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

Example 21 with MolecularType

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

the class MolecularTypeTreeModel 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;
    Object userObject = selectedNode.getUserObject();
    try {
        if (newValue instanceof String) {
            String inputString = (String) newValue;
            if (inputString == null || inputString.length() == 0) {
                return;
            }
            if (userObject instanceof MolecularType) {
                String mangled = TokenMangler.fixTokenStrict(inputString);
                if (!mangled.equals(inputString)) {
                    String errMsg = ((Displayable) userObject).getDisplayType() + " '" + inputString + "' not legal identifier, try '" + mangled + "'";
                    throw new RuntimeException(errMsg);
                }
                ((MolecularType) userObject).setName(inputString);
            } else if (userObject instanceof MolecularComponent) {
                String mangled = TokenMangler.fixTokenStrict(inputString);
                if (!mangled.equals(inputString)) {
                    String errMsg = ((Displayable) userObject).getDisplayType() + " '" + inputString + "' not legal identifier, try '" + mangled + "'";
                    throw new RuntimeException(errMsg);
                }
                ((MolecularComponent) userObject).setName(inputString);
            } else if (userObject instanceof ComponentStateDefinition) {
                if (inputString.matches("[A-Z_a-z0-9]+")) {
                    ((ComponentStateDefinition) userObject).setName(inputString);
                }
            }
        }
    } catch (Exception ex) {
        DialogUtils.showErrorDialog(ownerTree, ex.getMessage());
    }
}

Example 22 with MolecularType

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

the class MolecularTypeTreeModel 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 {
        populateTree();
        Object object = evt.getSource();
        if (object instanceof MolecularType) {
            List<MolecularComponent> oldValue = (List<MolecularComponent>) evt.getOldValue();
            for (MolecularComponent molecularComponent : oldValue) {
                molecularComponent.removePropertyChangeListener(this);
                for (ComponentStateDefinition componentState : molecularComponent.getComponentStateDefinitions()) {
                    componentState.removePropertyChangeListener(this);
                }
            }
            List<MolecularComponent> newValue = (List<MolecularComponent>) evt.getNewValue();
            for (MolecularComponent molecularComponent : newValue) {
                molecularComponent.addPropertyChangeListener(this);
                for (ComponentStateDefinition componentState : molecularComponent.getComponentStateDefinitions()) {
                    componentState.addPropertyChangeListener(this);
                }
            }
        } else if (object instanceof MolecularComponent) {
            List<ComponentStateDefinition> oldValue = (List<ComponentStateDefinition>) evt.getOldValue();
            for (ComponentStateDefinition componentState : oldValue) {
                componentState.removePropertyChangeListener(this);
            }
            List<ComponentStateDefinition> newValue = (List<ComponentStateDefinition>) evt.getNewValue();
            for (ComponentStateDefinition componentState : newValue) {
                componentState.addPropertyChangeListener(this);
            }
        }
    }
}

Example 23 with MolecularType

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

the class BioModel method propertyChange.

/**
 * This method gets called when a bound property is changed.
 * @param evt A PropertyChangeEvent object describing the event source
 *   	and the property that has changed.
 */
public void propertyChange(java.beans.PropertyChangeEvent evt) {
    // 
    if (evt.getSource() instanceof SimulationContext && evt.getPropertyName().equals("mathDescription") && evt.getNewValue() != null) {
        if (fieldSimulations != null) {
            for (int i = 0; i < fieldSimulations.length; i++) {
                if (fieldSimulations[i].getMathDescription() == evt.getOldValue()) {
                    try {
                        fieldSimulations[i].setMathDescription((MathDescription) evt.getNewValue());
                    } catch (PropertyVetoException e) {
                        System.out.println("error propagating math from SimulationContext '" + ((SimulationContext) evt.getSource()).getName() + "' to Simulation '" + fieldSimulations[i].getName());
                        e.printStackTrace(System.out);
                    }
                }
            }
        }
    }
    // 
    if (evt.getSource() == this && evt.getPropertyName().equals(PropertyConstants.PROPERTY_NAME_SIMULATIONS) && evt.getNewValue() != null) {
        // 
        if (evt.getOldValue() != null) {
            Simulation[] simulations = (Simulation[]) evt.getOldValue();
            for (int i = 0; i < simulations.length; i++) {
                simulations[i].removeVetoableChangeListener(this);
                simulations[i].removePropertyChangeListener(this);
            }
        }
        // 
        if (evt.getOldValue() != null) {
            Simulation[] simulations = (Simulation[]) evt.getNewValue();
            for (int i = 0; i < simulations.length; i++) {
                simulations[i].addVetoableChangeListener(this);
                simulations[i].addPropertyChangeListener(this);
            }
        }
    }
    if (evt.getSource() == this && evt.getPropertyName().equals(PROPERTY_NAME_SIMULATION_CONTEXTS) && evt.getNewValue() != null) {
        // 
        if (evt.getOldValue() != null) {
            SimulationContext[] simulationContexts = (SimulationContext[]) evt.getOldValue();
            for (int i = 0; i < simulationContexts.length; i++) {
                simulationContexts[i].removeVetoableChangeListener(this);
                simulationContexts[i].removePropertyChangeListener(this);
            }
        }
        // 
        if (evt.getOldValue() != null) {
            SimulationContext[] simulationContexts = (SimulationContext[]) evt.getNewValue();
            for (int i = 0; i < simulationContexts.length; i++) {
                simulationContexts[i].addVetoableChangeListener(this);
                simulationContexts[i].addPropertyChangeListener(this);
            }
        }
    }
    if (evt.getSource() == fieldModel && (evt.getPropertyName().equals(Model.PROPERTY_NAME_SPECIES_CONTEXTS) || evt.getPropertyName().equals(Model.PROPERTY_NAME_REACTION_STEPS))) {
        // remove the relationship objects if the biomodelEntity objects were removed
        Set<BioModelEntityObject> removedObjects = relationshipModel.getBioModelEntityObjects();
        for (SpeciesContext sc : fieldModel.getSpeciesContexts()) {
            removedObjects.remove(sc);
        }
        for (ReactionStep rs : fieldModel.getReactionSteps()) {
            removedObjects.remove(rs);
        }
        for (MolecularType mt : fieldModel.getRbmModelContainer().getMolecularTypeList()) {
            removedObjects.remove(mt);
        }
        for (ReactionRule rr : fieldModel.getRbmModelContainer().getReactionRuleList()) {
            removedObjects.remove(rr);
        }
        relationshipModel.removeRelationshipObjects(removedObjects);
    }
    // adjust the relationship model when a molecule gets deleted
    if (evt.getSource() == fieldModel && (evt.getPropertyName().equals(RbmModelContainer.PROPERTY_NAME_MOLECULAR_TYPE_LIST))) {
        @SuppressWarnings("unchecked") List<MolecularType> oldListCopy = new ArrayList<MolecularType>((List<MolecularType>) evt.getOldValue());
        @SuppressWarnings("unchecked") List<MolecularType> newList = (List<MolecularType>) evt.getNewValue();
        if (newList != null && oldListCopy != null && oldListCopy.size() > newList.size()) {
            // something got deleted
            oldListCopy.removeAll(newList);
            for (MolecularType removedMt : oldListCopy) {
                relationshipModel.removeRelationshipObject(removedMt);
            }
        }
    }
    if (evt.getSource() == fieldModel && (evt.getPropertyName().equals(RbmModelContainer.PROPERTY_NAME_REACTION_RULE_LIST))) {
        @SuppressWarnings("unchecked") List<ReactionRule> oldListCopy = new ArrayList<ReactionRule>((List<ReactionRule>) evt.getOldValue());
        @SuppressWarnings("unchecked") List<ReactionRule> newList = (List<ReactionRule>) evt.getNewValue();
        if (newList != null && oldListCopy != null && oldListCopy.size() > newList.size()) {
            // something got deleted
            oldListCopy.removeAll(newList);
            for (ReactionRule removedRr : oldListCopy) {
                relationshipModel.removeRelationshipObject(removedRr);
            }
        }
    }
}

Example 24 with MolecularType

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

the class BioModel method getVCID.

public VCID getVCID(Identifiable identifiable) {
    String localName;
    String className;
    if (identifiable instanceof SpeciesContext) {
        localName = ((SpeciesContext) identifiable).getName();
        className = "SpeciesContext";
    } else if (identifiable instanceof Species) {
        localName = ((Species) identifiable).getCommonName();
        className = VCID.CLASS_SPECIES;
    } else if (identifiable instanceof Structure) {
        localName = ((Structure) identifiable).getName();
        className = "Structure";
    } else if (identifiable instanceof ReactionStep) {
        localName = ((ReactionStep) identifiable).getName();
        className = VCID.CLASS_REACTION_STEP;
    } else if (identifiable instanceof BioModel) {
        localName = ((BioModel) identifiable).getName();
        className = VCID.CLASS_BIOMODEL;
    // }else if (identifiable instanceof SimulationContext){
    // localName = ((SimulationContext)identifiable).getName();
    // className = "Application";
    } else if (identifiable instanceof BioPaxObject) {
        localName = ((BioPaxObject) identifiable).getID();
        className = "BioPaxObject";
    } else if (identifiable instanceof MolecularType) {
        localName = ((MolecularType) identifiable).getName();
        className = "MolecularType";
    } else if (identifiable instanceof ReactionRule) {
        localName = ((ReactionRule) identifiable).getName();
        className = "ReactionRule";
    } else if (identifiable instanceof RbmObservable) {
        localName = ((RbmObservable) identifiable).getName();
        className = "RbmObservable";
    } else {
        throw new RuntimeException("unsupported Identifiable class");
    }
    localName = TokenMangler.mangleVCId(localName);
    VCID vcid;
    try {
        vcid = VCID.fromString(className + "(" + localName + ")");
    } catch (VCID.InvalidVCIDException e) {
        e.printStackTrace();
        throw new RuntimeException(e.getMessage());
    }
    return vcid;
}

Example 25 with MolecularType

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

the class MolecularComponentSmallShape method paintComponent.

// ----------------------------------------------------------------------------------------------
private void paintComponent(Graphics g) {
    Graphics2D g2 = (Graphics2D) g;
    Color colorOld = g.getColor();
    Color componentColor = setComponentColor();
    g2.setColor(componentColor);
    // g.fillRect(xPos, yPos, width, height);
    g2.fillOval(xPos, yPos, componentDiameter, componentDiameter);
    g2.setColor(getDefaultColor(Color.black));
    g2.drawOval(xPos, yPos, componentDiameter, componentDiameter);
    if (mc.getComponentStateDefinitions().size() > 0) {
        if (getDisplayRequirements() == DisplayRequirements.highlightBonds) {
            g2.setColor(componentVeryLightGray);
        } else {
            g2.setColor(componentVeryLightGray);
            if (owner instanceof MolecularType) {
                if (hasErrorIssues(owner, mc)) {
                    g2.setColor(Color.red);
                } else {
                    if (shapeManager != null && !shapeManager.isShowMoleculeColor()) {
                        g2.setColor(componentVeryLightGray);
                    } else {
                        g2.setColor(Color.yellow);
                    }
                }
            } else if (mcp != null) {
                ComponentStatePattern csp = mcp.getComponentStatePattern();
                if (csp != null && !csp.isAny()) {
                    if (shapeManager != null && !shapeManager.isShowMoleculeColor()) {
                        g2.setColor(componentVeryLightGray);
                    } else {
                        g2.setColor(Color.yellow);
                    }
                }
            }
        }
        g2.fillOval(xPos + width - 5, yPos - 2, 5, 5);
        g.setColor(getDefaultColor(Color.darkGray));
        g2.drawOval(xPos + width - 5, yPos - 2, 5, 5);
    }
    g.setColor(colorOld);
}