Examples with SimulationContext cbit.vcell.mapping.SimulationContext used on opensource projects

Example 91 with SimulationContext

use of cbit.vcell.mapping.SimulationContext in project vcell by virtualcell.

the class DataSymbolsTableModel method simulationContextChange.

/**
 * Sets the simulationContext property (cbit.vcell.mapping.SimulationContext) value.
 * @param simulationContext The new value for the property.
 * @see #getSimulationContext
 */
@Override
protected void simulationContextChange(java.beans.PropertyChangeEvent evt) {
    super.simulationContextChange(evt);
    SimulationContext oldValue = (SimulationContext) evt.getOldValue();
    if (oldValue != null) {
        oldValue.getDataContext().removePropertyChangeListener(this);
        for (DataSymbol ds : oldValue.getDataContext().getDataSymbols()) {
            ds.removePropertyChangeListener(this);
        }
    }
    SimulationContext newValue = (SimulationContext) evt.getNewValue();
    if (newValue != null) {
        newValue.getDataContext().addPropertyChangeListener(this);
        for (DataSymbol ds : newValue.getDataContext().getDataSymbols()) {
            ds.addPropertyChangeListener(this);
        }
    }
}

Example 92 with SimulationContext

use of cbit.vcell.mapping.SimulationContext in project vcell by virtualcell.

the class ElectricalMembraneMappingPanel method setsimulationContext1.

/**
 * Set the simulationContext1 to a new value.
 * @param newValue cbit.vcell.mapping.SimulationContext
 */
/* WARNING: THIS METHOD WILL BE REGENERATED. */
private void setsimulationContext1(SimulationContext newValue) {
    if (ivjsimulationContext1 != newValue) {
        try {
            SimulationContext oldValue = getsimulationContext1();
            ivjsimulationContext1 = newValue;
            connPtoP2SetSource();
            connEtoM1(ivjsimulationContext1);
            connEtoM6(ivjsimulationContext1);
            firePropertyChange("simulationContext", oldValue, newValue);
        } catch (java.lang.Throwable ivjExc) {
            handleException(ivjExc);
        }
    }
    ;
}

Example 93 with SimulationContext

use of cbit.vcell.mapping.SimulationContext in project vcell by virtualcell.

the class ElectricalMembraneMappingPanel method setSimulationContext.

/**
 * Sets the simulationContext property (cbit.vcell.mapping.SimulationContext) value.
 * @param simulationContext The new value for the property.
 * @see #getSimulationContext
 */
public void setSimulationContext(SimulationContext simulationContext) {
    SimulationContext oldValue = fieldSimulationContext;
    fieldSimulationContext = simulationContext;
    firePropertyChange("simulationContext", oldValue, simulationContext);
}

Example 94 with SimulationContext

use of cbit.vcell.mapping.SimulationContext in project vcell by virtualcell.

the class ElectricalStimulusPanel method setSimulationContext.

/**
 * Sets the simulationContext property (cbit.vcell.mapping.SimulationContext) value.
 * @param simulationContext The new value for the property.
 * @see #getSimulationContext
 */
public void setSimulationContext(SimulationContext simulationContext) {
    SimulationContext oldValue = fieldSimulationContext;
    fieldSimulationContext = simulationContext;
    firePropertyChange("simulationContext", oldValue, simulationContext);
}

Example 95 with SimulationContext

use of cbit.vcell.mapping.SimulationContext in project vcell by virtualcell.

the class GeneratedReactionTableRow method deriveRule.

private void deriveRule(String inputString, Model tempModel) {
    if (owner != null && owner.getSimulationContext() != null) {
        List<MolecularType> mtList = owner.getSimulationContext().getModel().getRbmModelContainer().getMolecularTypeList();
        try {
            tempModel.getRbmModelContainer().setMolecularTypeList(mtList);
        } catch (PropertyVetoException e1) {
            e1.printStackTrace();
            throw new RuntimeException("Unexpected exception setting " + MolecularType.typeName + " list: " + e1.getMessage(), e1);
        }
    } else {
        // This should not be possible
        throw new RuntimeException("Owner or SimulationContext are null.");
    }
    int arrowIndex = inputString.indexOf("<->");
    boolean bReversible = true;
    if (arrowIndex < 0) {
        arrowIndex = inputString.indexOf("->");
        bReversible = false;
    }
    String left = inputString.substring(0, arrowIndex).trim();
    String right = inputString.substring(arrowIndex + (bReversible ? 3 : 2)).trim();
    if (left.length() == 0 && right.length() == 0) {
        return;
    }
    String name = reactionObject.getRuleName();
    if (name.contains(GeneratedReactionTableModel.reverse)) {
        name = name.substring(GeneratedReactionTableModel.reverse.length());
    }
    if (name.endsWith(ReactionRule.DirectHalf)) {
        name = name.substring(0, name.indexOf(ReactionRule.DirectHalf));
    }
    if (name.endsWith(ReactionRule.InverseHalf)) {
        name = name.substring(0, name.indexOf(ReactionRule.InverseHalf));
    }
    // try to get the name of the original structure from the original rule and make here another structure with the same name
    String strStructure = null;
    Structure ruleStructure;
    SimulationContext sc = owner.getSimulationContext();
    ReactionRule rr = sc.getModel().getRbmModelContainer().getReactionRule(name);
    if (rr != null && rr.getStructure() != null) {
        strStructure = rr.getStructure().getName();
    }
    if (strStructure != null) {
        if (tempModel.getStructure(strStructure) == null) {
            try {
                tempModel.addFeature(strStructure);
            } catch (ModelException | PropertyVetoException e) {
                e.printStackTrace();
            }
        }
        ruleStructure = tempModel.getStructure(strStructure);
    } else {
        throw new RuntimeException("Failed to recover a Structure name from the Reaction Rule: " + name);
    }
    // making the fake rules just for display purpose, actually they are the flattened reactions resulted from bngl
    // the name is probably not unique, it's likely that many flattened reactions are derived from the same rule
    reactionRule = tempModel.getRbmModelContainer().createReactionRule(name, ruleStructure, bReversible);
    String regex = "[^!]\\+";
    String[] patterns = left.split(regex);
    for (String spString : patterns) {
        try {
            spString = spString.trim();
            // if compartments are present, we're making some fake compartments in the tempModel just for compartment name display purposes
            SpeciesPattern speciesPattern = (SpeciesPattern) RbmUtils.parseSpeciesPattern(spString, tempModel);
            strStructure = RbmUtils.parseCompartment(spString, tempModel);
            speciesPattern.resolveBonds();
            Structure structure;
            if (strStructure != null) {
                if (tempModel.getStructure(strStructure) == null) {
                    tempModel.addFeature(strStructure);
                }
                structure = tempModel.getStructure(strStructure);
            } else {
                // if nothing explicit for a participant, we use by default the structure of the rule
                structure = ruleStructure;
            }
            reactionRule.addReactant(new ReactantPattern(speciesPattern, structure));
        } catch (Throwable ex) {
            ex.printStackTrace();
            return;
        }
    }
    patterns = right.split(regex);
    for (String spString : patterns) {
        try {
            spString = spString.trim();
            SpeciesPattern speciesPattern = (SpeciesPattern) RbmUtils.parseSpeciesPattern(spString, tempModel);
            strStructure = RbmUtils.parseCompartment(spString, tempModel);
            speciesPattern.resolveBonds();
            Structure structure;
            if (strStructure != null) {
                if (tempModel.getStructure(strStructure) == null) {
                    tempModel.addFeature(strStructure);
                }
                structure = tempModel.getStructure(strStructure);
            } else {
                structure = ruleStructure;
            }
            reactionRule.addProduct(new ProductPattern(speciesPattern, structure));
        } catch (Throwable ex) {
            ex.printStackTrace();
            return;
        }
    }
}