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

Example 21 with MathModel

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

the class RuleBasedTest method main.

public static void main(String[] args) {
    try {
        PropertyLoader.loadProperties();
    } catch (Exception e) {
        e.printStackTrace();
    }
    final int numTrials = 40;
    VCDatabaseVisitor vcDatabaseVisitor = new VCDatabaseVisitor() {

        @Override
        public void visitMathModel(MathModel mathModel, PrintStream logFilePrintStream) {
            throw new IllegalArgumentException("Not Implemented");
        }

        @Override
        public void visitGeometry(Geometry geometry, PrintStream logFilePrintStream) {
            throw new IllegalArgumentException("Not Implemented");
        }

        @Override
        public void visitBioModel(BioModel bioModel, PrintStream logFilePrintStream) {
            SimulationContext[] simulationContexts = bioModel.getSimulationContexts();
            for (SimulationContext simContext : simulationContexts) {
                if ((simContext.getApplicationType() == Application.NETWORK_STOCHASTIC) && simContext.getGeometry().getDimension() == 0) {
                    File baseDirectory = createDirFile(simContext);
                    try {
                        checkNonspatialStochasticSimContext(simContext, baseDirectory, numTrials);
                    } catch (Exception e) {
                        e.printStackTrace();
                        if (!e.getMessage().contains("Only Mass Action Kinetics supported ")) {
                            writeMessageTofile(baseDirectory, e.getMessage());
                        }
                    }
                }
            }
        }

        @Override
        public boolean filterMathModel(MathModelInfo mathModelInfo) {
            return false;
        }

        @Override
        public boolean filterGeometry(GeometryInfo geometryInfo) {
            return false;
        }

        @Override
        public boolean filterBioModel(BioModelInfo bioModelInfo) {
            return // bioModelInfo.getVersion().getName().equals("model");
            bioModelInfo.getVersion().getName().equals("simpleModel_Network_orig");
        }
    };
    String currentUserID = "schaff";
    String[] allUsers = new String[] { /*-all*/
    currentUserID, "-" };
    VCDatabaseScanner.scanBioModels(allUsers, vcDatabaseVisitor, false);
}

Example 22 with MathModel

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

the class MathGenerationDebugger method compareMath_4_8.

private void compareMath_4_8() {
    try {
        MathModel mathModel1 = new MathModel(null);
        MathModel mathModel2 = new MathModel(null);
        mathModel1.setMathDescription(mathGenerationResults.mathDesc_original);
        mathModel2.setMathDescription(mathGenerationResults.mathDesc_4_8);
        getMathDebuggerPanel().setMathModel1(mathModel1);
        getMathDebuggerPanel().setMathModel2(mathModel2);
    } catch (Exception e) {
        e.printStackTrace(System.out);
        DialogUtils.showErrorDialog(this, e.getMessage(), e);
    }
}

Example 23 with MathModel

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

the class MathModelEditorTreeCellRenderer method getTreeCellRendererComponent.

// public void setMathModel(MathModel mm) {
// mathModel = mm;
// }
public Component getTreeCellRendererComponent(JTree tree, Object value, boolean sel, boolean expanded, boolean leaf, int row, boolean hasFocus) {
    super.getTreeCellRendererComponent(tree, value, sel, expanded, leaf, row, hasFocus);
    if (regularFont == null) {
        regularFont = getFont();
        boldFont = regularFont.deriveFont(Font.BOLD);
    }
    Font font = regularFont;
    Icon icon = null;
    String labelText = null;
    String toolTipPrefix = "";
    String toolTipSuffix = "";
    if (value instanceof BioModelNode) {
        BioModelNode node = (BioModelNode) value;
        if (node.getChildCount() > 0) {
            icon = getIcon();
        }
        Object userObj = node.getUserObject();
        if (userObj instanceof MathModel) {
            font = boldFont;
            icon = VCellIcons.documentIcon;
            labelText = ((MathModel) userObj).getName();
            toolTipPrefix = "MathModel: ";
        } else if (userObj instanceof DocumentEditorTreeFolderNode) {
            // --- 1st level folders
            DocumentEditorTreeFolderNode folder = (DocumentEditorTreeFolderNode) userObj;
            labelText = folder.getName();
            if (folder.isBold()) {
                font = boldFont;
            }
            DocumentEditorTreeFolderClass folderClass = folder.getFolderClass();
            switch(folderClass) {
                case MATH_VCML_NODE:
                    icon = VCellIcons.textNotesIcon;
                    break;
                case MATH_GEOMETRY_NODE:
                    icon = VCellIcons.geometryIcon;
                    break;
                case MATH_SIMULATIONS_NODE:
                    icon = VCellIcons.simulationIcon;
                    break;
                case MATH_OUTPUT_FUNCTIONS_NODE:
                    icon = VCellIcons.getOutputFunctionIcon();
                    break;
            }
        }
    }
    setIcon(icon);
    setFont(font);
    setText(labelText);
    if (toolTipSuffix.length() == 0) {
        toolTipSuffix = labelText;
    }
    setToolTipText(toolTipPrefix + toolTipSuffix);
    return this;
}

Example 24 with MathModel

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

the class MathModelEditorTreeModel method setMathModel.

public void setMathModel(MathModel newValue) {
    if (mathModel == newValue) {
        return;
    }
    MathModel oldValue = this.mathModel;
    mathModel = newValue;
    populateRoot();
    if (oldValue != null) {
        oldValue.removePropertyChangeListener(this);
    }
    if (newValue != null) {
        newValue.addPropertyChangeListener(this);
    }
}

Example 25 with MathModel

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

the class VCMLEditorPanel method setMathModel.

/**
 * Sets the mathModel property (cbit.vcell.mathmodel.MathModel) value.
 * @param mathModel The new value for the property.
 * @see #getMathModel
 */
public void setMathModel(MathModel newValue) {
    if (fieldMathModel == newValue) {
        return;
    }
    MathModel oldValue = fieldMathModel;
    if (oldValue != null) {
        oldValue.removePropertyChangeListener(ivjEventHandler);
        if (oldValue.getGeometry() != null) {
            oldValue.getGeometry().getGeometrySpec().removePropertyChangeListener(ivjEventHandler);
        }
    }
    fieldMathModel = newValue;
    if (newValue != null) {
        newValue.addPropertyChangeListener(ivjEventHandler);
        if (newValue.getGeometry() != null) {
            newValue.getGeometry().getGeometrySpec().addPropertyChangeListener(ivjEventHandler);
        }
        getMathDescEditor().setMathDescription(fieldMathModel.getMathDescription());
    }
}