalRender->setProgramName("Ralph Gauges");
5504 pGlobalRender->setProgramVersion("1.0");
5505 pGlobalRender->setBackgroundColor("#FFFFFFFF");
5506 // color definitions
5507 ColorDefinition* pColorDefinition=pGlobalRender->createColorDefinition();
5508 pColorDefinition->setId("white");
5509 pColorDefinition->setColorValue("#FFFFFF");
5510 pColorDefinition=pGlobalRender->createColorDefinition();
5511 pColorDefinition->setId("black");
5512 pColorDefinition->setColorValue("#000000");
5513 // styles
5514 // style for compartment glyphs
5515 GlobalStyle* pGlobalStyle=pGlobalRender->createStyle("compartmentGlyphStyle");
5516 pGlobalStyle->addType("COMPARTMENTGLYPH");
5517 RenderGroup* pGroup=pGlobalStyle->getGroup();
5518 pGroup->setStroke("black");
5519 pGroup->setStrokeWidth(1.0);
5520 Rectangle* pRectangle=pGroup->createRectangle();
5521 pRectangle->setCoordinatesAndSize(RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0),RelAbsVector(0.0,100.0),RelAbsVector(0.0,100.0));
5522 pRectangle->setRadiusX(RelAbsVector(0.0,0.0));
5523
5524 // style for species glyphs
5525 pGlobalStyle=pGlobalRender->createStyle("speciesGlyphStyle");
5526 pGlobalStyle->addType("SPECIESGLYPH");
5527 pGroup=pGlobalStyle->getGroup();
5528 pGroup->setStroke("black");
5529 pGroup->setStrokeWidth(1.0);
5530 pRectangle=pGroup->createRectangle();
5531 pRectangle->setCoordinatesAndSize(RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0),RelAbsVector(0.0,100.0),RelAbsVector(0.0,100.0));
5532 pRectangle->setRadiusX(RelAbsVector(0.0,0.0));
5533
5534 // style for all other glyphs
5535 pGlobalStyle=pGlobalRender->createStyle("reactionGlyphStyle");
5536 pGlobalStyle->addType("SPECIESREFERENCEGLYPH");
5537 pGlobalStyle->addType("REACTIONGLYPH");
5538 pGlobalStyle->addType("TEXTGLYPH");
5539 pGroup=pGlobalStyle->getGroup();
5540 pGroup->setStroke("black");
5541 pGroup->setStrokeWidth(1.0);
5542 pGroup->setFontSize(RelAbsVector(12.0,0.0));
5543 pGroup->setTextAnchor(Text::ANCHOR_MIDDLE);
5544
5545 // second render information
5546 pGlobalRender=lolPlugin->createGlobalRenderInformation();
5547 pGlobalRender->setId("defaultGrayStyle");
5548 pGlobalRender->setName("grayscale style");
5549 pGlobalRender->setProgramName("Ralph Gauges");
5550 pGlobalRender->setProgramVersion("1.0");
5551 pGlobalRender->setBackgroundColor("#FFFFFFFF");
5552 // color definitions
5553 pColorDefinition=pGlobalRender->createColorDefinition();
5554 pColorDefinition->setId("lightGray");
5555 pColorDefinition->setColorValue("#CECECE");
5556 pColorDefinition=pGlobalRender->createColorDefinition();
5557 pColorDefinition->setId("white");
5558 pColorDefinition->setColorValue("#FFFFFF");
5559 pColorDefinition=pGlobalRender->createColorDefinition();
5560 pColorDefinition->setId("black");
5561 pColorDefinition->setColorValue("#000000");
5562 pColorDefinition=pGlobalRender->createColorDefinition();
5563 pColorDefinition->setId("lightGray2");
5564 pColorDefinition->setColorValue("#F0F0F0");
5565 pColorDefinition=pGlobalRender->createColorDefinition();
5566 pColorDefinition->setId("gray");
5567 pColorDefinition->setColorValue("#0B0B0B");
5568 // gradient definitions
5569 RadialGradient* pRadialGradient=pGlobalRender->createRadialGradientDefinition();
5570 pRadialGradient->setId("speciesGlyphGradient");
5571 GradientStop* pStop=pRadialGradient->createGradientStop();
5572 pStop->setOffset(RelAbsVector(0.0,0.0));
5573 pStop->setStopColor("white");
5574 pStop=pRadialGradient->createGradientStop();
5575 pStop->setOffset(RelAbsVector(0.0,100.0));
5576 pStop->setStopColor("lightGray");
5577 // line endings
5578 LineEnding* pLineEnding=pGlobalRender->createLineEnding();
5579 pLineEnding->setId("simpleHead_black");
5580 p=Point(&layoutns, -8,-3);
5581 Dimensions d(&layoutns, 10,6);
5582 pLineEnding->getBoundingBox()->setPosition(&p);
5583 pLineEnding->getBoundingBox()->setDimensions(&d);
5584 pGroup=pLineEnding->getGroup();
5585 pGroup->setStroke("black");
5586 pGroup->setStrokeWidth(1.0);
5587 pGroup->setFillColor("black");
5588 Polygon* pPolygon=pGroup->createPolygon();
5589 RenderPoint* pR=pPolygon->createPoint();
5590 pR->setCoordinates(RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0));
5591 pR=pPolygon->createPoint();
5592 pR->setCoordinates(RelAbsVector(10.0,0.0),RelAbsVector(3.0,0.0));
5593 pR=pPolygon->createPoint();
5594 pR->setCoordinates(RelAbsVector(0.0,0.0),RelAbsVector(6.0,0.0));
5595
5596 // styles
5597 // style for compartment glyphs
5598 pGlobalStyle=pGlobalRender->createStyle("compartmentGlyphStyle");
5599 pGlobalStyle->addType("COMPARTMENTGLYPH");
5600 pGroup=pGlobalStyle->getGroup();
5601 pGroup->setStroke("gray");
5602 pGroup->setStrokeWidth(1.0);
5603 pRectangle=pGroup->createRectangle();
5604 pRectangle->setCoordinatesAndSize(RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0),RelAbsVector(0.0,100.0),RelAbsVector(0.0,100.0));
5605 pRectangle->setRadiusX(RelAbsVector(0.0,5.0));
5606 pRectangle->setFillColor("lightGray2");
5607
5608 // style for species glyphs
5609 pGlobalStyle=pGlobalRender->createStyle("speciesGlyphStyle");
5610 pGlobalStyle->addType("SPECIESGLYPH");
5611 pGroup=pGlobalStyle->getGroup();
5612 pGroup->setStroke("black");
5613 pGroup->setStrokeWidth(1.0);
5614 pRectangle=pGroup->createRectangle();
5615 pRectangle->setCoordinatesAndSize(RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0),RelAbsVector(0.0,100.0),RelAbsVector(0.0,100.0));
5616 pRectangle->setRadiusX(RelAbsVector(0.0,5.0));
5617 pRectangle->setFillColor("speciesGlyphGradient");
5618
5619 // style for reaction and text glyphs
5620 pGlobalStyle=pGlobalRender->createStyle("reactionGlyphStyle");
5621 pGlobalStyle->addType("REACTIONGLYPH");
5622 pGlobalStyle->addType("TEXTGLYPH");
5623 pGroup=pGlobalStyle->getGroup();
5624 pGroup->setStroke("black");
5625 pGroup->setStrokeWidth(1.0);
5626 pGroup->setFontSize(RelAbsVector(12.0,0.0));
5627 pGroup->setTextAnchor(Text::ANCHOR_MIDDLE);
5628
5629 // style for substrate and product species reference glyphs
5630 pGlobalStyle=pGlobalRender->createStyle("reactantSpeciesReferenceGlyphStyle");
5631 pGlobalStyle->addRole("substrate");
5632 pGlobalStyle->addRole("sidesubstrate");
5633 pGlobalStyle->addRole("product");
5634 pGlobalStyle->addRole("sideproduct");
5635 pGroup=pGlobalStyle->getGroup();
5636 pGroup->setStroke("#000000");
5637 pGroup->setStrokeWidth(1.0);
5638
5639 // style for activator species reference glyphs
5640 pGlobalStyle=pGlobalRender->createStyle("activatorSpeciesReferenceGlyphStyle");
5641 pGlobalStyle->addRole("activator");
5642 pGroup=pGlobalStyle->getGroup();
5643 pGroup->setStroke("#000000");
5644 pGroup->setStrokeWidth(1.0);
5645
5646 // style for modifier species reference glyphs
5647 pGlobalStyle=pGlobalRender->createStyle("modifierSpeciesReferenceGlyphStyle");
5648 pGlobalStyle->addRole("modifier");
5649 pGroup=pGlobalStyle->getGroup();
5650 pGroup->setStroke("#000000");
5651 pGroup->setStrokeWidth(1.0);
5652
5653 // style for inhibitor species reference glyphs
5654 pGlobalStyle=pGlobalRender->createStyle("inhibitorSpeciesReferenceGlyphStyle");
5655 pGlobalStyle->addRole("inhibitor");
5656 pGroup=pGlobalStyle->getGroup();
5657 pGroup->setStroke("#000000");
5658 pGroup->setStrokeWidth(1.0);
5659
5660 // short gray style which uses the default style and just redefines some colors
5661 // second render information
5662 pGlobalRender=lolPlugin->createGlobalRenderInformation();
5663 pGlobalRender->setId("shortGrayStyle");
5664 pGlobalRender->setName("modified default style to grayscale");
5665 pGlobalRender->setReferenceRenderInformationId("defaultStyle");
5666 pGlobalRender->setProgramName("Ralph Gauges");
5667 pGlobalRender->setProgramVersion("1.0");
5668 pGlobalRender->setBackgroundColor("#FFFFFFFF");
5669 // color definitions
5670 pColorDefinition=pGlobalRender->createColorDefinition();
5671 pColorDefinition->setId("lightBlue");
5672 pColorDefinition->setColorValue("#CECECE");
5673 pColorDefinition=pGlobalRender->createColorDefinition();
5674 pColorDefinition->setId("white");
5675 pColorDefinition->setColorValue("#FFFFFF");
5676 pColorDefinition=pGlobalRender->createColorDefinition();
5677 pColorDefinition->setId("black");
5678 pColorDefinition->setColorValue("#000000");
5679 pColorDefinition=pGlobalRender->createColorDefinition();
5680 pColorDefinition->setId("red");
5681 pColorDefinition->setColorValue("#000000");
5682 pColorDefinition=pGlobalRender->createColorDefinition();
5683 pColorDefinition->setId("green");
5684 pColorDefinition->setColorValue("#000000");
5685 pColorDefinition=pGlobalRender->createColorDefinition();
5686 pColorDefinition->setId("blue");
5687 pColorDefinition->setColorValue("#000000");
5688 pColorDefinition=pGlobalRender->createColorDefinition();
5689 pColorDefinition->setId("lightYellow");
5690 pColorDefinition->setColorValue("#F0F0F0");
5691 pColorDefinition=pGlobalRender->createColorDefinition();
5692 pColorDefinition->setId("darkGreen");
5693 pColorDefinition->setColorValue("#0B0B0B");
5694
5695 // render information for the default color style
5696 lolPlugin = (RenderListOfLayoutsPlugin*)pListOfLayouts->getPlugin("render");
5697 pGlobalRender=lolPlugin->createGlobalRenderInformation();
5698 pGlobalRender->setId("defaultStyle");
5699 pGlobalRender->setName("default style");
5700 pGlobalRender->setProgramName("Ralph Gauges");
5701 pGlobalRender->setProgramVersion("1.0");
5702 pGlobalRender->setBackgroundColor("#FFFFFFFF");
5703 // color definitions
5704 pColorDefinition=pGlobalRender->createColorDefinition();
5705 pColorDefinition->setId("lightBlue");
5706 pColorDefinition->setColorValue("#ADD8E6");
5707 pColorDefinition=pGlobalRender->createColorDefinition();
5708 pColorDefinition->setId("white");
5709 pColorDefinition->setColorValue("#FFFFFF");
5710 pColorDefinition=pGlobalRender->createColorDefinition();
5711 pColorDefinition->setId("black");
5712 pColorDefinition->setColorValue("#000000");
5713 pColorDefinition=pGlobalRender->createColorDefinition();
5714 pColorDefinition->setId("red");
5715 pColorDefinition->setColorValue("#FF0000");
5716 pColorDefinition=pGlobalRender->createColorDefinition();
5717 pColorDefinition->setId("green");
5718 pColorDefinition->setColorValue("#00FF00");
5719 pColorDefinition=pGlobalRender->createColorDefinition();
5720 pColorDefinition->setId("blue");
5721 pColorDefinition->setColorValue("#0000FF");
5722 pColorDefinition=pGlobalRender->createColorDefinition();
5723 pColorDefinition->setId("lightYellow");
5724 pColorDefinition->setColorValue("#FFFFD1");
5725 pColorDefinition=pGlobalRender->createColorDefinition();
5726 pColorDefinition->setId("darkGreen");
5727 pColorDefinition->setColorValue("#002000");
5728 // gradient definitions
5729 pRadialGradient=pGlobalRender->createRadialGradientDefinition();
5730 pRadialGradient->setId("speciesGlyphGradient");
5731 pStop=pRadialGradient->createGradientStop();
5732 pStop->setOffset(RelAbsVector(0.0,0.0));
5733 pStop->setStopColor("white");
5734 pStop=pRadialGradient->createGradientStop();
5735 pStop->setOffset(RelAbsVector(0.0,100.0));
5736 pStop->setStopColor("lightBlue");
5737 // line endings
5738 pLineEnding=pGlobalRender->createLineEnding();
5739 pLineEnding->setId("simpleHead_black");
5740 pLineEnding->getBoundingBox()->setPosition(&p);
5741 pLineEnding->getBoundingBox()->setDimensions(&d);
5742 pGroup=pLineEnding->getGroup();
5743 pGroup->setStroke("black");
5744 pGroup->setStrokeWidth(1.0);
5745 pGroup->setFillColor("black");
5746 pPolygon=pGroup->createPolygon();
5747 pR=pPolygon->createPoint();
5748 pR->setCoordinates(RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0));
5749 pR=pPolygon->createPoint();
5750 pR->setCoordinates(RelAbsVector(10.0,0.0),RelAbsVector(3.0,0.0));
5751 pR=pPolygon->createPoint();
5752 pR->setCoordinates(RelAbsVector(0.0,0.0),RelAbsVector(6.0,0.0));
5753 pLineEnding=pGlobalRender->createLineEnding();
5754 pLineEnding->setId("simpleHead_red");
5755 pLineEnding->getBoundingBox()->setPosition(&p);
5756 pLineEnding->getBoundingBox()->setDimensions(&d);
5757 pGroup=pLineEnding->getGroup();
5758 pGroup->setStroke("red");
5759 pGroup->setStrokeWidth(1.0);
5760 pGroup->setFillColor("red");
5761 pPolygon=pGroup->createPolygon();
5762 pR=pPolygon->createPoint();
5763 pR->setCoordinates(RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0));
5764 pR=pPolygon->createPoint();
5765 pR->setCoordinates(RelAbsVector(10.0,0.0),RelAbsVector(3.0,0.0));
5766 pR=pPolygon->createPoint();
5767 pR->setCoordinates(RelAbsVector(0.0,0.0),RelAbsVector(6.0,0.0));
5768 pLineEnding=pGlobalRender->createLineEnding();
5769 pLineEnding->setId("simpleHead_green");
5770 pLineEnding->getBoundingBox()->setPosition(&p);
5771 pLineEnding->getBoundingBox()->setDimensions(&d);
5772 pGroup=pLineEnding->getGroup();
5773 pGroup->setStroke("green");
5774 pGroup->setStrokeWidth(1.0);
5775 pGroup->setFillColor("green");
5776 pPolygon=pGroup->createPolygon();
5777 pR=pPolygon->createPoint();
5778 pR->setCoordinates(RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0));
5779 pR=pPolygon->createPoint();
5780 pR->setCoordinates(RelAbsVector(10.0,0.0),RelAbsVector(3.0,0.0));
5781 pR=pPolygon->createPoint();
5782 pR->setCoordinates(RelAbsVector(0.0,0.0),RelAbsVector(6.0,0.0));
5783 pLineEnding=pGlobalRender->createLineEnding();
5784 pLineEnding->setId("simpleHead_blue");
5785 pLineEnding->getBoundingBox()->setPosition(&p);
5786 pLineEnding->getBoundingBox()->setDimensions(&d);
5787 pGroup=pLineEnding->getGroup();
5788 pGroup->setStroke("blue");
5789 pGroup->setStrokeWidth(1.0);
5790 pGroup->setFillColor("blue");
5791 pPolygon=pGroup->createPolygon();
5792 pR=pPolygon->createPoint();
5793 pR->setCoordinates(RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0));
5794 pR=pPolygon->createPoint();
5795 pR->setCoordinates(RelAbsVector(10.0,0.0),RelAbsVector(3.0,0.0));
5796 pR=pPolygon->createPoint();
5797 pR->setCoordinates(RelAbsVector(0.0,0.0),RelAbsVector(6.0,0.0));
5798
5799 // styles
5800 // style for compartment glyphs
5801 pGlobalStyle=pGlobalRender->createStyle("compartmentGlyphStyle");
5802 pGlobalStyle->addType("COMPARTMENTGLYPH");
5803 pGroup=pGlobalStyle->getGroup();
5804 pGroup->setStroke("darkGreen");
5805 pGroup->setStrokeWidth(1.0);
5806 pRectangle=pGroup->createRectangle();
5807 pRectangle->setCoordinatesAndSize(RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0),RelAbsVector(0.0,100.0),RelAbsVector(0.0,100.0));
5808 pRectangle->setRadiusX(RelAbsVector(0.0,10.0));
5809 pRectangle->setRadiusY(RelAbsVector(0.0,10.0));
5810 pRectangle->setFillColor("lightYellow");
5811
5812 // style for species glyphs
5813 pGlobalStyle=pGlobalRender->createStyle("speciesGlyphStyle");
5814 pGlobalStyle->addType("SPECIESGLYPH");
5815 pGroup=pGlobalStyle->getGroup();
5816 pGroup->setStroke("black");
5817 pGroup->setStrokeWidth(1.0);
5818 pRectangle=pGroup->createRectangle();
5819 pRectangle->setCoordinatesAndSize(RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0),RelAbsVector(0.0,100.0),RelAbsVector(0.0,100.0));
5820 pRectangle->setRadiusX(RelAbsVector(5.0,0.0));
5821 pRectangle->setRadiusY(RelAbsVector(0.0,50.0));
5822 pRectangle->setFillColor("speciesGlyphGradient");
5823
5824 // style for reaction and text glyphs
5825 pGlobalStyle=pGlobalRender->createStyle("reactionGlyphStyle");
5826 pGlobalStyle->addType("REACTIONGLYPH");
5827 pGlobalStyle->addType("TEXTGLYPH");
5828 pGroup=pGlobalStyle->getGroup();
5829 pGroup->setStroke("black");
5830 pGroup->setStrokeWidth(1.0);
5831 pGroup->setFontSize(RelAbsVector(12.0,0.0));
5832 pGroup->setTextAnchor(Text::ANCHOR_MIDDLE);
5833
5834 // style for substrate and product species reference glyphs
5835 pGlobalStyle=pGlobalRender->createStyle("reactantSpeciesReferenceGlyphStyle");
5836 pGlobalStyle->addRole("substrate");
5837 pGlobalStyle->addRole("sidesubstrate");
5838 pGlobalStyle->addRole("product");
5839 pGlobalStyle->addRole("sideproduct");
5840 pGroup=pGlobalStyle->getGroup();
5841 pGroup->setStroke("#000000");
5842 pGroup->setStrokeWidth(1.0);
5843 pGroup->setEndHead("simpleHead_black");
5844
5845 // style for activator species reference glyphs
5846 pGlobalStyle=pGlobalRender->createStyle("activatorSpeciesReferenceGlyphStyle");
5847 pGlobalStyle->addRole("activator");
5848 pGroup=pGlobalStyle->getGroup();
5849 pGroup->setStroke("green");
5850 pGroup->setStrokeWidth(1.0);
5851 pGroup->setEndHead("simpleHead_green");
5852
5853 // style for modifier species reference glyphs
5854 pGlobalStyle=pGlobalRender->createStyle("modifierSpeciesReferenceGlyphStyle");
5855 pGlobalStyle->addRole("modifier");
5856 pGroup=pGlobalStyle->getGroup();
5857 pGroup->setStroke("blue");
5858 pGroup->setStrokeWidth(1.0);
5859 pGroup->setEndHead("simpleHead_blue");
5860
5861 // style for inhibitor species reference glyphs
5862 pGlobalStyle=pGlobalRender->createStyle("inhibitorSpeciesReferenceGlyphStyle");
5863 pGlobalStyle->addRole("inhibitor");
5864 pGroup=pGlobalStyle->getGroup();
5865 pGroup->setStroke("red");
5866 pGroup->setStrokeWidth(1.0);
5867 pGroup->setEndHead("simpleHead_red");
5868
5869
5870 // local style that references a global style and redefines some things
5871 RenderLayoutPlugin* rPlugin=(RenderLayoutPlugin*)layout->getPlugin("render");
5872 LocalRenderInformation* pLocalRender=rPlugin->createLocalRenderInformation();
5873 pLocalRender->setId("highlightGlucose");
5874 pLocalRender->setReferenceRenderInformationId("defaultStyle");
5875 pLocalRender->setProgramName("Ralph Gauges");
5876 pLocalRender->setProgramVersion("1.0");
5877 pLocalRender->setBackgroundColor("#FFFFFFFF");
5878 // color definitions
5879 pColorDefinition=pLocalRender->createColorDefinition();
5880 pColorDefinition->setId("lightRed");
5881 pColorDefinition->setColorValue("#E6ADD8");
5882 pColorDefinition=pLocalRender->createColorDefinition();
5883 pColorDefinition->setId("white");
5884 pColorDefinition->setColorValue("#FFFFFF");
5885 // gradient definitions
5886 pRadialGradient=pLocalRender->createRadialGradientDefinition();
5887 pRadialGradient->setId("highlightedSpeciesGlyphGradient");
5888 pStop=pRadialGradient->createGradientStop();
5889 pStop->setOffset(RelAbsVector(0.0,0.0));
5890 pStop->setStopColor("white");
5891 pStop=pRadialGradient->createGradientStop();
5892 pStop->setOffset(RelAbsVector(0.0,100.0));
5893 pStop->setStopColor("lightRed");
5894
5895 // style for highligted species glyph
5896 LocalStyle* pLocalStyle=pLocalRender->createStyle("highlightedGlucose");
5897 pLocalStyle->addId("SpeciesGlyph_Glucose");
5898 pGroup=pLocalStyle->getGroup();
5899 pGroup->setStroke("black");
5900 pGroup->setStrokeWidth(1.0);
5901 pRectangle=pGroup->createRectangle();
5902 pRectangle->setCoordinatesAndSize(RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0),RelAbsVector(0.0,100.0),RelAbsVector(0.0,100.0));
5903 pRectangle->setRadiusX(RelAbsVector(5.0,0.0));
5904 pRectangle->setRadiusY(RelAbsVector(0.0,50.0));
5905 pRectangle->setFillColor("highlightedSpeciesGlyphGradient");
5906
5907 SBMLWriter writer;
5908
5909 //bool result=writeSBML(document,"example6.xml");
5910 char* writtenContent=writer.writeToString(document);
5911
5912 XMLInputStream stream2(writtenContent,false);
5913 XMLNode node2(stream2);
5914 free(writtenContent);
5915 // we need to check the namespaces on node2
5916 // it must contain a namespace for the layout and one for the
5917 // render extension
5918 // It must also contain a required attribute for each of the two packages
5919 const XMLNamespaces* pXMLNamespaces=&node.getNamespaces();
5920 int index=pXMLNamespaces->getIndex("http://www.sbml.org/sbml/level3/version1/layout/version1");
5921 fail_unless(index != -1);
5922 std::string prefix=pXMLNamespaces->getPrefix(index);
5923 fail_unless(!prefix.empty());
5924 const XMLAttributes* pXMLAttributes=&node2.getAttributes();
5925 fail_unless(pXMLAttributes->getLength() > 0);
5926 int i;
5927 for(i=0;i<pXMLAttributes->getLength();++i)
5928 {
5929 if(pXMLAttributes->getName(i) == "required" && pXMLAttributes->getPrefix(i) == prefix)
5930 {
5931 break;
5932 }
5933 }
5934 fail_unless(i < pXMLAttributes->getLength());
5935 // same check for the render extension
5936 index=pXMLNamespaces->getIndex("http://www.sbml.org/sbml/level3/version1/render/version1");
5937 fail_unless(index != -1);
5938 prefix=pXMLNamespaces->getPrefix(index);
5939 fail_unless(!prefix.empty());
5940 pXMLAttributes=&node2.getAttributes();
5941 fail_unless(pXMLAttributes->getLength() > 0);
5942 for(i=0;i<pXMLAttributes->getLength();++i)
5943 {
5944 if(pXMLAttributes->getName(i) == "required" && pXMLAttributes->getPrefix(i) == prefix)
5945 {
5946 break;
5947 }
5948 }
5949 fail_unless(i < pXMLAttributes->getLength());
5950
5951 const XMLNode* listOfLayouts1,*listOfLayouts2;
5952 listOfLayouts1=&node;
5953 fail_unless(listOfLayouts1->getName()=="sbml");
5954 int iMax=listOfLayouts1->getNumChildren();
5955 for(i=0;i<iMax;++i)
5956 {
5957 if(listOfLayouts1->getChild(i).getName()=="model")
5958 {
5959 listOfLayouts1=&listOfLayouts1->getChild(i);
5960 break;
5961 }
5962 }
5963 fail_unless(listOfLayouts1->getName()=="model");
5964 iMax=listOfLayouts1->getNumChildren();
5965 for(i=0;i<iMax;++i)
5966 {
5967 if(listOfLayouts1->getChild(i).getName()=="listOfLayouts")
5968 {
5969 listOfLayouts1=&listOfLayouts1->getChild(i);
5970 break;
5971 }
5972 }
5973 fail_unless(listOfLayouts1->getName()=="listOfLayouts");
5974
5975 listOfLayouts2=&node2;
5976 fail_unless(listOfLayouts2->getName()=="sbml");
5977 iMax=listOfLayouts2->getNumChildren();
5978 for(i=0;i<iMax;++i)
5979 {
5980 if(listOfLayouts2->getChild(i).getName()=="model")
5981 {
5982 listOfLayouts2=&listOfLayouts2->getChild(i);
5983 break;
5984 }
5985 }
5986 fail_unless(listOfLayouts2->getName()=="model");
5987 iMax=listOfLayouts2->getNumChildren();
5988 for(i=0;i<iMax;++i)
5989 {
5990 // make sure no annotation (with layout) has been written
5991 fail_unless(listOfLayouts2->getChild(i).getName() != "annotation");
5992 if(listOfLayouts2->getChild(i).getName()=="listOfLayouts")
5993 {
5994 listOfLayouts2=&listOfLayouts2->getChild(i);
5995 break;
5996 }
5997 }
5998 fail_unless(listOfLayouts2->getName()=="listOfLayouts");
5999
6000
6001 //std::string l1 = listOfLayouts1->toXMLString();
6002 //std::string l2 = listOfLayouts2->toXMLString();
6003 //std::string docString = writeSBMLToString(document);
6004
6005 // until the sbml element gets a namespace, we only compare the listOfLayouts element and all its children.
6006 fail_unless(listOfLayouts1->equals(*listOfLayouts2));
6007
6008 delete document;
6009 }
6010 END_TEST
6011
START_TEST(test_RenderWriting_write_L3_model_2)6012 START_TEST (test_RenderWriting_write_L3_model_2)
6013 {
6014 const char* s = \
6015 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
6016 "<sbml xmlns=\"http://www.sbml.org/sbml/level3/version1/core\" level=\"3\" version=\"1\"\n"
6017 " xmlns:layout=\"http://www.sbml.org/sbml/level3/version1/layout/version1\"\n"
6018 " xmlns:render=\"http://www.sbml.org/sbml/level3/version1/render/version1\"\n"
6019 " layout:required=\"false\"\n"
6020 " render:required=\"false\">\n"
6021 " <model id=\"TestModel\">\n"
6022 " <layout:listOfLayouts xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\">\n"
6023 " <layout:layout id=\"TextTest\">\n"
6024 " <layout:dimensions width=\"510\" height=\"106\"/>\n"
6025 " <layout:listOfAdditionalGraphicalObjects>\n"
6026 " <layout:graphicalObject id=\"graphical_object_1\">\n"
6027 " <layout:boundingBox>\n"
6028 " <layout:position x=\"5\" y=\"5\"/>\n"
6029 " <layout:dimensions width=\"500\" height=\"40\"/>\n"
6030 " </layout:boundingBox>\n"
6031 " </layout:graphicalObject>\n"
6032 " <layout:graphicalObject id=\"graphical_object_2\">\n"
6033 " <layout:boundingBox>\n"
6034 " <layout:position x=\"5\" y=\"53\"/>\n"
6035 " <layout:dimensions width=\"500\" height=\"40\"/>\n"
6036 " </layout:boundingBox>\n"
6037 " </layout:graphicalObject>\n"
6038 " </layout:listOfAdditionalGraphicalObjects>\n"
6039 " <listOfRenderInformation>\n"
6040 " <renderInformation id=\"TextRenderInfo\">\n"
6041 " <listOfStyles>\n"
6042 " <style id=\"style_for_graphical_object_1\" idList=\"graphical_object_1\">\n"
6043 " <g stroke=\"#000000\" stroke-width=\"1\" font-size=\"20\" font-family=\"sans\" text-anchor=\"start\">\n"
6044 " <rectangle fill=\"#aaaaff\" x=\"0\" y=\"0\" width=\"100%\" height=\"100%\"/>\n"
6045 " <text x=\"0\" y=\"0\">ABCDEFGHIJKLMNOPQRSTUVWXYZ</text>\n"
6046 " </g>\n"
6047 " </style>\n"
6048 " <style id=\"style_for_graphical_object_2\" idList=\"graphical_object_2\">\n"
6049 " <g stroke=\"#000000\" stroke-width=\"1\" font-size=\"20\" font-family=\"sans\" text-anchor=\"start\">\n"
6050 " <rectangle fill=\"#aaaaff\" x=\"0\" y=\"0\" width=\"100%\" height=\"100%\"/>\n"
6051 " <text x=\"0\" y=\"0\">abcdefghijklmnopqrstuvwxyz</text>\n"
6052 " </g>\n"
6053 " </style>\n"
6054 " </listOfStyles>\n"
6055 " </renderInformation>\n"
6056 " </listOfRenderInformation>\n"
6057 " </layout:layout>\n"
6058 " </layout:listOfLayouts>\n"
6059 " </model>\n"
6060 "</sbml>";
6061
6062 XMLInputStream stream(s,false);
6063 XMLNode node(stream);
6064 // create the document
6065
6066 SBMLDocument *document=new SBMLDocument(3,1);
6067
6068 // enable layout and render
6069 document->enablePackage(LayoutExtension::getXmlnsL3V1V1(), "layout", true);
6070 document->enablePackage(RenderExtension::getXmlnsL3V1V1(), "render", true);
6071
6072 // create the Model
6073
6074 Model* pModel=document->createModel();
6075 pModel->setId("TestModel");
6076 document->setModel(pModel);
6077
6078 // now we create a new layout
6079 LayoutModelPlugin* mPlugin=(LayoutModelPlugin*)pModel->getPlugin("layout");
6080 Layout* pLayout=mPlugin->createLayout();
6081 pLayout->setId("TextTest");
6082 double y=5.0,x=5.0;
6083 // draw each text in a 500x40 box
6084 const double WIDTH=500.0;
6085 double HEIGHT=40.0;
6086 std::ostringstream os;
6087 unsigned int object_index=1;
6088 const std::string TEXT="ABCDEFGHIJKLMNOPQRSTUVWXYZ";
6089 const std::string text="abcdefghijklmnopqrstuvwxyz";
6090 // the dimensions of the whole layout will be
6091 Dimensions dim(layoutns,WIDTH+10,2*HEIGHT*1.2+10);
6092 pLayout->setDimensions(&dim);
6093 // create the render information
6094 RenderLayoutPlugin* rPlugin=(RenderLayoutPlugin*)pLayout->getPlugin("render");
6095 LocalRenderInformation* pRenderInfo=rPlugin->createLocalRenderInformation();
6096 pRenderInfo->setId("TextRenderInfo");
6097 Dimensions d(layoutns,WIDTH,HEIGHT);
6098 // create a graphical object with the correct bounding box
6099 // left alligned capital letters
6100 os.str("");
6101 os << "graphical_object_" << object_index++;
6102 GraphicalObject* pObject=pLayout->createAdditionalGraphicalObject();
6103 pObject->setId(os.str());
6104 // we set the bound
6105 BoundingBox bb;
6106 Point p(layoutns,x,y);
6107 bb.setPosition(&p);
6108 bb.setDimensions(&d);
6109 pObject->setBoundingBox(&bb);
6110 // we create a style for the object
6111 LocalStyle* pStyle=pRenderInfo->createStyle("style_for_"+os.str());
6112 pStyle->addId(pObject->getId());
6113 RenderGroup* pGroup=pStyle->getGroup();
6114 pGroup->setStroke("#000000");
6115 pGroup->setStrokeWidth(1.0);
6116 pGroup->setFontFamily("sans");
6117 pGroup->setFontSize(20.0);
6118 pGroup->setTextAnchor(Text::ANCHOR_START);
6119 // add a rectangle to the group
6120 Rectangle* pRectangle=pGroup->createRectangle();
6121 pRectangle->setCoordinates(RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0));
6122 pRectangle->setSize(RelAbsVector(0.0,100.0),RelAbsVector(0.0,100.0));
6123 pRectangle->setFillColor("#aaaaff");
6124 // add a text element to the group
6125 Text* pText=pGroup->createText();
6126 pText->setText(TEXT);
6127 y+=HEIGHT*1.2;
6128 // create a graphical object with the correct bounding box
6129 // left alligned lowercase letters
6130 os.str("");
6131 os << "graphical_object_" << object_index++;
6132 pObject=pLayout->createAdditionalGraphicalObject();
6133 pObject->setId(os.str());
6134 // we set the bound
6135 p=Point(layoutns,x,y);
6136 bb.setPosition(&p);
6137 bb.setDimensions(&d);
6138 pObject->setBoundingBox(&bb);
6139 // we create a style for the object
6140 pStyle=pRenderInfo->createStyle("style_for_"+os.str());
6141 pStyle->addId(pObject->getId());
6142 pGroup=pStyle->getGroup();
6143 pGroup->setStroke("#000000");
6144 pGroup->setStrokeWidth(1.0);
6145 pGroup->setFontFamily("sans");
6146 pGroup->setFontSize(20.0);
6147 pGroup->setTextAnchor(Text::ANCHOR_START);
6148 // add a rectangle to the group
6149 pRectangle=pGroup->createRectangle();
6150 pRectangle->setCoordinates(RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0),RelAbsVector(0.0,0.0));
6151 pRectangle->setSize(RelAbsVector(0.0,100.0),RelAbsVector(0.0,100.0));
6152 pRectangle->setFillColor("#aaaaff");
6153 // add a text element to the group
6154 pText=pGroup->createText();
6155 pText->setText(text);
6156
6157 // write the document
6158 std::string writtenContent=writeSBMLToStdString(document);
6159 fail_unless(!writtenContent.empty());
6160 // now we read the written content
6161 SBMLReader reader;
6162 SBMLDocument* pDocument2=reader.readSBMLFromString(writtenContent);
6163 fail_unless(pDocument2 != NULL);
6164 const Model *pModel2=pDocument2->getModel();
6165 LayoutModelPlugin* plugin = (LayoutModelPlugin*)pModel2->getPlugin("layout");
6166 fail_unless(pModel2 != NULL);
6167 fail_unless(plugin->getListOfLayouts()->size() == 1);
6168 const Layout* pLayout2=plugin->getLayout(0);
6169 fail_unless(pLayout2 != NULL);
6170 fail_unless(pLayout->getListOfAdditionalGraphicalObjects()->size() == 2);
6171 // there should be one piece of render information
6172 RenderLayoutPlugin* rPlugin1 = (RenderLayoutPlugin*) pLayout->getPlugin("render");
6173 RenderLayoutPlugin* rPlugin2 = (RenderLayoutPlugin*) pLayout2->getPlugin("render");
6174 fail_unless(rPlugin1->getListOfLocalRenderInformation()->size() == 1);
6175 fail_unless(rPlugin2 != NULL);
6176 if (rPlugin2 == NULL) return;
6177
6178 const LocalRenderInformation* pLocalRenderInfo2=rPlugin2->getRenderInformation(0);
6179 fail_unless(pLocalRenderInfo2 != NULL);
6180 if (pLocalRenderInfo2 == NULL) return;
6181
6182 fail_unless(pLocalRenderInfo2->getId() == "TextRenderInfo");
6183 fail_unless(pLocalRenderInfo2->getNumColorDefinitions() == 0);
6184 fail_unless(pLocalRenderInfo2->getNumGradientDefinitions() == 0);
6185 fail_unless(pLocalRenderInfo2->getNumLineEndings() == 0);
6186 fail_unless(pLocalRenderInfo2->getNumStyles() == 2);
6187 const LocalStyle* pStyle2_1=pLocalRenderInfo2->getStyle(0),*pStyle2_2=NULL;
6188 fail_unless(pStyle2_1 != NULL);
6189 if(pStyle2_1->getId() == "style_for_graphical_object_2")
6190 {
6191 pStyle2_1=pLocalRenderInfo2->getStyle(1);
6192 }
6193 else
6194 {
6195 pStyle2_2=pLocalRenderInfo2->getStyle(1);
6196 fail_unless(pStyle2_2->getId() == "style_for_graphical_object_2");
6197 }
6198 fail_unless(pStyle2_2 != NULL);
6199 fail_unless(pStyle2_2->getId() == "style_for_graphical_object_2");
6200 fail_unless(pStyle2_1->getId() == "style_for_graphical_object_1");
6201 // check both id lists
6202 fail_unless(pStyle2_1->getIdList().size() == 1);
6203 fail_unless(pStyle2_1->isInIdList("graphical_object_1"));
6204 fail_unless(pStyle2_2->getIdList().size() == 1);
6205 fail_unless(pStyle2_2->isInIdList("graphical_object_2"));
6206 //
6207 // check both groups and their attributes
6208 const RenderGroup* pGroup2_1 = pStyle2_1->getGroup();
6209 fail_unless(pGroup2_1 != NULL);
6210 fail_unless(pGroup2_1->isSetStroke());
6211 fail_unless(pGroup2_1->getStroke() == "#000000");
6212 fail_unless(pGroup2_1->isSetStrokeWidth());
6213 fail_unless(fabs(pGroup2_1->getStrokeWidth() - 1.0) < 1e-12);
6214 fail_unless(pGroup2_1->isSetFontSize());
6215 fail_unless(pGroup2_1->getFontSize() == RelAbsVector(20.0,0.0));
6216 fail_unless(pGroup2_1->isSetFontFamily());
6217 fail_unless(pGroup2_1->getFontFamily() == "sans");
6218 fail_unless(pGroup2_1->isSetTextAnchor());
6219 fail_unless(pGroup2_1->getTextAnchor() == Text::ANCHOR_START);
6220 const RenderGroup* pGroup2_2 = pStyle2_2->getGroup();
6221 fail_unless(pGroup2_2 != NULL);
6222 fail_unless(pGroup2_2->isSetStroke());
6223 fail_unless(pGroup2_2->getStroke() == "#000000");
6224 fail_unless(pGroup2_2->isSetStrokeWidth());
6225 fail_unless(fabs(pGroup2_2->getStrokeWidth() -1.0) < 1e-12);
6226 fail_unless(pGroup2_2->isSetFontSize());
6227 fail_unless(pGroup2_2->getFontSize() == RelAbsVector(20.0,0.0));
6228 fail_unless(pGroup2_2->isSetFontFamily());
6229 fail_unless(pGroup2_2->getFontFamily() == "sans");
6230 fail_unless(pGroup2_2->isSetTextAnchor());
6231 fail_unless(pGroup2_2->getTextAnchor() == Text::ANCHOR_START);
6232 //
6233 // check the elements of both groups and their attributes
6234 fail_unless(pGroup2_1->getNumElements() == 2);
6235 const Rectangle* pRectangle2_1 = dynamic_cast<const Rectangle*>(pGroup->getElement(0));
6236 fail_unless(pRectangle2_1 != NULL);
6237 fail_unless(pRectangle2_1->isSetFillColor());
6238 fail_unless(pRectangle2_1->getFillColor() == "#aaaaff");
6239 fail_unless(pRectangle2_1->getX() == RelAbsVector(0.0,0.0));
6240 fail_unless(pRectangle2_1->getY() == RelAbsVector(0.0,0.0));
6241 fail_unless(pRectangle2_1->getWidth() == RelAbsVector(0.0,100.0));
6242 fail_unless(pRectangle2_1->getHeight() == RelAbsVector(0.0,100.0));
6243 const Text* pText2_1=dynamic_cast<const Text*>(pGroup2_1->getElement(1));
6244 fail_unless(pText2_1 != NULL);
6245 fail_unless(pText2_1->getX() == RelAbsVector(0.0,0.0));
6246 fail_unless(pText2_1->getY() == RelAbsVector(0.0,0.0));
6247 fail_unless(pText2_1->getText() == TEXT);
6248 fail_unless(pGroup2_2->getNumElements() == 2);
6249 const Rectangle* pRectangle2_2 = dynamic_cast<const Rectangle*>(pGroup->getElement(0));
6250 fail_unless(pRectangle2_2 != NULL);
6251 fail_unless(pRectangle2_2->isSetFillColor());
6252 fail_unless(pRectangle2_2->getFillColor() == "#aaaaff");
6253 fail_unless(pRectangle2_2->getX() == RelAbsVector(0.0,0.0));
6254 fail_unless(pRectangle2_2->getY() == RelAbsVector(0.0,0.0));
6255 fail_unless(pRectangle2_2->getWidth() == RelAbsVector(0.0,100.0));
6256 fail_unless(pRectangle2_2->getHeight() == RelAbsVector(0.0,100.0));
6257 const Text* pText2_2=dynamic_cast<const Text*>(pGroup2_2->getElement(1));
6258 fail_unless(pText2_2 != NULL);
6259 fail_unless(pText2_2->getX() == RelAbsVector(0.0,0.0));
6260 fail_unless(pText2_2->getY() == RelAbsVector(0.0,0.0));
6261 fail_unless(pText2_2->getText() == text);
6262 delete document;
6263 delete pDocument2;
6264 }
6265 END_TEST
6266
6267
6268 Suite *
create_suite_RenderWriting(void)6269 create_suite_RenderWriting (void)
6270 {
6271 Suite *suite = suite_create("RenderWriting");
6272 TCase *tcase = tcase_create("RenderWriting");
6273
6274
6275 tcase_add_checked_fixture( tcase,
6276 RenderWriting_setup,
6277 RenderWriting_teardown );
6278
6279 tcase_add_test( tcase, test_RenderWriting_write_l2_ojectrole );
6280 tcase_add_test( tcase, test_RenderWriting_write_model_1 );
6281 tcase_add_test( tcase, test_RenderWriting_write_L3_model_1 );
6282 tcase_add_test( tcase, test_RenderWriting_write_L3_model_2 );
6283
6284 suite_add_tcase(suite, tcase);
6285
6286 return suite;
6287 }
6288
6289
6290
6291 END_C_DECLS
6292