use of cbit.vcell.model.ModelQuantity in project vcell by virtualcell.
the class ParameterTableModel method isCellEditable.
/**
* Insert the method's description here.
* Creation date: (2/24/01 12:27:46 AM)
* @return boolean
* @param rowIndex int
* @param columnIndex int
*/
public boolean isCellEditable(int rowIndex, int columnIndex) {
if (!bEditable) {
return false;
}
Parameter parameter = getValueAt(rowIndex);
if (reactionStep != null && parameter instanceof KineticsParameter) {
KineticsParameter kp = (KineticsParameter) parameter;
if (kp.getRole() == Kinetics.ROLE_KReverse) {
if (!reactionStep.isReversible()) {
// disable Kr if rule is not reversible
return false;
}
}
}
switch(columnIndex) {
case COLUMN_NAME:
return parameter.isNameEditable();
case COLUMN_DESCRIPTION:
return false;
case COLUMN_IS_GLOBAL:
// if the parameter is reaction rate param or a ReservedSymbol in the model, it should not be editable
if ((parameter instanceof KineticsParameter) && (((KineticsParameter) parameter).getRole() != Kinetics.ROLE_UserDefined)) {
return false;
}
if (parameter instanceof UnresolvedParameter) {
return false;
}
if (parameter instanceof KineticsProxyParameter) {
KineticsProxyParameter kpp = (KineticsProxyParameter) parameter;
SymbolTableEntry ste = kpp.getTarget();
if ((ste instanceof Model.ReservedSymbol) || (ste instanceof SpeciesContext) || (ste instanceof ModelQuantity)) {
return false;
}
}
return true;
case COLUMN_VALUE:
return parameter.isExpressionEditable();
case COLUMN_UNITS:
return parameter.isUnitEditable();
}
return false;
}
use of cbit.vcell.model.ModelQuantity in project vcell by virtualcell.
the class ReactionRulePropertiesTableModel method isCellEditable.
/**
* Insert the method's description here.
* Creation date: (2/24/01 12:27:46 AM)
* @return boolean
* @param rowIndex int
* @param columnIndex int
*/
public boolean isCellEditable(int rowIndex, int columnIndex) {
if (!bEditable) {
return false;
}
Object o = getValueAt(rowIndex);
if (!(o instanceof Parameter)) {
return false;
}
Parameter parameter = (Parameter) o;
if (reactionRule != null && reactionRule.getKineticLaw().getLocalParameter(RbmKineticLawParameterType.MassActionReverseRate) == parameter) {
if (!reactionRule.isReversible()) {
// disable Kr if rule is not reversible
return false;
}
}
switch(columnIndex) {
case COLUMN_NAME:
return parameter.isNameEditable();
case COLUMN_DESCRIPTION:
return false;
case COLUMN_IS_GLOBAL:
// if the parameter is reaction rate param or a ReservedSymbol in the model, it should not be editable
if ((parameter instanceof LocalParameter) && (((LocalParameter) parameter).getRole() != RbmKineticLaw.RbmKineticLawParameterType.UserDefined)) {
return false;
}
if (parameter instanceof UnresolvedParameter) {
return false;
}
if (parameter instanceof LocalProxyParameter) {
LocalProxyParameter kpp = (LocalProxyParameter) parameter;
SymbolTableEntry ste = kpp.getTarget();
if ((ste instanceof Model.ReservedSymbol) || (ste instanceof SpeciesContext) || (ste instanceof ModelQuantity)) {
return false;
}
}
return true;
case COLUMN_VALUE:
return parameter.isExpressionEditable();
case COLUMN_UNITS:
return parameter.isUnitEditable();
}
return false;
}
use of cbit.vcell.model.ModelQuantity in project vcell by virtualcell.
the class ReactionRulePropertiesTableModel method setValueAt.
public void setValueAt(Object aValue, int rowIndex, int columnIndex) {
Object o = getValueAt(rowIndex);
if (!(o instanceof Parameter)) {
return;
}
Parameter parameter = (Parameter) o;
// try {
switch(columnIndex) {
case COLUMN_NAME:
{
try {
if (aValue instanceof String) {
String newName = (String) aValue;
if (!parameter.getName().equals(newName)) {
if (parameter instanceof LocalParameter) {
reactionRule.getKineticLaw().renameParameter(parameter.getName(), newName);
} else if (parameter instanceof LocalProxyParameter) {
parameter.setName(newName);
}
fireTableRowsUpdated(rowIndex, rowIndex);
}
}
} catch (ExpressionException e) {
e.printStackTrace(System.out);
PopupGenerator.showErrorDialog(ownerTable, "Error changing parameter name:\n" + e.getMessage());
} catch (PropertyVetoException e) {
e.printStackTrace(System.out);
PopupGenerator.showErrorDialog(ownerTable, "Error changing parameter name:\n" + e.getMessage());
}
break;
}
case COLUMN_IS_GLOBAL:
{
if (aValue.equals(Boolean.FALSE)) {
// check box has been <unset> (<true> to <false>) : change param from global to local
if ((parameter instanceof LocalProxyParameter) && ((((LocalProxyParameter) parameter).getTarget() instanceof Model.ReservedSymbol) || (((LocalProxyParameter) parameter).getTarget() instanceof SpeciesContext) || (((LocalProxyParameter) parameter).getTarget() instanceof ModelQuantity))) {
PopupGenerator.showErrorDialog(ownerTable, "Parameter : \'" + parameter.getName() + "\' is a " + ((LocalProxyParameter) parameter).getTarget().getClass() + " in the model; cannot convert it to a local kinetic parameter.");
} else {
try {
reactionRule.getKineticLaw().convertParameterType(parameter, false);
} catch (PropertyVetoException pve) {
pve.printStackTrace(System.out);
PopupGenerator.showErrorDialog(ownerTable, "Unable to convert parameter : \'" + parameter.getName() + "\' to local kinetics parameter : " + pve.getMessage());
} catch (ExpressionBindingException e) {
e.printStackTrace(System.out);
PopupGenerator.showErrorDialog(ownerTable, "Unable to convert parameter : \'" + parameter.getName() + "\' to local kinetics parameter : " + e.getMessage());
}
}
} else {
// check box has been <set> (<false> to <true>) : change param from local to global
if ((parameter instanceof LocalParameter) && (((LocalParameter) parameter).getRole() != RbmKineticLaw.RbmKineticLawParameterType.UserDefined)) {
PopupGenerator.showErrorDialog(ownerTable, "Parameter : \'" + parameter.getName() + "\' is a pre-defined kinetics parameter (not user-defined); cannot convert it to a model level (global) parameter.");
} else {
ModelParameter mp = reactionRule.getModel().getModelParameter(parameter.getName());
// model already had the model parameter 'param', but check if 'param' value is different from
// model parameter with same name. If it is, the local value will be overridden by global (model) param
// value, and user should be warned.
String choice = "Ok";
if (mp != null && !(mp.getExpression().compareEqual(parameter.getExpression()))) {
String msgStr = "Model already has a global parameter named : \'" + parameter.getName() + "\'; with value = \'" + mp.getExpression().infix() + "\'; This local parameter \'" + parameter.getName() + "\' with value = \'" + parameter.getExpression().infix() + "\' will be overridden by the global value. \nPress \'Ok' to override " + "local value with global value of \'" + parameter.getName() + "\'. \nPress \'Cancel\' to retain new local value.";
choice = PopupGenerator.showWarningDialog(ownerTable, msgStr, new String[] { "Ok", "Cancel" }, "Ok");
}
if (choice.equals("Ok")) {
try {
// Now 'parameter' is a local kinetic parameter. If it is not numeric, and if its expression
// contains other local kinetic parameters, warn user that 'parameter' cannot be promoted because
// of its expression containing other local parameters.
boolean bPromoteable = true;
if (!parameter.getExpression().isNumeric()) {
String[] symbols = parameter.getExpression().getSymbols();
for (int i = 0; i < symbols.length; i++) {
if (reactionRule.getKineticLaw().getLocalParameter(symbols[i]) != null) {
PopupGenerator.showErrorDialog(ownerTable, "Parameter \'" + parameter.getName() + "\' contains other local kinetic parameters; Cannot convert it to global until the referenced parameters are global.");
bPromoteable = false;
}
}
}
if (bPromoteable) {
reactionRule.getKineticLaw().convertParameterType(parameter, true);
}
} catch (PropertyVetoException pve) {
pve.printStackTrace(System.out);
PopupGenerator.showErrorDialog(ownerTable, "Cannot convert parameter \'" + parameter.getName() + "\' to global parameter : " + pve.getMessage());
} catch (ExpressionBindingException e) {
e.printStackTrace(System.out);
PopupGenerator.showErrorDialog(ownerTable, "Cannot convert parameter \'" + parameter.getName() + "\' to global parameter : " + e.getMessage());
}
}
}
}
fireTableRowsUpdated(rowIndex, rowIndex);
break;
}
case COLUMN_VALUE:
{
try {
if (aValue instanceof ScopedExpression) {
// }
throw new RuntimeException("unexpected value type ScopedExpression");
} else if (aValue instanceof String) {
String newExpressionString = (String) aValue;
if (parameter instanceof LocalParameter) {
LocalParameter localParameter = (LocalParameter) parameter;
reactionRule.getKineticLaw().setParameterValue(localParameter, new Expression(newExpressionString), true);
} else if (parameter instanceof LocalProxyParameter) {
parameter.setExpression(new Expression(newExpressionString));
}
}
reactionRule.getKineticLaw().resolveUndefinedUnits();
fireTableRowsUpdated(rowIndex, rowIndex);
} catch (java.beans.PropertyVetoException e) {
e.printStackTrace(System.out);
PopupGenerator.showErrorDialog(ownerTable, "Error:\n" + e.getMessage());
} catch (ExpressionException e) {
e.printStackTrace(System.out);
PopupGenerator.showErrorDialog(ownerTable, "Expression error:\n" + e.getMessage());
}
break;
}
case COLUMN_UNITS:
{
try {
if (aValue instanceof String && parameter instanceof LocalParameter && ((LocalParameter) parameter).getRole() == RbmKineticLaw.RbmKineticLawParameterType.UserDefined) {
String newUnitString = (String) aValue;
LocalParameter kineticsParm = (LocalParameter) parameter;
ModelUnitSystem modelUnitSystem = reactionRule.getModel().getUnitSystem();
if (!kineticsParm.getUnitDefinition().getSymbol().equals(newUnitString)) {
kineticsParm.setUnitDefinition(modelUnitSystem.getInstance(newUnitString));
reactionRule.getKineticLaw().resolveUndefinedUnits();
fireTableRowsUpdated(rowIndex, rowIndex);
}
}
} catch (VCUnitException e) {
e.printStackTrace(System.out);
PopupGenerator.showErrorDialog(ownerTable, "Error changing parameter unit:\n" + e.getMessage());
}
break;
}
}
// }catch (java.beans.PropertyVetoException e){
// e.printStackTrace(System.out);
// }
}
use of cbit.vcell.model.ModelQuantity in project vcell by virtualcell.
the class ParameterTableModel method setValueAt.
public void setValueAt(Object aValue, int rowIndex, int columnIndex) {
Parameter parameter = getValueAt(rowIndex);
// try {
switch(columnIndex) {
case COLUMN_NAME:
{
try {
if (aValue instanceof String) {
String newName = (String) aValue;
if (!parameter.getName().equals(newName)) {
if (parameter instanceof Kinetics.KineticsParameter) {
reactionStep.getKinetics().renameParameter(parameter.getName(), newName);
} else if (parameter instanceof Kinetics.KineticsProxyParameter) {
parameter.setName(newName);
}
fireTableRowsUpdated(rowIndex, rowIndex);
}
}
} catch (ExpressionException e) {
e.printStackTrace(System.out);
PopupGenerator.showErrorDialog(ownerTable, "Error changing parameter name:\n" + e.getMessage());
} catch (java.beans.PropertyVetoException e) {
e.printStackTrace(System.out);
PopupGenerator.showErrorDialog(ownerTable, "Error changing parameter name:\n" + e.getMessage());
}
break;
}
case COLUMN_IS_GLOBAL:
{
if (aValue.equals(Boolean.FALSE)) {
// check box has been <unset> (<true> to <false>) : change param from global to local
if ((parameter instanceof KineticsProxyParameter) && ((((KineticsProxyParameter) parameter).getTarget() instanceof Model.ReservedSymbol) || (((KineticsProxyParameter) parameter).getTarget() instanceof SpeciesContext) || (((KineticsProxyParameter) parameter).getTarget() instanceof ModelQuantity))) {
PopupGenerator.showErrorDialog(ownerTable, "Parameter : \'" + parameter.getName() + "\' is a " + ((KineticsProxyParameter) parameter).getTarget().getClass() + " in the model; cannot convert it to a local kinetic parameter.");
} else {
try {
reactionStep.getKinetics().convertParameterType(parameter, false);
} catch (PropertyVetoException pve) {
pve.printStackTrace(System.out);
PopupGenerator.showErrorDialog(ownerTable, "Unable to convert parameter : \'" + parameter.getName() + "\' to local kinetics parameter : " + pve.getMessage());
} catch (ExpressionBindingException e) {
e.printStackTrace(System.out);
PopupGenerator.showErrorDialog(ownerTable, "Unable to convert parameter : \'" + parameter.getName() + "\' to local kinetics parameter : " + e.getMessage());
}
}
} else {
// check box has been <set> (<false> to <true>) : change param from local to global
if ((parameter instanceof KineticsParameter) && (((KineticsParameter) parameter).getRole() != Kinetics.ROLE_UserDefined)) {
PopupGenerator.showErrorDialog(ownerTable, "Parameter : \'" + parameter.getName() + "\' is a pre-defined kinetics parameter (not user-defined); cannot convert it to a model level (global) parameter.");
} else {
ModelParameter mp = reactionStep.getKinetics().getReactionStep().getModel().getModelParameter(parameter.getName());
// model already had the model parameter 'param', but check if 'param' value is different from
// model parameter with same name. If it is, the local value will be overridden by global (model) param
// value, and user should be warned.
String choice = "Ok";
if (mp != null && !(mp.getExpression().compareEqual(parameter.getExpression()))) {
String msgStr = "Model already has a global parameter named : \'" + parameter.getName() + "\'; with value = \'" + mp.getExpression().infix() + "\'; This local parameter \'" + parameter.getName() + "\' with value = \'" + parameter.getExpression().infix() + "\' will be overridden by the global value. \nPress \'Ok' to override " + "local value with global value of \'" + parameter.getName() + "\'. \nPress \'Cancel\' to retain new local value.";
choice = PopupGenerator.showWarningDialog(ownerTable, msgStr, new String[] { "Ok", "Cancel" }, "Ok");
}
if (choice.equals("Ok")) {
try {
// Now 'parameter' is a local kinetic parameter. If it is not numeric, and if its expression
// contains other local kinetic parameters, warn user that 'parameter' cannot be promoted because
// of its expression containing other local parameters.
boolean bPromoteable = true;
if (!parameter.getExpression().isNumeric()) {
String[] symbols = parameter.getExpression().getSymbols();
for (int i = 0; i < symbols.length; i++) {
if (reactionStep.getKinetics().getKineticsParameter(symbols[i]) != null) {
PopupGenerator.showErrorDialog(ownerTable, "Parameter \'" + parameter.getName() + "\' contains other local kinetic parameters; Cannot convert it to global until the referenced parameters are global.");
bPromoteable = false;
}
}
}
if (bPromoteable) {
reactionStep.getKinetics().convertParameterType(parameter, true);
}
} catch (PropertyVetoException pve) {
pve.printStackTrace(System.out);
PopupGenerator.showErrorDialog(ownerTable, "Cannot convert parameter \'" + parameter.getName() + "\' to global parameter : " + pve.getMessage());
} catch (ExpressionBindingException e) {
e.printStackTrace(System.out);
PopupGenerator.showErrorDialog(ownerTable, "Cannot convert parameter \'" + parameter.getName() + "\' to global parameter : " + e.getMessage());
}
}
}
}
fireTableRowsUpdated(rowIndex, rowIndex);
break;
}
case COLUMN_VALUE:
{
try {
if (aValue instanceof ScopedExpression) {
// }
throw new RuntimeException("unexpected value type ScopedExpression");
} else if (aValue instanceof String) {
String newExpressionString = (String) aValue;
if (parameter instanceof Kinetics.KineticsParameter) {
reactionStep.getKinetics().setParameterValue((Kinetics.KineticsParameter) parameter, new Expression(newExpressionString));
} else if (parameter instanceof Kinetics.KineticsProxyParameter) {
parameter.setExpression(new Expression(newExpressionString));
}
}
reactionStep.getKinetics().resolveUndefinedUnits();
fireTableRowsUpdated(rowIndex, rowIndex);
} catch (java.beans.PropertyVetoException e) {
e.printStackTrace(System.out);
PopupGenerator.showErrorDialog(ownerTable, "Error:\n" + e.getMessage());
} catch (ExpressionException e) {
e.printStackTrace(System.out);
PopupGenerator.showErrorDialog(ownerTable, "Expression error:\n" + e.getMessage());
}
break;
}
case COLUMN_UNITS:
{
try {
if (aValue instanceof String && parameter instanceof Kinetics.KineticsParameter && ((Kinetics.KineticsParameter) parameter).getRole() == Kinetics.ROLE_UserDefined) {
String newUnitString = (String) aValue;
Kinetics.KineticsParameter kineticsParm = (Kinetics.KineticsParameter) parameter;
ModelUnitSystem modelUnitSystem = reactionStep.getModel().getUnitSystem();
if (!kineticsParm.getUnitDefinition().getSymbol().equals(newUnitString)) {
kineticsParm.setUnitDefinition(modelUnitSystem.getInstance(newUnitString));
reactionStep.getKinetics().resolveUndefinedUnits();
fireTableRowsUpdated(rowIndex, rowIndex);
}
}
} catch (VCUnitException e) {
e.printStackTrace(System.out);
PopupGenerator.showErrorDialog(ownerTable, "Error changing parameter unit:\n" + e.getMessage());
}
break;
}
}
// }catch (java.beans.PropertyVetoException e){
// e.printStackTrace(System.out);
// }
}
use of cbit.vcell.model.ModelQuantity in project vcell by virtualcell.
the class SEDMLExporter method getSymbolTableEntryForModelEntity.
private SymbolTableEntry getSymbolTableEntryForModelEntity(MathSymbolMapping mathSymbolMapping, String paramName) {
cbit.vcell.math.Variable mathVar = mathSymbolMapping.findVariableByName(paramName);
SymbolTableEntry[] stEntries = mathSymbolMapping.getBiologicalSymbol(mathVar);
if (stEntries == null || stEntries.length == 0) {
throw new NullPointerException("No matching biological symbol for : " + paramName);
}
// if the extra stes in the array are KineticsProxyParameters/ModelQuantities, remove them from array. Should be left with only one entry for overriddenConstantName
if (stEntries.length > 1) {
//
// If there are more than one stEntries, usually, it is a regular ste (species, global parameter, structure, etc) together with
// kineticsProxyParameters (that have the regular ste as target) or Model quantities (structure size, membrane voltage).
// So filtering out the kinticProxyParametes should leave only the regular parameter,
// which is what we want. If there are more, then there is a problem.
//
ArrayList<SymbolTableEntry> steList = new ArrayList<SymbolTableEntry>(Arrays.asList(stEntries));
for (int i = 0; i < stEntries.length; i++) {
if (stEntries[i] instanceof ProxyParameter) {
SymbolTableEntry ppTargetSte = ((ProxyParameter) stEntries[i]).getTarget();
if (steList.contains(ppTargetSte) || ppTargetSte instanceof ModelQuantity) {
steList.remove(stEntries[i]);
}
}
if (stEntries[i] instanceof ModelQuantity) {
if (steList.contains(stEntries[i])) {
steList.remove(stEntries[i]);
}
}
}
// after removing proxy parameters, cannot have more than one ste in list
if (steList.size() == 0) {
throw new RuntimeException("No mapping entry for constant : '" + paramName + "'.");
}
if (steList.size() > 1) {
throw new RuntimeException("Cannot have more than one mapping entry for constant : '" + paramName + "'.");
}
SymbolTableEntry[] stes = (SymbolTableEntry[]) steList.toArray(new SymbolTableEntry[0]);
return stes[0];
} else {
return stEntries[0];
}
}
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