Examples with RbmObservable cbit.vcell.model.RbmObservable used on opensource projects

Example 1 with RbmObservable

use of cbit.vcell.model.RbmObservable in project vcell by virtualcell.

the class ViewObservablesMapPanel method initialize.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

            SpeciesPatternSmallShape spss = null;

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

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

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

            SpeciesPatternSmallShape spss = null;

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

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

Example 2 with RbmObservable

use of cbit.vcell.model.RbmObservable in project vcell by virtualcell.

the class ViewObservablesMapPanel method updateShapeObservable.

private void updateShapeObservable(int selectedRow) {
    spsList.clear();
    if (selectedRow == -1) {
        shapePanelObservable.repaint();
        return;
    }
    ObservablesGroupTableRow observablesTableRow = observablesTableModel.getValueAt(selectedRow);
    String obsName = observablesTableRow.getObservableGroupObject().getObservableGroupName();
    RbmObservable observable = observablesTableRow.getObservable(obsName);
    int maxXOffset = xOffsetInitial;
    int maxYOffset = 8;
    if (observable != null && observable.getSpeciesPatternList() != null && observable.getSpeciesPatternList().size() > 0) {
        // if more than one sp per observable, since non-editable we show them all on a single row
        for (int i = 0; i < observable.getSpeciesPatternList().size(); i++) {
            SpeciesPattern sp = observable.getSpeciesPatternList().get(i);
            SpeciesPatternLargeShape sps = new SpeciesPatternLargeShape(maxXOffset, maxYOffset, 80, sp, shapePanelObservable, observable, issueManager);
            spsList.add(sps);
            int xOffset = sps.getRightEnd();
            maxXOffset = xOffset + 40;
        }
    }
    Dimension preferredSize = new Dimension(maxXOffset + 200, maxYOffset);
    shapePanelObservable.setPreferredSize(preferredSize);
    shapePanelObservable.repaint();
}

Example 3 with RbmObservable

use of cbit.vcell.model.RbmObservable in project vcell by virtualcell.

the class ObservablesGroupTableModel method getValueAt.

public Object getValueAt(int iRow, int iCol) {
    ObservablesGroupTableRow observablesTableRow = getValueAt(iRow);
    String obsName = observablesTableRow.getObservableGroupObject().getObservableGroupName();
    RbmObservable obs = observablesTableRow.getObservable(obsName);
    String obsDefinition = ObservablesGroupTableRow.toBnglString(obs);
    switch(iCol) {
        case iColOriginalName:
            return obsName;
        case iColStructure:
            {
                if (obsDefinition.startsWith("@") && obsDefinition.contains(":")) {
                    String structName = obsDefinition.substring(1, obsDefinition.indexOf(":"));
                    return structName;
                } else {
                    SimulationContext sc = owner.getSimulationContext();
                    if (sc.getModel().getStructures().length > 1) {
                        // if we have more than 1 compartments
                        return "?";
                    } else {
                        Structure struct = sc.getModel().getStructure(0);
                        return struct.getName();
                    }
                }
            }
        case iColDepiction:
            return obsDefinition;
        case iColDefinition:
            switch(obs.getSequence()) {
                case Multimolecular:
                    return obsDefinition;
                case PolymerLengthEqual:
                    return obsDefinition + "=" + obs.getSequenceLength();
                case PolymerLengthGreater:
                    return obsDefinition + ">" + obs.getSequenceLength();
                default:
                    return obsDefinition;
            }
        case iColExpression:
            String exp;
            BNGSpecies[] speciesList = observablesTableRow.getObservableGroupObject().getListofSpecies();
            if (speciesList == null || speciesList.length == 0) {
                exp = "<html><font color=\"red\">No generated species</html>";
            } else {
                exp = getExpressionAsString(observablesTableRow.getObservableGroupObject());
            }
            return exp;
        case iColCount:
            return obs.getType().name();
        default:
            return null;
    }
}

Example 4 with RbmObservable

use of cbit.vcell.model.RbmObservable in project vcell by virtualcell.

the class ObservablePropertiesPanel method onSelectedObjectsChange.

@Override
protected void onSelectedObjectsChange(Object[] selectedObjects) {
    RbmObservable observable = null;
    if (selectedObjects.length == 1 && selectedObjects[0] instanceof RbmObservable) {
        observable = (RbmObservable) selectedObjects[0];
    }
    setObservable(observable);
    updateSequence();
}

Example 5 with RbmObservable

use of cbit.vcell.model.RbmObservable in project vcell by virtualcell.

the class ObservableTreeModel method valueForPathChanged.

@Override
public void valueForPathChanged(TreePath path, Object newValue) {
    Object obj = path.getLastPathComponent();
    if (obj == null || !(obj instanceof BioModelNode)) {
        return;
    }
    BioModelNode selectedNode = (BioModelNode) obj;
    BioModelNode parentNode = (BioModelNode) selectedNode.getParent();
    Object userObject = selectedNode.getUserObject();
    try {
        if (newValue instanceof String) {
            String inputString = (String) newValue;
            if (inputString == null || inputString.length() == 0) {
                return;
            }
            String mangled = TokenMangler.fixTokenStrict(inputString);
            if (!mangled.equals(inputString)) {
                String errMsg = ((Displayable) userObject).getDisplayType() + " '" + inputString + "' not legal identifier, try '" + mangled + "'";
                throw new RuntimeException(errMsg);
            }
            if (userObject instanceof RbmObservable) {
                // TODO: untested!!!
                ((RbmObservable) userObject).setName(inputString);
            }
        } else if (newValue instanceof MolecularComponentPattern) {
            MolecularComponentPattern newMcp = (MolecularComponentPattern) newValue;
            Object parentObject = parentNode == null ? null : parentNode.getUserObject();
            if (parentObject instanceof MolecularTypePattern) {
                MolecularTypePattern mtp = (MolecularTypePattern) parentObject;
                MolecularComponent mc = newMcp.getMolecularComponent();
                MolecularComponentPattern mcp = mtp.getMolecularComponentPattern(mc);
                mcp.setComponentStatePattern(newMcp.getComponentStatePattern());
                BondType bp = mcp.getBondType();
                BondType newbp = newMcp.getBondType();
                mcp.setBondType(newbp);
                // specified -> specified
                if (bp == BondType.Specified && newbp == BondType.Specified) {
                // bond didn't change
                } else if (bp == BondType.Specified && newbp != BondType.Specified) {
                    // specified -> non specified
                    // change the partner to possible
                    mcp.getBond().molecularComponentPattern.setBondType(BondType.Possible);
                    mcp.setBond(null);
                } else if (bp != BondType.Specified && newbp == BondType.Specified) {
                    // non specified -> specified
                    int newBondId = newMcp.getBondId();
                    mcp.setBondId(newBondId);
                    mcp.setBond(newMcp.getBond());
                    mcp.getBond().molecularComponentPattern.setBondId(newBondId);
                    for (SpeciesPattern sp : observable.getSpeciesPatternList()) {
                        sp.resolveBonds();
                    }
                } else {
                }
            }
        }
    } catch (Exception ex) {
        DialogUtils.showErrorDialog(ownerTree, ex.getMessage());
    }
}