Examples with StructureToolShapeIcon cbit.vcell.graph.gui.StructureToolShapeIcon used on opensource projects

Example 1 with StructureToolShapeIcon

use of cbit.vcell.graph.gui.StructureToolShapeIcon in project vcell by virtualcell.

the class BioModelEditorModelPanel method newButton2Pressed.

private void newButton2Pressed() throws ModelException, PropertyVetoException {
    computeCurrentSelectedTable();
    if (currentSelectedTable == reactionsTable) {
        if (bioModel.getModel().getRbmModelContainer().getMolecularTypeList().isEmpty()) {
            PopupGenerator.showInfoDialog(this, VCellErrorMessages.MustBeRuleBased);
            return;
        }
        if (bioModel.getModel().getNumStructures() == 1) {
            Structure s = bioModel.getModel().getStructure(0);
            newObject = makeReactionRule(s);
            if (newObject != null) {
                for (int i = 0; i < currentSelectedTableModel.getRowCount(); i++) {
                    if (currentSelectedTableModel.getValueAt(i) == newObject) {
                        currentSelectedTable.setRowSelectionInterval(i, i);
                        break;
                    }
                }
            }
        } else if (bioModel.getModel().getNumStructures() > 1) {
            final JPopupMenu menu = new JPopupMenu("Choose compartment");
            for (int i = 0; i < bioModel.getModel().getNumStructures(); i++) {
                Structure s = bioModel.getModel().getStructure(i);
                String sName = s.getName();
                JMenuItem menuItem = new JMenuItem("In " + s.getTypeName() + " " + sName);
                menuItem.setIcon(new StructureToolShapeIcon(17));
                menu.add(menuItem);
                menuItem.addActionListener(new ActionListener() {

                    public void actionPerformed(ActionEvent e) {
                        newObject = makeReactionRule(s);
                        if (newObject != null) {
                            for (int i = 0; i < currentSelectedTableModel.getRowCount(); i++) {
                                if (currentSelectedTableModel.getValueAt(i) == newObject) {
                                    currentSelectedTable.setRowSelectionInterval(i, i);
                                    break;
                                }
                            }
                        }
                    }
                });
            }
            menu.show(newButton2, 0, newButton2.getHeight());
        }
    }
}

Example 2 with StructureToolShapeIcon

use of cbit.vcell.graph.gui.StructureToolShapeIcon in project vcell by virtualcell.

the class BioModelEditorModelPanel method newButtonPressed.

private void newButtonPressed() throws ModelException, PropertyVetoException {
    newObject = null;
    computeCurrentSelectedTable();
    if (currentSelectedTable == speciesTable) {
        if (bioModel.getModel().getNumStructures() == 1) {
            newObject = bioModel.getModel().createSpeciesContext(bioModel.getModel().getStructures()[0]);
        } else if (bioModel.getModel().getNumStructures() > 1) {
            final JPopupMenu menu = new JPopupMenu("Choose compartment");
            for (int i = 0; i < bioModel.getModel().getNumStructures(); i++) {
                Structure s = bioModel.getModel().getStructure(i);
                String sName = s.getName();
                JMenuItem menuItem = new JMenuItem("In " + s.getTypeName() + " " + sName);
                menuItem.setIcon(new StructureToolShapeIcon(17));
                menu.add(menuItem);
                menuItem.addActionListener(new ActionListener() {

                    public void actionPerformed(ActionEvent e) {
                        newObject = bioModel.getModel().createSpeciesContext(s);
                    }
                });
            }
            menu.show(newButton, 0, newButton.getHeight());
        }
    } else if (currentSelectedTable == molecularTypeTable) {
        if (bioModel.getModel().getRbmModelContainer() != null) {
            MolecularType mt = bioModel.getModel().getRbmModelContainer().createMolecularType();
            bioModel.getModel().getRbmModelContainer().addMolecularType(mt, true);
            newObject = mt;
        }
    } else if (currentSelectedTable == observablesTable) {
        if (bioModel.getModel().getRbmModelContainer() != null) {
            if (bioModel.getModel().getRbmModelContainer().getMolecularTypeList().isEmpty()) {
                PopupGenerator.showInfoDialog(this, VCellErrorMessages.MustBeRuleBased);
                return;
            }
            if (bioModel.getModel().getNumStructures() == 1) {
                RbmObservable o = bioModel.getModel().getRbmModelContainer().createObservable(RbmObservable.ObservableType.Molecules);
                bioModel.getModel().getRbmModelContainer().addObservable(o);
                SpeciesPattern sp = new SpeciesPattern();
                o.addSpeciesPattern(sp);
                newObject = o;
            } else if (bioModel.getModel().getNumStructures() > 1) {
                final JPopupMenu menu = new JPopupMenu("Choose compartment");
                for (int i = 0; i < bioModel.getModel().getNumStructures(); i++) {
                    Structure s = bioModel.getModel().getStructure(i);
                    String sName = s.getName();
                    JMenuItem menuItem = new JMenuItem("In " + s.getTypeName() + " " + sName);
                    menuItem.setIcon(new StructureToolShapeIcon(17));
                    menu.add(menuItem);
                    menuItem.addActionListener(new ActionListener() {

                        public void actionPerformed(ActionEvent e) {
                            RbmObservable o = bioModel.getModel().getRbmModelContainer().createObservable(RbmObservable.ObservableType.Molecules, null, s);
                            o.setStructure(s);
                            try {
                                bioModel.getModel().getRbmModelContainer().addObservable(o);
                            } catch (ModelException | PropertyVetoException e1) {
                                e1.printStackTrace();
                                throw new RuntimeException(e1.getMessage(), e1);
                            }
                            SpeciesPattern sp = new SpeciesPattern();
                            o.addSpeciesPattern(sp);
                            newObject = o;
                            if (newObject != null) {
                                for (int i = 0; i < currentSelectedTableModel.getRowCount(); i++) {
                                    if (currentSelectedTableModel.getValueAt(i) == newObject) {
                                        currentSelectedTable.setRowSelectionInterval(i, i);
                                        break;
                                    }
                                }
                            }
                        }
                    });
                }
                menu.show(newButton, 0, newButton.getHeight());
            }
        }
    } else if (currentSelectedTable == structuresTable) {
        try {
            Feature feature = bioModel.getModel().createFeature();
            newObject = feature;
        } catch (Exception e) {
            e.printStackTrace();
            DialogUtils.showErrorDialog(this, e.getMessage(), e);
        }
    } else if (currentSelectedTable == reactionsTable) {
        if (bioModel.getModel().getNumStructures() == 1) {
            SimpleReaction reactionStep = bioModel.getModel().createSimpleReaction(bioModel.getModel().getStructures()[0]);
            newObject = reactionStep;
        } else {
            addNewReaction();
        }
    }
    if (newObject != null) {
        for (int i = 0; i < currentSelectedTableModel.getRowCount(); i++) {
            if (currentSelectedTableModel.getValueAt(i) == newObject) {
                currentSelectedTable.setRowSelectionInterval(i, i);
                break;
            }
        }
    }
}

Example 3 with StructureToolShapeIcon

use of cbit.vcell.graph.gui.StructureToolShapeIcon in project vcell by virtualcell.

the class BioModelEditorModelPanel method duplicateButtonPressed.

private void duplicateButtonPressed() {
    computeCurrentSelectedTable();
    int row = currentSelectedTable.getSelectedRow();
    System.out.println("Duplicate Button Pressed for row " + row);
    if (currentSelectedTable == reactionsTable) {
        ModelProcess mp = reactionTableModel.getValueAt(row);
        if (!(mp instanceof ReactionRule)) {
            return;
        }
        ReactionRule oldRule = (ReactionRule) mp;
        if (bioModel.getModel().getNumStructures() == 1) {
            duplicateReactionRule(oldRule, oldRule.getStructure());
        } else if (bioModel.getModel().getNumStructures() > 1) {
            final JPopupMenu menu = new JPopupMenu("Choose compartment");
            for (int i = 0; i < bioModel.getModel().getNumStructures(); i++) {
                String ourType = oldRule.getStructure().getTypeName();
                Structure s = bioModel.getModel().getStructure(i);
                String theirType = s.getTypeName();
                if (!ourType.equals(theirType)) {
                    // offer to duplicate only within structures of the same type as the original,
                    continue;
                // otherwise units will be meaningless (surface vs volume)
                }
                String sName = s.getName();
                JMenuItem menuItem = new JMenuItem("In " + s.getTypeName() + " " + sName);
                menuItem.setIcon(new StructureToolShapeIcon(17));
                menu.add(menuItem);
                menuItem.addActionListener(new ActionListener() {

                    @Override
                    public void actionPerformed(ActionEvent e) {
                        newObject = duplicateReactionRule(oldRule, s);
                    // moves selection on the newly created object
                    // if (newObject != null) {
                    // for (int i = 0; i < currentSelectedTableModel.getRowCount(); i ++) {
                    // if (currentSelectedTableModel.getValueAt(i) == newObject) {
                    // currentSelectedTable.setRowSelectionInterval(i, i);
                    // break;
                    // }
                    // }
                    // }
                    }
                });
            }
            menu.show(duplicateButton, 0, duplicateButton.getHeight());
        }
    } else if (currentSelectedTable == speciesTable) {
        SpeciesContext sc = speciesTableModel.getValueAt(row);
        if (!sc.hasSpeciesPattern()) {
            return;
        }
        if (bioModel.getModel().getNumStructures() == 1) {
            duplicateSpecies(sc, sc.getStructure(), bioModel.getModel());
        } else if (bioModel.getModel().getNumStructures() > 1) {
            final JPopupMenu menu = new JPopupMenu("Choose compartment");
            for (int i = 0; i < bioModel.getModel().getNumStructures(); i++) {
                String ourType = sc.getStructure().getTypeName();
                Structure s = bioModel.getModel().getStructure(i);
                String theirType = s.getTypeName();
                if (!ourType.equals(theirType)) {
                    continue;
                }
                String sName = s.getName();
                JMenuItem menuItem = new JMenuItem("In " + s.getTypeName() + " " + sName);
                menuItem.setIcon(new StructureToolShapeIcon(17));
                menu.add(menuItem);
                menuItem.addActionListener(new ActionListener() {

                    @Override
                    public void actionPerformed(ActionEvent e) {
                        newObject = duplicateSpecies(sc, s, bioModel.getModel());
                    }
                });
            }
            menu.show(duplicateButton, 0, duplicateButton.getHeight());
        }
    } else if (currentSelectedTable == observablesTable) {
        RbmObservable o = observableTableModel.getValueAt(row);
        if (o.getSpeciesPatternList().isEmpty()) {
            return;
        }
        if (bioModel.getModel().getNumStructures() == 1) {
            duplicateObservable(o, o.getStructure(), bioModel.getModel());
        } else if (bioModel.getModel().getNumStructures() > 1) {
            final JPopupMenu menu = new JPopupMenu("Choose compartment");
            for (int i = 0; i < bioModel.getModel().getNumStructures(); i++) {
                Structure s = bioModel.getModel().getStructure(i);
                String sName = s.getName();
                JMenuItem menuItem = new JMenuItem("In " + s.getTypeName() + " " + sName);
                menuItem.setIcon(new StructureToolShapeIcon(17));
                menu.add(menuItem);
                menuItem.addActionListener(new ActionListener() {

                    @Override
                    public void actionPerformed(ActionEvent e) {
                        newObject = duplicateObservable(o, s, bioModel.getModel());
                    }
                });
            }
            menu.show(duplicateButton, 0, duplicateButton.getHeight());
        }
    }
}