Examples with MathModel cbit.vcell.mathmodel.MathModel used on opensource projects

Example 26 with MathModel

use of cbit.vcell.mathmodel.MathModel in project vcell by virtualcell.

the class SimulationWorkspaceModelInfo method getContextName.

/**
 * Insert the method's description here.
 * Creation date: (9/25/2005 11:04:29 AM)
 * @return java.lang.String
 */
public java.lang.String getContextName() {
    String results = null;
    if (simulationOwner instanceof MathModel) {
        MathModel mathModel = (MathModel) simulationOwner;
        results = mathModel.getName();
    } else if (simulationOwner instanceof SimulationContext) {
        SimulationContext simContext = (SimulationContext) simulationOwner;
        results = simContext.getBioModel().getName() + "::" + simContext.getName();
    }
    return results;
}

Example 27 with MathModel

use of cbit.vcell.mathmodel.MathModel in project vcell by virtualcell.

the class VCellClientDataServiceImpl method createSimulationDataSetRef.

public static SimulationDataSetRef createSimulationDataSetRef(Simulation simulation, VCDocument modelDocument, int jobIndex, boolean isLocal) {
    SimulationDataSetRef simulationDataSetReference = new SimulationDataSetRef();
    Origin origin = simulation.getMathDescription().getGeometry().getOrigin();
    Extent extent = simulation.getMathDescription().getGeometry().getExtent();
    SimulationInfo simInfo = simulation.getSimulationInfo();
    simulationDataSetReference.setSimName(simInfo.getName());
    // String simName = simInfo.getName();
    // if (jobIndex!=0){
    // simName = simName + " job#"+String.valueOf(jobIndex);
    // }
    final String modelId;
    final boolean isMathModel;
    final String modelName;
    final String simContextName;
    if (modelDocument != null) {
        modelId = modelDocument.getVersion().getVersionKey().toString();
        isMathModel = (modelDocument instanceof MathModel);
        modelName = modelDocument.getName();
        if (modelDocument instanceof BioModel && simulation.getSimulationOwner() != null) {
            simContextName = simulation.getSimulationOwner().getName();
        } else {
            simContextName = null;
        }
    } else {
        modelId = "no id";
        isMathModel = false;
        modelName = "no model";
        simContextName = null;
    }
    simulationDataSetReference.setSimId(simInfo.getAuthoritativeVCSimulationIdentifier().getSimulationKey().toString());
    simulationDataSetReference.setModelId(modelId);
    simulationDataSetReference.setUsername(simInfo.getVersion().getOwner().getName());
    simulationDataSetReference.setUserkey(simInfo.getVersion().getOwner().getID().toString());
    simulationDataSetReference.setIsMathModel(isMathModel);
    simulationDataSetReference.setJobIndex(jobIndex);
    simulationDataSetReference.setModelName(modelName);
    simulationDataSetReference.setOriginXYZ(Arrays.asList(new Double[] { origin.getX(), origin.getY(), origin.getZ() }));
    simulationDataSetReference.setExtentXYZ(Arrays.asList(new Double[] { extent.getX(), extent.getY(), extent.getZ() }));
    if (simContextName != null) {
        simulationDataSetReference.setSimulationContextName(simContextName);
    }
    simulationDataSetReference.setSimName(simInfo.getName());
    boolean movingBoundarySolver = simulation.getSolverTaskDescription().getSolverDescription().isMovingBoundarySolver();
    simulationDataSetReference.setIsTimeVaryingMesh(movingBoundarySolver);
    simulationDataSetReference.setIsLocal(isLocal);
    return simulationDataSetReference;
}

Example 28 with MathModel

use of cbit.vcell.mathmodel.MathModel in project vcell by virtualcell.

the class MathDebuggerPanel method getMathModel2.

public MathModel getMathModel2() throws PropertyVetoException {
    MathDescription mathDesc = mathDescEditor2.getMathDescription();
    if (mathDesc == null) {
        return null;
    } else {
        MathModel mathModel = new MathModel(null);
        mathModel.setName("MATH 2");
        mathModel.setMathDescription(mathDesc);
        return mathModel;
    }
}

Example 29 with MathModel

use of cbit.vcell.mathmodel.MathModel in project vcell by virtualcell.

the class MathDebuggerPanel method main.

public static void main(java.lang.String[] args) {
    try {
        javax.swing.JFrame frame = new javax.swing.JFrame();
        MathDebuggerPanel aMathDebuggerPanel;
        aMathDebuggerPanel = new MathDebuggerPanel();
        frame.setContentPane(aMathDebuggerPanel);
        frame.setTitle("Math Descriptions Comparator");
        frame.setSize(aMathDebuggerPanel.getSize());
        frame.addWindowListener(new java.awt.event.WindowAdapter() {

            public void windowClosing(java.awt.event.WindowEvent e) {
                System.exit(0);
            }
        });
        MathModel mathModel1 = new MathModel(null);
        mathModel1.setName("math1");
        Geometry geometry1 = new Geometry("geo", 0);
        MathDescription mathDesc1 = mathModel1.getMathDescription();
        mathDesc1.setGeometry(geometry1);
        mathDesc1.addSubDomain(new CompartmentSubDomain("Compartment", CompartmentSubDomain.NON_SPATIAL_PRIORITY));
        MathModel mathModel2 = new MathModel(null);
        mathModel2.setName("math2");
        Geometry geometry2 = new Geometry("geo", 0);
        MathDescription mathDesc2 = mathModel2.getMathDescription();
        mathDesc2.setGeometry(geometry2);
        mathDesc2.addSubDomain(new CompartmentSubDomain("Compartment", CompartmentSubDomain.NON_SPATIAL_PRIORITY));
        aMathDebuggerPanel.setMathModel1(mathModel1);
        aMathDebuggerPanel.setMathModel2(mathModel2);
        frame.setSize(1500, 800);
        frame.setVisible(true);
    } catch (Throwable exception) {
        System.err.println("Exception occurred in main() of javax.swing.JPanel");
        exception.printStackTrace(System.out);
    }
}

Example 30 with MathModel

use of cbit.vcell.mathmodel.MathModel in project vcell by virtualcell.

the class MathDebuggerPanel method paste.

private void paste() throws PropertyVetoException, MathException, XmlParseException {
    String copiedText = (String) VCellTransferable.getFromClipboard(DataFlavor.stringFlavor);
    if (!copiedText.contains("BEGINMATH:") && !copiedText.contains("ENDMATH")) {
        throw new RuntimeException("Make sure each math description is enclosed with 'BEGINMATH:' and 'ENDMATH' tags for the 'Paste' operation to work.");
    }
    String[] mathStrings = copiedText.split("BEGINMATH:");
    String mathString1 = null;
    String mathString2 = null;
    for (int i = 0; i < mathStrings.length; i++) {
        mathStrings[i] = mathStrings[i].trim();
        if (mathStrings[i].trim().startsWith("MathDescription {")) {
            int endIndex = mathStrings[i].indexOf("ENDMATH");
            if (endIndex > 0) {
                if (mathString1 == null) {
                    mathString1 = mathStrings[i].substring(0, endIndex);
                } else if (mathString2 == null) {
                    mathString2 = mathStrings[i].substring(0, endIndex);
                } else {
                    throw new RuntimeException("too many math Descriptions (expecting only two)");
                }
            }
        }
    }
    if (mathString1 != null) {
        MathDescription mathDesc = MathDescription.fromEditor(getMathDescEditor1().getMathDescription(), mathString1);
        MathModel mathModel = new MathModel(null);
        mathModel.setName("Math1");
        mathModel.setMathDescription(mathDesc);
        setMathModel1(mathModel);
    }
    if (mathString2 != null) {
        MathDescription mathDesc = MathDescription.fromEditor(getMathDescEditor2().getMathDescription(), mathString2);
        MathModel mathModel = new MathModel(null);
        mathModel.setName("Math2");
        mathModel.setMathDescription(mathDesc);
        setMathModel2(mathModel);
    }
    compareTree();
}