Examples with ReactantPattern cbit.vcell.model.ReactantPattern used on opensource projects

Example 21 with ReactantPattern

use of cbit.vcell.model.ReactantPattern in project vcell by virtualcell.

the class ReactionRulePropertiesTreeModel method propertyChange.

public void propertyChange(PropertyChangeEvent evt) {
    if (evt.getPropertyName().equals(PropertyConstants.PROPERTY_NAME_NAME)) {
        nodeChanged(rootNode);
    } else if (evt.getPropertyName().equals("entityChange")) {
        nodeChanged(rootNode);
    } else if (evt.getSource() == reactionRule || evt.getSource() instanceof SpeciesPattern || evt.getSource() instanceof MolecularTypePattern) {
        populateTree();
        Object source = evt.getSource();
        if (source == reactionRule) {
            if (participantType == ReactionRuleParticipantType.Reactant && evt.getPropertyName().equals(ReactionRule.PROPERTY_NAME_REACTANT_PATTERNS)) {
                List<ReactantPattern> oldValue = (List<ReactantPattern>) evt.getOldValue();
                if (oldValue != null) {
                    for (ReactantPattern sp : oldValue) {
                        RbmUtils.removePropertyChangeListener(sp.getSpeciesPattern(), this);
                    }
                }
                List<ReactantPattern> newValue = (List<ReactantPattern>) evt.getNewValue();
                if (newValue != null) {
                    for (ReactantPattern sp : newValue) {
                        RbmUtils.addPropertyChangeListener(sp.getSpeciesPattern(), this);
                    }
                }
            } else if (participantType == ReactionRuleParticipantType.Product && evt.getPropertyName().equals(ReactionRule.PROPERTY_NAME_PRODUCT_PATTERNS)) {
                List<ProductPattern> oldValue = (List<ProductPattern>) evt.getOldValue();
                if (oldValue != null) {
                    for (ProductPattern sp : oldValue) {
                        RbmUtils.removePropertyChangeListener(sp.getSpeciesPattern(), this);
                    }
                }
                List<ProductPattern> newValue = (List<ProductPattern>) evt.getNewValue();
                if (newValue != null) {
                    for (ProductPattern sp : newValue) {
                        RbmUtils.addPropertyChangeListener(sp.getSpeciesPattern(), 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)) {
                ComponentStatePattern oldValue = (ComponentStatePattern) evt.getOldValue();
                if (oldValue != null) {
                    oldValue.removePropertyChangeListener(this);
                }
                ComponentStatePattern newValue = (ComponentStatePattern) evt.getNewValue();
                if (newValue != null) {
                    newValue.addPropertyChangeListener(this);
                }
            }
        }
    }
}

Example 22 with ReactantPattern

use of cbit.vcell.model.ReactantPattern in project vcell by virtualcell.

the class ReactionRulePropertiesTreeModel method valueForPathChanged.

@Override
public void valueForPathChanged(TreePath path, Object newValue) {
    Object obj = path.getLastPathComponent();
    if (obj == null || !(obj instanceof BioModelNode)) {
        return;
    }
    BioModelNode selectedNode = (BioModelNode) obj;
    BioModelNode parentNode = (BioModelNode) selectedNode.getParent();
    Object userObject = selectedNode.getUserObject();
    try {
        if (newValue instanceof String) {
            String inputString = (String) newValue;
            if (inputString == null || inputString.length() == 0) {
                return;
            }
            if (userObject instanceof ReactionRule) {
                // TODO: untested!!!
                ((ReactionRule) userObject).setName(inputString);
            }
        } else if (newValue instanceof MolecularComponentPattern) {
            MolecularComponentPattern newMcp = (MolecularComponentPattern) newValue;
            Object parentObject = parentNode == null ? null : parentNode.getUserObject();
            if (parentObject instanceof MolecularTypePattern) {
                MolecularTypePattern mtp = (MolecularTypePattern) parentObject;
                MolecularComponent mc = newMcp.getMolecularComponent();
                MolecularComponentPattern mcp = mtp.getMolecularComponentPattern(mc);
                mcp.setComponentStatePattern(newMcp.getComponentStatePattern());
                BondType bp = mcp.getBondType();
                BondType newbp = newMcp.getBondType();
                mcp.setBondType(newbp);
                // specified -> specified
                if (bp == BondType.Specified && newbp == BondType.Specified) {
                // bond didn't change
                } else if (bp == BondType.Specified && newbp != BondType.Specified) {
                    // specified -> non specified
                    // change the partner to possible
                    mcp.getBond().molecularComponentPattern.setBondType(BondType.Possible);
                    mcp.setBond(null);
                } else if (bp != BondType.Specified && newbp == BondType.Specified) {
                    // non specified -> specified
                    int newBondId = newMcp.getBondId();
                    mcp.setBondId(newBondId);
                    mcp.setBond(newMcp.getBond());
                    mcp.getBond().molecularComponentPattern.setBondId(newBondId);
                    for (ReactantPattern rp : reactionRule.getReactantPatterns()) {
                        rp.getSpeciesPattern().resolveBonds();
                    }
                    for (ProductPattern pp : reactionRule.getProductPatterns()) {
                        pp.getSpeciesPattern().resolveBonds();
                    }
                } else {
                }
            }
        }
    } catch (Exception ex) {
        DialogUtils.showErrorDialog(ownerTree, ex.getMessage());
    }
}