Examples with ComponentStateDefinition org.vcell.model.rbm.ComponentStateDefinition used on opensource projects

Example 21 with ComponentStateDefinition

use of org.vcell.model.rbm.ComponentStateDefinition in project vcell by virtualcell.

the class ObservableTreeModel method propertyChange.

public void propertyChange(PropertyChangeEvent evt) {
    if (evt.getPropertyName().equals(PropertyConstants.PROPERTY_NAME_NAME)) {
        nodeChanged(rootNode);
    } else if (evt.getSource() == observable && evt.getPropertyName().equals(RbmObservable.PROPERTY_NAME_TYPE)) {
        nodeChanged(rootNode);
    } else if (evt.getPropertyName().equals("entityChange")) {
        nodeChanged(rootNode);
    } else {
        populateTree();
        Object source = evt.getSource();
        if (source == observable) {
            if (evt.getPropertyName().equals(RbmObservable.PROPERTY_NAME_SPECIES_PATTERN_LIST)) {
                List<SpeciesPattern> oldValue = (List<SpeciesPattern>) evt.getOldValue();
                if (oldValue != null) {
                    for (SpeciesPattern sp : oldValue) {
                        RbmUtils.removePropertyChangeListener(sp, this);
                    }
                }
                List<SpeciesPattern> newValue = (List<SpeciesPattern>) evt.getNewValue();
                if (newValue != null) {
                    for (SpeciesPattern sp : newValue) {
                        RbmUtils.addPropertyChangeListener(sp, this);
                    }
                }
            } else if (evt.getPropertyName().equals(RbmObservable.PROPERTY_NAME_SPECIES_PATTERN)) {
                SpeciesPattern newValue = (SpeciesPattern) evt.getNewValue();
                if (newValue != null) {
                    RbmUtils.addPropertyChangeListener(newValue, this);
                }
            }
        } else if (source instanceof SpeciesPattern) {
            if (evt.getPropertyName().equals(SpeciesPattern.PROPERTY_NAME_MOLECULAR_TYPE_PATTERNS)) {
                List<MolecularTypePattern> oldValue = (List<MolecularTypePattern>) evt.getOldValue();
                if (oldValue != null) {
                    for (MolecularTypePattern mtp : oldValue) {
                        RbmUtils.removePropertyChangeListener(mtp, this);
                    }
                }
                List<MolecularTypePattern> newValue = (List<MolecularTypePattern>) evt.getNewValue();
                if (newValue != null) {
                    for (MolecularTypePattern mtp : newValue) {
                        RbmUtils.addPropertyChangeListener(mtp, this);
                    }
                }
            }
        } else if (source instanceof MolecularTypePattern) {
            if (evt.getPropertyName().equals(MolecularTypePattern.PROPERTY_NAME_COMPONENT_PATTERN_LIST)) {
                List<MolecularComponentPattern> oldValue = (List<MolecularComponentPattern>) evt.getOldValue();
                if (oldValue != null) {
                    for (MolecularComponentPattern mcp : oldValue) {
                        RbmUtils.removePropertyChangeListener(mcp, this);
                    }
                }
                List<MolecularComponentPattern> newValue = (List<MolecularComponentPattern>) evt.getNewValue();
                if (newValue != null) {
                    for (MolecularComponentPattern mcp : newValue) {
                        RbmUtils.addPropertyChangeListener(mcp, this);
                    }
                }
            }
        } else if (source instanceof MolecularComponentPattern) {
            if (evt.getSource().equals(MolecularComponentPattern.PROPERTY_NAME_COMPONENT_STATE)) {
                ComponentStateDefinition oldValue = (ComponentStateDefinition) evt.getOldValue();
                if (oldValue != null) {
                    oldValue.removePropertyChangeListener(this);
                }
                ComponentStateDefinition newValue = (ComponentStateDefinition) evt.getNewValue();
                if (newValue != null) {
                    newValue.addPropertyChangeListener(this);
                }
            }
        }
    }
}

Example 22 with ComponentStateDefinition

use of org.vcell.model.rbm.ComponentStateDefinition in project vcell by virtualcell.

the class MolecularTypeTreeModel method createMolecularComponentNode.

private BioModelNode createMolecularComponentNode(MolecularComponent molecularComponent) {
    BioModelNode node = new BioModelNode(molecularComponent, true);
    for (ComponentStateDefinition componentState : molecularComponent.getComponentStateDefinitions()) {
        BioModelNode n = new BioModelNode(componentState, false);
        node.add(n);
    }
    return node;
}

Example 23 with ComponentStateDefinition

use of org.vcell.model.rbm.ComponentStateDefinition in project vcell by virtualcell.

the class MolecularTypeTreeModel method setMolecularType.

public void setMolecularType(MolecularType newValue) {
    if (newValue == molecularType) {
        return;
    }
    MolecularType oldValue = molecularType;
    if (oldValue != null) {
        oldValue.removePropertyChangeListener(this);
        for (MolecularComponent molecularComponent : oldValue.getComponentList()) {
            molecularComponent.removePropertyChangeListener(this);
            for (ComponentStateDefinition componentState : molecularComponent.getComponentStateDefinitions()) {
                componentState.removePropertyChangeListener(this);
            }
        }
    }
    molecularType = newValue;
    populateTree();
    if (newValue != null) {
        newValue.addPropertyChangeListener(this);
        for (MolecularComponent molecularComponent : newValue.getComponentList()) {
            molecularComponent.addPropertyChangeListener(this);
            for (ComponentStateDefinition componentState : molecularComponent.getComponentStateDefinitions()) {
                componentState.addPropertyChangeListener(this);
            }
        }
    }
}

Example 24 with ComponentStateDefinition

use of org.vcell.model.rbm.ComponentStateDefinition in project vcell by virtualcell.

the class ObservableTableModel method propertyChange.

@Override
public void propertyChange(PropertyChangeEvent evt) {
    super.propertyChange(evt);
    Object source = evt.getSource();
    // if (source == getModel().getRbmModelContainer()) {
    if (source == getModel()) {
        if (evt.getPropertyName().equals(RbmModelContainer.PROPERTY_NAME_OBSERVABLE_LIST)) {
            refreshData();
            List<RbmObservable> oldValue = (List<RbmObservable>) evt.getOldValue();
            if (oldValue != null) {
                for (RbmObservable observable : oldValue) {
                    observable.removePropertyChangeListener(this);
                    SpeciesPattern speciesPattern = observable.getSpeciesPattern(0);
                    RbmUtils.removePropertyChangeListener(speciesPattern, this);
                }
            }
            List<RbmObservable> newValue = (List<RbmObservable>) evt.getNewValue();
            if (newValue != null) {
                for (RbmObservable observable : newValue) {
                    observable.addPropertyChangeListener(this);
                    SpeciesPattern speciesPattern = observable.getSpeciesPattern(0);
                    RbmUtils.addPropertyChangeListener(speciesPattern, this);
                }
            }
        } else if (evt.getPropertyName().equals(RbmModelContainer.PROPERTY_NAME_MOLECULAR_TYPE_LIST)) {
            // we need this?
            refreshData();
        }
    } else if (source instanceof RbmObservable) {
        RbmObservable mt = (RbmObservable) source;
        int changeRow = getRowIndex(mt);
        if (changeRow >= 0) {
            fireTableRowsUpdated(changeRow, changeRow);
        }
    // if (evt.getPropertyName().equals(RbmObservable.PROPERTY_NAME_SPECIES_PATTERN_LIST)) {
    // SpeciesPattern oldValue = (SpeciesPattern) evt.getOldValue();
    // if (oldValue != null) {
    // RbmUtils.removePropertyChangeListener(oldValue, this);
    // }
    // SpeciesPattern newValue = (SpeciesPattern) evt.getNewValue();
    // if (newValue != null) {
    // RbmUtils.addPropertyChangeListener(newValue, this);
    // }
    // }
    } else if (source instanceof SpeciesPattern) {
        fireTableRowsUpdated(0, getRowCount() - 1);
        if (evt.getPropertyName().equals(SpeciesPattern.PROPERTY_NAME_MOLECULAR_TYPE_PATTERNS)) {
            List<MolecularTypePattern> oldValue = (List<MolecularTypePattern>) evt.getOldValue();
            if (oldValue != null) {
                for (MolecularTypePattern mtp : oldValue) {
                    RbmUtils.removePropertyChangeListener(mtp, this);
                }
            }
            List<MolecularTypePattern> newValue = (List<MolecularTypePattern>) evt.getNewValue();
            if (newValue != null) {
                for (MolecularTypePattern mtp : newValue) {
                    RbmUtils.addPropertyChangeListener(mtp, this);
                }
            }
        }
    } else if (source instanceof MolecularTypePattern) {
        fireTableRowsUpdated(0, getRowCount() - 1);
        if (evt.getPropertyName().equals(MolecularTypePattern.PROPERTY_NAME_COMPONENT_PATTERN_LIST)) {
            List<MolecularComponentPattern> oldValue = (List<MolecularComponentPattern>) evt.getOldValue();
            if (oldValue != null) {
                for (MolecularComponentPattern mcp : oldValue) {
                    RbmUtils.removePropertyChangeListener(mcp, this);
                }
            }
            List<MolecularComponentPattern> newValue = (List<MolecularComponentPattern>) evt.getNewValue();
            if (newValue != null) {
                for (MolecularComponentPattern mcp : newValue) {
                    RbmUtils.addPropertyChangeListener(mcp, this);
                }
            }
        }
    } else if (source instanceof MolecularComponentPattern) {
        fireTableRowsUpdated(0, getRowCount() - 1);
        if (source.equals(MolecularComponentPattern.PROPERTY_NAME_COMPONENT_STATE)) {
            ComponentStateDefinition oldValue = (ComponentStateDefinition) evt.getOldValue();
            if (oldValue != null) {
                oldValue.removePropertyChangeListener(this);
            }
            ComponentStateDefinition newValue = (ComponentStateDefinition) evt.getNewValue();
            if (newValue != null) {
                newValue.addPropertyChangeListener(this);
            }
        }
    } else if (evt.getSource() instanceof MolecularComponent) {
        fireTableRowsUpdated(0, getRowCount() - 1);
    } else if (evt.getSource() instanceof ComponentStateDefinition) {
        fireTableRowsUpdated(0, getRowCount() - 1);
    }
// updateStructureComboBox();
}

Example 25 with ComponentStateDefinition

use of org.vcell.model.rbm.ComponentStateDefinition in project vcell by virtualcell.

the class ReactionRuleEditorPropertiesPanel method reflectStateToProduct.

private void reflectStateToProduct(MolecularComponentPattern mcpReactant, ComponentStatePattern cspReactant) {
    MolecularTypePattern mtpReactant = reactionRule.getReactantMoleculeOfComponent(mcpReactant);
    MolecularTypePattern mtpProduct = reactionRule.getMatchingProductMolecule(mtpReactant);
    if (mtpProduct == null) {
        return;
    }
    for (MolecularComponentPattern mcpProduct : mtpProduct.getComponentPatternList()) {
        if (mcpProduct.getMolecularComponent() != mcpReactant.getMolecularComponent()) {
            continue;
        }
        // use this if isAny
        ComponentStatePattern csp = new ComponentStatePattern();
        if (!cspReactant.isAny()) {
            ComponentStateDefinition csd = cspReactant.getComponentStateDefinition();
            csp = new ComponentStatePattern(csd);
        }
        mcpProduct.setComponentStatePattern(csp);
    }
}