Exemplo n.º 1
0
    public static int Main(string[] args)
    {
        if (args.Length != 1)
        {
            Console.WriteLine("Usage: create_sedml output-filename.");
            return(2);
        }

        // create the document
        SedDocument doc = new SedDocument();

        doc.setLevel(1);
        doc.setVersion(1);

        {
            // create a first model referencing an sbml file
            SedModel model = doc.createModel();
            model.setId("model1");
            model.setSource("file.xml");
            model.setLanguage("urn:sedml:sbml");

            // create a second model modifying a variable of that other sbml file
            model = doc.createModel();
            model.setId("model2");
            model.setSource("model1");
            model.setLanguage("urn:sedml:sbml");

            // change a paramerter 'k' to 0.1
            SedChangeAttribute change = model.createChangeAttribute();
            change.setTarget("/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='k']/@value");
            change.setNewValue("0.1");

            // remove species 's1'
            SedRemoveXML remove = model.createRemoveXML();
            remove.setTarget("/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='S1']");

            // now for something tricky we want to update the initialConcentration of 'S2' to be
            // half what it was in the original model
            SedComputeChange compute = model.createComputeChange();
            compute.setTarget("/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id="S2"]/@initialConcentration");
            SedVariable variable = compute.createVariable();
            variable.setId("S2");
            variable.setModelReference("model1");
            variable.setTarget("/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='S2']");
            compute.setMath(libsedml.parseFormula("S2 / 2"));
        }

        // create simulation
        SedUniformTimeCourse tc = doc.createUniformTimeCourse();

        tc.setId("sim1");
        tc.setInitialTime(0.0);
        tc.setOutputStartTime(0.0);
        tc.setOutputEndTime(10.0);
        tc.setNumberOfPoints(1000);
        // need to set the correct KISAO Term
        SedAlgorithm alg = tc.createAlgorithm();

        alg.setKisaoID("KISAO:0000019");

        // create a task that uses the simulation and the model above
        SedTask task = doc.createTask();

        task.setId("task1");
        task.setModelReference("model1");
        task.setSimulationReference("sim1");

        // add a DataGenerator to hold the output for time
        SedDataGenerator dg = doc.createDataGenerator();

        dg.setId("time");
        dg.setName("time");
        SedVariable var = dg.createVariable();

        var.setId("v0");
        var.setName("time");
        var.setTaskReference("task1");
        var.setSymbol("urn:sedml:symbol:time");
        dg.setMath(libsedml.parseFormula("v0"));

        // and one for S1
        dg = doc.createDataGenerator();
        dg.setId("S1");
        dg.setName("S1");
        var = dg.createVariable();
        var.setId("v1");
        var.setName("S1");
        var.setTaskReference("task1");
        var.setTarget("/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='S1']");
        dg.setMath(libsedml.parseFormula("v1"));

        // add a report
        SedReport report = doc.createReport();

        report.setId("r1");
        report.setName("report 1");
        SedDataSet set = report.createDataSet();

        set.setId("ds1");
        set.setLabel("time");
        set.setDataReference("time");
        set = report.createDataSet();
        set.setId("ds2");
        set.setLabel("S1");
        set.setDataReference("S1");

        // add a 2d plot
        SedPlot2D plot = doc.createPlot2D();

        plot.setId("p1");
        plot.setName("S1 Timecourse");
        SedCurve curve = plot.createCurve();

        curve.setId("c1");
        curve.setName("S1");
        curve.setLogX(false);
        curve.setLogY(false);
        curve.setXDataReference("time");
        curve.setYDataReference("S1");

        // add a 3D Plot
        SedPlot3D plot2 = doc.createPlot3D();

        plot2.setId("p2");
        plot2.setName("dunno");
        SedSurface surf = plot2.createSurface();

        surf.setId("surf1");
        surf.setName("S1");
        surf.setLogX(false);
        surf.setLogY(false);
        surf.setLogZ(false);
        surf.setXDataReference("time");
        surf.setYDataReference("S1");
        surf.setZDataReference("S1");

        // write the document
        libsedml.writeSedML(doc, args[0]);

        return(0);
    }
Exemplo n.º 2
0
    public static int Main(string[] args)
    {
        if (args.Length != 1)
        {
            Console.WriteLine("{0}Usage: print_sedml input-filename{0}{0}", Environment.NewLine);
            return(2);
        }

        SedDocument doc = libsedml.readSedML(args[0]);

        if (doc.getErrorLog().getNumFailsWithSeverity(libsedml.LIBSEDML_SEV_ERROR) > 0)
        {
            Console.WriteLine(doc.getErrorLog().toString());
            return(2);
        }

        Console.WriteLine("The document has " + doc.getNumSimulations() + " simulation(s)." + Environment.NewLine);
        for (int i = 0; i < doc.getNumSimulations(); ++i)
        {
            SedSimulation current = doc.getSimulation(i);
            switch (current.getTypeCode())
            {
            case libsedml.SEDML_SIMULATION_UNIFORMTIMECOURSE:
            {
                SedUniformTimeCourse tc = (SedUniformTimeCourse)(current);
                Console.WriteLine("\tTimecourse id=" + tc.getId() + " start=" + tc.getOutputStartTime() + " end=" + tc.getOutputEndTime() + " numPoints=" + tc.getNumberOfPoints() + " kisao=" + (tc.isSetAlgorithm() ? tc.getAlgorithm().getKisaoID() : "none") + Environment.NewLine);
                break;
            }

            default:
                Console.WriteLine("\tUncountered unknown simulation. " + current.getId() + Environment.NewLine);
                break;
            }
        }

        Console.WriteLine(Environment.NewLine);
        Console.WriteLine("The document has " + doc.getNumModels() + " model(s)." + Environment.NewLine);
        for (int i = 0; i < doc.getNumModels(); ++i)
        {
            SedModel current = doc.getModel(i);
            Console.WriteLine("\tModel id=" + current.getId() + " language=" + current.getLanguage() + " source=" + current.getSource() + " numChanges=" + current.getNumChanges() + Environment.NewLine);
        }

        Console.WriteLine(Environment.NewLine);
        Console.WriteLine("The document has " + doc.getNumTasks() + " task(s)." + Environment.NewLine);
        for (int i = 0; i < doc.getNumTasks(); ++i)
        {
            SedTask current = doc.getTask(i);
            Console.WriteLine("\tTask id=" + current.getId() + " model=" + current.getModelReference() + " sim=" + current.getSimulationReference() + Environment.NewLine);
        }

        Console.WriteLine(Environment.NewLine);
        Console.WriteLine("The document has " + doc.getNumDataGenerators() + " datagenerators(s)." + Environment.NewLine);
        for (int i = 0; i < doc.getNumDataGenerators(); ++i)
        {
            SedDataGenerator current = doc.getDataGenerator(i);
            Console.WriteLine("\tDG id=" + current.getId() + " math=" + libsedml.formulaToString(current.getMath()) + Environment.NewLine);
        }

        Console.WriteLine(Environment.NewLine);
        Console.WriteLine("The document has " + doc.getNumOutputs() + " output(s)." + Environment.NewLine);
        for (int i = 0; i < doc.getNumOutputs(); ++i)
        {
            SedOutput current = doc.getOutput(i);
            switch (current.getTypeCode())
            {
            case libsedml.SEDML_OUTPUT_REPORT:
            {
                SedReport r = (SedReport)(current);
                Console.WriteLine("\tReport id=" + current.getId() + " numDataSets=" + r.getNumDataSets() + Environment.NewLine);
                break;
            }

            case libsedml.SEDML_OUTPUT_PLOT2D:
            {
                SedPlot2D p = (SedPlot2D)(current);
                Console.WriteLine("\tPlot2d id=" + current.getId() + " numCurves=" + p.getNumCurves() + Environment.NewLine);
                break;
            }

            case libsedml.SEDML_OUTPUT_PLOT3D:
            {
                SedPlot3D p = (SedPlot3D)(current);
                Console.WriteLine("\tPlot3d id=" + current.getId() + " numSurfaces=" + p.getNumSurfaces() + Environment.NewLine);
                break;
            }

            default:
                Console.WriteLine("\tEncountered unknown output " + current.getId() + Environment.NewLine);
                break;
            }
        }

        return(0);
    }