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

Example 66 with MolecularType

use of org.vcell.model.rbm.MolecularType 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 67 with MolecularType

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

the class ObservablePropertiesPanel method showPopupMenu.

private void showPopupMenu(MouseEvent e, PointLocationInShapeContext locationContext) {
    if (popupFromShapeMenu == null) {
        popupFromShapeMenu = new JPopupMenu();
    }
    if (popupFromShapeMenu.isShowing()) {
        return;
    }
    boolean bDelete = false;
    boolean bAdd = false;
    boolean bEdit = false;
    boolean bRename = false;
    popupFromShapeMenu.removeAll();
    Point mousePoint = e.getPoint();
    final Object deepestShape = locationContext.getDeepestShape();
    final RbmElementAbstract selectedObject;
    if (deepestShape == null) {
        selectedObject = null;
        // when cursor is outside any species pattern we offer to add a new one
        System.out.println("outside");
        popupFromShapeMenu.add(getAddSpeciesPatternFromShapeMenuItem());
    } else if (deepestShape instanceof ComponentStateLargeShape) {
        System.out.println("inside state");
        if (((ComponentStateLargeShape) deepestShape).isHighlighted()) {
            selectedObject = ((ComponentStateLargeShape) deepestShape).getComponentStatePattern();
        } else {
            return;
        }
    } else if (deepestShape instanceof MolecularComponentLargeShape) {
        System.out.println("inside component");
        if (((MolecularComponentLargeShape) deepestShape).isHighlighted()) {
            selectedObject = ((MolecularComponentLargeShape) deepestShape).getMolecularComponentPattern();
        } else {
            return;
        }
    } else if (deepestShape instanceof MolecularTypeLargeShape) {
        System.out.println("inside molecule");
        if (((MolecularTypeLargeShape) deepestShape).isHighlighted()) {
            selectedObject = ((MolecularTypeLargeShape) deepestShape).getMolecularTypePattern();
        } else {
            return;
        }
    } else if (deepestShape instanceof SpeciesPatternLargeShape) {
        System.out.println("inside species pattern");
        if (((SpeciesPatternLargeShape) deepestShape).isHighlighted()) {
            selectedObject = ((SpeciesPatternLargeShape) deepestShape).getSpeciesPattern();
        } else {
            return;
        }
    } else {
        selectedObject = null;
        System.out.println("inside something else?");
        return;
    }
    if (selectedObject instanceof SpeciesPattern) {
        getAddFromShapeMenu().setText(VCellErrorMessages.AddMolecularTypes);
        getAddFromShapeMenu().removeAll();
        for (final MolecularType mt : bioModel.getModel().getRbmModelContainer().getMolecularTypeList()) {
            JMenuItem menuItem = new JMenuItem(mt.getName());
            Graphics gc = splitPaneHorizontal.getGraphics();
            Icon icon = new MolecularTypeSmallShape(4, 4, mt, null, gc, mt, null, issueManager);
            menuItem.setIcon(icon);
            getAddFromShapeMenu().add(menuItem);
            menuItem.addActionListener(new ActionListener() {

                public void actionPerformed(ActionEvent e) {
                    MolecularTypePattern molecularTypePattern = new MolecularTypePattern(mt);
                    ((SpeciesPattern) selectedObject).addMolecularTypePattern(molecularTypePattern);
                    SwingUtilities.invokeLater(new Runnable() {

                        public void run() {
                        }
                    });
                }
            });
        }
        JMenu compartmentMenuItem = new JMenu("Specify structure (for all)");
        compartmentMenuItem.removeAll();
        for (final Structure struct : bioModel.getModel().getStructures()) {
            JMenuItem menuItem = new JMenuItem(struct.getName());
            compartmentMenuItem.add(menuItem);
            menuItem.addActionListener(new ActionListener() {

                public void actionPerformed(ActionEvent e) {
                    String nameStruct = e.getActionCommand();
                    Structure struct = bioModel.getModel().getStructure(nameStruct);
                    observable.setStructure(struct);
                    SwingUtilities.invokeLater(new Runnable() {

                        public void run() {
                            // repaint tree
                            observableTreeModel.populateTree();
                        // observableTree.scrollPathToVisible(path);	// scroll back up to show the observable
                        }
                    });
                }
            });
        }
        JMenuItem deleteMenuItem = new JMenuItem("Delete Species Pattern");
        deleteMenuItem.addActionListener(new ActionListener() {

            public void actionPerformed(ActionEvent e) {
                // observable.getSpeciesPatternList().remove((SpeciesPattern)selectedObject);
                observable.removeSpeciesPattern((SpeciesPattern) selectedObject);
                final TreePath path = observableTreeModel.findObjectPath(null, observable);
                observableTree.setSelectionPath(path);
                SwingUtilities.invokeLater(new Runnable() {

                    public void run() {
                        // repaint tree
                        observableTreeModel.populateTree();
                        // scroll back up to show the observable
                        observableTree.scrollPathToVisible(path);
                    }
                });
            }
        });
        popupFromShapeMenu.add(deleteMenuItem);
        popupFromShapeMenu.add(new JSeparator());
        popupFromShapeMenu.add(getAddFromShapeMenu());
        popupFromShapeMenu.add(compartmentMenuItem);
    } else if (selectedObject instanceof MolecularTypePattern) {
        MolecularTypePattern mtp = (MolecularTypePattern) selectedObject;
        String moveRightMenuText = "Move <b>" + "right" + "</b>";
        moveRightMenuText = "<html>" + moveRightMenuText + "</html>";
        JMenuItem moveRightMenuItem = new JMenuItem(moveRightMenuText);
        Icon icon = VCellIcons.moveRightIcon;
        moveRightMenuItem.setIcon(icon);
        moveRightMenuItem.addActionListener(new ActionListener() {

            public void actionPerformed(ActionEvent e) {
                MolecularTypePattern from = (MolecularTypePattern) selectedObject;
                SpeciesPattern sp = locationContext.sps.getSpeciesPattern();
                sp.shiftRight(from);
                observableTreeModel.populateTree();
            }
        });
        popupFromShapeMenu.add(moveRightMenuItem);
        String moveLeftMenuText = "Move <b>" + "left" + "</b>";
        moveLeftMenuText = "<html>" + moveLeftMenuText + "</html>";
        JMenuItem moveLeftMenuItem = new JMenuItem(moveLeftMenuText);
        icon = VCellIcons.moveLeftIcon;
        moveLeftMenuItem.setIcon(icon);
        moveLeftMenuItem.addActionListener(new ActionListener() {

            public void actionPerformed(ActionEvent e) {
                MolecularTypePattern from = (MolecularTypePattern) selectedObject;
                SpeciesPattern sp = locationContext.sps.getSpeciesPattern();
                sp.shiftLeft(from);
                observableTreeModel.populateTree();
            }
        });
        popupFromShapeMenu.add(moveLeftMenuItem);
        popupFromShapeMenu.add(new JSeparator());
        String deleteMenuText = "Delete <b>" + mtp.getMolecularType().getName() + "</b>";
        deleteMenuText = "<html>" + deleteMenuText + "</html>";
        JMenuItem deleteMenuItem = new JMenuItem(deleteMenuText);
        deleteMenuItem.addActionListener(new ActionListener() {

            public void actionPerformed(ActionEvent e) {
                MolecularTypePattern mtp = (MolecularTypePattern) selectedObject;
                SpeciesPattern sp = locationContext.sps.getSpeciesPattern();
                sp.removeMolecularTypePattern(mtp);
            }
        });
        popupFromShapeMenu.add(deleteMenuItem);
    } else if (selectedObject instanceof MolecularComponentPattern) {
        manageComponentPatternFromShape(selectedObject, locationContext, ShowWhat.ShowBond);
        bDelete = false;
    } else if (selectedObject instanceof ComponentStatePattern) {
        MolecularComponentPattern mcp = ((ComponentStateLargeShape) deepestShape).getMolecularComponentPattern();
        manageComponentPatternFromShape(mcp, locationContext, ShowWhat.ShowState);
    }
    if (bRename) {
        popupFromShapeMenu.add(getRenameFromShapeMenuItem());
    }
    if (bDelete) {
        popupFromShapeMenu.add(getDeleteFromShapeMenuItem());
    }
    if (bEdit) {
        popupFromShapeMenu.add(getEditFromShapeMenuItem());
    }
    if (bAdd) {
        popupFromShapeMenu.add(new JSeparator());
        popupFromShapeMenu.add(getAddFromShapeMenu());
    }
    popupFromShapeMenu.show(e.getComponent(), mousePoint.x, mousePoint.y);
}

Example 68 with MolecularType

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

the class ObservableTableModel method isCellEditable.

public boolean isCellEditable(int row, int columnIndex) {
    Column col = Column.values()[columnIndex];
    if (col == Column.name) {
        return true;
    }
    RbmObservable o = getValueAt(row);
    if (o == null) {
        return false;
    }
    if (col == Column.structure) {
        return false;
    }
    if (col == Column.type) {
        return true;
    }
    if (col == Column.depiction) {
        return false;
    }
    final List<SpeciesPattern> spList = o.getSpeciesPatternList();
    for (SpeciesPattern sp : spList) {
        final List<MolecularTypePattern> mtpList = sp.getMolecularTypePatterns();
        for (MolecularTypePattern mtp : mtpList) {
            MolecularType mt = mtp.getMolecularType();
            if (mt.getComponentList().size() != 0) {
                return false;
            }
        }
    }
    return true;
}

Example 69 with MolecularType

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

the class ObservableTreeModel method createMolecularTypePatternNode.

private BioModelNode createMolecularTypePatternNode(MolecularTypePattern molecularTypePattern) {
    MolecularType molecularType = molecularTypePattern.getMolecularType();
    BioModelNode node = new BioModelNode(molecularTypePattern, true);
    for (MolecularComponent mc : molecularType.getComponentList()) {
        if (bShowDetails || molecularTypePattern.getMolecularComponentPattern(mc).isbVisible()) {
            BioModelNode n = createMolecularComponentPatternNode(molecularTypePattern.getMolecularComponentPattern(mc));
            if (n != null) {
                node.add(n);
            }
        }
    }
    return node;
}

Example 70 with MolecularType

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

the class PhysiologyRelationshipTableModel method refreshData.

private void refreshData() {
    ArrayList<PhysiologyRelationshipTableRow> pathwayObjectList = new ArrayList<PhysiologyRelationshipTableRow>();
    if (bioModel != null) {
        HashSet<RelationshipObject> relationshipObjects = null;
        if (bioModelEntityObject != null) {
            relationshipObjects = bioModel.getRelationshipModel().getRelationshipObjects(bioModelEntityObject);
        }
        List<PhysiologyRelationshipTableRow> allPathwayObjectList = new ArrayList<PhysiologyRelationshipTableRow>();
        for (BioPaxObject bpObject1 : bioModel.getPathwayModel().getBiopaxObjects()) {
            if ((bpObject1 instanceof PhysicalEntity && (bioModelEntityObject == null || bioModelEntityObject instanceof SpeciesContext)) || (bpObject1 instanceof Conversion && (bioModelEntityObject == null || bioModelEntityObject instanceof ModelProcess)) || (bpObject1 instanceof PhysicalEntity && (bioModelEntityObject == null || bioModelEntityObject instanceof MolecularType))) {
                PhysiologyRelationshipTableRow entityRow = new PhysiologyRelationshipTableRow(bpObject1);
                if (relationshipObjects != null) {
                    for (RelationshipObject ro : relationshipObjects) {
                        if (ro.getBioPaxObject() == entityRow.getBioPaxObject()) {
                            entityRow.setSelected(true);
                            break;
                        }
                    }
                }
                if (!bShowLinkOnly || entityRow.selected) {
                    allPathwayObjectList.add(entityRow);
                }
            }
        }
        if (searchText == null || searchText.length() == 0) {
            pathwayObjectList.addAll(allPathwayObjectList);
        } else {
            for (PhysiologyRelationshipTableRow rs : allPathwayObjectList) {
                BioPaxObject bpObject = rs.getBioPaxObject();
                String lowerCaseSearchText = searchText.toLowerCase();
                if (getLabel(bpObject).toLowerCase().contains(lowerCaseSearchText) || getType(bpObject).toLowerCase().contains(lowerCaseSearchText)) {
                    pathwayObjectList.add(rs);
                }
            }
        }
    }
    setData(pathwayObjectList);
    GuiUtils.flexResizeTableColumns(ownerTable);
}