use of cbit.vcell.mapping.spatial.processes.PointKinematics in project vcell by virtualcell.
the class DefaultScrollTableCellRenderer method getTableCellRendererComponent.
/**
* Insert the method's description here.
* Creation date: (3/27/2001 1:07:02 PM)
* @return java.awt.Component
* @param table javax.swing.JTable
* @param value java.lang.Object
* @param isSelected boolean
* @param hasFocus boolean
* @param row int
* @param column int
*/
public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
defaultToolTipText = null;
super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
defaultToolTipText = getToolTipText();
setBorder(DEFAULT_GAP);
if (isSelected) {
setBackground(table.getSelectionBackground());
setForeground(table.getSelectionForeground());
} else {
if (table instanceof ScrollTable && ((ScrollTable) table).getHoverRow() == row) {
setBackground(hoverColor);
} else {
setBackground(row % 2 == 0 ? table.getBackground() : everyOtherRowColor);
}
if (table.getModel() instanceof SpatialProcessTableModel) /* && column == SpatialProcessTableModel.COLUMN_SpatialProcess_SPATIALOBJECTS */
{
boolean found = isMatchWithSelectedObject(table, row);
if (found == true) {
setBackground(Color.yellow);
}
} else if (table.getModel() instanceof SpatialObjectTableModel) /* && column == SpatialObjectTableModel.COLUMN_SpatialObject_NAME */
{
boolean found = isMatchWithSelectedProcess(table, row);
if (found == true) {
setBackground(Color.yellow);
}
}
setForeground(table.getForeground());
}
TableModel tableModel = table.getModel();
if (bEnableUneditableForeground && (!table.isEnabled() || !tableModel.isCellEditable(row, column))) {
if (!isSelected) {
setForeground(uneditableForeground);
}
}
if (value instanceof Double) {
Double doubleValue = (Double) value;
setText(nicelyFormattedDouble(doubleValue));
} else if (value instanceof JComponent) {
JComponent jc = (JComponent) value;
if (hasFocus) {
jc.setBorder(focusHighlightBorder);
} else {
jc.setBorder(noFocusBorder);
}
return jc;
}
if (BioModelEditorRightSideTableModel.ADD_NEW_HERE_TEXT.equals(value)) {
setText(BioModelEditorRightSideTableModel.ADD_NEW_HERE_HTML);
} else if (value instanceof ModelProcessEquation && BioModelEditorRightSideTableModel.ADD_NEW_HERE_REACTION_TEXT.equals(((ModelProcessEquation) value).toString())) {
setText(BioModelEditorRightSideTableModel.ADD_NEW_REACTION_OR_RULE_HTML);
}
if (tableModel instanceof BioModelEditorApplicationsTableModel) {
// for the applications table we show the icons with the app type
Icon icon = null;
String toolTipSuffix = "";
BioModelEditorApplicationsTableModel bmeatm = (BioModelEditorApplicationsTableModel) tableModel;
SimulationContext simContext = (SimulationContext) (bmeatm.getValueAt(row));
if (simContext.isRuleBased()) {
if (simContext.getGeometry().getDimension() == 0) {
icon = VCellIcons.appRbmNonspIcon;
toolTipSuffix = "Rule Based / Non spatial";
}
} else if (simContext.isStoch()) {
if (simContext.getGeometry().getDimension() == 0) {
icon = VCellIcons.appStoNonspIcon;
toolTipSuffix = "Stochastic / Non spatial";
} else {
icon = VCellIcons.appStoSpatialIcon;
toolTipSuffix = "Stochastic / Spatial";
}
} else {
// deterministic
if (simContext.getGeometry().getDimension() == 0) {
icon = VCellIcons.appDetNonspIcon;
toolTipSuffix = "Deterministic / Non spatial";
} else {
icon = VCellIcons.appDetSpatialIcon;
toolTipSuffix = "Deterministic / Spatial";
}
}
String toolTipPrefix = "Application: ";
setToolTipText(toolTipPrefix + toolTipSuffix);
if (column == 0) {
setIcon(icon);
} else {
setIcon(null);
}
} else if (column == 2 && tableModel instanceof SpatialProcessTableModel) {
Icon icon = null;
SpatialProcess spatialProcess = (SpatialProcess) (((SpatialProcessTableModel) tableModel).getValueAt(row));
if (spatialProcess instanceof PointLocation) {
icon = VCellIcons.spatialPointIcon;
} else if (spatialProcess instanceof PointKinematics) {
icon = VCellIcons.spatialPointIcon;
} else if (spatialProcess instanceof SurfaceKinematics) {
icon = VCellIcons.spatialMembraneIcon;
} else {
icon = VCellIcons.spatialVolumeIcon;
}
setIcon(icon);
} else if (tableModel instanceof SortTableModel) {
// for most other tables we reserve the icon spot to display issues
DefaultScrollTableCellRenderer.issueRenderer(this, defaultToolTipText, table, row, column, (SortTableModel) tableModel);
}
return this;
}
use of cbit.vcell.mapping.spatial.processes.PointKinematics in project vcell by virtualcell.
the class DiffEquMathMapping method addSpatialProcesses.
private void addSpatialProcesses(VariableHash varHash, ArrayList<CompartmentSubdomainContext> compartmentSubdomainContexts, ArrayList<MembraneSubdomainContext> membraneSubdomainContexts) throws MathException, MappingException, ExpressionException {
if (simContext.getGeometry().getDimension() == 0) {
return;
}
//
for (SpatialObject spatialObject : simContext.getSpatialObjects()) {
if (spatialObject instanceof PointObject) {
PointObject pointObject = (PointObject) spatialObject;
//
// if true, have to solve for this category
//
boolean bPosition = pointObject.isQuantityCategoryEnabled(QuantityCategory.PointPosition);
boolean bVelocity = pointObject.isQuantityCategoryEnabled(QuantityCategory.PointVelocity);
boolean bDirection = pointObject.isQuantityCategoryEnabled(QuantityCategory.DirectionToPoint);
boolean bDistance = pointObject.isQuantityCategoryEnabled(QuantityCategory.PointDistanceMap);
//
// either make a point subdomain, or just define functions.
//
ArrayList<PointLocation> pointLocationProcesses = new ArrayList<PointLocation>();
ArrayList<PointKinematics> pointKinematicsProcesses = new ArrayList<PointKinematics>();
for (SpatialProcess spatialProcess : simContext.getSpatialProcesses()) {
if (spatialProcess instanceof PointLocation && ((PointLocation) spatialProcess).getPointObject() == pointObject) {
pointLocationProcesses.add((PointLocation) spatialProcess);
}
if (spatialProcess instanceof PointKinematics && ((PointKinematics) spatialProcess).getPointObject() == pointObject) {
pointKinematicsProcesses.add((PointKinematics) spatialProcess);
}
}
if (pointLocationProcesses.size() == 1 && pointKinematicsProcesses.size() == 0 && !bVelocity) {
GeometryClass gc = null;
PointLocation pointLocation = pointLocationProcesses.get(0);
if (bPosition) {
if (simContext.getGeometry().getDimension() == 1) {
SpatialQuantity posXQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.X);
LocalParameter posXParam = pointLocation.getParameter(SpatialProcessParameterType.PointPositionX);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(posXParam, gc), getIdentifierSubstitutions(posXParam.getExpression(), posXParam.getUnitDefinition(), gc), gc));
Expression posXExp = new Expression(posXParam, pointLocation.getNameScope());
Expression xExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.X), simContext.getModel().getNameScope());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(posXQuantity, gc), getIdentifierSubstitutions(posXExp, posXQuantity.getUnitDefinition(), gc), gc));
Expression posX_minus_X = Expression.add(posXExp, Expression.negate(xExp));
Expression signum_posX_minus_X = Expression.function(FunctionType.MIN, new Expression(1.0), Expression.function(FunctionType.MAX, Expression.mult(new Expression(1e10), posX_minus_X), new Expression(-1)));
if (bDirection) {
SpatialQuantity dirXQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.X);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirXQuantity, gc), getIdentifierSubstitutions(signum_posX_minus_X, dirXQuantity.getUnitDefinition(), gc), gc));
}
if (bDistance) {
Expression abs_X_minux_posX = Expression.function(FunctionType.ABS, posX_minus_X);
SpatialQuantity distanceQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointDistanceMap, QuantityComponent.Scalar);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(distanceQuantity, gc), getIdentifierSubstitutions(abs_X_minux_posX, distanceQuantity.getUnitDefinition(), gc), gc));
}
}
if (simContext.getGeometry().getDimension() == 2) {
SpatialQuantity posXQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.X);
LocalParameter posXParam = pointLocation.getParameter(SpatialProcessParameterType.PointPositionX);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(posXParam, gc), getIdentifierSubstitutions(posXParam.getExpression(), posXParam.getUnitDefinition(), gc), gc));
Expression posXExp = new Expression(posXParam, pointLocation.getNameScope());
Expression xExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.X), simContext.getModel().getNameScope());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(posXQuantity, gc), getIdentifierSubstitutions(new Expression(posXParam, pointLocation.getNameScope()), posXQuantity.getUnitDefinition(), gc), gc));
SpatialQuantity posYQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.Y);
LocalParameter posYParam = pointLocation.getParameter(SpatialProcessParameterType.PointPositionY);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(posYParam, gc), getIdentifierSubstitutions(posYParam.getExpression(), posYParam.getUnitDefinition(), gc), gc));
Expression posYExp = new Expression(posYParam, pointLocation.getNameScope());
Expression yExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.Y), simContext.getModel().getNameScope());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(posYQuantity, gc), getIdentifierSubstitutions(new Expression(posYParam, pointLocation.getNameScope()), posYQuantity.getUnitDefinition(), gc), gc));
Expression posX_minux_X = Expression.add(posXExp, Expression.negate(xExp));
Expression posY_minux_Y = Expression.add(posYExp, Expression.negate(yExp));
Expression DX2 = Expression.mult(posX_minux_X, posX_minux_X);
Expression DY2 = Expression.mult(posY_minux_Y, posY_minux_Y);
Expression sqrt_DX2_DY2 = Expression.function(FunctionType.SQRT, Expression.add(DX2, DY2));
Expression dirX = Expression.div(posX_minux_X, Expression.add(sqrt_DX2_DY2, new Expression(1e-8)));
Expression dirY = Expression.div(posY_minux_Y, Expression.add(sqrt_DX2_DY2, new Expression(1e-8)));
if (bDirection) {
SpatialQuantity dirXQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.X);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirXQuantity, gc), getIdentifierSubstitutions(dirX, dirXQuantity.getUnitDefinition(), gc), gc));
SpatialQuantity dirYQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.Y);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirYQuantity, gc), getIdentifierSubstitutions(dirY, dirYQuantity.getUnitDefinition(), gc), gc));
}
if (bDistance) {
SpatialQuantity distanceQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointDistanceMap, QuantityComponent.Scalar);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(distanceQuantity, gc), getIdentifierSubstitutions(sqrt_DX2_DY2, distanceQuantity.getUnitDefinition(), gc), gc));
}
}
if (simContext.getGeometry().getDimension() == 3) {
SpatialQuantity posXQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.X);
LocalParameter posXParam = pointLocation.getParameter(SpatialProcessParameterType.PointPositionX);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(posXParam, gc), getIdentifierSubstitutions(posXParam.getExpression(), posXParam.getUnitDefinition(), gc), gc));
Expression posXExp = new Expression(posXParam, pointLocation.getNameScope());
Expression xExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.X), simContext.getModel().getNameScope());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(posXQuantity, gc), getIdentifierSubstitutions(new Expression(posXParam, pointLocation.getNameScope()), posXQuantity.getUnitDefinition(), gc), gc));
SpatialQuantity posYQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.Y);
LocalParameter posYParam = pointLocation.getParameter(SpatialProcessParameterType.PointPositionY);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(posYParam, gc), getIdentifierSubstitutions(posYParam.getExpression(), posYParam.getUnitDefinition(), gc), gc));
Expression posYExp = new Expression(posYParam, pointLocation.getNameScope());
Expression yExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.Y), simContext.getModel().getNameScope());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(posYQuantity, gc), getIdentifierSubstitutions(new Expression(posYParam, pointLocation.getNameScope()), posYQuantity.getUnitDefinition(), gc), gc));
SpatialQuantity posZQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.Z);
LocalParameter posZParam = pointLocation.getParameter(SpatialProcessParameterType.PointPositionZ);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(posZParam, gc), getIdentifierSubstitutions(posZParam.getExpression(), posZParam.getUnitDefinition(), gc), gc));
Expression posZExp = new Expression(posZParam, pointLocation.getNameScope());
Expression zExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.Z), simContext.getModel().getNameScope());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(posZQuantity, gc), getIdentifierSubstitutions(new Expression(posZParam, pointLocation.getNameScope()), posZQuantity.getUnitDefinition(), gc), gc));
Expression posX_minux_X = Expression.add(posXExp, Expression.negate(xExp));
Expression posY_minux_Y = Expression.add(posYExp, Expression.negate(yExp));
Expression posZ_minux_Z = Expression.add(posZExp, Expression.negate(zExp));
Expression DX2 = Expression.mult(posX_minux_X, posX_minux_X);
Expression DY2 = Expression.mult(posY_minux_Y, posY_minux_Y);
Expression DZ2 = Expression.mult(posZ_minux_Z, posZ_minux_Z);
Expression sqrt_DX2_DY2_DZ2 = Expression.function(FunctionType.SQRT, Expression.add(DX2, DY2, DZ2));
Expression dirX = Expression.div(posX_minux_X, Expression.add(sqrt_DX2_DY2_DZ2, new Expression(1e-8)));
Expression dirY = Expression.div(posY_minux_Y, Expression.add(sqrt_DX2_DY2_DZ2, new Expression(1e-8)));
Expression dirZ = Expression.div(posZ_minux_Z, Expression.add(sqrt_DX2_DY2_DZ2, new Expression(1e-8)));
if (bDirection) {
SpatialQuantity dirXQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.X);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirXQuantity, gc), getIdentifierSubstitutions(dirX, dirXQuantity.getUnitDefinition(), gc), gc));
SpatialQuantity dirYQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.Y);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirYQuantity, gc), getIdentifierSubstitutions(dirY, dirYQuantity.getUnitDefinition(), gc), gc));
SpatialQuantity dirZQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.Z);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirZQuantity, gc), getIdentifierSubstitutions(dirZ, dirZQuantity.getUnitDefinition(), gc), gc));
}
if (bDistance) {
SpatialQuantity distanceQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointDistanceMap, QuantityComponent.Scalar);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(distanceQuantity, gc), getIdentifierSubstitutions(sqrt_DX2_DY2_DZ2, distanceQuantity.getUnitDefinition(), gc), gc));
}
}
} else {
throw new MappingException("PointLocation process defined for pointObject '" + pointObject.getName() + "' but Position not enabled");
}
} else if (pointLocationProcesses.size() == 0 && pointKinematicsProcesses.size() == 1) {
GeometryClass gc = null;
PointKinematics pointKinematics = pointKinematicsProcesses.get(0);
if (bPosition && bVelocity) {
LocalParameter velXParam = pointKinematics.getParameter(SpatialProcessParameterType.PointVelocityX);
LocalParameter iniPosXParam = pointKinematics.getParameter(SpatialProcessParameterType.PointInitialPositionX);
SpatialQuantity posXQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.X);
SpatialQuantity velXQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointVelocity, QuantityComponent.X);
Expression posXExp = new Expression(posXQuantity, simContext.getNameScope());
Expression xExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.X), simContext.getModel().getNameScope());
Expression posX_minux_X = Expression.add(posXExp, Expression.negate(xExp));
LocalParameter velYParam = pointKinematics.getParameter(SpatialProcessParameterType.PointVelocityY);
LocalParameter iniPosYParam = pointKinematics.getParameter(SpatialProcessParameterType.PointInitialPositionY);
SpatialQuantity posYQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.Y);
SpatialQuantity velYQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointVelocity, QuantityComponent.Y);
Expression posYExp = new Expression(posYQuantity, simContext.getNameScope());
Expression yExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.Y), simContext.getModel().getNameScope());
Expression posY_minux_Y = Expression.add(posYExp, Expression.negate(yExp));
LocalParameter velZParam = pointKinematics.getParameter(SpatialProcessParameterType.PointVelocityZ);
LocalParameter iniPosZParam = pointKinematics.getParameter(SpatialProcessParameterType.PointInitialPositionZ);
SpatialQuantity posZQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.Z);
SpatialQuantity velZQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointVelocity, QuantityComponent.Z);
Expression posZExp = new Expression(posZQuantity, simContext.getNameScope());
Expression zExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.Z), simContext.getModel().getNameScope());
Expression posZ_minux_Z = Expression.add(posZExp, Expression.negate(zExp));
String pointSubdomainName = pointObject.getName();
Domain domain = new Domain(pointSubdomainName);
PointSubDomain pointSubdomain = new PointSubDomain(pointSubdomainName);
mathDesc.addSubDomain(pointSubdomain);
if (simContext.getGeometry().getDimension() >= 1) {
PointVariable posXVar = new PointVariable(getMathSymbol(posXQuantity, gc), domain);
varHash.addVariable(posXVar);
Expression initXExp = getIdentifierSubstitutions(new Expression(iniPosXParam, pointKinematics.getNameScope()), iniPosXParam.getUnitDefinition(), gc);
Expression rateXExp = getIdentifierSubstitutions(new Expression(velXParam, pointKinematics.getNameScope()), velXParam.getUnitDefinition(), gc);
OdeEquation odeX = new OdeEquation(posXVar, initXExp, rateXExp);
pointSubdomain.addEquation(odeX);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(iniPosXParam, gc), getIdentifierSubstitutions(new Expression(iniPosXParam.getExpression()), iniPosXParam.getUnitDefinition(), gc), gc));
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velXParam, gc), getIdentifierSubstitutions(new Expression(velXParam.getExpression()), velXParam.getUnitDefinition(), gc), gc));
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velXQuantity, gc), getIdentifierSubstitutions(new Expression(velXParam, pointKinematics.getNameScope()), velXQuantity.getUnitDefinition(), gc), gc));
pointSubdomain.setPositionX(getIdentifierSubstitutions(new Expression(posXQuantity, simContext.getNameScope()), posXQuantity.getUnitDefinition(), gc));
}
if (simContext.getGeometry().getDimension() >= 2) {
PointVariable posYVar = new PointVariable(getMathSymbol(posYQuantity, gc), domain);
varHash.addVariable(posYVar);
Expression initYExp = getIdentifierSubstitutions(new Expression(iniPosYParam, pointKinematics.getNameScope()), iniPosYParam.getUnitDefinition(), gc);
Expression rateYExp = getIdentifierSubstitutions(new Expression(velYParam, pointKinematics.getNameScope()), velYParam.getUnitDefinition(), gc);
OdeEquation odeY = new OdeEquation(posYVar, initYExp, rateYExp);
pointSubdomain.addEquation(odeY);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(iniPosYParam, gc), getIdentifierSubstitutions(new Expression(iniPosYParam.getExpression()), iniPosYParam.getUnitDefinition(), gc), gc));
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velYParam, gc), getIdentifierSubstitutions(new Expression(velYParam.getExpression()), velYParam.getUnitDefinition(), gc), gc));
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velYQuantity, gc), getIdentifierSubstitutions(new Expression(velYParam, pointKinematics.getNameScope()), velYQuantity.getUnitDefinition(), gc), gc));
pointSubdomain.setPositionY(getIdentifierSubstitutions(new Expression(posYQuantity, simContext.getNameScope()), posYQuantity.getUnitDefinition(), gc));
}
if (simContext.getGeometry().getDimension() == 3) {
PointVariable posZVar = new PointVariable(getMathSymbol(posZQuantity, gc), domain);
varHash.addVariable(posZVar);
Expression initZExp = getIdentifierSubstitutions(new Expression(iniPosZParam, pointKinematics.getNameScope()), iniPosZParam.getUnitDefinition(), gc);
Expression rateZExp = getIdentifierSubstitutions(new Expression(velZParam, pointKinematics.getNameScope()), velZParam.getUnitDefinition(), gc);
OdeEquation odeZ = new OdeEquation(posZVar, initZExp, rateZExp);
pointSubdomain.addEquation(odeZ);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(iniPosZParam, gc), getIdentifierSubstitutions(new Expression(iniPosZParam.getExpression()), iniPosZParam.getUnitDefinition(), gc), gc));
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velZParam, gc), getIdentifierSubstitutions(new Expression(velZParam.getExpression()), velZParam.getUnitDefinition(), gc), gc));
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velZQuantity, gc), getIdentifierSubstitutions(new Expression(velZParam, pointKinematics.getNameScope()), velZQuantity.getUnitDefinition(), gc), gc));
pointSubdomain.setPositionZ(getIdentifierSubstitutions(new Expression(posZQuantity, simContext.getNameScope()), posZQuantity.getUnitDefinition(), gc));
}
if (simContext.getGeometry().getDimension() == 1) {
Expression signum_posX_minus_X = Expression.function(FunctionType.MIN, new Expression(1.0), Expression.function(FunctionType.MAX, Expression.mult(new Expression(1e10), posX_minux_X), new Expression(-1)));
if (bDirection) {
SpatialQuantity dirXQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.X);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirXQuantity, gc), getIdentifierSubstitutions(signum_posX_minus_X, dirXQuantity.getUnitDefinition(), gc), gc));
}
if (bDistance) {
Expression abs_X_minux_posX = Expression.function(FunctionType.ABS, posX_minux_X);
SpatialQuantity distanceQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointDistanceMap, QuantityComponent.Scalar);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(distanceQuantity, gc), getIdentifierSubstitutions(abs_X_minux_posX, distanceQuantity.getUnitDefinition(), gc), gc));
}
}
if (simContext.getGeometry().getDimension() == 2) {
Expression DX2 = Expression.mult(posX_minux_X, posX_minux_X);
Expression DY2 = Expression.mult(posY_minux_Y, posY_minux_Y);
Expression sqrt_DX2_DY2 = Expression.function(FunctionType.SQRT, Expression.add(DX2, DY2));
Expression dirX = Expression.div(posX_minux_X, Expression.add(sqrt_DX2_DY2, new Expression(1e-8)));
Expression dirY = Expression.div(posY_minux_Y, Expression.add(sqrt_DX2_DY2, new Expression(1e-8)));
if (bDirection) {
SpatialQuantity dirXQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.X);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirXQuantity, gc), getIdentifierSubstitutions(dirX, dirXQuantity.getUnitDefinition(), gc), gc));
SpatialQuantity dirYQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.Y);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirYQuantity, gc), getIdentifierSubstitutions(dirY, dirYQuantity.getUnitDefinition(), gc), gc));
}
if (bDistance) {
SpatialQuantity distanceQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointDistanceMap, QuantityComponent.Scalar);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(distanceQuantity, gc), getIdentifierSubstitutions(sqrt_DX2_DY2, distanceQuantity.getUnitDefinition(), gc), gc));
}
}
if (simContext.getGeometry().getDimension() == 3) {
Expression DX2 = Expression.mult(posX_minux_X, posX_minux_X);
Expression DY2 = Expression.mult(posY_minux_Y, posY_minux_Y);
Expression DZ2 = Expression.mult(posZ_minux_Z, posZ_minux_Z);
Expression sqrt_DX2_DY2_DZ2 = Expression.function(FunctionType.SQRT, Expression.add(DX2, DY2, DZ2));
Expression dirX = Expression.div(posX_minux_X, Expression.add(sqrt_DX2_DY2_DZ2, new Expression(1e-8)));
Expression dirY = Expression.div(posY_minux_Y, Expression.add(sqrt_DX2_DY2_DZ2, new Expression(1e-8)));
Expression dirZ = Expression.div(posZ_minux_Z, Expression.add(sqrt_DX2_DY2_DZ2, new Expression(1e-8)));
if (bDirection) {
SpatialQuantity dirXQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.X);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirXQuantity, gc), getIdentifierSubstitutions(dirX, dirXQuantity.getUnitDefinition(), gc), gc));
SpatialQuantity dirYQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.Y);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirYQuantity, gc), getIdentifierSubstitutions(dirY, dirYQuantity.getUnitDefinition(), gc), gc));
SpatialQuantity dirZQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.Z);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirZQuantity, gc), getIdentifierSubstitutions(dirZ, dirZQuantity.getUnitDefinition(), gc), gc));
}
if (bDistance) {
SpatialQuantity distanceQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointDistanceMap, QuantityComponent.Scalar);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(distanceQuantity, gc), getIdentifierSubstitutions(sqrt_DX2_DY2_DZ2, distanceQuantity.getUnitDefinition(), gc), gc));
}
}
} else {
throw new MappingException(pointKinematics.getDescription() + " process defined for pointObject '" + pointObject.getName() + "' but Position and Velocity not enabled");
}
} else {
throw new MappingException("expecting 1 location or kinematics process for point '" + pointObject.getName() + "'");
}
} else if (spatialObject instanceof SurfaceRegionObject) {
SurfaceRegionObject surfaceRegionObject = (SurfaceRegionObject) spatialObject;
SubVolume insideSubvolume = surfaceRegionObject.getInsideSubVolume();
SubVolume outsideSubvolume = surfaceRegionObject.getOutsideSubVolume();
SurfaceClass surfaceClass = simContext.getGeometry().getGeometrySurfaceDescription().getSurfaceClass(insideSubvolume, outsideSubvolume);
MembraneSubdomainContext memSubdomainContext = null;
for (MembraneSubdomainContext context : membraneSubdomainContexts) {
if (context.surfaceClass == surfaceClass) {
memSubdomainContext = context;
}
}
//
// if true, have to solve for this category
//
boolean bNormal = surfaceRegionObject.isQuantityCategoryEnabled(QuantityCategory.Normal);
boolean bVelocity = surfaceRegionObject.isQuantityCategoryEnabled(QuantityCategory.SurfaceVelocity);
boolean bDistance = surfaceRegionObject.isQuantityCategoryEnabled(QuantityCategory.SurfaceDistanceMap);
boolean bDirection = surfaceRegionObject.isQuantityCategoryEnabled(QuantityCategory.DirectionToSurface);
boolean bSize = surfaceRegionObject.isQuantityCategoryEnabled(QuantityCategory.SurfaceSize);
if (bVelocity) {
ArrayList<SurfaceKinematics> surfaceKinematicsList = new ArrayList<SurfaceKinematics>();
for (SpatialProcess spatialProcess : simContext.getSpatialProcesses()) {
if (spatialProcess instanceof SurfaceKinematics && ((SurfaceKinematics) spatialProcess).getSurfaceRegionObject() == surfaceRegionObject) {
surfaceKinematicsList.add((SurfaceKinematics) spatialProcess);
}
}
if (surfaceKinematicsList.size() == 1) {
SurfaceKinematics surfaceKinematics = surfaceKinematicsList.get(0);
if (simContext.getGeometry().getDimension() >= 1) {
SpatialQuantity velXQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.SurfaceVelocity, QuantityComponent.X);
LocalParameter velXParam = surfaceKinematics.getParameter(SpatialProcessParameterType.SurfaceVelocityX);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velXParam, surfaceClass), getIdentifierSubstitutions(velXParam.getExpression(), velXParam.getUnitDefinition(), surfaceClass), surfaceClass));
Expression velXExp = new Expression(velXParam, surfaceKinematics.getNameScope());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velXQuantity, surfaceClass), getIdentifierSubstitutions(velXExp, velXQuantity.getUnitDefinition(), surfaceClass), surfaceClass));
if (bNormal) {
SpatialQuantity normXQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.Normal, QuantityComponent.X);
Expression normXExp = new Expression(MathFunctionDefinitions.FUNCTION_normalX);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(normXQuantity, surfaceClass), getIdentifierSubstitutions(normXExp, normXQuantity.getUnitDefinition(), surfaceClass), surfaceClass));
}
}
if (simContext.getGeometry().getDimension() >= 2) {
SpatialQuantity velYQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.SurfaceVelocity, QuantityComponent.Y);
LocalParameter velYParam = surfaceKinematics.getParameter(SpatialProcessParameterType.SurfaceVelocityY);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velYParam, surfaceClass), getIdentifierSubstitutions(velYParam.getExpression(), velYParam.getUnitDefinition(), surfaceClass), surfaceClass));
Expression velYExp = new Expression(velYParam, surfaceKinematics.getNameScope());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velYQuantity, surfaceClass), getIdentifierSubstitutions(velYExp, velYQuantity.getUnitDefinition(), surfaceClass), surfaceClass));
if (bNormal) {
SpatialQuantity normYQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.Normal, QuantityComponent.Y);
Expression normYExp = new Expression(MathFunctionDefinitions.FUNCTION_normalY);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(normYQuantity, surfaceClass), getIdentifierSubstitutions(normYExp, normYQuantity.getUnitDefinition(), surfaceClass), surfaceClass));
}
}
if (simContext.getGeometry().getDimension() >= 3) {
SpatialQuantity velZQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.SurfaceVelocity, QuantityComponent.Z);
LocalParameter velZParam = surfaceKinematics.getParameter(SpatialProcessParameterType.SurfaceVelocityZ);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velZParam, surfaceClass), getIdentifierSubstitutions(velZParam.getExpression(), velZParam.getUnitDefinition(), surfaceClass), surfaceClass));
Expression velYExp = new Expression(velZParam, surfaceKinematics.getNameScope());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velZQuantity, surfaceClass), getIdentifierSubstitutions(velYExp, velZQuantity.getUnitDefinition(), surfaceClass), surfaceClass));
if (bNormal) {
SpatialQuantity normZQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.Normal, QuantityComponent.Z);
// MathFunctionDefinitions.FUNCTION_normalZ);
Expression normZExp = new Expression("normalZ_not_implemented()");
varHash.addVariable(newFunctionOrConstant(getMathSymbol(normZQuantity, surfaceClass), getIdentifierSubstitutions(normZExp, normZQuantity.getUnitDefinition(), surfaceClass), surfaceClass));
}
}
} else {
throw new MappingException("expecting 1 Surface Kinematics process for Surface Object '" + surfaceRegionObject.getName() + "'");
}
}
if (bSize) {
SpatialQuantity sizeQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.SurfaceSize, QuantityComponent.Scalar);
String funcName = MathFunctionDefinitions.Function_regionArea_current.getFunctionName();
Expression sizeExp = Expression.function(funcName, new Expression[] { new Expression("'" + surfaceClass.getName() + "'") });
varHash.addVariable(newFunctionOrConstant(getMathSymbol(sizeQuantity, surfaceClass), getIdentifierSubstitutions(sizeExp, sizeQuantity.getUnitDefinition(), surfaceClass), surfaceClass));
}
if (bDirection) {
SpatialQuantity directionXQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.DirectionToSurface, QuantityComponent.X);
SpatialQuantity directionYQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.DirectionToSurface, QuantityComponent.Y);
SpatialQuantity directionZQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.DirectionToSurface, QuantityComponent.Z);
for (SubVolume adjacentSubvolume : surfaceClass.getAdjacentSubvolumes()) {
Domain domain = new Domain(adjacentSubvolume);
CompartmentSubDomain compSubdomain = mathDesc.getCompartmentSubDomain(adjacentSubvolume.getName());
if (simContext.getGeometry().getDimension() >= 1) {
String name = adjacentSubvolume.getName() + "_dirX_" + memSubdomainContext.membraneSubdomain.getName();
LocalizedDirectionToMembraneQuantity localDirectionXQuantity = addLocalizedDirectionToMembraneQuantity(name, surfaceClass, adjacentSubvolume, QuantityComponent.X);
VolVariable distanceVar = new VolVariable(getMathSymbol(localDirectionXQuantity, adjacentSubvolume), domain);
varHash.addVariable(distanceVar);
ComputeMembraneMetricEquation membraneMetricEquation = new ComputeMembraneMetricEquation(distanceVar, MembraneMetricComponent.directionToMembraneX);
membraneMetricEquation.setTargetMembraneName(memSubdomainContext.membraneSubdomain.getName());
compSubdomain.addEquation(membraneMetricEquation);
}
if (simContext.getGeometry().getDimension() >= 2) {
String name = adjacentSubvolume.getName() + "_dirY_" + memSubdomainContext.membraneSubdomain.getName();
LocalizedDirectionToMembraneQuantity localDirectionYQuantity = addLocalizedDirectionToMembraneQuantity(name, surfaceClass, adjacentSubvolume, QuantityComponent.Y);
VolVariable distanceVar = new VolVariable(getMathSymbol(localDirectionYQuantity, adjacentSubvolume), domain);
varHash.addVariable(distanceVar);
ComputeMembraneMetricEquation membraneMetricEquation = new ComputeMembraneMetricEquation(distanceVar, MembraneMetricComponent.directionToMembraneY);
membraneMetricEquation.setTargetMembraneName(memSubdomainContext.membraneSubdomain.getName());
compSubdomain.addEquation(membraneMetricEquation);
}
if (simContext.getGeometry().getDimension() == 3) {
String name = adjacentSubvolume.getName() + "_dirZ_" + memSubdomainContext.membraneSubdomain.getName();
LocalizedDirectionToMembraneQuantity localDirectionZQuantity = addLocalizedDirectionToMembraneQuantity(name, surfaceClass, adjacentSubvolume, QuantityComponent.Z);
VolVariable distanceVar = new VolVariable(getMathSymbol(localDirectionZQuantity, adjacentSubvolume), domain);
varHash.addVariable(distanceVar);
ComputeMembraneMetricEquation membraneMetricEquation = new ComputeMembraneMetricEquation(distanceVar, MembraneMetricComponent.directionToMembraneZ);
membraneMetricEquation.setTargetMembraneName(memSubdomainContext.membraneSubdomain.getName());
compSubdomain.addEquation(membraneMetricEquation);
}
}
}
if (bDistance) {
SpatialQuantity distanceQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.SurfaceDistanceMap, QuantityComponent.Scalar);
for (SubVolume adjacentSubvolume : surfaceClass.getAdjacentSubvolumes()) {
String name = adjacentSubvolume.getName() + "_distanceTo_" + memSubdomainContext.membraneSubdomain.getName();
LocalizedDistanceToMembraneQuantity localDistanceQuantity = addLocalizedDistanceToMembraneQuantity(name, surfaceClass, adjacentSubvolume);
CompartmentSubDomain compSubdomain = mathDesc.getCompartmentSubDomain(adjacentSubvolume.getName());
Domain domain = new Domain(adjacentSubvolume);
VolVariable distanceVar = new VolVariable(getMathSymbol(localDistanceQuantity, adjacentSubvolume), domain);
varHash.addVariable(distanceVar);
ComputeMembraneMetricEquation membraneMetricEquation = new ComputeMembraneMetricEquation(distanceVar, MembraneMetricComponent.distanceToMembrane);
membraneMetricEquation.setTargetMembraneName(memSubdomainContext.membraneSubdomain.getName());
compSubdomain.addEquation(membraneMetricEquation);
}
}
} else if (spatialObject instanceof VolumeRegionObject) {
VolumeRegionObject volumeRegionObject = (VolumeRegionObject) spatialObject;
SubVolume subvolume = volumeRegionObject.getSubVolume();
boolean bCentroid = volumeRegionObject.isQuantityCategoryEnabled(QuantityCategory.DirectionToSurface);
boolean bSize = volumeRegionObject.isQuantityCategoryEnabled(QuantityCategory.VolumeSize);
boolean bVelocity = volumeRegionObject.isQuantityCategoryEnabled(QuantityCategory.InteriorVelocity);
if (bVelocity) {
ArrayList<VolumeKinematics> volumeKinematicsList = new ArrayList<VolumeKinematics>();
for (SpatialProcess spatialProcess : simContext.getSpatialProcesses()) {
if (spatialProcess instanceof VolumeKinematics && ((VolumeKinematics) spatialProcess).getVolumeRegionObject() == volumeRegionObject) {
volumeKinematicsList.add((VolumeKinematics) spatialProcess);
}
}
if (volumeKinematicsList.size() == 1) {
VolumeKinematics volumeKinematics = volumeKinematicsList.get(0);
if (simContext.getGeometry().getDimension() >= 1) {
SpatialQuantity velXQuantity = volumeRegionObject.getSpatialQuantity(QuantityCategory.InteriorVelocity, QuantityComponent.X);
LocalParameter velXParam = volumeKinematics.getParameter(SpatialProcessParameterType.InternalVelocityX);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velXParam, subvolume), getIdentifierSubstitutions(velXParam.getExpression(), velXParam.getUnitDefinition(), subvolume), subvolume));
Expression velXExp = new Expression(velXParam, volumeKinematics.getNameScope());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velXQuantity, subvolume), getIdentifierSubstitutions(velXExp, velXQuantity.getUnitDefinition(), subvolume), subvolume));
}
if (simContext.getGeometry().getDimension() >= 2) {
SpatialQuantity velYQuantity = volumeRegionObject.getSpatialQuantity(QuantityCategory.InteriorVelocity, QuantityComponent.Y);
LocalParameter velYParam = volumeKinematics.getParameter(SpatialProcessParameterType.InternalVelocityY);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velYParam, subvolume), getIdentifierSubstitutions(velYParam.getExpression(), velYParam.getUnitDefinition(), subvolume), subvolume));
Expression velYExp = new Expression(velYParam, volumeKinematics.getNameScope());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velYQuantity, subvolume), getIdentifierSubstitutions(velYExp, velYQuantity.getUnitDefinition(), subvolume), subvolume));
}
if (simContext.getGeometry().getDimension() == 3) {
SpatialQuantity velZQuantity = volumeRegionObject.getSpatialQuantity(QuantityCategory.InteriorVelocity, QuantityComponent.Z);
LocalParameter velZParam = volumeKinematics.getParameter(SpatialProcessParameterType.InternalVelocityZ);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velZParam, subvolume), getIdentifierSubstitutions(velZParam.getExpression(), velZParam.getUnitDefinition(), subvolume), subvolume));
Expression velZExp = new Expression(velZParam, volumeKinematics.getNameScope());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(velZQuantity, subvolume), getIdentifierSubstitutions(velZExp, velZQuantity.getUnitDefinition(), subvolume), subvolume));
}
} else {
throw new MappingException("expecting 1 Volume Kinematics process for Volume Object '" + volumeRegionObject.getName() + "'");
}
}
if (bSize) {
SpatialQuantity sizeQuantity = volumeRegionObject.getSpatialQuantity(QuantityCategory.VolumeSize, QuantityComponent.Scalar);
String funcName = MathFunctionDefinitions.Function_regionVolume_current.getFunctionName();
Expression sizeExp = Expression.function(funcName, new Expression[] { new Expression("'" + subvolume.getName() + "'") });
varHash.addVariable(newFunctionOrConstant(getMathSymbol(sizeQuantity, subvolume), getIdentifierSubstitutions(sizeExp, sizeQuantity.getUnitDefinition(), subvolume), subvolume));
}
if (bCentroid) {
throw new MappingException(QuantityCategory.Centroid.description + " not yet implemented in math generation");
}
}
}
}
use of cbit.vcell.mapping.spatial.processes.PointKinematics in project vcell by virtualcell.
the class DefaultScrollTableCellRenderer method issueRenderer.
public static void issueRenderer(JLabel renderer, String defaultToolTipText, JTable table, int row, int column, SortTableModel tableModel) {
List<Issue> issueListError = tableModel.getIssues(row, column, Issue.Severity.ERROR);
List<Issue> issueListWarning = tableModel.getIssues(row, column, Issue.Severity.WARNING);
Icon icon = null;
Point mousePosition = table.getMousePosition();
// hue, saturation, brightness
Color red = Color.getHSBColor(0f, 0.4f, 1.0f);
if (issueListError.size() > 0) {
if (column == 0) {
icon = VCellIcons.issueErrorIcon;
if (mousePosition != null && mousePosition.getX() > LEFT_ICON_MARGIN && mousePosition.getX() <= (icon.getIconWidth() + LEFT_ICON_MARGIN)) {
String tt = Issue.getHtmlIssueMessage(issueListError);
renderer.setToolTipText(tt);
} else {
renderer.setToolTipText(defaultToolTipText);
}
// Color.red
renderer.setBorder(new MatteBorder(1, 1, 1, 0, red));
} else if (column == table.getColumnCount() - 1) {
renderer.setBorder(new MatteBorder(1, 0, 1, 1, red));
} else {
renderer.setBorder(new MatteBorder(1, 0, 1, 0, red));
}
} else if (issueListWarning.size() > 0) {
if (column == 0) {
icon = VCellIcons.issueWarningIcon;
if (mousePosition != null && mousePosition.getX() > LEFT_ICON_MARGIN && mousePosition.getX() <= (icon.getIconWidth() + LEFT_ICON_MARGIN)) {
renderer.setToolTipText(Issue.getHtmlIssueMessage(issueListWarning));
} else {
renderer.setToolTipText(defaultToolTipText);
}
renderer.setBorder(new MatteBorder(1, 1, 1, 0, Color.orange));
} else if (column == table.getColumnCount() - 1) {
renderer.setBorder(new MatteBorder(1, 0, 1, 1, Color.orange));
} else {
renderer.setBorder(new MatteBorder(1, 0, 1, 0, Color.orange));
}
} else {
if (column == 0) {
icon = VCellIcons.issueGoodIcon;
// no tooltip for column 0 when we have no issues on that line
renderer.setToolTipText(null);
}
if (column != 0 && defaultToolTipText != null && !defaultToolTipText.isEmpty()) {
renderer.setToolTipText(defaultToolTipText);
} else {
renderer.setToolTipText(null);
}
renderer.setBorder(DEFAULT_GAP);
}
if (column == 0 && icon != null) {
// for some tables we combine (concatenate) the issue icon with an entity icon
if (tableModel instanceof SpatialProcessTableModel) {
Icon icon2 = null;
SpatialProcess spatialProcess = (SpatialProcess) (((SpatialProcessTableModel) tableModel).getValueAt(row));
if (spatialProcess instanceof PointLocation) {
icon2 = VCellIcons.spatialLocationIcon;
} else if (spatialProcess instanceof PointKinematics) {
icon2 = VCellIcons.spatialKinematicsIcon;
} else if (spatialProcess instanceof SurfaceKinematics) {
icon2 = VCellIcons.spatialKinematicsIcon;
} else {
icon2 = VCellIcons.spatialKinematicsIcon;
}
icon = VCellIcons.addIcon(icon, icon2);
} else if (tableModel instanceof SpatialObjectTableModel) {
Icon icon2 = null;
SpatialObject spatialObject = (SpatialObject) (((SpatialObjectTableModel) tableModel).getValueAt(row));
if (spatialObject instanceof PointObject) {
icon2 = VCellIcons.spatialPointIcon;
} else if (spatialObject instanceof SurfaceRegionObject) {
icon2 = VCellIcons.spatialMembraneIcon;
} else if (spatialObject instanceof VolumeRegionObject) {
icon2 = VCellIcons.spatialVolumeIcon;
} else {
icon2 = VCellIcons.spatialVolumeIcon;
}
icon = VCellIcons.addIcon(icon, icon2);
}
}
renderer.setIcon(icon);
}
use of cbit.vcell.mapping.spatial.processes.PointKinematics in project vcell by virtualcell.
the class SimulationContext method createPointKinematics.
public PointKinematics createPointKinematics(PointObject pointObject) {
String pointProcName = "pproc_0";
while (getSpatialProcess(pointProcName) != null) {
pointProcName = TokenMangler.getNextEnumeratedToken(pointProcName);
}
PointKinematics pointKinematics = new PointKinematics(pointProcName, this);
pointKinematics.setPointObject(pointObject);
try {
addSpatialProcess(pointKinematics);
} catch (PropertyVetoException e) {
throw new RuntimeException(e.getMessage(), e);
}
return pointKinematics;
}
use of cbit.vcell.mapping.spatial.processes.PointKinematics in project vcell by virtualcell.
the class Xmlproducer method getXML.
public Element getXML(SpatialProcess[] spatialProcesses) throws XmlParseException {
Element spatialProcessesElement = new Element(XMLTags.SpatialProcessesTag);
for (SpatialProcess spatialProcess : spatialProcesses) {
Element spatialProcessElement = new Element(XMLTags.SpatialProcessTag);
spatialProcessElement.setAttribute(XMLTags.NameAttrTag, mangle(spatialProcess.getName()));
if (spatialProcess instanceof PointKinematics) {
spatialProcessElement.setAttribute(XMLTags.SpatialProcessTypeAttrTag, XMLTags.SpatialProcessTypeAttrValue_PointKinematics);
spatialProcessElement.setAttribute(XMLTags.SpatialProcessPointObjectAttrTag, ((PointKinematics) spatialProcess).getPointObject().getName());
} else if (spatialProcess instanceof PointLocation) {
spatialProcessElement.setAttribute(XMLTags.SpatialProcessTypeAttrTag, XMLTags.SpatialProcessTypeAttrValue_PointLocation);
spatialProcessElement.setAttribute(XMLTags.SpatialProcessPointObjectAttrTag, ((PointLocation) spatialProcess).getPointObject().getName());
} else if (spatialProcess instanceof SurfaceKinematics) {
spatialProcessElement.setAttribute(XMLTags.SpatialProcessTypeAttrTag, XMLTags.SpatialProcessTypeAttrValue_SurfaceKinematics);
spatialProcessElement.setAttribute(XMLTags.SpatialProcessSurfaceObjectAttrTag, ((SurfaceKinematics) spatialProcess).getSurfaceRegionObject().getName());
} else if (spatialProcess instanceof VolumeKinematics) {
spatialProcessElement.setAttribute(XMLTags.SpatialProcessTypeAttrTag, XMLTags.SpatialProcessTypeAttrValue_VolumeKinematics);
spatialProcessElement.setAttribute(XMLTags.SpatialProcessVolumeObjectAttrTag, ((VolumeKinematics) spatialProcess).getVolumeRegionObject().getName());
} else {
throw new RuntimeException("spatialProcess type " + spatialProcess.getClass().getSimpleName() + " not yet supported for persistence.");
}
LocalParameter[] parameters = spatialProcess.getParameters();
for (LocalParameter parm : parameters) {
if (parm.getExpression() != null) {
Element tempparameter = new Element(XMLTags.ParameterTag);
// Get parameter attributes
tempparameter.setAttribute(XMLTags.NameAttrTag, mangle(parm.getName()));
tempparameter.setAttribute(XMLTags.ParamRoleAttrTag, spatialProcess.getParameterType(parm).getRoleXmlName());
VCUnitDefinition unit = parm.getUnitDefinition();
if (unit != null) {
tempparameter.setAttribute(XMLTags.VCUnitDefinitionAttrTag, unit.getSymbol());
}
tempparameter.addContent(mangleExpression(parm.getExpression()));
spatialProcessElement.addContent(tempparameter);
}
}
spatialProcessesElement.addContent(spatialProcessElement);
}
System.out.println(XmlUtil.xmlToString(spatialProcessesElement));
return spatialProcessesElement;
}
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