Examples with BoundaryConditionType cbit.vcell.math.BoundaryConditionType used on opensource projects

Example 6 with BoundaryConditionType

use of cbit.vcell.math.BoundaryConditionType 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;
                }
        }
    }
}

Example 7 with BoundaryConditionType

use of cbit.vcell.math.BoundaryConditionType in project vcell by virtualcell.

the class StructureMappingTableRenderer method getTableCellRendererComponent.

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);
    if (table.getModel() instanceof StructureMappingTableModel) {
        StructureMappingTableModel structureMappingTableModel = (StructureMappingTableModel) table.getModel();
        String toolTip = structureMappingTableModel.getToolTip(row, column);
        if (value instanceof Structure) {
            Structure structure = (Structure) value;
            setText(structure.getName());
        } else if (value instanceof Double && structureMappingTableModel.isNewSizeColumn(column)) {
            StructureMapping structureMapping = structureMappingTableModel.getStructureMapping(row);
            if (structureMappingTableModel.isNonSpatial()) {
                VCUnitDefinition unitDefinition = structureMapping.getStructure().getStructureSize().getUnitDefinition();
                TextIcon sizeIcon = unitIconHash.get(unitDefinition.getSymbol());
                if (sizeIcon == null) {
                    sizeIcon = new TextIcon("[ " + unitDefinition.getSymbolUnicode() + " ]");
                    unitIconHash.put(unitDefinition.getSymbol(), sizeIcon);
                }
                setIcon(sizeIcon);
            } else {
                // spatial
                if (structureMapping.getUnitSizeParameter() != null) {
                    VCUnitDefinition unitDefinition = structureMapping.getUnitSizeParameter().getUnitDefinition();
                    TextIcon sizeIcon = unitIconHash.get(unitDefinition.getSymbol());
                    if (sizeIcon == null) {
                        sizeIcon = new TextIcon("[ " + unitDefinition.getSymbolUnicode() + " ]");
                        unitIconHash.put(unitDefinition.getSymbol(), sizeIcon);
                    }
                    setIcon(sizeIcon);
                }
            }
        }
        if (structureMappingTableModel.isSubdomainColumn(column)) {
            // can be null
            if (value == null) {
                setText("Unmapped");
                setForeground(Color.red);
                setIcon(null);
            } else {
                if (value instanceof GeometryClass) {
                    setText(((GeometryClass) value).getName());
                    if (value instanceof SubVolume) {
                        SubVolume subVolume = (SubVolume) value;
                        java.awt.Color handleColor = new java.awt.Color(colormap[subVolume.getHandle()]);
                        // small square icon with subdomain color
                        Icon icon = new ColorIcon(10, 10, handleColor, true);
                        setHorizontalTextPosition(SwingConstants.RIGHT);
                        setIcon(icon);
                    } else if (value instanceof SurfaceClass) {
                        SurfaceClass sc = (SurfaceClass) value;
                        Set<SubVolume> sv = sc.getAdjacentSubvolumes();
                        Iterator<SubVolume> iterator = sv.iterator();
                        SubVolume sv1 = iterator.next();
                        SubVolume sv2 = iterator.next();
                        java.awt.Color c1 = new java.awt.Color(colormap[sv2.getHandle()]);
                        java.awt.Color c2 = new java.awt.Color(colormap[sv1.getHandle()]);
                        Icon icon = new ColorIconEx(10, 10, c1, c2);
                        setIcon(icon);
                        setHorizontalTextPosition(SwingConstants.RIGHT);
                    }
                } else {
                    setText(value.toString());
                    setIcon(null);
                }
            }
        }
        if (value instanceof BoundaryConditionType) {
            // we get here only for spatial
            Object candidate = structureMappingTableModel.getValueAt(row, StructureMappingTableModel.SPATIAL_COLUMN_SUBDOMAIN);
            if (candidate instanceof SurfaceClass) {
                SurfaceClass surfaceClass = (SurfaceClass) candidate;
                cbit.vcell.model.Model model = structureMappingTableModel.getGeometryContext().getModel();
                SimulationContext simContext = structureMappingTableModel.getGeometryContext().getSimulationContext();
                Pair<SubVolume, SubVolume> ret = DiffEquMathMapping.computeBoundaryConditionSource(model, simContext, surfaceClass);
                SubVolume innerSubVolume = ret.one;
                java.awt.Color handleColor = new java.awt.Color(colormap[innerSubVolume.getHandle()]);
                // small square icon with subdomain color
                Icon icon = new ColorIcon(8, 8, handleColor, true);
                setHorizontalTextPosition(SwingConstants.LEFT);
                setIcon(icon);
                setText("from");
                // override default tooltip
                toolTip = "Boundary condition inherited from Subdomain '" + innerSubVolume.getName() + "'";
                setToolTipText(toolTip);
            } else {
                setText(((BoundaryConditionType) value).boundaryTypeStringValue());
            }
        }
        List<Issue> issueList = structureMappingTableModel.getIssues(row, column, Issue.SEVERITY_ERROR);
        if (issueList.size() > 0) {
            // override default tooltip
            setToolTipText(Issue.getHtmlIssueMessage(issueList));
            if (column == 0) {
                setBorder(new MatteBorder(1, 1, 1, 0, Color.red));
            } else if (column == table.getColumnCount() - 1) {
                setBorder(new MatteBorder(1, 0, 1, 1, Color.red));
            } else {
                setBorder(new MatteBorder(1, 0, 1, 0, Color.red));
            }
        } else {
            setToolTipText(toolTip);
            setBorder(DEFAULT_GAP);
        }
    }
    return this;
}

Example 8 with BoundaryConditionType

use of cbit.vcell.math.BoundaryConditionType in project vcell by virtualcell.

the class StructureMapping method setBoundaryConditionTypeZm.

/**
 * This method was created by a SmartGuide.
 * @param bct java.lang.String
 * @exception java.lang.Exception The exception description.
 */
public void setBoundaryConditionTypeZm(BoundaryConditionType bc) {
    BoundaryConditionType oldBCType = getBoundaryConditionTypeZm();
    setBoundaryCondition(BoundaryLocation.getZM(), bc);
    BoundaryConditionType newBCType = getBoundaryConditionTypeZm();
    firePropertyChange("boundaryConditionTypeZm", oldBCType, newBCType);
}

Example 9 with BoundaryConditionType

use of cbit.vcell.math.BoundaryConditionType in project vcell by virtualcell.

the class StructureMapping method setBoundaryConditionTypeXp.

/**
 * This method was created by a SmartGuide.
 * @param bct java.lang.String
 * @exception java.lang.Exception The exception description.
 */
public void setBoundaryConditionTypeXp(BoundaryConditionType bc) {
    BoundaryConditionType oldBCType = getBoundaryConditionTypeXp();
    setBoundaryCondition(BoundaryLocation.getXP(), bc);
    BoundaryConditionType newBCType = getBoundaryConditionTypeXp();
    firePropertyChange("boundaryConditionTypeXp", oldBCType, newBCType);
}

Example 10 with BoundaryConditionType

use of cbit.vcell.math.BoundaryConditionType in project vcell by virtualcell.

the class StructureMapping method setBoundaryConditionTypeYm.

/**
 * This method was created by a SmartGuide.
 * @param bct java.lang.String
 * @exception java.lang.Exception The exception description.
 */
public void setBoundaryConditionTypeYm(BoundaryConditionType bc) {
    BoundaryConditionType oldBCType = getBoundaryConditionTypeYm();
    setBoundaryCondition(BoundaryLocation.getYM(), bc);
    BoundaryConditionType newBCType = getBoundaryConditionTypeYm();
    firePropertyChange("boundaryConditionTypeYm", oldBCType, newBCType);
}