Examples with MIRIAMQualifier org.vcell.sybil.models.miriam.MIRIAMQualifier used on opensource projects

Example 11 with MIRIAMQualifier

use of org.vcell.sybil.models.miriam.MIRIAMQualifier in project vcell by virtualcell.

the class VCMetaDataMiriamManager method queryAllMiriamRefGroups.

private Map<MiriamRefGroup, MIRIAMQualifier> queryAllMiriamRefGroups(Identifiable identifiable) {
    Entry entry = vcMetaData.getRegistry().getEntry(identifiable);
    if (entry.getResource() == null) {
        return null;
    }
    MIRIAMizer miriamizer = new MIRIAMizer();
    Graph rdfData = vcMetaData.getRdfData();
    Resource resource = entry.getResource();
    Map<RefGroup, MIRIAMQualifier> allRefGroups = miriamizer.getAllRefGroups(rdfData, resource);
    Map<MiriamRefGroup, MIRIAMQualifier> wrappedRefGroups = new HashMap<MiriamRefGroup, MIRIAMQualifier>();
    for (RefGroup refGroup : allRefGroups.keySet()) {
        MiriamRefGroup miriamRefGroup = new VCMetaDataMiriamRefGroup(refGroup);
        MIRIAMQualifier miriamQualifier = allRefGroups.get(refGroup);
        wrappedRefGroups.put(miriamRefGroup, miriamQualifier);
    }
    return wrappedRefGroups;
}

Example 12 with MIRIAMQualifier

use of org.vcell.sybil.models.miriam.MIRIAMQualifier in project vcell by virtualcell.

the class VCMetaDataMiriamManager method getMiriamTreeMap.

public synchronized TreeMap<Identifiable, Map<MiriamRefGroup, MIRIAMQualifier>> getMiriamTreeMap() {
    if (miriamTreeMap == null) {
        final IdentifiableProvider identifiableProvider = vcMetaData.getIdentifiableProvider();
        IdentifiableComparator ic = new IdentifiableComparator(identifiableProvider);
        miriamTreeMap = new TreeMap<Identifiable, Map<MiriamRefGroup, MIRIAMQualifier>>(ic);
        Registry registry = vcMetaData.getRegistry();
        Set<Entry> allEntries = registry.getAllEntries();
        for (Entry entry : allEntries) {
            if (entry.getResource() != null) {
                Identifiable identifiable = entry.getIdentifiable();
                Map<MiriamRefGroup, MIRIAMQualifier> refGroupMap = queryAllMiriamRefGroups(identifiable);
                if (refGroupMap.size() > 0) {
                    miriamTreeMap.put(entry.getIdentifiable(), refGroupMap);
                }
            }
        }
    }
    return miriamTreeMap;
}

Example 13 with MIRIAMQualifier

use of org.vcell.sybil.models.miriam.MIRIAMQualifier in project vcell by virtualcell.

the class VCMetaData method createBioPaxObjects.

public void createBioPaxObjects(BioModel bioModel) {
    AnnotationMapping annoMapping = new AnnotationMapping();
    VCMetaData vcMetaData = bioModel.getVCMetaData();
    Set<Identifiable> identifiables = vcMetaData.getIdentifiableProvider().getAllIdentifiables();
    TreeMap<Identifiable, Map<MiriamRefGroup, MIRIAMQualifier>> miriamDescrHeir = miriamManager.getMiriamTreeMap();
    for (Identifiable identifiable : identifiables) {
        Map<MiriamRefGroup, MIRIAMQualifier> refGroupMap = miriamDescrHeir.get(identifiable);
        if (refGroupMap != null) {
            // Here we make a biopax object based on an annotation
            // TODO: some biomodels database was moved permanently, this call may fail
            String info = annoMapping.annotation2BioPaxObject(bioModel, identifiable);
            boolean printInfo = false;
            if (printInfo) {
                System.out.println(info);
            }
        }
    }
}

Example 14 with MIRIAMQualifier

use of org.vcell.sybil.models.miriam.MIRIAMQualifier in project vcell by virtualcell.

the class SpeciesContextShape method paintSelf.

@Override
public void paintSelf(Graphics2D g, int absPosX, int absPosY) {
    boolean isBound = false;
    SpeciesContext sc = (SpeciesContext) getModelObject();
    boolean bHasPCLink = false;
    if (graphModel instanceof ModelCartoon) {
        ModelCartoon mc = (ModelCartoon) graphModel;
        // check if species has Pathway Commons link by querying VCMetadata : if it does, need to change color of speciesContext.
        try {
            MiriamManager miriamManager = mc.getModel().getVcMetaData().getMiriamManager();
            Map<MiriamRefGroup, MIRIAMQualifier> miriamRefGroups = miriamManager.getAllMiriamRefGroups(sc.getSpecies());
            if (miriamRefGroups != null && miriamRefGroups.size() > 0) {
                bHasPCLink = true;
            }
        } catch (Exception e) {
            e.printStackTrace(System.out);
        }
    }
    if (sc.getSpecies().getDBSpecies() != null || bHasPCLink) {
        isBound = true;
    }
    int shapeHeight = getSpaceManager().getSize().height;
    int shapeWidth = getSpaceManager().getSize().width;
    int offsetX = (shapeWidth - circleDiameter) / 2;
    int offsetY = (shapeHeight - circleDiameter) / 2;
    Graphics2D g2D = g;
    // if (icon == null) {
    icon = new Area();
    icon.add(new Area(new Ellipse2D.Double(offsetX, offsetY, circleDiameter, circleDiameter)));
    // icon.add(new Area(new RoundRectangle2D.Double(offsetX, offsetY,circleDiameter,circleDiameter,circleDiameter/2,circleDiameter/2)));
    // }
    Area movedIcon = icon.createTransformedArea(AffineTransform.getTranslateInstance(absPosX, absPosY));
    if (sc.getSpeciesPattern() == null) {
        defaultBG = java.awt.Color.green;
    } else {
        defaultBG = java.awt.Color.blue;
    }
    if (isCatalyst == true) {
        defaultBG = java.awt.Color.magenta;
    }
    backgroundColor = defaultBG;
    darkerBackground = backgroundColor.darker().darker();
    // g.setColor((!isBound && !isSelected()?darkerBackground:backgroundColor));
    g2D.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
    Color exterior = !isBound && !isSelected() ? darkerBackground : backgroundColor;
    // Color interior = exterior.brighter().brighter();
    Point2D center = new Point2D.Float(absPosX + circleDiameter * 0.5f, absPosY + circleDiameter * 0.5f);
    float radius = circleDiameter * 0.5f;
    Point2D focus = new Point2D.Float(absPosX + circleDiameter * 0.4f, absPosY + circleDiameter * 0.4f);
    float[] dist = { 0.1f, 1.0f };
    Color[] colors = { Color.white, exterior };
    // Color[] colors = {interior, exterior};
    RadialGradientPaint p = new RadialGradientPaint(center, radius, focus, dist, colors, CycleMethod.NO_CYCLE);
    g2D.setPaint(p);
    g2D.fill(movedIcon);
    g.setColor(forgroundColor);
    g2D.draw(movedIcon);
    // draw label
    if (getLabel() != null && getLabel().length() > 0) {
        if (isSelected()) {
            // clear background and outline to make selected label stand out
            Rectangle outlineRectangle = getLabelOutline(absPosX, absPosY);
            drawRaisedOutline(outlineRectangle.x, outlineRectangle.y, outlineRectangle.width, outlineRectangle.height, g, Color.white, forgroundColor, Color.gray);
        }
        g.setColor(forgroundColor);
        g.drawString((isSelected() || smallLabel == null ? getLabel() : smallLabel), (isSelected() || smallLabel == null ? getLabelPos().x : smallLabelPos.x) + absPosX, getLabelPos().y + absPosY);
    }
    if (linkText != null && linkText != "") {
        ShapePaintUtil.paintLinkMark(g2D, this, Color.BLACK);
    }
}

Example 15 with MIRIAMQualifier

use of org.vcell.sybil.models.miriam.MIRIAMQualifier 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);
    // Link to biopax object Table Cell Renderer
    DefaultScrollTableCellRenderer linkTableCellRenderer = 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;
        }
    };
    // Annotations icon column renderer
    DefaultScrollTableCellRenderer annotationTableCellRenderer = new DefaultScrollTableCellRenderer() {

        final Color lightBlueBackground = new Color(214, 234, 248);

        @Override
        public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
            super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
            Identifiable entity = null;
            if (table.getModel() instanceof VCellSortTableModel<?>) {
                if (table.getModel() == reactionTableModel) {
                    entity = (BioModelEntityObject) reactionTableModel.getValueAt(row);
                } else if (table.getModel() == speciesTableModel) {
                    entity = speciesTableModel.getValueAt(row);
                } else if (table.getModel() == molecularTypeTableModel) {
                    entity = molecularTypeTableModel.getValueAt(row);
                } else if (table.getModel() == observableTableModel) {
                    entity = observableTableModel.getValueAt(row);
                } else if (table.getModel() == structureTableModel) {
                    entity = structureTableModel.getValueAt(row);
                }
                if (entity != null) {
                    if (isSelected) {
                        setBackground(lightBlueBackground);
                    }
                    Identifiable identifiable = AnnotationsPanel.getIdentifiable(entity);
                    String freeText = bioModel.getVCMetaData().getFreeTextAnnotation(identifiable);
                    MiriamManager miriamManager = bioModel.getVCMetaData().getMiriamManager();
                    TreeMap<Identifiable, Map<MiriamRefGroup, MIRIAMQualifier>> miriamDescrHeir = miriamManager.getMiriamTreeMap();
                    Map<MiriamRefGroup, MIRIAMQualifier> refGroupMap = miriamDescrHeir.get(identifiable);
                    Icon icon1 = VCellIcons.issueGoodIcon;
                    Icon icon2 = VCellIcons.issueGoodIcon;
                    if (freeText != null && !freeText.isEmpty()) {
                        icon2 = VCellIcons.noteIcon;
                    // icon = VCellIcons.bookmarkIcon;
                    // icon = VCellIcons.addIcon(icon, VCellIcons.linkIcon);
                    // icon = VCellIcons.addIcon(icon, VCellIcons.certificateIcon);
                    // icon = VCellIcons.addIcon(icon, VCellIcons.noteIcon);
                    }
                    if (refGroupMap != null && !refGroupMap.isEmpty()) {
                        icon1 = VCellIcons.linkIcon;
                    }
                    Icon icon = VCellIcons.addIcon(icon1, icon2);
                    setIcon(icon);
                }
            }
            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;
        }
    };
    DefaultScrollTableCellRenderer reactionNameCellRenderer = 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);
                }
                setToolTipText(null);
                if (selectedObject != null) {
                    if (selectedObject instanceof ReactionStep) {
                        ReactionStep rs = (ReactionStep) selectedObject;
                        String sbmlName = rs.getSbmlName();
                        if (sbmlName != null && !sbmlName.isEmpty()) {
                            String text = "<html>";
                            text += sbmlName;
                            text += "</html>";
                            setToolTipText(text);
                        } else {
                            setToolTipText(rs.getDisplayName());
                        }
                    } else if (selectedObject instanceof ReactionRule) {
                        ReactionRule rr = (ReactionRule) selectedObject;
                        setToolTipText(rr.getDisplayName());
                    }
                }
            }
            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_NAME).setCellRenderer(reactionNameCellRenderer);
    reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_LINK).setCellRenderer(linkTableCellRenderer);
    reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_EQUATION).setCellRenderer(rbmReactionExpressionCellRenderer);
    reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_DEFINITION).setCellRenderer(rbmReactionDefinitionCellRenderer);
    reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_NOTES).setCellRenderer(annotationTableCellRenderer);
    speciesTable.getColumnModel().getColumn(BioModelEditorSpeciesTableModel.COLUMN_NAME).setCellRenderer(rbmSpeciesNameCellRenderer);
    speciesTable.getColumnModel().getColumn(BioModelEditorSpeciesTableModel.COLUMN_LINK).setCellRenderer(linkTableCellRenderer);
    speciesTable.getColumnModel().getColumn(BioModelEditorSpeciesTableModel.COLUMN_NOTES).setCellRenderer(annotationTableCellRenderer);
    molecularTypeTable.getColumnModel().getColumn(MolecularTypeTableModel.Column.link.ordinal()).setCellRenderer(linkTableCellRenderer);
    molecularTypeTable.getColumnModel().getColumn(MolecularTypeTableModel.Column.notes.ordinal()).setCellRenderer(annotationTableCellRenderer);
    observablesTable.getColumnModel().getColumn(ObservableTableModel.Column.species_pattern.ordinal()).setCellRenderer(rbmObservablePatternCellRenderer);
    observablesTable.getColumnModel().getColumn(ObservableTableModel.Column.structure.ordinal()).setCellRenderer(tableRenderer);
    observablesTable.getColumnModel().getColumn(ObservableTableModel.Column.notes.ordinal()).setCellRenderer(annotationTableCellRenderer);
    structuresTable.getColumnModel().getColumn(BioModelEditorStructureTableModel.COLUMN_NOTES).setCellRenderer(annotationTableCellRenderer);
    // fixed width columns
    final int notesWidth = 65;
    molecularTypeTable.getColumnModel().getColumn(MolecularTypeTableModel.Column.depiction.ordinal()).setMaxWidth(180);
    molecularTypeTable.getColumnModel().getColumn(MolecularTypeTableModel.Column.notes.ordinal()).setPreferredWidth(notesWidth);
    molecularTypeTable.getColumnModel().getColumn(MolecularTypeTableModel.Column.notes.ordinal()).setMaxWidth(notesWidth);
    speciesTable.getColumnModel().getColumn(BioModelEditorSpeciesTableModel.COLUMN_NOTES).setPreferredWidth(notesWidth);
    speciesTable.getColumnModel().getColumn(BioModelEditorSpeciesTableModel.COLUMN_NOTES).setMaxWidth(notesWidth);
    observablesTable.getColumnModel().getColumn(ObservableTableModel.Column.notes.ordinal()).setPreferredWidth(notesWidth);
    observablesTable.getColumnModel().getColumn(ObservableTableModel.Column.notes.ordinal()).setMaxWidth(notesWidth);
    reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_DEPICTION).setPreferredWidth(180);
    reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_NOTES).setPreferredWidth(notesWidth);
    reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_NOTES).setMaxWidth(notesWidth);
    structuresTable.getColumnModel().getColumn(BioModelEditorStructureTableModel.COLUMN_NOTES).setPreferredWidth(notesWidth);
    structuresTable.getColumnModel().getColumn(BioModelEditorStructureTableModel.COLUMN_NOTES).setMaxWidth(notesWidth);
    // all "depictions" have their own renderer
    molecularTypeTable.getColumnModel().getColumn(MolecularTypeTableModel.Column.depiction.ordinal()).setCellRenderer(rbmMolecularTypeShapeDepictionCellRenderer);
    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);
    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.addMouseListener(eventHandler);
    structuresTable.addKeyListener(eventHandler);
}