Examples with RelationshipObject org.vcell.relationship.RelationshipObject used on opensource projects

Example 16 with RelationshipObject

use of org.vcell.relationship.RelationshipObject in project vcell by virtualcell.

the class BioModelEditorConversionTableModel method createTableRowForTransportParticipant.

private ConversionTableRow createTableRowForTransportParticipant(BioPaxObject bpObject, String interactionId, String interactionLabel, String participantType, double stoich, HashSet<RelationshipObject> relationshipObjects) {
    String location = "";
    ConversionTableRow conversionTableRow = new ConversionTableRow(bpObject);
    conversionTableRow.setInteractionId(interactionId);
    conversionTableRow.setInteractionLabel(interactionLabel);
    conversionTableRow.setParticipantType(participantType);
    // stoichiometry and location
    Model model = bioModel.getModel();
    StructureTopology structTopology = model.getStructureTopology();
    if (participantType.equals("Reactant")) {
        // stoichiometry
        if (stoich != 0)
            conversionTableRow.setStoich(stoich);
        else
            conversionTableRow.setStoich(1.0);
        // else{
        if (model.getMembranes().size() > 0)
            location = structTopology.getOutsideFeature(model.getMembranes().get(0)).getName();
        else
            location = model.getStructures()[0].getName();
        // }
        conversionTableRow.setLocation(location);
    } else if (participantType.equals("Product")) {
        // stoichiometry
        if (stoich != 0)
            conversionTableRow.setStoich(stoich);
        else
            conversionTableRow.setStoich(1.0);
        // else{
        if (model.getMembranes().size() > 0)
            location = structTopology.getInsideFeature(model.getMembranes().get(0)).getName();
        else
            location = model.getStructures()[0].getName();
        // }
        conversionTableRow.setLocation(location);
    } else {
        conversionTableRow.setStoich(1.0);
        // else
        if (bpObject instanceof Transport) {
            if (model.getMembranes().size() > 0)
                location = model.getMembranes().get(0).getName();
            else
                location = model.getStructures()[0].getName();
        } else
            location = model.getStructures()[0].getName();
        conversionTableRow.setLocation(location);
    }
    // id
    if (relationshipObjects == null) {
        if (bpObject instanceof Entity) {
            String id = (BioPAXUtil.getName((Entity) bpObject) + "_" + location).trim();
            if (isValid(id))
                conversionTableRow.setId(id);
            else
                conversionTableRow.setId(changeID(id));
        }
    } else {
        String id = null;
        for (RelationshipObject relationshipObject : relationshipObjects) {
            if (relationshipObject.getBioModelEntityObject().getStructure().getName().equalsIgnoreCase(location)) {
                id = relationshipObject.getBioModelEntityObject().getName();
            }
        }
        if (id != null) {
            // the linked bmObject with the same location will be used
            conversionTableRow.setId(id);
        } else {
            // a new bmObject will be created if no linked bmObject in the same location
            if (bpObject instanceof Entity) {
                id = (BioPAXUtil.getName((Entity) bpObject) + "_" + location).trim();
                if (isValid(id))
                    conversionTableRow.setId(id);
                else
                    conversionTableRow.setId(changeID(id));
            }
        }
    }
    return conversionTableRow;
}

Example 17 with RelationshipObject

use of org.vcell.relationship.RelationshipObject in project vcell by virtualcell.

the class BioModelEditorModelPanel method initialize.

private void initialize() {
    newButton = new JButton("New");
    newButton2 = new JButton("New Rule");
    newMemButton = new JButton("New Membrane");
    deleteButton = new JButton("Delete");
    duplicateButton = new JButton("Duplicate");
    pathwayButton = new JButton("Pathway Links", new DownArrowIcon());
    pathwayButton.setHorizontalTextPosition(SwingConstants.LEFT);
    textFieldSearch = new JTextField();
    textFieldSearch.putClientProperty("JTextField.variant", "search");
    structuresTable = new EditorScrollTable();
    reactionsTable = new EditorScrollTable();
    speciesTable = new EditorScrollTable();
    molecularTypeTable = new EditorScrollTable();
    observablesTable = new EditorScrollTable();
    structureTableModel = new BioModelEditorStructureTableModel(structuresTable);
    reactionTableModel = new BioModelEditorReactionTableModel(reactionsTable);
    speciesTableModel = new BioModelEditorSpeciesTableModel(speciesTable);
    molecularTypeTableModel = new MolecularTypeTableModel(molecularTypeTable);
    observableTableModel = new ObservableTableModel(observablesTable);
    structuresTable.setModel(structureTableModel);
    reactionsTable.setModel(reactionTableModel);
    speciesTable.setModel(speciesTableModel);
    molecularTypeTable.setModel(molecularTypeTableModel);
    observablesTable.setModel(observableTableModel);
    reactionCartoonEditorPanel = new ReactionCartoonEditorPanel();
    reactionCartoonEditorPanel.addPropertyChangeListener(eventHandler);
    reactionCartoonEditorPanel.getReactionCartoonFull().addPropertyChangeListener(eventHandler);
    reactionCartoonEditorPanel.getReactionCartoonMolecule().addPropertyChangeListener(eventHandler);
    reactionCartoonEditorPanel.getReactionCartoonRule().addPropertyChangeListener(eventHandler);
    // cartoonEditorPanel  = new CartoonEditorPanelFixed();
    // cartoonEditorPanel.getStructureCartoon().addPropertyChangeListener(eventHandler);
    /* button panel */
    buttonPanel = new JPanel();
    buttonPanel.setLayout(new GridBagLayout());
    GridBagConstraints gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = 0;
    gbc.insets = new Insets(4, 4, 4, 4);
    gbc.anchor = GridBagConstraints.LINE_END;
    buttonPanel.add(newButton, gbc);
    gbc = new GridBagConstraints();
    gbc.gridx = 1;
    gbc.gridy = 0;
    gbc.insets = new Insets(4, 4, 4, 4);
    gbc.anchor = GridBagConstraints.LINE_END;
    buttonPanel.add(newButton2, gbc);
    gbc = new GridBagConstraints();
    gbc.gridx = 2;
    gbc.gridy = 0;
    gbc.insets = new Insets(4, 4, 4, 4);
    gbc.anchor = GridBagConstraints.LINE_END;
    buttonPanel.add(newMemButton, gbc);
    gbc = new GridBagConstraints();
    gbc.gridx = 3;
    gbc.insets = new Insets(4, 4, 4, 4);
    gbc.gridy = 0;
    gbc.anchor = GridBagConstraints.LINE_END;
    buttonPanel.add(duplicateButton, gbc);
    gbc = new GridBagConstraints();
    gbc.gridx = 4;
    gbc.insets = new Insets(4, 4, 4, 4);
    gbc.gridy = 0;
    gbc.anchor = GridBagConstraints.LINE_END;
    buttonPanel.add(deleteButton, gbc);
    gbc = new GridBagConstraints();
    gbc.gridx = 5;
    gbc.insets = new Insets(4, 4, 4, 4);
    gbc.gridy = 0;
    gbc.anchor = GridBagConstraints.LINE_END;
    buttonPanel.add(pathwayButton, gbc);
    gbc = new GridBagConstraints();
    gbc.gridx = 6;
    gbc.gridy = 0;
    gbc.weightx = 0.5;
    gbc.fill = GridBagConstraints.HORIZONTAL;
    gbc.insets = new Insets(4, 4, 4, 4);
    buttonPanel.add(Box.createRigidArea(new Dimension(5, 5)), gbc);
    gbc = new GridBagConstraints();
    gbc.gridx = 7;
    gbc.gridy = 0;
    gbc.anchor = GridBagConstraints.LINE_END;
    gbc.insets = new Insets(4, 4, 4, 4);
    buttonPanel.add(new JLabel("Search "), gbc);
    gbc = new GridBagConstraints();
    gbc.gridx = 8;
    gbc.gridy = 0;
    gbc.weightx = 1.5;
    gbc.anchor = GridBagConstraints.LINE_START;
    gbc.fill = GridBagConstraints.HORIZONTAL;
    gbc.insets = new Insets(4, 4, 4, 4);
    buttonPanel.add(textFieldSearch, gbc);
    /* button panel */
    tabbedPane = new JTabbedPaneEnhanced();
    tabbedPane.setTabLayoutPolicy(JTabbedPane.SCROLL_TAB_LAYOUT);
    modelPanelTabs[ModelPanelTabID.reaction_diagram.ordinal()] = new ModelPanelTab(ModelPanelTabID.reaction_diagram, reactionCartoonEditorPanel, VCellIcons.diagramIcon);
    // modelPanelTabs[ModelPanelTabID.structure_diagram.ordinal()] = new ModelPanelTab(ModelPanelTabID.structure_diagram, cartoonEditorPanel, VCellIcons.structureIcon);
    modelPanelTabs[ModelPanelTabID.reaction_table.ordinal()] = new ModelPanelTab(ModelPanelTabID.reaction_table, reactionsTable.getEnclosingScrollPane(), VCellIcons.tableIcon);
    modelPanelTabs[ModelPanelTabID.structure_table.ordinal()] = new ModelPanelTab(ModelPanelTabID.structure_table, structuresTable.getEnclosingScrollPane(), VCellIcons.tableIcon);
    modelPanelTabs[ModelPanelTabID.species_table.ordinal()] = new ModelPanelTab(ModelPanelTabID.species_table, speciesTable.getEnclosingScrollPane(), VCellIcons.tableIcon);
    modelPanelTabs[ModelPanelTabID.species_definitions_table.ordinal()] = new ModelPanelTab(ModelPanelTabID.species_definitions_table, molecularTypeTable.getEnclosingScrollPane(), VCellIcons.tableIcon);
    modelPanelTabs[ModelPanelTabID.observables_table.ordinal()] = new ModelPanelTab(ModelPanelTabID.observables_table, observablesTable.getEnclosingScrollPane(), VCellIcons.tableIcon);
    tabbedPane.addChangeListener(eventHandler);
    tabbedPane.addMouseListener(eventHandler);
    for (ModelPanelTab tab : modelPanelTabs) {
        tab.getComponent().setBorder(GuiConstants.TAB_PANEL_BORDER);
        tabbedPane.addTab(tab.getName(), tab.getIcon(), tab.getComponent());
    }
    // tabbedPane.addChangeListener(changeListener);
    setLayout(new BorderLayout());
    add(tabbedPane, BorderLayout.CENTER);
    add(buttonPanel, BorderLayout.SOUTH);
    newButton.addActionListener(eventHandler);
    newButton2.addActionListener(eventHandler);
    newMemButton.addActionListener(eventHandler);
    duplicateButton.addActionListener(eventHandler);
    duplicateButton.setEnabled(false);
    deleteButton.addActionListener(eventHandler);
    deleteButton.setEnabled(false);
    pathwayButton.addActionListener(eventHandler);
    pathwayButton.setEnabled(false);
    textFieldSearch.addActionListener(eventHandler);
    textFieldSearch.getDocument().addDocumentListener(eventHandler);
    structuresTable.getSelectionModel().addListSelectionListener(eventHandler);
    reactionsTable.getSelectionModel().addListSelectionListener(eventHandler);
    speciesTable.getSelectionModel().addListSelectionListener(eventHandler);
    molecularTypeTable.getSelectionModel().addListSelectionListener(eventHandler);
    observablesTable.getSelectionModel().addListSelectionListener(eventHandler);
    DefaultScrollTableCellRenderer tableRenderer = 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 (value instanceof Structure) {
                setText(((Structure) value).getName());
            } else if (value instanceof Kinetics) {
                setText(((Kinetics) value).getKineticsDescription().getDescription());
            } else if (value instanceof RbmKineticLaw) {
                setText(((RbmKineticLaw) value).getRateLawType().name());
            }
            return this;
        }
    };
    RbmTableRenderer rbmTableRenderer = new RbmTableRenderer();
    structuresTable.setDefaultRenderer(Structure.class, tableRenderer);
    speciesTable.setDefaultRenderer(Structure.class, tableRenderer);
    reactionsTable.setDefaultRenderer(Structure.class, tableRenderer);
    reactionsTable.setDefaultRenderer(Kinetics.class, tableRenderer);
    reactionsTable.setDefaultRenderer(RbmKineticLaw.class, tableRenderer);
    reactionsTable.setDefaultRenderer(ModelProcessDynamics.class, tableRenderer);
    DefaultScrollTableCellRenderer tableCellRenderer = 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);
            BioModelEntityObject bioModelEntityObject = null;
            if (table.getModel() instanceof VCellSortTableModel<?>) {
                if (table.getModel() == reactionTableModel && reactionTableModel.getValueAt(row) instanceof BioModelEntityObject) {
                    bioModelEntityObject = (BioModelEntityObject) reactionTableModel.getValueAt(row);
                } else if (table.getModel() == speciesTableModel) {
                    bioModelEntityObject = speciesTableModel.getValueAt(row);
                } else if (table.getModel() == molecularTypeTableModel) {
                    bioModelEntityObject = molecularTypeTableModel.getValueAt(row);
                }
                if (bioModelEntityObject != null) {
                    Set<RelationshipObject> relationshipSet = bioModel.getRelationshipModel().getRelationshipObjects(bioModelEntityObject);
                    if (relationshipSet.size() > 0) {
                        StringBuilder tooltip = new StringBuilder("<html>Links to Pathway objects:<br>");
                        for (RelationshipObject ro : relationshipSet) {
                            tooltip.append("<li>" + ro.getBioPaxObject() + "</li>");
                        }
                        if (!isSelected) {
                            setForeground(Color.blue);
                        }
                        String finalName = null;
                        BioPaxObject bioPaxObject = relationshipSet.iterator().next().getBioPaxObject();
                        if (bioPaxObject instanceof EntityImpl && ((EntityImpl) bioPaxObject).getName() != null && ((EntityImpl) bioPaxObject).getName().size() > 0) {
                            finalName = ((EntityImpl) bioPaxObject).getName().get(0);
                        } else if (bioPaxObject instanceof Conversion) {
                            Conversion mp = (Conversion) bioPaxObject;
                            finalName = "[" + bioPaxObject.getIDShort() + "]";
                        } else {
                            finalName = bioModelEntityObject.getName();
                        }
                        final int LIMIT = 40;
                        final String DOTS = "...";
                        if (finalName != null && finalName.length() > LIMIT) {
                            finalName = finalName.substring(0, LIMIT - DOTS.length() - 1) + DOTS;
                        }
                        setText("<html><u>" + finalName + "</u></html>");
                        setToolTipText(tooltip.toString());
                    }
                }
            }
            return this;
        }
    };
    DefaultScrollTableCellRenderer rbmReactionExpressionCellRenderer = 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 VCellSortTableModel<?>) {
                Object selectedObject = null;
                if (table.getModel() == reactionTableModel) {
                    selectedObject = reactionTableModel.getValueAt(row);
                }
                if (selectedObject != null) {
                    if (selectedObject instanceof ReactionRule && value instanceof ModelProcessEquation) {
                        String text = "<html>";
                        text += "Reaction Rule";
                        text += "</html>";
                        setText(text);
                    } else {
                        // plain reaction, check if reactants have species pattern
                        ReactionStep rs = (ReactionStep) selectedObject;
                        String text = "<html>";
                        for (int i = 0; i < rs.getNumReactants(); i++) {
                            Reactant p = rs.getReactant(i);
                            if (p.getSpeciesContext().hasSpeciesPattern()) {
                                text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
                                // text += "<b>" + p.getName() + "</b>";
                                text += p.getName();
                            } else {
                                text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
                                text += p.getName();
                            }
                            if (i < rs.getNumReactants() - 1) {
                                text += " + ";
                            }
                        }
                        text += " -&gt; ";
                        for (int i = 0; i < rs.getNumProducts(); i++) {
                            Product p = rs.getProduct(i);
                            if (p.getSpeciesContext().hasSpeciesPattern()) {
                                text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
                                // text += "<b>" + p.getName() + "</b>";
                                text += p.getName();
                            } else {
                                text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
                                text += p.getName();
                            }
                            if (i < rs.getNumProducts() - 1) {
                                text += " + ";
                            }
                        }
                        text += "</html>";
                        setText(text);
                    }
                }
            }
            return this;
        }
    };
    DefaultScrollTableCellRenderer rbmReactionDefinitionCellRenderer = 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 VCellSortTableModel<?>) {
                Object selectedObject = null;
                if (table.getModel() == reactionTableModel) {
                    selectedObject = reactionTableModel.getValueAt(row);
                }
                if (selectedObject != null) {
                    if (selectedObject instanceof ReactionRule && value instanceof ModelProcessEquation) {
                        ReactionRule rr = (ReactionRule) selectedObject;
                        String text = "<html>";
                        for (int i = 0; i < rr.getReactantPatterns().size(); i++) {
                            ReactantPattern rp = rr.getReactantPattern(i);
                            if (rp.getStructure() != null && !rp.getSpeciesPattern().getMolecularTypePatterns().isEmpty()) {
                                text += "@" + rp.getStructure().getName() + ":";
                            }
                            text += RbmUtils.toBnglString(rp.getSpeciesPattern(), null, CompartmentMode.hide, 0);
                            // text += RbmTableRenderer.toHtml(rp.getSpeciesPattern(), isSelected);
                            if (i < rr.getReactantPatterns().size() - 1) {
                                text += "+";
                            }
                        }
                        if (rr.isReversible()) {
                            // &lt;-&gt;  <->
                            text += " &lt;-&gt; ";
                        } else {
                            text += " -&gt; ";
                        }
                        for (int i = 0; i < rr.getProductPatterns().size(); i++) {
                            ProductPattern pp = rr.getProductPattern(i);
                            if (pp.getStructure() != null && !pp.getSpeciesPattern().getMolecularTypePatterns().isEmpty()) {
                                text += "@" + pp.getStructure().getName() + ":";
                            }
                            text += RbmUtils.toBnglString(pp.getSpeciesPattern(), null, CompartmentMode.hide, 0);
                            if (i < rr.getProductPatterns().size() - 1) {
                                text += "+";
                            }
                        }
                        text += "</html>";
                        setText(text);
                    } else {
                        // plain reaction, check if reactants have species pattern
                        ReactionStep rs = (ReactionStep) selectedObject;
                        String text = "<html>";
                        for (int i = 0; i < rs.getNumReactants(); i++) {
                            Reactant p = rs.getReactant(i);
                            if (p.getSpeciesContext().hasSpeciesPattern()) {
                                text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
                                text += p.getName();
                            } else {
                                text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
                                text += p.getName();
                            }
                            if (i < rs.getNumReactants() - 1) {
                                text += " + ";
                            }
                        }
                        if (rs.isReversible()) {
                            // &lt;-&gt;  <->
                            text += " &lt;-&gt; ";
                        } else {
                            text += " -&gt; ";
                        }
                        for (int i = 0; i < rs.getNumProducts(); i++) {
                            Product p = rs.getProduct(i);
                            if (p.getSpeciesContext().hasSpeciesPattern()) {
                                text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
                                text += p.getName();
                            } else {
                                text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
                                text += p.getName();
                            }
                            if (i < rs.getNumProducts() - 1) {
                                text += " + ";
                            }
                        }
                        text += "</html>";
                        setText(text);
                    }
                }
            }
            return this;
        }
    };
    DefaultScrollTableCellRenderer rbmObservablePatternCellRenderer = 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 VCellSortTableModel<?>) {
                Object selectedObject = null;
                if (table.getModel() == observableTableModel) {
                    selectedObject = observableTableModel.getValueAt(row);
                }
                if (selectedObject != null) {
                    if (selectedObject instanceof RbmObservable && value instanceof String) {
                        RbmObservable o = (RbmObservable) selectedObject;
                        String text = "<html>";
                        for (int i = 0; i < o.getSpeciesPatternList().size(); i++) {
                            SpeciesPattern sp = o.getSpeciesPattern(i);
                            text += RbmTableRenderer.toHtml(sp, isSelected);
                            if (i < o.getSpeciesPatternList().size() - 1) {
                                text += " ";
                            }
                        }
                        text = RbmUtils.appendSequence(text, o);
                        text += "</html>";
                        setText(text);
                    }
                }
            }
            return this;
        }
    };
    DefaultScrollTableCellRenderer rbmSpeciesNameCellRenderer = 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 VCellSortTableModel<?>) {
                Object selectedObject = null;
                if (table.getModel() == speciesTableModel) {
                    selectedObject = speciesTableModel.getValueAt(row);
                }
                if (selectedObject != null) {
                    if (selectedObject instanceof SpeciesContext) {
                        SpeciesContext sc = (SpeciesContext) selectedObject;
                        String text = "<html>";
                        if (sc.hasSpeciesPattern()) {
                            text += "<b>" + sc.getName() + "</b>";
                        } else {
                            text += sc.getName();
                        }
                        text += "</html>";
                        setText(text);
                    }
                }
            }
            return this;
        }
    };
    // 
    // this renderer only paints the molecular type small shape in the MolecularType Table
    // 
    DefaultScrollTableCellRenderer rbmMolecularTypeShapeDepictionCellRenderer = new DefaultScrollTableCellRenderer() {

        MolecularTypeSmallShape stls = 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() == molecularTypeTableModel) {
                    selectedObject = molecularTypeTableModel.getValueAt(row);
                }
                if (selectedObject != null) {
                    if (selectedObject instanceof MolecularType) {
                        MolecularType mt = (MolecularType) selectedObject;
                        Graphics cellContext = table.getGraphics();
                        if (mt != null) {
                            stls = new MolecularTypeSmallShape(4, 3, mt, null, cellContext, mt, null, issueManager);
                        }
                    }
                } else {
                    stls = null;
                }
            }
            return this;
        }

        @Override
        public void paintComponent(Graphics g) {
            super.paintComponent(g);
            if (stls != null) {
                stls.paintSelf(g);
            }
        }
    };
    // painting of species patterns small shapes inside the species context 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 SpeciesContext) {
                        SpeciesContext sc = (SpeciesContext) selectedObject;
                        // sp may be null for "plain" species contexts
                        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);
            }
        }
    };
    // ---------------------------------------------------------------------------------------------------------------------------------
    DefaultScrollTableCellRenderer rbmReactionShapeDepictionCellRenderer = 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() == reactionTableModel) {
                    selectedObject = reactionTableModel.getValueAt(row);
                }
                if (selectedObject != null) {
                    if (selectedObject instanceof ReactionRule) {
                        ReactionRule rr = (ReactionRule) selectedObject;
                        Graphics panelContext = table.getGraphics();
                        spssList.clear();
                        List<ReactantPattern> rpList = rr.getReactantPatterns();
                        int xPos = 4;
                        for (int i = 0; i < rpList.size(); i++) {
                            SpeciesPattern sp = rr.getReactantPattern(i).getSpeciesPattern();
                            spss = new SpeciesPatternSmallShape(xPos, 2, sp, null, panelContext, rr, isSelected, issueManager);
                            if (i < rpList.size() - 1) {
                                spss.addEndText("+");
                            } else {
                                if (rr.isReversible()) {
                                    spss.addEndText("<->");
                                    xPos += 7;
                                } else {
                                    spss.addEndText("->");
                                }
                            }
                            xPos += spss.getWidth() + 15;
                            spssList.add(spss);
                        }
                        List<ProductPattern> ppList = rr.getProductPatterns();
                        xPos += 7;
                        for (int i = 0; i < ppList.size(); i++) {
                            SpeciesPattern sp = rr.getProductPattern(i).getSpeciesPattern();
                            spss = new SpeciesPatternSmallShape(xPos, 2, sp, null, panelContext, rr, isSelected, issueManager);
                            if (i < ppList.size() - 1) {
                                spss.addEndText("+");
                            }
                            xPos += spss.getWidth() + 15;
                            spssList.add(spss);
                        }
                    } else {
                        ReactionStep rs = (ReactionStep) selectedObject;
                        Graphics panelContext = table.getGraphics();
                        spssList.clear();
                        int xPos = 4;
                        int extraSpace = 0;
                        for (int i = 0; i < rs.getNumReactants(); i++) {
                            SpeciesPattern sp = rs.getReactant(i).getSpeciesContext().getSpeciesPattern();
                            spss = new SpeciesPatternSmallShape(xPos, 2, sp, panelContext, rs, isSelected, issueManager);
                            if (i < rs.getNumReactants() - 1) {
                                spss.addEndText("+");
                            } else {
                                if (rs.isReversible()) {
                                    spss.addEndText("<->");
                                    extraSpace += 7;
                                } else {
                                    spss.addEndText("->");
                                }
                            }
                            int offset = sp == null ? 17 : 15;
                            offset += extraSpace;
                            int w = spss.getWidth();
                            xPos += w + offset;
                            spssList.add(spss);
                        }
                        xPos += 8;
                        for (int i = 0; i < rs.getNumProducts(); i++) {
                            SpeciesPattern sp = rs.getProduct(i).getSpeciesContext().getSpeciesPattern();
                            if (i == 0 && rs.getNumReactants() == 0) {
                                xPos += 14;
                            }
                            spss = new SpeciesPatternSmallShape(xPos, 2, sp, panelContext, rs, isSelected, issueManager);
                            if (i == 0 && rs.getNumReactants() == 0) {
                                spss.addStartText("->");
                            }
                            if (i < rs.getNumProducts() - 1) {
                                spss.addEndText("+");
                            }
                            int offset = sp == null ? 17 : 15;
                            int w = spss.getWidth();
                            xPos += w + offset;
                            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);
            }
        }
    };
    // -------------------------------------------------------------------------------------------------------------------------------
    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() == observableTableModel) {
                    selectedObject = observableTableModel.getValueAt(row);
                }
                if (selectedObject != null) {
                    if (selectedObject instanceof RbmObservable) {
                        RbmObservable observable = (RbmObservable) selectedObject;
                        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);
            }
        }
    };
    // TODO: here are the renderers associated with the columns
    reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_LINK).setCellRenderer(tableCellRenderer);
    reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_EQUATION).setCellRenderer(rbmReactionExpressionCellRenderer);
    reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_DEFINITION).setCellRenderer(rbmReactionDefinitionCellRenderer);
    speciesTable.getColumnModel().getColumn(BioModelEditorSpeciesTableModel.COLUMN_NAME).setCellRenderer(rbmSpeciesNameCellRenderer);
    speciesTable.getColumnModel().getColumn(BioModelEditorSpeciesTableModel.COLUMN_LINK).setCellRenderer(tableCellRenderer);
    molecularTypeTable.getColumnModel().getColumn(MolecularTypeTableModel.Column.link.ordinal()).setCellRenderer(tableCellRenderer);
    observablesTable.getColumnModel().getColumn(ObservableTableModel.Column.species_pattern.ordinal()).setCellRenderer(rbmObservablePatternCellRenderer);
    observablesTable.getColumnModel().getColumn(ObservableTableModel.Column.structure.ordinal()).setCellRenderer(tableRenderer);
    // all "depictions" have their own renderer
    molecularTypeTable.getColumnModel().getColumn(MolecularTypeTableModel.Column.depiction.ordinal()).setCellRenderer(rbmMolecularTypeShapeDepictionCellRenderer);
    molecularTypeTable.getColumnModel().getColumn(MolecularTypeTableModel.Column.depiction.ordinal()).setMaxWidth(180);
    speciesTable.getColumnModel().getColumn(BioModelEditorSpeciesTableModel.COLUMN_DEPICTION).setCellRenderer(rbmSpeciesShapeDepictionCellRenderer);
    speciesTable.getColumnModel().getColumn(BioModelEditorSpeciesTableModel.COLUMN_DEFINITION).setCellRenderer(rbmTableRenderer);
    observablesTable.getColumnModel().getColumn(ObservableTableModel.Column.depiction.ordinal()).setCellRenderer(rbmObservableShapeDepictionCellRenderer);
    reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_DEPICTION).setCellRenderer(rbmReactionShapeDepictionCellRenderer);
    reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_DEPICTION).setPreferredWidth(180);
    observablesTable.getColumnModel().getColumn(ObservableTableModel.Column.type.ordinal()).setCellEditor(observableTableModel.getObservableTypeComboBoxEditor());
    observableTableModel.updateObservableTypeComboBox();
    reactionsTable.addMouseListener(eventHandler);
    reactionsTable.addKeyListener(eventHandler);
    speciesTable.addMouseListener(eventHandler);
    speciesTable.addKeyListener(eventHandler);
    molecularTypeTable.addMouseListener(eventHandler);
    molecularTypeTable.addKeyListener(eventHandler);
    observablesTable.addMouseListener(eventHandler);
    observablesTable.addKeyListener(eventHandler);
    structuresTable.addKeyListener(eventHandler);
}

Example 18 with RelationshipObject

use of org.vcell.relationship.RelationshipObject in project vcell by virtualcell.

the class BioModelEditorModelPanel method showPathwayLinks.

private void showPathwayLinks() {
    BioModelEntityObject selectedBioModelEntityObject = getSelectedBioModelEntityObject();
    if (selectedBioModelEntityObject != null) {
        Set<RelationshipObject> relationshipSet = bioModel.getRelationshipModel().getRelationshipObjects(selectedBioModelEntityObject);
        if (relationshipSet.size() > 0) {
            ArrayList<BioPaxObject> selectedBioPaxObjects = new ArrayList<BioPaxObject>();
            for (RelationshipObject re : relationshipSet) {
                selectedBioPaxObjects.add(re.getBioPaxObject());
            }
            selectionManager.followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.PATHWAY_NODE, ActiveViewID.pathway), selectedBioPaxObjects.toArray(new BioPaxObject[0]));
        }
    }
}

Example 19 with RelationshipObject

use of org.vcell.relationship.RelationshipObject in project vcell by virtualcell.

the class ReactionPropertiesPanel method listLinkedPathwayObjects.

private String listLinkedPathwayObjects() {
    // Kinetics kinetics = reactionStep.getKinetics();
    if (reactionStep == null) {
        return "no selected reaction";
    }
    if (bioModel == null || bioModel.getModel() == null) {
        return "no biomodel";
    }
    JPanel panel = new JPanel();
    panel.setLayout(new BoxLayout(panel, BoxLayout.X_AXIS));
    String linkedPOlist = "";
    for (RelationshipObject relObject : bioModel.getRelationshipModel().getRelationshipObjects(reactionStep)) {
        if (relObject == null) {
            continue;
        }
        final BioPaxObject bpObject = relObject.getBioPaxObject();
        if (bpObject == null) {
            continue;
        }
        if (bpObject instanceof Entity) {
            String name = new String();
            if (((Entity) bpObject).getName().isEmpty()) {
                name = ((Entity) bpObject).getID();
            } else {
                name = ((Entity) bpObject).getName().get(0);
            }
            if (name.contains("#")) {
                name = name.substring(name.indexOf("#") + 1);
            }
            JLabel label = new JLabel("<html><u>" + name + "</u></html>");
            label.setForeground(Color.blue);
            label.addMouseListener(new MouseAdapter() {

                public void mouseClicked(MouseEvent e) {
                    if (e.getClickCount() == 2) {
                        selectionManager.followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.PATHWAY_DIAGRAM_NODE, ActiveViewID.pathway_diagram), new Object[] { bpObject });
                    }
                }
            });
            panel.add(label);
        }
    }
    Dimension dim = new Dimension(200, 20);
    panel.setMinimumSize(dim);
    panel.setPreferredSize(dim);
    linkedPOScrollPane.setViewportView(panel);
    return linkedPOlist;
}

Example 20 with RelationshipObject

use of org.vcell.relationship.RelationshipObject in project vcell by virtualcell.

the class MolecularTypePropertiesPanel method listLinkedPathwayObjects.

private String listLinkedPathwayObjects() {
    if (molecularType == null) {
        return "no selected molecule";
    }
    if (bioModel == null || bioModel.getModel() == null) {
        return "no biomodel";
    }
    JPanel panel = new JPanel();
    panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS));
    String linkedPOlist = "";
    for (RelationshipObject relObject : bioModel.getRelationshipModel().getRelationshipObjects(molecularType)) {
        final BioPaxObject bpObject = relObject.getBioPaxObject();
        if (bpObject instanceof Entity) {
            JLabel label = new JLabel("<html><u>" + ((Entity) bpObject).getName().get(0) + "</u></html>");
            label.setForeground(Color.blue);
            label.addMouseListener(new MouseAdapter() {

                public void mouseClicked(MouseEvent e) {
                    if (e.getClickCount() == 2) {
                        selectionManager.followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.PATHWAY_DIAGRAM_NODE, ActiveViewID.pathway_diagram), new Object[] { bpObject });
                    }
                }
            });
            panel.add(label);
        }
    }
    Dimension dim = new Dimension(200, 20);
    panel.setMinimumSize(dim);
    panel.setPreferredSize(dim);
    linkedPOScrollPane.setViewportView(panel);
    return linkedPOlist;
}