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

Example 1 with MolecularTypePattern

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

the class ViewObservablesMapPanel method initialize.

private void initialize() {
    try {
        // --------------------------------------- the split panels
        setName("ViewGeneratedSpeciesPanel");
        setLayout(new BorderLayout());
        JPanel topPanel = new JPanel();
        topPanel.setLayout(new GridBagLayout());
        JPanel bottomPanel = new JPanel();
        bottomPanel.setLayout(new GridBagLayout());
        JSplitPane splitPaneHorizontal = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
        splitPaneHorizontal.setDividerSize(10);
        splitPaneHorizontal.setOneTouchExpandable(true);
        splitPaneHorizontal.setDividerLocation(260);
        splitPaneHorizontal.setResizeWeight(0.5);
        splitPaneHorizontal.setTopComponent(topPanel);
        splitPaneHorizontal.setBottomComponent(bottomPanel);
        add(splitPaneHorizontal, BorderLayout.CENTER);
        // ---------------------------------------- species shape panel
        shapePanelSpecies = new LargeShapePanel() {

            @Override
            public void paintComponent(Graphics g) {
                super.paintComponent(g);
                if (spls != null) {
                    spls.paintSelf(g);
                }
            }

            @Override
            public DisplayMode getDisplayMode() {
                return DisplayMode.other;
            }

            @Override
            public RuleAnalysisChanged hasStateChanged(String reactionRuleName, MolecularComponentPattern molecularComponentPattern) {
                return RuleAnalysisChanged.UNCHANGED;
            }

            @Override
            public RuleAnalysisChanged hasStateChanged(MolecularComponentPattern molecularComponentPattern) {
                return RuleAnalysisChanged.UNCHANGED;
            }

            @Override
            public RuleAnalysisChanged hasBondChanged(String reactionRuleName, MolecularComponentPattern molecularComponentPattern) {
                return RuleAnalysisChanged.UNCHANGED;
            }

            @Override
            public RuleAnalysisChanged hasBondChanged(MolecularComponentPattern molecularComponentPattern) {
                return RuleAnalysisChanged.UNCHANGED;
            }

            @Override
            public RuleAnalysisChanged hasNoMatch(String reactionRuleName, MolecularTypePattern mtp) {
                return RuleAnalysisChanged.UNCHANGED;
            }

            @Override
            public RuleAnalysisChanged hasNoMatch(MolecularTypePattern molecularTypePattern) {
                return RuleAnalysisChanged.UNCHANGED;
            }

            @Override
            public RuleParticipantSignature getSignature() {
                return null;
            }

            @Override
            public GroupingCriteria getCriteria() {
                return null;
            }

            @Override
            public boolean isViewSingleRow() {
                return true;
            }
        };
        shapePanelSpecies.setLayout(new GridBagLayout());
        shapePanelSpecies.setBackground(Color.white);
        // not really editable but we don't want the brown contours here
        shapePanelSpecies.setEditable(true);
        shapePanelSpecies.setShowMoleculeColor(true);
        shapePanelSpecies.setShowNonTrivialOnly(true);
        Border loweredBevelBorder = BorderFactory.createLoweredBevelBorder();
        JScrollPane scrollPaneSpecies = new JScrollPane(shapePanelSpecies);
        scrollPaneSpecies.setBorder(loweredBevelBorder);
        scrollPaneSpecies.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
        scrollPaneSpecies.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_NEVER);
        JPanel optionsPanelSpecies = new JPanel();
        optionsPanelSpecies.setLayout(new GridBagLayout());
        getZoomSmallerButtonSpecies().setEnabled(true);
        getZoomLargerButtonSpecies().setEnabled(true);
        shapePanelSpecies.zoomSmaller();
        shapePanelSpecies.zoomSmaller();
        GridBagConstraints gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = 0;
        gbc.insets = new Insets(0, 0, 0, 10);
        gbc.anchor = GridBagConstraints.WEST;
        optionsPanelSpecies.add(getZoomLargerButtonSpecies(), gbc);
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = 1;
        gbc.insets = new Insets(2, 0, 4, 10);
        gbc.anchor = GridBagConstraints.WEST;
        optionsPanelSpecies.add(getZoomSmallerButtonSpecies(), gbc);
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = 2;
        gbc.weightx = 1;
        // fake cell used for filling all the vertical empty space
        gbc.weighty = 1;
        gbc.anchor = GridBagConstraints.WEST;
        gbc.insets = new Insets(4, 4, 4, 10);
        optionsPanelSpecies.add(new JLabel(""), gbc);
        JPanel containerOfScrollPanelSpecies = new JPanel();
        containerOfScrollPanelSpecies.setLayout(new BorderLayout());
        containerOfScrollPanelSpecies.add(optionsPanelSpecies, BorderLayout.WEST);
        containerOfScrollPanelSpecies.add(scrollPaneSpecies, BorderLayout.CENTER);
        Dimension dimS = new Dimension(500, 125);
        // dimension of shape panel
        containerOfScrollPanelSpecies.setPreferredSize(dimS);
        containerOfScrollPanelSpecies.setMinimumSize(dimS);
        containerOfScrollPanelSpecies.setMaximumSize(dimS);
        shapePanelObservable = new LargeShapePanel() {

            @Override
            public void paintComponent(Graphics g) {
                super.paintComponent(g);
                for (SpeciesPatternLargeShape sps : spsList) {
                    if (sps == null) {
                        continue;
                    }
                    sps.paintSelf(g);
                }
            }

            @Override
            public DisplayMode getDisplayMode() {
                return DisplayMode.other;
            }

            @Override
            public RuleAnalysisChanged hasStateChanged(String reactionRuleName, MolecularComponentPattern molecularComponentPattern) {
                return RuleAnalysisChanged.UNCHANGED;
            }

            @Override
            public RuleAnalysisChanged hasStateChanged(MolecularComponentPattern molecularComponentPattern) {
                return RuleAnalysisChanged.UNCHANGED;
            }

            @Override
            public RuleAnalysisChanged hasBondChanged(String reactionRuleName, MolecularComponentPattern molecularComponentPattern) {
                return RuleAnalysisChanged.UNCHANGED;
            }

            @Override
            public RuleAnalysisChanged hasBondChanged(MolecularComponentPattern molecularComponentPattern) {
                return RuleAnalysisChanged.UNCHANGED;
            }

            @Override
            public RuleAnalysisChanged hasNoMatch(String reactionRuleName, MolecularTypePattern mtp) {
                return RuleAnalysisChanged.UNCHANGED;
            }

            @Override
            public RuleAnalysisChanged hasNoMatch(MolecularTypePattern molecularTypePattern) {
                return RuleAnalysisChanged.UNCHANGED;
            }

            @Override
            public RuleParticipantSignature getSignature() {
                return null;
            }

            @Override
            public GroupingCriteria getCriteria() {
                return null;
            }

            @Override
            public boolean isViewSingleRow() {
                return true;
            }
        };
        // 
        DefaultScrollTableCellRenderer rbmSpeciesPatternCellRenderer = new DefaultScrollTableCellRenderer() {

            @Override
            public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
                super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
                if (table.getModel() instanceof GeneratedSpeciesTableModel2) {
                    Object selectedObject = null;
                    if (table.getModel() == speciesTableModel) {
                        selectedObject = speciesTableModel.getValueAt(row);
                    }
                    if (selectedObject != null) {
                        if (selectedObject instanceof GeneratedSpeciesTableRow && value instanceof String) {
                            SpeciesPattern sp = ((GeneratedSpeciesTableRow) selectedObject).getSpecies().getSpeciesPattern();
                            String text = "<html>";
                            text += RbmTableRenderer.toHtml(sp, isSelected);
                            text += "</html>";
                            setText(text);
                        }
                    }
                }
                return this;
            }
        };
        // shapePanelObservable.setLayout(null);
        shapePanelObservable.setLayout(new GridBagLayout());
        shapePanelObservable.setBackground(Color.white);
        shapePanelObservable.setEditable(true);
        shapePanelObservable.setShowMoleculeColor(true);
        shapePanelObservable.setShowNonTrivialOnly(true);
        JScrollPane scrollPaneObservable = new JScrollPane(shapePanelObservable);
        scrollPaneObservable.setBorder(loweredBevelBorder);
        scrollPaneObservable.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
        scrollPaneObservable.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_NEVER);
        JPanel optionsPanelObservable = new JPanel();
        optionsPanelObservable.setLayout(new GridBagLayout());
        getZoomSmallerButtonObservable().setEnabled(true);
        getZoomLargerButtonObservable().setEnabled(true);
        shapePanelObservable.zoomSmaller();
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = 0;
        gbc.insets = new Insets(0, 0, 0, 10);
        gbc.anchor = GridBagConstraints.WEST;
        optionsPanelObservable.add(getZoomLargerButtonObservable(), gbc);
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = 1;
        gbc.insets = new Insets(2, 0, 4, 10);
        gbc.anchor = GridBagConstraints.WEST;
        optionsPanelObservable.add(getZoomSmallerButtonObservable(), gbc);
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = 2;
        gbc.weightx = 1;
        // fake cell used for filling all the vertical empty space
        gbc.weighty = 1;
        gbc.anchor = GridBagConstraints.WEST;
        gbc.insets = new Insets(4, 4, 4, 10);
        optionsPanelObservable.add(new JLabel(""), gbc);
        JPanel containerOfScrollPanelObservable = new JPanel();
        containerOfScrollPanelObservable.setLayout(new BorderLayout());
        containerOfScrollPanelObservable.add(optionsPanelObservable, BorderLayout.WEST);
        containerOfScrollPanelObservable.add(scrollPaneObservable, BorderLayout.CENTER);
        Dimension dimO = new Dimension(500, 100);
        // dimension of shape panel
        containerOfScrollPanelObservable.setPreferredSize(dimO);
        containerOfScrollPanelObservable.setMinimumSize(dimO);
        containerOfScrollPanelObservable.setMaximumSize(dimO);
        // -------------- connection between tables, table models, selection models, renderers, event handlers
        speciesTable = new EditorScrollTable();
        speciesTableModel = new GeneratedSpeciesTableModel2(speciesTable, owner);
        speciesTable.setModel(speciesTableModel);
        speciesTable.getSelectionModel().addListSelectionListener(eventHandlerS);
        speciesTable.getModel().addTableModelListener(eventHandlerS);
        observablesTable = new EditorScrollTable();
        observablesTableModel = new ObservablesGroupTableModel(observablesTable, owner, speciesTableModel);
        observablesTable.setModel(observablesTableModel);
        observablesTable.getSelectionModel().addListSelectionListener(eventHandlerO);
        observablesTable.getModel().addTableModelListener(eventHandlerO);
        speciesTable.getColumnModel().getColumn(GeneratedSpeciesTableModel2.iColDefinition).setCellRenderer(rbmSpeciesPatternCellRenderer);
        DefaultTableCellRenderer rightRenderer = new DefaultTableCellRenderer();
        rightRenderer.setHorizontalAlignment(JLabel.RIGHT);
        // speciesTable.getColumnModel().getColumn(GeneratedSpeciesTableModel2.iColMultiplier).setCellRenderer(rightRenderer);	// right align
        // left column wide enough for title
        speciesTable.getColumnModel().getColumn(GeneratedSpeciesTableModel2.iColMultiplier).setMaxWidth(70);
        speciesTable.addMouseMotionListener(new // add toolTipText for each table cell
        MouseMotionAdapter() {

            public void mouseMoved(MouseEvent e) {
                Point p = e.getPoint();
                int row = speciesTable.rowAtPoint(p);
                int column = speciesTable.columnAtPoint(p);
                speciesTable.setToolTipText(String.valueOf(speciesTable.getValueAt(row, column)));
            }
        });
        // ---------------------------------------------- top panel
        int gridy = 0;
        gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.weightx = 1.0;
        gbc.weighty = 1.0;
        gbc.gridwidth = 8;
        gbc.fill = GridBagConstraints.BOTH;
        gbc.insets = new Insets(4, 4, 4, 4);
        observablesTable.setPreferredScrollableViewportSize(new Dimension(400, 200));
        topPanel.add(observablesTable.getEnclosingScrollPane(), gbc);
        gridy++;
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.anchor = GridBagConstraints.LINE_END;
        gbc.insets = new Insets(4, 4, 4, 4);
        topPanel.add(new JLabel("Search "), gbc);
        textFieldSearchObservables = new JTextField(70);
        textFieldSearchObservables.addActionListener(eventHandlerO);
        textFieldSearchObservables.getDocument().addDocumentListener(eventHandlerO);
        textFieldSearchObservables.putClientProperty("JTextField.variant", "search");
        gbc = new java.awt.GridBagConstraints();
        gbc.weightx = 1.0;
        gbc.gridx = 1;
        gbc.gridy = gridy;
        gbc.gridwidth = 3;
        gbc.anchor = GridBagConstraints.LINE_START;
        gbc.fill = java.awt.GridBagConstraints.HORIZONTAL;
        gbc.insets = new Insets(4, 0, 4, 4);
        topPanel.add(textFieldSearchObservables, gbc);
        gbc = new GridBagConstraints();
        gbc.gridx = 4;
        gbc.gridy = gridy;
        gbc.fill = GridBagConstraints.HORIZONTAL;
        gbc.insets = new Insets(4, 4, 4, 10);
        topPanel.add(totalObservablesLabel, gbc);
        gridy++;
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        // gbc.weightx = 1.0;
        gbc.gridwidth = 8;
        gbc.anchor = GridBagConstraints.LINE_END;
        gbc.fill = java.awt.GridBagConstraints.BOTH;
        gbc.insets = new Insets(4, 4, 4, 4);
        topPanel.add(containerOfScrollPanelObservable, gbc);
        // -------------------------------------------- bottom panel
        gridy = 0;
        gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.weightx = 1.0;
        gbc.weighty = 1.0;
        gbc.gridwidth = 8;
        gbc.fill = GridBagConstraints.BOTH;
        gbc.insets = new Insets(4, 4, 4, 4);
        speciesTable.setPreferredScrollableViewportSize(new Dimension(400, 200));
        bottomPanel.add(speciesTable.getEnclosingScrollPane(), gbc);
        gridy++;
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.anchor = GridBagConstraints.LINE_END;
        gbc.insets = new Insets(4, 4, 4, 4);
        bottomPanel.add(new JLabel("Search "), gbc);
        textFieldSearchSpecies = new JTextField(70);
        textFieldSearchSpecies.addActionListener(eventHandlerS);
        textFieldSearchSpecies.getDocument().addDocumentListener(eventHandlerS);
        textFieldSearchSpecies.putClientProperty("JTextField.variant", "search");
        gbc = new java.awt.GridBagConstraints();
        gbc.weightx = 1.0;
        gbc.gridx = 1;
        gbc.gridy = gridy;
        gbc.gridwidth = 3;
        gbc.anchor = GridBagConstraints.LINE_START;
        gbc.fill = java.awt.GridBagConstraints.HORIZONTAL;
        gbc.insets = new Insets(4, 0, 4, 4);
        bottomPanel.add(textFieldSearchSpecies, gbc);
        gbc = new GridBagConstraints();
        gbc.gridx = 4;
        gbc.gridy = gridy;
        gbc.fill = GridBagConstraints.HORIZONTAL;
        gbc.insets = new Insets(4, 4, 4, 10);
        bottomPanel.add(totalSpeciesLabel, gbc);
        gridy++;
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        // gbc.weightx = 1.0;
        gbc.gridwidth = 8;
        gbc.anchor = GridBagConstraints.LINE_END;
        gbc.fill = java.awt.GridBagConstraints.BOTH;
        gbc.insets = new Insets(4, 4, 4, 4);
        bottomPanel.add(containerOfScrollPanelSpecies, gbc);
        // rendering the small shapes of the flattened species in the Depiction column of this viewer table)
        // TODO: this renderer is almost identical with the one in BioModelEditorModelPanel (which paints the small shapes
        // of a species context in the Depiction column of the species table)
        DefaultScrollTableCellRenderer rbmSpeciesShapeDepictionCellRenderer = new DefaultScrollTableCellRenderer() {

            SpeciesPatternSmallShape spss = null;

            @Override
            public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
                super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
                if (table.getModel() instanceof VCellSortTableModel<?>) {
                    Object selectedObject = null;
                    if (table.getModel() == speciesTableModel) {
                        selectedObject = speciesTableModel.getValueAt(row);
                    }
                    if (selectedObject != null) {
                        if (selectedObject instanceof GeneratedSpeciesTableRow) {
                            SpeciesContext sc = ((GeneratedSpeciesTableRow) selectedObject).getSpecies();
                            // sp cannot be null
                            SpeciesPattern sp = sc.getSpeciesPattern();
                            Graphics panelContext = table.getGraphics();
                            spss = new SpeciesPatternSmallShape(4, 2, sp, panelContext, sc, isSelected, issueManager);
                        }
                    } else {
                        spss = null;
                    }
                }
                setText("");
                return this;
            }

            @Override
            public void paintComponent(Graphics g) {
                super.paintComponent(g);
                if (spss != null) {
                    spss.paintSelf(g);
                }
            }
        };
        speciesTable.getColumnModel().getColumn(GeneratedSpeciesTableModel2.iColDepiction).setCellRenderer(rbmSpeciesShapeDepictionCellRenderer);
        speciesTable.getColumnModel().getColumn(GeneratedSpeciesTableModel2.iColDepiction).setPreferredWidth(400);
        speciesTable.getColumnModel().getColumn(GeneratedSpeciesTableModel2.iColDepiction).setMinWidth(400);
        speciesTable.getColumnModel().getColumn(GeneratedSpeciesTableModel2.iColDefinition).setPreferredWidth(30);
        speciesTable.setAutoResizeMode(JTable.AUTO_RESIZE_LAST_COLUMN);
        DefaultScrollTableCellRenderer rbmObservableShapeDepictionCellRenderer = new DefaultScrollTableCellRenderer() {

            List<SpeciesPatternSmallShape> spssList = new ArrayList<SpeciesPatternSmallShape>();

            SpeciesPatternSmallShape spss = null;

            @Override
            public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
                super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
                if (table.getModel() instanceof VCellSortTableModel<?>) {
                    Object selectedObject = null;
                    if (table.getModel() == observablesTableModel) {
                        selectedObject = observablesTableModel.getValueAt(row);
                    }
                    if (selectedObject != null && selectedObject instanceof ObservablesGroupTableRow) {
                        ObservablesGroupTableRow ogtr = ((ObservablesGroupTableRow) selectedObject);
                        String obsName = ogtr.getObservableGroupObject().getObservableGroupName();
                        RbmObservable observable = ogtr.getObservable(obsName);
                        Graphics panelContext = table.getGraphics();
                        int xPos = 4;
                        spssList.clear();
                        for (int i = 0; i < observable.getSpeciesPatternList().size(); i++) {
                            SpeciesPattern sp = observable.getSpeciesPatternList().get(i);
                            spss = new SpeciesPatternSmallShape(xPos, 2, sp, panelContext, observable, isSelected, issueManager);
                            xPos += spss.getWidth() + 6;
                            spssList.add(spss);
                        }
                    } else {
                        spssList.clear();
                    }
                }
                setText("");
                return this;
            }

            @Override
            public void paintComponent(Graphics g) {
                super.paintComponent(g);
                for (SpeciesPatternSmallShape spss : spssList) {
                    if (spss == null) {
                        continue;
                    }
                    spss.paintSelf(g);
                }
            }
        };
        observablesTable.getColumnModel().getColumn(ObservablesGroupTableModel.iColDepiction).setCellRenderer(rbmObservableShapeDepictionCellRenderer);
        observablesTable.getColumnModel().getColumn(ObservablesGroupTableModel.iColDepiction).setPreferredWidth(150);
        observablesTable.getColumnModel().getColumn(ObservablesGroupTableModel.iColDepiction).setMinWidth(150);
        observablesTable.getColumnModel().getColumn(ObservablesGroupTableModel.iColDefinition).setPreferredWidth(80);
        observablesTable.getColumnModel().getColumn(ObservablesGroupTableModel.iColExpression).setPreferredWidth(100);
        observablesTable.setAutoResizeMode(JTable.AUTO_RESIZE_LAST_COLUMN);
    } catch (java.lang.Throwable ivjExc) {
        handleException(ivjExc);
    }
}

Example 2 with MolecularTypePattern

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

the class ViewGeneratedReactionsPanel method updateShape.

public void updateShape(int selectedRow) {
    GeneratedReactionTableRow reactionTableRow = tableModel.getValueAt(selectedRow);
    String inputString = reactionTableRow.getExpression();
    System.out.println(selectedRow + ": " + inputString);
    // ReactionRule newReactionRule = (ReactionRule)RbmUtils.parseReactionRule(inputString, bioModel);
    Model tempModel = null;
    try {
        tempModel = new Model("MyTempModel");
        tempModel.addFeature("c0");
    } catch (ModelException | PropertyVetoException e1) {
        e1.printStackTrace();
    }
    if (owner != null && owner.getSimulationContext() != null) {
        List<MolecularType> mtList = owner.getSimulationContext().getModel().getRbmModelContainer().getMolecularTypeList();
        try {
            tempModel.getRbmModelContainer().setMolecularTypeList(mtList);
        } catch (PropertyVetoException e1) {
            e1.printStackTrace();
            throw new RuntimeException("Unexpected exception setting " + MolecularType.typeName + " list: " + e1.getMessage(), e1);
        }
    } else {
        // This should not be possible
        throw new RuntimeException("Owner or SimulationContext are null.");
    }
    int arrowIndex = inputString.indexOf("<->");
    boolean bReversible = true;
    if (arrowIndex < 0) {
        arrowIndex = inputString.indexOf("->");
        bReversible = false;
    }
    String left = inputString.substring(0, arrowIndex).trim();
    String right = inputString.substring(arrowIndex + (bReversible ? 3 : 2)).trim();
    if (left.length() == 0 && right.length() == 0) {
        return;
    }
    // we recover the original rule that generated the flattened reaction we now try to transform back into a fake rule
    BNGReaction reactionObject = reactionTableRow.getReactionObject();
    String name = reactionObject.getRuleName();
    if (name.contains(GeneratedReactionTableModel.reverse)) {
        name = name.substring(GeneratedReactionTableModel.reverse.length());
    }
    if (name.endsWith(ReactionRule.DirectHalf)) {
        name = name.substring(0, name.indexOf(ReactionRule.DirectHalf));
    }
    if (name.endsWith(ReactionRule.InverseHalf)) {
        name = name.substring(0, name.indexOf(ReactionRule.InverseHalf));
    }
    // get the name of the original structure from the original rule and make here another structure with the same name
    String strStructure = null;
    Structure ruleStructure;
    SimulationContext sc = owner.getSimulationContext();
    ReactionRule rr = sc.getModel().getRbmModelContainer().getReactionRule(name);
    if (rr != null && rr.getStructure() != null) {
        strStructure = rr.getStructure().getName();
    }
    if (strStructure != null) {
        if (tempModel.getStructure(strStructure) == null) {
            try {
                if (rr.getStructure().getTypeName().equals(Structure.TYPE_NAME_MEMBRANE)) {
                    tempModel.addMembrane(strStructure);
                } else {
                    tempModel.addFeature(strStructure);
                }
            } catch (ModelException | PropertyVetoException e) {
                e.printStackTrace();
            }
        }
        ruleStructure = tempModel.getStructure(strStructure);
    } else {
        throw new RuntimeException("Failed to recover a Structure name from the Reaction Rule: " + name);
    }
    // making the fake rules just for display purpose, actually they are the flattened reactions resulted from bngl
    // the name is probably not unique, it's likely that many flattened reactions are derived from the same rule
    ReactionRule reactionRule = tempModel.getRbmModelContainer().createReactionRule(name, ruleStructure, bReversible);
    String regex = "[^!]\\+";
    String[] patterns = left.split(regex);
    for (String spString : patterns) {
        try {
            spString = spString.trim();
            // if compartments are present, we're cheating big time making some fake compartments just for compartment name display purposes
            SpeciesPattern speciesPattern = (SpeciesPattern) RbmUtils.parseSpeciesPattern(spString, tempModel);
            strStructure = RbmUtils.parseCompartment(spString, tempModel);
            speciesPattern.resolveBonds();
            Structure structure;
            if (strStructure != null) {
                if (tempModel.getStructure(strStructure) == null) {
                    if (sc.getModel().getStructure(strStructure).getTypeName().equals(Structure.TYPE_NAME_MEMBRANE)) {
                        tempModel.addMembrane(strStructure);
                    } else {
                        tempModel.addFeature(strStructure);
                    }
                }
                structure = tempModel.getStructure(strStructure);
            } else {
                // if nothing explicit for a participant, we use by default the structure of the rule
                structure = ruleStructure;
            }
            reactionRule.addReactant(new ReactantPattern(speciesPattern, structure));
        } catch (Throwable ex) {
            ex.printStackTrace();
            // error (red circle)
            SpeciesPatternLargeShape spls = new SpeciesPatternLargeShape(20, 20, -1, shapePanel, true, issueManager);
            reactantPatternShapeList.clear();
            productPatternShapeList.clear();
            reactantPatternShapeList.add(spls);
            shapePanel.repaint();
            return;
        }
    }
    patterns = right.split(regex);
    for (String spString : patterns) {
        try {
            spString = spString.trim();
            SpeciesPattern speciesPattern = (SpeciesPattern) RbmUtils.parseSpeciesPattern(spString, tempModel);
            strStructure = RbmUtils.parseCompartment(spString, tempModel);
            speciesPattern.resolveBonds();
            Structure structure;
            if (strStructure != null) {
                if (tempModel.getStructure(strStructure) == null) {
                    if (sc.getModel().getStructure(strStructure).getTypeName().equals(Structure.TYPE_NAME_MEMBRANE)) {
                        tempModel.addMembrane(strStructure);
                    } else {
                        tempModel.addFeature(strStructure);
                    }
                }
                structure = tempModel.getStructure(strStructure);
            } else {
                structure = ruleStructure;
            }
            // BNGLParser parser = new BNGLParser(new StringReader(sp));
            // ASTSpeciesPattern astSpeciesPattern = parser.SpeciesPattern();
            // BnglObjectConstructionVisitor constructionVisitor = new BnglObjectConstructionVisitor(tempModel, null, false);
            // SpeciesPattern speciesPattern = (SpeciesPattern) astSpeciesPattern.jjtAccept(constructionVisitor, null);
            // for(MolecularTypePattern mtp : speciesPattern.getMolecularTypePatterns()) {
            // mtp.setParticipantMatchLabel("*");
            // }
            // System.out.println(speciesPattern.toString());
            reactionRule.addProduct(new ProductPattern(speciesPattern, structure));
        } catch (Throwable ex) {
            ex.printStackTrace();
            // error (red circle)
            SpeciesPatternLargeShape spls = new SpeciesPatternLargeShape(20, 20, -1, shapePanel, true, issueManager);
            reactantPatternShapeList.clear();
            productPatternShapeList.clear();
            reactantPatternShapeList.add(spls);
            shapePanel.repaint();
            return;
        }
    }
    // ----------------------------------------------------------------------------------------------------
    List<ReactantPattern> rpList = reactionRule.getReactantPatterns();
    reactantPatternShapeList.clear();
    int xOffset = 20;
    int xOffsetRound = 20;
    if (rpList != null && rpList.size() > 0) {
        for (int i = 0; i < rpList.size(); i++) {
            SpeciesPattern sp = rpList.get(i).getSpeciesPattern();
            for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
                mtp.setParticipantMatchLabel("*");
            }
            SpeciesPatternLargeShape sps = new SpeciesPatternLargeShape(xOffset, 20, -1, sp, shapePanel, reactionRule, issueManager);
            // SpeciesPatternRoundShape sps = new SpeciesPatternRoundShape(xOffsetRound, 20, -1, sp, shapePanel, reactionRule);
            if (i < rpList.size() - 1) {
                sps.addEndText("+");
            } else {
                if (reactionRule.isReversible()) {
                    sps.addEndText("<->");
                } else {
                    sps.addEndText("->");
                }
            }
            xOffset = sps.getRightEnd() + 45;
            xOffsetRound = sps.getRightEnd() + 45;
            reactantPatternShapeList.add(sps);
        }
    }
    // space for the <-> sign
    xOffset += 15;
    List<ProductPattern> ppList = reactionRule.getProductPatterns();
    productPatternShapeList.clear();
    if (ppList != null && ppList.size() > 0) {
        for (int i = 0; i < ppList.size(); i++) {
            SpeciesPattern sp = ppList.get(i).getSpeciesPattern();
            for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
                mtp.setParticipantMatchLabel("*");
            }
            SpeciesPatternLargeShape sps = new SpeciesPatternLargeShape(xOffset, 20, -1, sp, shapePanel, reactionRule, issueManager);
            // SpeciesPatternRoundShape sps = new SpeciesPatternRoundShape(xOffset, 20, -1, sp, shapePanel, reactionRule);
            if (i < ppList.size() - 1) {
                sps.addEndText("+");
            }
            xOffset = sps.getRightEnd() + 45;
            productPatternShapeList.add(sps);
        }
    }
    Dimension preferredSize = new Dimension(xOffset + 90, 50);
    shapePanel.setPreferredSize(preferredSize);
    shapePanel.repaint();
}

Example 3 with MolecularTypePattern

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

the class SpeciesPropertiesPanel method initialize.

/**
 * Initialize the class.
 */
private void initialize() {
    try {
        Border border = BorderFactory.createLineBorder(Color.gray);
        shapePanel = new // glyph (shape) panel
        LargeShapePanel() {

            @Override
            public void paintComponent(Graphics g) {
                super.paintComponent(g);
                if (spls != null) {
                    spls.paintSelf(g);
                }
            }

            @Override
            public DisplayMode getDisplayMode() {
                return DisplayMode.other;
            }

            @Override
            public RuleAnalysisChanged hasStateChanged(String reactionRuleName, MolecularComponentPattern molecularComponentPattern) {
                return RuleAnalysisChanged.UNCHANGED;
            }

            @Override
            public RuleAnalysisChanged hasStateChanged(MolecularComponentPattern molecularComponentPattern) {
                return RuleAnalysisChanged.UNCHANGED;
            }

            @Override
            public RuleAnalysisChanged hasBondChanged(String reactionRuleName, MolecularComponentPattern molecularComponentPattern) {
                return RuleAnalysisChanged.UNCHANGED;
            }

            @Override
            public RuleAnalysisChanged hasBondChanged(MolecularComponentPattern molecularComponentPattern) {
                return RuleAnalysisChanged.UNCHANGED;
            }

            @Override
            public RuleAnalysisChanged hasNoMatch(String reactionRuleName, MolecularTypePattern mtp) {
                return RuleAnalysisChanged.UNCHANGED;
            }

            @Override
            public RuleAnalysisChanged hasNoMatch(MolecularTypePattern molecularTypePattern) {
                return RuleAnalysisChanged.UNCHANGED;
            }

            @Override
            public RuleParticipantSignature getSignature() {
                return null;
            }

            @Override
            public GroupingCriteria getCriteria() {
                return null;
            }

            @Override
            public boolean isViewSingleRow() {
                return true;
            }
        };
        shapePanel.setBorder(border);
        shapePanel.setBackground(Color.white);
        shapePanel.setZoomFactor(-1);
        shapePanel.setEditable(true);
        shapePanel.setShowMoleculeColor(true);
        shapePanel.setShowNonTrivialOnly(true);
        // Dimension ms = new Dimension(350, 80);
        // shapePanel.setMinimumSize(ms);
        shapePanel.addMouseListener(new MouseAdapter() {

            @Override
            public void mouseClicked(MouseEvent e) {
                super.mouseClicked(e);
                if (e.getButton() == 1) {
                    // left click selects the object (we highlight it)
                    Point whereClicked = e.getPoint();
                    PointLocationInShapeContext locationContext = new PointLocationInShapeContext(whereClicked);
                    manageMouseActivity(locationContext);
                } else if (e.getButton() == 3) {
                    // right click invokes popup menu (only if the object is highlighted)
                    Point whereClicked = e.getPoint();
                    PointLocationInShapeContext locationContext = new PointLocationInShapeContext(whereClicked);
                    manageMouseActivity(locationContext);
                    if (locationContext.getDeepestShape() != null && !locationContext.getDeepestShape().isHighlighted()) {
                    // TODO: (maybe) add code here to highlight the shape if it's not highlighted already but don't show the menu
                    // return;
                    }
                    showPopupMenu(e, locationContext);
                }
            }

            private void manageMouseActivity(PointLocationInShapeContext locationContext) {
                Graphics g = shapePanel.getGraphics();
                spls.turnHighlightOffRecursive(g);
                if (spls.contains(locationContext)) {
                    // check if mouse is inside shape
                    System.out.println("left click inside shape " + locationContext.getDeepestShape().toString());
                }
                locationContext.highlightDeepestShape();
                locationContext.paintDeepestShape(g);
            }
        });
        shapePanel.addMouseMotionListener(new MouseMotionAdapter() {

            public void mouseMoved(MouseEvent e) {
                Point overWhat = e.getPoint();
                PointLocationInShapeContext locationContext = new PointLocationInShapeContext(overWhat);
                spls.contains(locationContext);
                HighlightableShapeInterface hsi = locationContext.getDeepestShape();
                if (hsi == null) {
                    shapePanel.setToolTipText(null);
                } else {
                    shapePanel.setToolTipText("Right click for " + hsi.getDisplayType() + " menus");
                }
                for (MolecularTypeLargeShape mtls : spls.getMolecularTypeLargeShapes()) {
                    Rectangle r = mtls.getAnchorHotspot();
                    if (r != null && r.contains(overWhat)) {
                        mtls.getMolecularType();
                        shapePanel.setToolTipText(mtls.getAnchorsHTML());
                        break;
                    }
                }
            }
        });
        // ----------------------------------------------------------------------------------
        leftPanel = new JPanel();
        GridBagLayout mgr = new GridBagLayout();
        mgr.rowHeights = new int[] { 100, 100 };
        leftPanel.setLayout(mgr);
        leftPanel.setBackground(Color.white);
        speciesPropertiesTree = new BioModelNodeEditableTree();
        speciesPropertiesTreeModel = new SpeciesPropertiesTreeModel(speciesPropertiesTree);
        speciesPropertiesTree.setModel(speciesPropertiesTreeModel);
        JPanel generalPanel = new JPanel();
        generalPanel.setLayout(new GridBagLayout());
        Dimension size = new Dimension(100, 150);
        generalPanel.setMinimumSize(size);
        nameTextField = new JTextField();
        nameTextField.setEditable(false);
        int gridy = 0;
        GridBagConstraints gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.insets = new Insets(2, 4, 2, 4);
        gbc.anchor = GridBagConstraints.LINE_END;
        JLabel label = new JLabel("Species Name");
        generalPanel.add(label, gbc);
        gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 1;
        gbc.gridy = gridy;
        // significantly longer than the sbmlName text field
        gbc.weightx = 0.7;
        gbc.fill = java.awt.GridBagConstraints.BOTH;
        gbc.insets = new Insets(2, 4, 2, 4);
        gbc.anchor = GridBagConstraints.LINE_START;
        generalPanel.add(nameTextField, gbc);
        sbmlNameTextField = new JTextField();
        sbmlNameTextField.setEditable(false);
        sbmlNameTextField.setEnabled(false);
        gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 2;
        gbc.gridy = gridy;
        gbc.insets = new Insets(2, 8, 2, 2);
        gbc.anchor = GridBagConstraints.LINE_END;
        generalPanel.add(new JLabel("Sbml Name"), gbc);
        gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 3;
        gbc.gridy = gridy;
        gbc.weightx = 0.3;
        gbc.fill = java.awt.GridBagConstraints.BOTH;
        gbc.insets = new Insets(2, 4, 2, 4);
        gbc.anchor = GridBagConstraints.LINE_START;
        generalPanel.add(sbmlNameTextField, gbc);
        gridy++;
        gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.insets = new Insets(2, 4, 2, 4);
        gbc.anchor = GridBagConstraints.FIRST_LINE_END;
        generalPanel.add(new JLabel("Linked Pathway Object(s)"), gbc);
        linkedPOScrollPane = new JScrollPane();
        gbc = new java.awt.GridBagConstraints();
        gbc.weightx = 1.0;
        gbc.weighty = 0.1;
        gbc.gridx = 1;
        gbc.gridy = gridy;
        gbc.gridwidth = 3;
        gbc.anchor = GridBagConstraints.LINE_START;
        gbc.fill = java.awt.GridBagConstraints.BOTH;
        gbc.insets = new Insets(2, 4, 2, 4);
        generalPanel.add(linkedPOScrollPane, gbc);
        GridBagConstraints gbc1 = new GridBagConstraints();
        gbc1.gridx = 0;
        gbc1.gridy = 0;
        gbc1.gridwidth = 1;
        gbc1.weightx = 1;
        gbc1.weighty = 1;
        gbc1.fill = GridBagConstraints.BOTH;
        leftPanel.add(generalPanel, gbc1);
        scrollPane = new JScrollPane(shapePanel);
        scrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
        scrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);
        // -----------------------------------------------------------
        JPanel optionsPanel = new JPanel();
        optionsPanel.setLayout(new GridBagLayout());
        getZoomSmallerButton().setEnabled(true);
        getZoomLargerButton().setEnabled(true);
        GridBagConstraints gbc2 = new GridBagConstraints();
        gbc2.gridx = 0;
        gbc2.gridy = 0;
        gbc2.insets = new Insets(4, 4, 0, 10);
        gbc2.anchor = GridBagConstraints.WEST;
        optionsPanel.add(getZoomLargerButton(), gbc2);
        gbc2 = new GridBagConstraints();
        gbc2.gridx = 0;
        gbc2.gridy = 1;
        gbc2.insets = new Insets(4, 4, 4, 10);
        gbc2.anchor = GridBagConstraints.WEST;
        optionsPanel.add(getZoomSmallerButton(), gbc2);
        gbc2 = new GridBagConstraints();
        gbc2.gridx = 0;
        gbc2.gridy = 2;
        gbc2.weightx = 1;
        // fake cell used for filling all the vertical empty space
        gbc2.weighty = 1;
        gbc2.anchor = GridBagConstraints.WEST;
        gbc2.insets = new Insets(4, 4, 4, 10);
        optionsPanel.add(new JLabel(""), gbc2);
        JPanel containerOfScrollPanel = new JPanel();
        containerOfScrollPanel.setLayout(new BorderLayout());
        containerOfScrollPanel.add(optionsPanel, BorderLayout.WEST);
        containerOfScrollPanel.add(scrollPane, BorderLayout.CENTER);
        // gbc1 = new GridBagConstraints();
        gbc1.gridx = 0;
        gbc1.gridy = 1;
        gbc1.weightx = 1;
        gbc1.weighty = 0.1;
        gbc1.fill = GridBagConstraints.BOTH;
        leftPanel.add(containerOfScrollPanel, gbc1);
        setName("SpeciesEditorPanel");
        setLayout(new BorderLayout());
        setBackground(Color.white);
        add(leftPanel, BorderLayout.CENTER);
        initConnections();
    } catch (java.lang.Throwable ivjExc) {
        handleException(ivjExc);
    }
}

Example 4 with MolecularTypePattern

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

the class SpeciesPropertiesPanel method showPopupMenu.

private void showPopupMenu(MouseEvent e, PointLocationInShapeContext locationContext) {
    if (popupFromShapeMenu == null) {
        popupFromShapeMenu = new JPopupMenu();
    }
    if (popupFromShapeMenu.isShowing()) {
        return;
    }
    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 {
            if (!fieldSpeciesContext.hasSpeciesPattern()) {
                selectedObject = new SpeciesPattern();
            } else {
                return;
            }
        }
    } else {
        selectedObject = null;
        System.out.println("inside something else?");
        return;
    }
    System.out.println(selectedObject);
    popupFromShapeMenu.removeAll();
    Point mousePoint = e.getPoint();
    if (selectedObject instanceof SpeciesPattern) {
        final SpeciesPattern sp = (SpeciesPattern) selectedObject;
        JMenu addMenuItem = new JMenu(VCellErrorMessages.SpecifyMolecularTypes);
        popupFromShapeMenu.add(addMenuItem);
        addMenuItem.removeAll();
        for (final MolecularType mt : bioModel.getModel().getRbmModelContainer().getMolecularTypeList()) {
            JMenuItem menuItem = new JMenuItem(mt.getName());
            Graphics gc = shapePanel.getGraphics();
            Icon icon = new MolecularTypeSmallShape(1, 4, mt, null, gc, mt, null, issueManager);
            menuItem.setIcon(icon);
            addMenuItem.add(menuItem);
            menuItem.addActionListener(new ActionListener() {

                public void actionPerformed(ActionEvent e) {
                    MolecularTypePattern molecularTypePattern = new MolecularTypePattern(mt);
                    for (MolecularComponentPattern mcp : molecularTypePattern.getComponentPatternList()) {
                        mcp.setBondType(BondType.None);
                    }
                    if (!fieldSpeciesContext.hasSpeciesPattern()) {
                        fieldSpeciesContext.setSpeciesPattern(sp);
                    }
                    fieldSpeciesContext.getSpeciesPattern().addMolecularTypePattern(molecularTypePattern);
                }
            });
        }
    // JMenu compartmentMenuItem = new JMenu("Specify structure");
    // popupFromShapeMenu.add(compartmentMenuItem);
    // 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);
    // fieldSpeciesContext.setStructure(struct);
    // }
    // });
    // }
    } 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);
                speciesPropertiesTreeModel.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);
                speciesPropertiesTreeModel.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);
                if (sp.getMolecularTypePatterns().isEmpty()) {
                    fieldSpeciesContext.setSpeciesPattern(null);
                }
            }
        });
        popupFromShapeMenu.add(deleteMenuItem);
    } else if (selectedObject instanceof MolecularComponentPattern) {
        manageComponentPatternFromShape(selectedObject, locationContext, ShowWhat.ShowBond);
    } else if (selectedObject instanceof ComponentStatePattern) {
        MolecularComponentPattern mcp = ((ComponentStateLargeShape) deepestShape).getMolecularComponentPattern();
        manageComponentPatternFromShape(mcp, locationContext, ShowWhat.ShowState);
    } else {
        System.out.println("Where am I ???");
    }
    popupFromShapeMenu.show(e.getComponent(), mousePoint.x, mousePoint.y);
}

Example 5 with MolecularTypePattern

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

the class SpeciesPropertiesPanel method manageComponentPatternFromShape.

public void manageComponentPatternFromShape(final RbmElementAbstract selectedObject, PointLocationInShapeContext locationContext, ShowWhat showWhat) {
    popupFromShapeMenu.removeAll();
    final MolecularComponentPattern mcp = (MolecularComponentPattern) selectedObject;
    final MolecularComponent mc = mcp.getMolecularComponent();
    // ------------------------------------------------------------------- State
    if (showWhat == ShowWhat.ShowState && mc.getComponentStateDefinitions().size() != 0) {
        String prefix = "State:  ";
        final Map<String, String> itemMap = new LinkedHashMap<String, String>();
        // itemList.add(ComponentStatePattern.strAny);			// any is not an option for state
        String csdCurrentName;
        for (final ComponentStateDefinition csd : mc.getComponentStateDefinitions()) {
            csdCurrentName = "";
            if (mcp.getComponentStatePattern() != null && !mcp.getComponentStatePattern().isAny()) {
                ComponentStateDefinition csdCurrent = mcp.getComponentStatePattern().getComponentStateDefinition();
                csdCurrentName = csdCurrent.getName();
            }
            String name = csd.getName();
            if (name.equals(csdCurrentName)) {
                // currently selected menu item is shown in bold
                name = "<html>" + prefix + "<b>" + name + "</b></html>";
            } else {
                name = "<html>" + prefix + name + "</html>";
            }
            itemMap.put(name, csd.getName());
        }
        for (String name : itemMap.keySet()) {
            JMenuItem menuItem = new JMenuItem(name);
            popupFromShapeMenu.add(menuItem);
            menuItem.setIcon(VCellIcons.rbmComponentStateIcon);
            menuItem.addActionListener(new ActionListener() {

                public void actionPerformed(ActionEvent e) {
                    String key = e.getActionCommand();
                    String name = itemMap.get(key);
                    if (name.equals(ComponentStatePattern.strAny)) {
                        ComponentStatePattern csp = new ComponentStatePattern();
                        mcp.setComponentStatePattern(csp);
                    } else {
                        ComponentStateDefinition csd = mcp.getMolecularComponent().getComponentStateDefinition(name);
                        if (csd == null) {
                            throw new RuntimeException("Missing ComponentStateDefinition " + name + " for Component " + mcp.getMolecularComponent().getName());
                        }
                        ComponentStatePattern csp = new ComponentStatePattern(csd);
                        mcp.setComponentStatePattern(csp);
                    }
                }
            });
        }
    }
    if (showWhat == ShowWhat.ShowState) {
        return;
    }
    // ---------------------------------------------------------------------------- Bonds
    final MolecularTypePattern mtp = locationContext.getMolecularTypePattern();
    final SpeciesPattern sp = locationContext.getSpeciesPattern();
    JMenu editBondMenu = new JMenu();
    final String specifiedString = mcp.getBondType() == BondType.Specified ? "<html><b>" + "Site bond specified" + "</b></html>" : "<html>" + "Site bond specified" + "</html>";
    editBondMenu.setText(specifiedString);
    editBondMenu.setToolTipText("Specified");
    editBondMenu.removeAll();
    final Map<String, Bond> itemMap = new LinkedHashMap<String, Bond>();
    String noneString = mcp.getBondType() == BondType.None ? "<html><b>" + "Site is unbound" + "</b></html>" : "<html>" + "Site is unbound" + "</html>";
    itemMap.put(noneString, null);
    // itemMap.put(possibleString, null);	// not a valid option for species
    if (mtp != null && sp != null) {
        List<Bond> bondPartnerChoices = sp.getAllBondPartnerChoices(mtp, mc);
        for (Bond b : bondPartnerChoices) {
            // if(b.equals(mcp.getBond())) {
            // continue;	// if the mcp has a bond already we don't offer it
            // }
            int index = 0;
            if (mcp.getBondType() == BondType.Specified) {
                index = mcp.getBondId();
            } else {
                index = sp.nextBondId();
            }
            itemMap.put(b.toHtmlStringLong(sp, mtp, mc, index), b);
        // itemMap.put(b.toHtmlStringLong(sp, index), b);
        }
    }
    int index = 0;
    Graphics gc = shapePanel.getGraphics();
    for (String name : itemMap.keySet()) {
        JMenuItem menuItem = new JMenuItem(name);
        if (index == 0) {
            menuItem.setIcon(VCellIcons.rbmBondNoneIcon);
            menuItem.setToolTipText("None");
            popupFromShapeMenu.add(menuItem);
        } else {
            Bond b = itemMap.get(name);
            // clone of the sp, with only the bond of interest
            SpeciesPattern spBond = new SpeciesPattern(bioModel.getModel(), sp);
            spBond.resetBonds();
            spBond.resetStates();
            MolecularTypePattern mtpFrom = spBond.getMolecularTypePattern(mtp.getMolecularType().getName(), mtp.getIndex());
            MolecularComponentPattern mcpFrom = mtpFrom.getMolecularComponentPattern(mc);
            MolecularTypePattern mtpTo = spBond.getMolecularTypePattern(b.molecularTypePattern.getMolecularType().getName(), b.molecularTypePattern.getIndex());
            MolecularComponentPattern mcpTo = mtpTo.getMolecularComponentPattern(b.molecularComponentPattern.getMolecularComponent());
            spBond.setBond(mtpTo, mcpTo, mtpFrom, mcpFrom);
            Icon icon = new SpeciesPatternSmallShape(3, 4, spBond, gc, fieldSpeciesContext, false, issueManager);
            ((SpeciesPatternSmallShape) icon).setDisplayRequirements(DisplayRequirements.highlightBonds);
            menuItem.setIcon(icon);
            editBondMenu.add(menuItem);
        }
        menuItem.addActionListener(new ActionListener() {

            public void actionPerformed(ActionEvent e) {
                String name = e.getActionCommand();
                BondType btBefore = mcp.getBondType();
                if (name.equals(noneString)) {
                    if (btBefore == BondType.Specified) {
                        // specified -> not specified
                        // change the partner to none since this is the only option
                        mcp.getBond().molecularComponentPattern.setBondType(BondType.None);
                        mcp.getBond().molecularComponentPattern.setBond(null);
                    }
                    mcp.setBondType(BondType.None);
                    mcp.setBond(null);
                    SwingUtilities.invokeLater(new Runnable() {

                        public void run() {
                            speciesPropertiesTreeModel.populateTree();
                        }
                    });
                } else {
                    if (btBefore != BondType.Specified) {
                        // if we go from a non-specified to a specified we need to find the next available
                        // bond id, so that we can choose the color for displaying the bond
                        // a bad bond id, like -1, will crash badly when trying to choose the color
                        int bondId = sp.nextBondId();
                        mcp.setBondId(bondId);
                    } else {
                        // specified -> specified
                        // change the old partner to none since it's the only available option, continue using the bond id
                        mcp.getBond().molecularComponentPattern.setBondType(BondType.None);
                        mcp.getBond().molecularComponentPattern.setBond(null);
                    }
                    mcp.setBondType(BondType.Specified);
                    Bond b = itemMap.get(name);
                    mcp.setBond(b);
                    mcp.getBond().molecularComponentPattern.setBondId(mcp.getBondId());
                    sp.resolveBonds();
                    SwingUtilities.invokeLater(new Runnable() {

                        public void run() {
                            speciesPropertiesTreeModel.populateTree();
                        }
                    });
                }
            }
        });
        index++;
    }
    popupFromShapeMenu.add(editBondMenu);
}