Examples with Conversion org.vcell.pathway.Conversion used on opensource projects

Example 6 with Conversion

use of org.vcell.pathway.Conversion in project vcell by virtualcell.

the class PathwayGraphModel method refreshGroupObject.

private void refreshGroupObject(GroupObject groupObject) {
    for (BioPaxObject bpObject : groupObject.getGroupedObjects()) {
        if (bpObject instanceof Conversion) {
            // Conversions inside groupObject
            Conversion conversion = (Conversion) bpObject;
            refreshInteraction(conversion);
        } else if (bpObject instanceof MolecularInteraction) {
            // molecularInteraction inside  groupObject
            MolecularInteraction molecularInteraction = (MolecularInteraction) bpObject;
            refreshInteraction(molecularInteraction);
        } else if (bpObject instanceof GroupObject) {
            // groupObject inside another groupObject
            refreshGroupObject((GroupObject) bpObject);
        }
    }
}

Example 7 with Conversion

use of org.vcell.pathway.Conversion in project vcell by virtualcell.

the class BioModelEditorPathwayDiagramPanel method deleteSelectedBioPaxObjects.

public static void deleteSelectedBioPaxObjects(Component guiRequester, BioModel bioModel, GraphModel graphModel) {
    StringBuilder warning = new StringBuilder("You can NOT delete the following pathway objects:\n\n");
    StringBuilder text = new StringBuilder("You are going to DELETE the following pathway objects:\n\n");
    // all objects required by user
    List<BioPaxObject> selected = getSelectedBioPaxObjects(graphModel);
    // the user required objects that can be deleted
    List<BioPaxObject> selectedBioPaxObjects = new ArrayList<BioPaxObject>();
    // all objects that will be deleted from the pathway model
    List<BioPaxObject> completeSelectedBioPaxObjects = new ArrayList<BioPaxObject>();
    // used for recover group objects
    HashSet<GroupObject> undeletedGroupObjects = new HashSet<GroupObject>();
    // all objects required by user + grouped elements contained in selected group objects
    List<BioPaxObject> allSelectedBioPaxObjects = new ArrayList<BioPaxObject>();
    // build a list of selected objects with selected grouped elements
    for (BioPaxObject bpObject : selected) {
        if (bpObject instanceof GroupObject) {
            // all elements of the groupObject will be deleted
            allSelectedBioPaxObjects.add(bpObject);
            // check all elements
            allSelectedBioPaxObjects.addAll(getAllGroupedObjects((GroupObject) bpObject));
        } else {
            allSelectedBioPaxObjects.add(bpObject);
        }
    }
    // if so, whether participants and catalysts of a selected reaction can be deleted
    for (BioPaxObject bpObject : allSelectedBioPaxObjects) {
        if (canDelete(bioModel, allSelectedBioPaxObjects, bpObject)) {
            selectedBioPaxObjects.add(bpObject);
            text.append("    " + bpObject.getTypeLabel() + ": \'" + PhysiologyRelationshipTableModel.getLabel(bpObject) + "\'\n");
            completeSelectedBioPaxObjects.add(bpObject);
            if (bpObject instanceof Conversion) {
                // check each participant
                for (InteractionParticipant ip : ((Conversion) bpObject).getParticipants()) {
                    if (canDelete(bioModel, allSelectedBioPaxObjects, ip.getPhysicalEntity())) {
                        completeSelectedBioPaxObjects.add(ip.getPhysicalEntity());
                        // the complex of the pysicalEntity will be removed
                        for (Complex complex : getComplex(bioModel, ip.getPhysicalEntity())) {
                            if (canDelete(bioModel, allSelectedBioPaxObjects, complex))
                                completeSelectedBioPaxObjects.add(complex);
                        }
                    }
                }
                // check catalysts
                for (BioPaxObject bp : bioModel.getPathwayModel().getBiopaxObjects()) {
                    if (bp instanceof Control) {
                        Control control = (Control) bp;
                        if (control.getControlledInteraction() == bpObject) {
                            completeSelectedBioPaxObjects.add(bp);
                            for (PhysicalEntity pe : control.getPhysicalControllers()) {
                                if (canDelete(bioModel, allSelectedBioPaxObjects, pe))
                                    completeSelectedBioPaxObjects.add(pe);
                            }
                        }
                    }
                }
            } else if (bpObject instanceof GroupObject) {
                // all elements of the groupObject will be deleted
                completeSelectedBioPaxObjects.add(bpObject);
                // check all elements
                completeSelectedBioPaxObjects.addAll(getAllGroupedObjects((GroupObject) bpObject));
            }
        } else {
            warning.append("    " + bpObject.getTypeLabel() + ": \'" + PhysiologyRelationshipTableModel.getLabel(bpObject) + "\'\n");
            if (bpObject instanceof GroupObject) {
                undeletedGroupObjects.add((GroupObject) bpObject);
            }
        }
    }
    warning.append("\nThey are either required by other reactions or linked with other physiological objects.\n\n");
    // for(GroupObject gObject : undeletedGroupObjects){
    // for (BioPaxObject bpo : gObject.getGroupedObjects()){
    // completeSelectedBioPaxObjects.remove(bpo);
    // }
    // }
    StringBuilder finalWarningMessage = new StringBuilder();
    if (allSelectedBioPaxObjects.size() > selectedBioPaxObjects.size()) {
        finalWarningMessage.append(warning.toString() + "\n\n");
    }
    if (selectedBioPaxObjects.size() > 0) {
        text.append("\nContinue?");
        finalWarningMessage.append(text.toString());
    }
    if (finalWarningMessage.length() == 0) {
        return;
    }
    String confirm = DialogUtils.showOKCancelWarningDialog(guiRequester, "Deleting pathway objects", finalWarningMessage.toString());
    if (confirm.equals(UserMessage.OPTION_CANCEL)) {
        return;
    }
    if (completeSelectedBioPaxObjects.size() > 0) {
        bioModel.getPathwayModel().remove(completeSelectedBioPaxObjects);
        bioModel.getPathwayModel().cleanGroupObjects();
        bioModel.getRelationshipModel().removeRelationshipObjects(completeSelectedBioPaxObjects);
    }
}

Example 8 with Conversion

use of org.vcell.pathway.Conversion in project vcell by virtualcell.

the class BioModelEditorConversionTableModel method refreshData.

private void refreshData() {
    if (bioModel == null || bioModel.getPathwayModel() == null || bioPaxObjects == null) {
        setData(null);
        return;
    }
    // function I :: get selected objects only
    // create ConversionTableRow objects
    allPathwayObjectList = new ArrayList<ConversionTableRow>();
    convertedBPObjects = new HashSet<BioPaxObject>();
    printObjects(bioPaxObjects);
    BioModel.printBpModelObjects(bioModel.getPathwayModel().getBiopaxObjects());
    // BioModel.printBpRelationshipObjects(bioModel.getRelationshipModel().getBioPaxObjects());	// derived; the bpObjects that are part of a relationship
    BioModel.printRelationships(bioModel.getRelationshipModel().getRelationshipObjects());
    System.out.println("----------------------------------------------------------------------");
    for (BioPaxObject bpo : bioPaxObjects) {
        if (bpo instanceof Conversion) {
            if (bioModel.getRelationshipModel().getRelationshipObjects(bpo).size() == 0) {
                Conversion conversion = (Conversion) bpo;
                ArrayList<String> nameList = conversion.getName();
                String interactionId = conversion.getID();
                String interactionLabel = nameList.isEmpty() ? conversion.getIDShort() : nameList.get(0);
                ConversionTableRow newConversionTableRow = createTableRow(conversion, interactionId, interactionLabel, "Conversion", 1.0, null);
                allPathwayObjectList.add(newConversionTableRow);
                convertedBPObjects.add(bpo);
                ArrayList<Stoichiometry> stoichiometryList = conversion.getParticipantStoichiometry();
                // stoichiometryMap problem:
                // how to deal with the case that the same object occurs on both left and right sides
                HashMap<PhysicalEntity, Double> stoichiometryMap = createStoichiometryMap(stoichiometryList);
                // reactant
                for (BioPaxObject bpObject1 : conversion.getLeft()) {
                    Double stoich = 1.0;
                    if (stoichiometryMap.get((PhysicalEntity) bpObject1) != null) {
                        stoich = stoichiometryMap.get((PhysicalEntity) bpObject1);
                    }
                    ConversionTableRow conversionTableRow;
                    if (bioModel.getRelationshipModel().getRelationshipObjects(bpObject1).isEmpty()) {
                        if (conversion instanceof Transport)
                            conversionTableRow = createTableRowForTransportParticipant(bpObject1, interactionId, interactionLabel, "Reactant", stoich, null);
                        else
                            conversionTableRow = createTableRow(bpObject1, interactionId, interactionLabel, "Reactant", stoich, null);
                    } else {
                        if (conversion instanceof Transport)
                            conversionTableRow = createTableRowForTransportParticipant(bpObject1, interactionId, interactionLabel, "Reactant", stoich, bioModel.getRelationshipModel().getRelationshipObjects(bpObject1));
                        else
                            conversionTableRow = createTableRow(bpObject1, interactionId, interactionLabel, "Reactant", stoich, bioModel.getRelationshipModel().getRelationshipObjects(bpObject1));
                    }
                    allPathwayObjectList.add(conversionTableRow);
                    convertedBPObjects.add(bpObject1);
                }
                // product
                for (BioPaxObject bpObject1 : conversion.getRight()) {
                    Double stoich = 1.0;
                    if (stoichiometryMap.get((PhysicalEntity) bpObject1) != null) {
                        stoich = stoichiometryMap.get((PhysicalEntity) bpObject1);
                    }
                    ConversionTableRow conversionTableRow;
                    if (bioModel.getRelationshipModel().getRelationshipObjects(bpObject1).isEmpty()) {
                        if (conversion instanceof Transport)
                            conversionTableRow = createTableRowForTransportParticipant(bpObject1, interactionId, interactionLabel, "Product", stoich, null);
                        else
                            conversionTableRow = createTableRow(bpObject1, interactionId, interactionLabel, "Product", stoich, null);
                    } else {
                        if (conversion instanceof Transport)
                            conversionTableRow = createTableRowForTransportParticipant(bpObject1, interactionId, interactionLabel, "Product", stoich, bioModel.getRelationshipModel().getRelationshipObjects(bpObject1));
                        else
                            conversionTableRow = createTableRow(bpObject1, interactionId, interactionLabel, "Product", stoich, bioModel.getRelationshipModel().getRelationshipObjects(bpObject1));
                    }
                    allPathwayObjectList.add(conversionTableRow);
                    convertedBPObjects.add(bpObject1);
                }
                // control
                for (BioPaxObject bpObject : bioModel.getPathwayModel().getBiopaxObjects()) {
                    if (bpObject instanceof Control) {
                        Control control = (Control) bpObject;
                        if (control instanceof Catalysis) {
                            // catalysis
                            if (BioPAXUtil.getControlledNonControlInteraction(control) == conversion) {
                                for (PhysicalEntity pe : ((Catalysis) control).getPhysicalControllers()) {
                                    ConversionTableRow conversionTableRow;
                                    if (bioModel.getRelationshipModel().getRelationshipObjects(pe).isEmpty()) {
                                        conversionTableRow = createTableRow(pe, interactionId, interactionLabel, "Catalyst", 1.0, null);
                                    } else {
                                        conversionTableRow = createTableRow(pe, interactionId, interactionLabel, "Catalyst", 1.0, bioModel.getRelationshipModel().getRelationshipObjects(pe));
                                    }
                                    allPathwayObjectList.add(conversionTableRow);
                                    convertedBPObjects.add(pe);
                                }
                            }
                        } else {
                            // other control types
                            if (BioPAXUtil.getControlledNonControlInteraction(control) == conversion) {
                                for (PhysicalEntity pe : control.getPhysicalControllers()) {
                                    ConversionTableRow conversionTableRow;
                                    if (bioModel.getRelationshipModel().getRelationshipObjects(pe).isEmpty()) {
                                        conversionTableRow = createTableRow(pe, interactionId, interactionLabel, "Control", 1.0, null);
                                    } else {
                                        conversionTableRow = createTableRow(pe, interactionId, interactionLabel, "Control", 1.0, bioModel.getRelationshipModel().getRelationshipObjects(pe));
                                    }
                                    allPathwayObjectList.add(conversionTableRow);
                                    convertedBPObjects.add(pe);
                                }
                            }
                        }
                    }
                }
            }
        } else if (bpo instanceof Catalysis) {
            for (PhysicalEntity pe : ((Catalysis) bpo).getPhysicalControllers()) {
                if (!convertedBPObjects.contains(pe)) {
                    ConversionTableRow conversionTableRow;
                    if (bioModel.getRelationshipModel().getRelationshipObjects(bpo).isEmpty()) {
                        conversionTableRow = createTableRow(pe, "", "", "Catalyst", 1.0, null);
                    } else {
                        conversionTableRow = createTableRow(pe, "", "", "Catalyst", 1.0, bioModel.getRelationshipModel().getRelationshipObjects(bpo));
                    }
                    allPathwayObjectList.add(conversionTableRow);
                    convertedBPObjects.add(pe);
                }
            }
            for (Pathway pathway : ((Catalysis) bpo).getPathwayControllers()) {
            // TODO
            }
        } else if (bpo instanceof Control) {
            for (PhysicalEntity pe : ((Catalysis) bpo).getPhysicalControllers()) {
                if (!convertedBPObjects.contains(pe)) {
                    ConversionTableRow conversionTableRow;
                    if (bioModel.getRelationshipModel().getRelationshipObjects(bpo).isEmpty()) {
                        conversionTableRow = createTableRow(pe, "", "", "Control", 1.0, null);
                    } else {
                        conversionTableRow = createTableRow(pe, "", "", "Control", 1.0, bioModel.getRelationshipModel().getRelationshipObjects(bpo));
                    }
                    allPathwayObjectList.add(conversionTableRow);
                    convertedBPObjects.add(pe);
                }
            }
            for (Pathway pathway : ((Catalysis) bpo).getPathwayControllers()) {
            // TODO
            }
        }
    }
    // 2nd pass - entities selected as themselves
    for (BioPaxObject bpo : bioPaxObjects) {
        if (bpo instanceof PhysicalEntity) {
            if (bioModel.getRelationshipModel().getRelationshipObjects(bpo).size() == 0) {
                PhysicalEntity physicalEntityObject = (PhysicalEntity) bpo;
                // we add standalone selected entities, only if they were not already added as part of any reaction
                if (!convertedBPObjects.contains(physicalEntityObject)) {
                    ConversionTableRow conversionTableRow = createTableRow(physicalEntityObject, "", "", "", 1.0, null);
                    allPathwayObjectList.add(conversionTableRow);
                    convertedBPObjects.add(physicalEntityObject);
                }
            }
        }
    }
    // apply text search function for particular columns
    ArrayList<ConversionTableRow> pathwayObjectList = new ArrayList<ConversionTableRow>();
    if (searchText == null || searchText.length() == 0) {
        pathwayObjectList.addAll(allPathwayObjectList);
    } else {
        String lowerCaseSearchText = searchText.toLowerCase();
        for (ConversionTableRow rs : allPathwayObjectList) {
            BioPaxObject bpObject = rs.getBioPaxObject();
            if (rs.interactionLabel().toLowerCase().contains(lowerCaseSearchText) || rs.participantType().toLowerCase().contains(lowerCaseSearchText) || getLabel(bpObject).toLowerCase().contains(lowerCaseSearchText) || getType(bpObject).toLowerCase().contains(lowerCaseSearchText)) {
                pathwayObjectList.add(rs);
            }
        }
    }
    setData(pathwayObjectList);
    GuiUtils.flexResizeTableColumns(ownerTable);
}

Example 9 with Conversion

use of org.vcell.pathway.Conversion 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 10 with Conversion

use of org.vcell.pathway.Conversion in project vcell by virtualcell.

the class PhysiologyRelationshipTableModel method refreshData.

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