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Provide specific time unit entity for sbml sim.
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org.insilico.vissim.sbscl/src/org/insilico/vissim/sbscl/simulation/SBMLSimulation.java

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -6,6 +6,7 @@
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import org.insilico.vissim.sbscl.utils.SBSCLUtils;
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import org.sbml.jsbml.Model;
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import org.sbml.jsbml.SBMLReader;
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import org.sbml.jsbml.UnitDefinition;
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import org.simulator.math.odes.AbstractDESSolver;
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import org.simulator.math.odes.MultiTable;
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import org.simulator.sbml.SBMLinterpreter;
@@ -24,17 +25,18 @@ public SimulationResult simulate(String path) throws Exception {
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SBMLReader reader = new SBMLReader();
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SimulationResult result = null;
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Model model = reader.readSBML(path).getModel();
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UnitDefinition timeUnitsInstance = model.getTimeUnitsInstance();
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SBMLinterpreter interpreter = new SBMLinterpreter(model);
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SBMLDialog sbmlDialog = new SBMLDialog();
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sbmlDialog.initDialog();
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AbstractDESSolver solver = getSolver(SBMLDialog.getSolverType());
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if (SBMLDialog.isCanceled() || solver == null) {
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throw new Exception();
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// TODO: Cancel scenario
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}
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double[] tp = getTimePoints(sbmlDialog);
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MultiTable solution = solver.solve(interpreter, interpreter.getInitialValues(), tp);
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result = new ResultAdapter(solution).getResult();
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result = new ResultAdapter(solution, timeUnitsInstance.getName()).getResult();
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return result;
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}
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