Examples with VCUnitDefinition cbit.vcell.units.VCUnitDefinition used on opensource projects

Example 61 with VCUnitDefinition

use of cbit.vcell.units.VCUnitDefinition in project vcell by virtualcell.

the class ITextWriter method writeReactionContext.

// ReactionContext - SpeciesContextSpec: ignored boundary conditions.
protected void writeReactionContext(Section simContextSection, SimulationContext simContext) throws DocumentException {
    ReactionContext rc = simContext.getReactionContext();
    if (rc == null) {
        return;
    }
    Section rcSection = null;
    // add reaction specs
    ReactionSpec[] reactionSpecs = rc.getReactionSpecs();
    Table reactionSpecTable = null;
    for (int i = 0; i < reactionSpecs.length; i++) {
        if (i == 0) {
            reactionSpecTable = getTable(4, 100, 1, 3, 3);
            // reactionSpecTable.setTableFitsPage(true);
            reactionSpecTable.addCell(createCell("Reaction Mapping", getBold(DEF_HEADER_FONT_SIZE), 4, 1, Element.ALIGN_CENTER, true));
            reactionSpecTable.addCell(createHeaderCell("Name", getBold(), 1));
            reactionSpecTable.addCell(createHeaderCell("Type", getBold(), 1));
            reactionSpecTable.addCell(createHeaderCell("Enabled (T/F)", getBold(), 1));
            reactionSpecTable.addCell(createHeaderCell("Fast (T/F)", getBold(), 1));
            reactionSpecTable.endHeaders();
        }
        String reactionName = reactionSpecs[i].getReactionStep().getName();
        String reactionType = reactionSpecs[i].getReactionStep().getDisplayType();
        reactionSpecTable.addCell(createCell(reactionName, getFont()));
        reactionSpecTable.addCell(createCell(reactionType, getFont()));
        reactionSpecTable.addCell(createCell((reactionSpecs[i].isExcluded() ? " F " : " T "), getFont()));
        reactionSpecTable.addCell(createCell((reactionSpecs[i].isFast() ? " T " : " F "), getFont()));
    }
    if (reactionSpecTable != null) {
        rcSection = simContextSection.addSection("Reaction Mapping For " + simContext.getName(), simContextSection.numberDepth() + 1);
        rcSection.add(reactionSpecTable);
    }
    // add species context specs
    SpeciesContextSpec[] speciesContSpecs = rc.getSpeciesContextSpecs();
    Table speciesSpecTable = null;
    int[] widths = { 2, 2, 4, 4, 1 };
    for (int i = 0; i < speciesContSpecs.length; i++) {
        if (i == 0) {
            speciesSpecTable = getTable(5, 100, 1, 3, 3);
            speciesSpecTable.addCell(createCell("Initial Conditions", getBold(DEF_HEADER_FONT_SIZE), 5, 1, Element.ALIGN_CENTER, true));
            speciesSpecTable.addCell(createHeaderCell("Species", getBold(), 1));
            speciesSpecTable.addCell(createHeaderCell("Structure", getBold(), 1));
            speciesSpecTable.addCell(createHeaderCell("Initial Conc.", getBold(), 1));
            speciesSpecTable.addCell(createHeaderCell("Diffusion Const.", getBold(), 1));
            speciesSpecTable.addCell(createHeaderCell("Fixed (T/F)", getBold(), 1));
            speciesSpecTable.endHeaders();
        }
        String speciesName = speciesContSpecs[i].getSpeciesContext().getSpecies().getCommonName();
        String structName = speciesContSpecs[i].getSpeciesContext().getStructure().getName();
        String diff = speciesContSpecs[i].getDiffusionParameter().getExpression().infix();
        VCUnitDefinition diffUnit = speciesContSpecs[i].getDiffusionParameter().getUnitDefinition();
        SpeciesContextSpecParameter initParam = speciesContSpecs[i].getInitialConditionParameter();
        String initConc = initParam == null ? "" : initParam.getExpression().infix();
        VCUnitDefinition initConcUnit = initParam == null ? null : initParam.getUnitDefinition();
        speciesSpecTable.addCell(createCell(speciesName, getFont()));
        speciesSpecTable.addCell(createCell(structName, getFont()));
        speciesSpecTable.addCell(createCell(initConc + (initConcUnit == null ? "" : "   " + initConcUnit.getSymbolUnicode()), getFont()));
        speciesSpecTable.addCell(createCell(diff + (diffUnit == null ? "" : "   " + diffUnit.getSymbolUnicode()), getFont()));
        speciesSpecTable.addCell(createCell((speciesContSpecs[i].isConstant() ? " T " : " F "), getFont()));
    }
    if (speciesSpecTable != null) {
        if (rcSection == null) {
            rcSection = simContextSection.addSection("Reaction Mapping For " + simContext.getName(), simContextSection.numberDepth() + 1);
        }
        speciesSpecTable.setWidths(widths);
        rcSection.add(speciesSpecTable);
    }
}

Example 62 with VCUnitDefinition

use of cbit.vcell.units.VCUnitDefinition in project vcell by virtualcell.

the class ITextWriter method writeKineticsParams.

protected void writeKineticsParams(Section reactionSection, ReactionStep rs) throws DocumentException {
    Kinetics.KineticsParameter[] kineticsParameters = rs.getKinetics().getKineticsParameters();
    Table paramTable = null;
    int[] widths = { 1, 4, 3, 2 };
    if (kineticsParameters.length > 0) {
        paramTable = getTable(4, 100, 1, 3, 3);
        paramTable.addCell(createCell("Kinetics Parameters", getBold(DEF_HEADER_FONT_SIZE), 4, 1, Element.ALIGN_CENTER, true));
        paramTable.addCell(createHeaderCell("Name", getBold(), 1));
        paramTable.addCell(createHeaderCell("Expression", getBold(), 1));
        paramTable.addCell(createHeaderCell("Role", getBold(), 1));
        paramTable.addCell(createHeaderCell("Unit", getBold(), 1));
        paramTable.endHeaders();
        for (int k = 0; k < kineticsParameters.length; k++) {
            String name = kineticsParameters[k].getName();
            Expression expression = kineticsParameters[k].getExpression();
            String role = rs.getKinetics().getDefaultParameterDesc(kineticsParameters[k].getRole());
            VCUnitDefinition unit = kineticsParameters[k].getUnitDefinition();
            paramTable.addCell(createCell(name, getFont()));
            paramTable.addCell(createCell((expression == null ? "" : expression.infix()), getFont()));
            paramTable.addCell(createCell(role, getFont()));
            // dimensionless will show as '1'.
            paramTable.addCell(createCell((unit == null ? "" : unit.getSymbolUnicode()), getFont()));
        }
    }
    if (paramTable != null) {
        paramTable.setWidths(widths);
        reactionSection.add(paramTable);
    }
}

Example 63 with VCUnitDefinition

use of cbit.vcell.units.VCUnitDefinition in project vcell by virtualcell.

the class ModelUnitSystem method createDefaultSBMLLevel2Units.

public static ModelUnitSystem createDefaultSBMLLevel2Units() {
    VCUnitSystem tempUnitSystem = new VCUnitSystem() {
    };
    VCUnitDefinition modelSubstanceUnit = tempUnitSystem.getInstance("mol");
    VCUnitDefinition modelVolumeUnit = tempUnitSystem.getInstance("litre");
    VCUnitDefinition modelAreaUnit = tempUnitSystem.getInstance("m2");
    VCUnitDefinition modelLengthUnit = tempUnitSystem.getInstance("m");
    VCUnitDefinition modelTimeUnit = tempUnitSystem.getInstance("s");
    ModelUnitSystem modelUnitSystem = ModelUnitSystem.createUnitSystem(modelSubstanceUnit, modelSubstanceUnit, modelSubstanceUnit, modelVolumeUnit, modelAreaUnit, modelLengthUnit, modelTimeUnit);
    return modelUnitSystem;
}

Example 64 with VCUnitDefinition

use of cbit.vcell.units.VCUnitDefinition in project vcell by virtualcell.

the class InitialConditionsPanel method initialize.

/**
 * Initialize the class.
 */
/* WARNING: THIS METHOD WILL BE REGENERATED. */
private void initialize() {
    try {
        // user code begin {1}
        // user code end
        setName("InitialConditionsPanel");
        setLayout(new BorderLayout());
        add(getRadioButtonAndCheckboxPanel(), BorderLayout.NORTH);
        add(getScrollPaneTable().getEnclosingScrollPane(), BorderLayout.CENTER);
        getScrollPaneTable().getSelectionModel().addListSelectionListener(ivjEventHandler);
        getJMenuItemPaste().addActionListener(ivjEventHandler);
        getJMenuItemCopy().addActionListener(ivjEventHandler);
        getJMenuItemCopyAll().addActionListener(ivjEventHandler);
        getJMenuItemPasteAll().addActionListener(ivjEventHandler);
        getAmountRadioButton().addActionListener(ivjEventHandler);
        getConcentrationRadioButton().addActionListener(ivjEventHandler);
        getRandomizeInitCondnCheckbox().addActionListener(ivjEventHandler);
        DefaultTableCellRenderer renderer = new DefaultScrollTableCellRenderer() {

            public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
                super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
                setIcon(null);
                defaultToolTipText = null;
                if (value instanceof Species) {
                    setText(((Species) value).getCommonName());
                    defaultToolTipText = getText();
                    setToolTipText(defaultToolTipText);
                } else if (value instanceof SpeciesContext) {
                    setText(((SpeciesContext) value).getName());
                    defaultToolTipText = getText();
                    setToolTipText(defaultToolTipText);
                } else if (value instanceof Structure) {
                    setText(((Structure) value).getName());
                    defaultToolTipText = getText();
                    setToolTipText(defaultToolTipText);
                } else if (value instanceof ScopedExpression) {
                    SpeciesContextSpec scSpec = tableModel.getValueAt(row);
                    VCUnitDefinition unit = null;
                    if (table.getColumnName(column).equals(SpeciesContextSpecsTableModel.ColumnType.COLUMN_INITIAL.label)) {
                        SpeciesContextSpecParameter initialConditionParameter = scSpec.getInitialConditionParameter();
                        unit = initialConditionParameter.getUnitDefinition();
                    } else if (table.getColumnName(column).equals(SpeciesContextSpecsTableModel.ColumnType.COLUMN_DIFFUSION.label)) {
                        SpeciesContextSpecParameter diffusionParameter = scSpec.getDiffusionParameter();
                        unit = diffusionParameter.getUnitDefinition();
                    }
                    if (unit != null) {
                        setHorizontalTextPosition(JLabel.LEFT);
                        setIcon(new TextIcon("[" + unit.getSymbolUnicode() + "]", DefaultScrollTableCellRenderer.uneditableForeground));
                    }
                    int rgb = 0x00ffffff & DefaultScrollTableCellRenderer.uneditableForeground.getRGB();
                    defaultToolTipText = "<html>" + StringEscapeUtils.escapeHtml4(getText()) + " <font color=#" + Integer.toHexString(rgb) + "> [" + unit.getSymbolUnicode() + "] </font></html>";
                    setToolTipText(defaultToolTipText);
                    if (unit != null) {
                        setText(defaultToolTipText);
                    }
                }
                TableModel tableModel = table.getModel();
                if (tableModel instanceof SortTableModel) {
                    DefaultScrollTableCellRenderer.issueRenderer(this, defaultToolTipText, table, row, column, (SortTableModel) tableModel);
                    setHorizontalTextPosition(JLabel.TRAILING);
                }
                return this;
            }
        };
        DefaultTableCellRenderer rbmSpeciesShapeDepictionCellRenderer = new DefaultScrollTableCellRenderer() {

            SpeciesPatternSmallShape spss = null;

            @Override
            public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
                super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
                if (table.getModel() instanceof VCellSortTableModel<?>) {
                    Object selectedObject = null;
                    if (table.getModel() == tableModel) {
                        selectedObject = tableModel.getValueAt(row);
                    }
                    if (selectedObject != null) {
                        if (selectedObject instanceof SpeciesContextSpec) {
                            SpeciesContextSpec scs = (SpeciesContextSpec) selectedObject;
                            SpeciesContext sc = scs.getSpeciesContext();
                            // sp may be null for "plain" species contexts
                            SpeciesPattern sp = sc.getSpeciesPattern();
                            Graphics panelContext = table.getGraphics();
                            spss = new SpeciesPatternSmallShape(4, 2, sp, shapeManager, panelContext, sc, isSelected, issueManager);
                        }
                    } else {
                        spss = null;
                    }
                }
                setText("");
                return this;
            }

            @Override
            public void paintComponent(Graphics g) {
                super.paintComponent(g);
                if (spss != null) {
                    spss.paintSelf(g);
                }
            }
        };
        getScrollPaneTable().setDefaultRenderer(SpeciesContext.class, renderer);
        getScrollPaneTable().setDefaultRenderer(Structure.class, renderer);
        getScrollPaneTable().setDefaultRenderer(SpeciesPattern.class, rbmSpeciesShapeDepictionCellRenderer);
        getScrollPaneTable().setDefaultRenderer(Species.class, renderer);
        getScrollPaneTable().setDefaultRenderer(ScopedExpression.class, renderer);
        getScrollPaneTable().setDefaultRenderer(Boolean.class, new ScrollTableBooleanCellRenderer());
    } catch (java.lang.Throwable ivjExc) {
        handleException(ivjExc);
    }
}

Example 65 with VCUnitDefinition

use of cbit.vcell.units.VCUnitDefinition in project vcell by virtualcell.

the class StructureMappingTableModel method setValueAt.

public void setValueAt(Object aValue, int rowIndex, int columnIndex) {
    if (rowIndex < 0 || rowIndex >= getRowCount()) {
        throw new RuntimeException("StructureMappingTableModel.setValueAt(), row = " + rowIndex + " out of range [" + 0 + "," + (getRowCount() - 1) + "]");
    }
    if (columnIndex < 0 || columnIndex >= getColumnCount()) {
        throw new RuntimeException("StructureMappingTableModel.setValueAt(), column = " + columnIndex + " out of range [" + 0 + "," + (getColumnCount() - 1) + "]");
    }
    StructureMapping structureMapping = getValueAt(rowIndex);
    Structure structure = structureMapping.getStructure();
    if (bNonSpatial) {
        switch(columnIndex) {
            case NONSPATIAL_COLUMN_SIZE:
                {
                    try {
                        Expression exp = null;
                        if (aValue instanceof String) {
                            exp = new Expression((String) aValue);
                        } else if (aValue instanceof Double) {
                            exp = new Expression(((Double) aValue).doubleValue());
                        }
                        // if the input volumn is null, leave it as it was.
                        if (exp != null) {
                            // for old ode model, once one size is input, solve the rest.                                                                                                          if it is unnamed compartment(the only one), we don't need to solve anything
                            if (!getGeometryContext().getSimulationContext().isStoch() && getGeometryContext().isAllSizeSpecifiedNull() && getGeometryContext().isAllVolFracAndSurfVolSpecified() && getGeometryContext().getStructureMappings().length > 1) {
                                structureMapping.getSizeParameter().setExpression(exp);
                                double size;
                                try {
                                    size = exp.evaluateConstant();
                                    VCUnitDefinition volumeUnit = getGeometryContext().getSimulationContext().getModel().getUnitSystem().getVolumeUnit();
                                    StructureSizeSolver.updateAbsoluteStructureSizes(getGeometryContext().getSimulationContext(), structure, size, volumeUnit);
                                    fireTableRowsUpdated(0, getRowCount());
                                } catch (ExpressionException ex) {
                                    ex.printStackTrace(System.out);
                                    PopupGenerator.showErrorDialog(ownerTable, "Size of Feature " + structure.getName() + " can not be solved as constant!");
                                } catch (Exception ex) {
                                    ex.printStackTrace(System.out);
                                    PopupGenerator.showErrorDialog(ownerTable, ex.getMessage());
                                }
                            } else {
                                structureMapping.getSizeParameter().setExpression(exp);
                                // set fraction in stoch math description, because these might be used when copy from stoch app to ode app.
                                if (getGeometryContext().isAllSizeSpecifiedPositive()) /*&& !getGeometryContext().getSimulationContext().isStoch()*/
                                {
                                    try {
                                        StructureSizeSolver.updateRelativeStructureSizes(getGeometryContext().getSimulationContext());
                                    } catch (Exception ex) {
                                        ex.printStackTrace(System.out);
                                        PopupGenerator.showErrorDialog(ownerTable, ex.getMessage());
                                    }
                                }
                            }
                        }
                    } catch (ExpressionException e) {
                        e.printStackTrace(System.out);
                        PopupGenerator.showErrorDialog(ownerTable, "expression error\n" + e.getMessage());
                    }
                    break;
                }
        }
    } else {
        switch(columnIndex) {
            case SPATIAL_COLUMN_SUBDOMAIN:
                {
                    GeometryClass geometryClass = null;
                    if (aValue instanceof String) {
                        String svname = (String) aValue;
                        geometryClass = getGeometryContext().getGeometry().getGeometryClass(svname);
                    } else if (aValue instanceof GeometryClass) {
                        geometryClass = (GeometryClass) aValue;
                    }
                    if (geometryClass != null) {
                        try {
                            getGeometryContext().assignStructure(structure, geometryClass);
                        } catch (PropertyVetoException e) {
                            e.printStackTrace(System.out);
                            PopupGenerator.showErrorDialog(ownerTable, e.getMessage());
                        } catch (IllegalMappingException e) {
                            e.printStackTrace(System.out);
                            PopupGenerator.showErrorDialog(ownerTable, e.getMessage());
                        } catch (MappingException e) {
                            e.printStackTrace(System.out);
                            PopupGenerator.showErrorDialog(ownerTable, e.getMessage());
                        }
                    }
                    break;
                }
            case SPATIAL_COLUMN_SIZERATIO:
                try {
                    Expression exp = null;
                    if (aValue instanceof String) {
                        exp = new Expression((String) aValue);
                    } else if (aValue instanceof Double) {
                        exp = new Expression(((Double) aValue).doubleValue());
                    }
                    if (exp != null) {
                        structureMapping.getUnitSizeParameter().setExpression(exp);
                        StructureSizeSolver.updateUnitStructureSizes(getGeometryContext().getSimulationContext(), structureMapping.getGeometryClass());
                    }
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "expression error\n" + e.getMessage());
                }
                break;
            case SPATIAL_COLUMN_X_MINUS:
                {
                    if (aValue != null) {
                        structureMapping.setBoundaryConditionTypeXm(new BoundaryConditionType((String) aValue));
                    }
                    break;
                }
            case SPATIAL_COLUMN_X_PLUS:
                {
                    if (aValue != null) {
                        structureMapping.setBoundaryConditionTypeXp(new BoundaryConditionType((String) aValue));
                    }
                    break;
                }
            case SPATIAL_COLUMN_Y_MINUS:
                {
                    if (aValue != null) {
                        structureMapping.setBoundaryConditionTypeYm(new BoundaryConditionType((String) aValue));
                    }
                    break;
                }
            case SPATIAL_COLUMN_Y_PLUS:
                {
                    if (aValue != null) {
                        structureMapping.setBoundaryConditionTypeYp(new BoundaryConditionType((String) aValue));
                    }
                    break;
                }
            case SPATIAL_COLUMN_Z_MINUS:
                {
                    if (aValue != null) {
                        structureMapping.setBoundaryConditionTypeZm(new BoundaryConditionType((String) aValue));
                    }
                    break;
                }
            case SPATIAL_COLUMN_Z_PLUS:
                {
                    if (aValue != null) {
                        structureMapping.setBoundaryConditionTypeZp(new BoundaryConditionType((String) aValue));
                    }
                    break;
                }
        }
    }
}