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

Example 86 with SpeciesContext

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

the class NetworkFreePanel method setSimulationContext.

public void setSimulationContext(SimulationContext simulationContext) {
    if (simulationContext == null) {
        return;
    }
    if (fieldSimulationContext != null) {
        fieldSimulationContext.removePropertyChangeListener(eventHandler);
    }
    fieldSimulationContext = simulationContext;
    fieldSimulationContext.addPropertyChangeListener(eventHandler);
    Model m = fieldSimulationContext.getModel();
    if (m != null) {
        m.removePropertyChangeListener(eventHandler);
        m.addPropertyChangeListener(eventHandler);
        for (SpeciesContext sc : m.getSpeciesContexts()) {
            sc.removePropertyChangeListener(eventHandler);
            sc.addPropertyChangeListener(eventHandler);
        }
    }
    refreshInterface();
}

Example 87 with SpeciesContext

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

the class ViewGeneratedSpeciesPanel method updateShape.

public void updateShape(int selectedRow) {
    GeneratedSpeciesTableRow speciesTableRow = tableModel.getValueAt(selectedRow);
    String inputString = speciesTableRow.getExpression();
    // System.out.println(selectedRows[0] + ": " + inputString);
    Model tempModel = null;
    try {
        tempModel = new Model("MyTempModel");
        tempModel.addFeature("c0");
    } catch (ModelException | PropertyVetoException e1) {
        e1.printStackTrace();
    }
    if (owner != null && owner.getSimulationContext() != null) {
        List<MolecularType> mtList = owner.getSimulationContext().getModel().getRbmModelContainer().getMolecularTypeList();
        try {
            tempModel.getRbmModelContainer().setMolecularTypeList(mtList);
        } catch (PropertyVetoException e1) {
            e1.printStackTrace();
            throw new RuntimeException("Unexpected exception setting " + MolecularType.typeName + " list: " + e1.getMessage(), e1);
        }
    } else {
        System.out.println("something is wrong, we just do nothing rather than crash");
        return;
    }
    try {
        String strStructure = null;
        if (inputString.contains(RbmUtils.SiteStruct)) {
            // we are in the mode where we emulate compartments by adding the compartment name as a fake site
            Pair<List<String>, String> p = RbmUtils.extractCompartment(inputString);
            // we'll just assume there's only one, may want to throw exception if more
            strStructure = p.one.get(0);
            inputString = p.two;
        } else {
            // should be the normal @comp:expression format - if it's not it will return null
            strStructure = RbmUtils.parseCompartment(inputString, tempModel);
        }
        Structure structure;
        if (strStructure != null) {
            if (tempModel.getStructure(strStructure) == null) {
                if (owner.getSimulationContext().getModel().getStructure(strStructure).getTypeName().equals(Structure.TYPE_NAME_MEMBRANE)) {
                    tempModel.addMembrane(strStructure);
                } else {
                    tempModel.addFeature(strStructure);
                }
            }
            structure = tempModel.getStructure(strStructure);
        } else {
            structure = tempModel.getStructure(0);
        }
        SpeciesPattern sp = (SpeciesPattern) RbmUtils.parseSpeciesPattern(inputString, tempModel);
        sp.resolveBonds();
        SpeciesContext sc = new SpeciesContext(new Species("a", ""), structure, sp);
        spls = new SpeciesPatternLargeShape(20, 20, -1, sp, shapePanel, sc, issueManager);
    } catch (ParseException | PropertyVetoException | ModelException e1) {
        e1.printStackTrace();
        // error (red circle)
        spls = new SpeciesPatternLargeShape(20, 20, -1, shapePanel, true, issueManager);
        shapePanel.repaint();
    }
    int xOffset = spls.getRightEnd() + 45;
    Dimension preferredSize = new Dimension(xOffset + 90, 50);
    shapePanel.setPreferredSize(preferredSize);
    shapePanel.repaint();
}

Example 88 with SpeciesContext

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

the class ViewGeneratedSpeciesPanel method initialize.

private void initialize() {
    try {
        setName("ViewGeneratedSpeciesPanel");
        setLayout(new GridBagLayout());
        shapePanel = 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;
            }
        };
        Border loweredBevelBorder = BorderFactory.createLoweredBevelBorder();
        shapePanel.setLayout(new GridBagLayout());
        shapePanel.setBackground(Color.white);
        // not really editable but we don't want the brown contours here
        shapePanel.setEditable(true);
        shapePanel.setShowMoleculeColor(true);
        shapePanel.setShowNonTrivialOnly(true);
        JScrollPane scrollPane = new JScrollPane(shapePanel);
        scrollPane.setBorder(loweredBevelBorder);
        scrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
        scrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_NEVER);
        JPanel optionsPanel = new JPanel();
        optionsPanel.setLayout(new GridBagLayout());
        getZoomSmallerButton().setEnabled(true);
        getZoomLargerButton().setEnabled(false);
        GridBagConstraints gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = 0;
        gbc.insets = new Insets(0, 0, 0, 10);
        gbc.anchor = GridBagConstraints.WEST;
        optionsPanel.add(getZoomLargerButton(), gbc);
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = 1;
        gbc.insets = new Insets(2, 0, 4, 10);
        gbc.anchor = GridBagConstraints.WEST;
        optionsPanel.add(getZoomSmallerButton(), 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);
        optionsPanel.add(new JLabel(""), gbc);
        JPanel containerOfScrollPanel = new JPanel();
        containerOfScrollPanel.setLayout(new BorderLayout());
        containerOfScrollPanel.add(optionsPanel, BorderLayout.WEST);
        containerOfScrollPanel.add(scrollPane, BorderLayout.CENTER);
        Dimension dim = new Dimension(500, 135);
        // dimension of shape panel
        containerOfScrollPanel.setPreferredSize(dim);
        containerOfScrollPanel.setMinimumSize(dim);
        containerOfScrollPanel.setMaximumSize(dim);
        // ------------------------------------------------------------------------
        table = new EditorScrollTable();
        tableModel = new GeneratedSpeciesTableModel(table, owner);
        table.setModel(tableModel);
        table.getSelectionModel().addListSelectionListener(eventHandler);
        table.getModel().addTableModelListener(eventHandler);
        DefaultTableCellRenderer rightRenderer = new DefaultTableCellRenderer();
        rightRenderer.setHorizontalAlignment(JLabel.RIGHT);
        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);
        table.setPreferredScrollableViewportSize(new Dimension(400, 200));
        add(table.getEnclosingScrollPane(), gbc);
        // gbc = new java.awt.GridBagConstraints();
        // gbc.gridx = 9;
        // gbc.gridy = gridy;
        // add toolTipText for each table cell
        table.addMouseMotionListener(new MouseMotionAdapter() {

            public void mouseMoved(MouseEvent e) {
                Point p = e.getPoint();
                int row = table.rowAtPoint(p);
                int column = table.columnAtPoint(p);
                table.setToolTipText(String.valueOf(table.getValueAt(row, column)));
            }
        });
        gridy++;
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.anchor = GridBagConstraints.LINE_END;
        gbc.insets = new Insets(4, 4, 4, 4);
        add(new JLabel("Search "), gbc);
        textFieldSearch = new JTextField(70);
        textFieldSearch.addActionListener(eventHandler);
        textFieldSearch.getDocument().addDocumentListener(eventHandler);
        textFieldSearch.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);
        add(textFieldSearch, gbc);
        gbc = new GridBagConstraints();
        gbc.gridx = 4;
        gbc.gridy = gridy;
        gbc.fill = GridBagConstraints.HORIZONTAL;
        gbc.insets = new Insets(4, 4, 4, 10);
        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);
        add(containerOfScrollPanel, 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() == tableModel) {
                        selectedObject = tableModel.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);
                }
            }
        };
        table.getColumnModel().getColumn(GeneratedSpeciesTableModel.iColDepiction).setCellRenderer(rbmSpeciesShapeDepictionCellRenderer);
        table.getColumnModel().getColumn(GeneratedSpeciesTableModel.iColDepiction).setPreferredWidth(400);
        table.getColumnModel().getColumn(GeneratedSpeciesTableModel.iColDepiction).setMinWidth(400);
        table.getColumnModel().getColumn(GeneratedReactionTableModel.iColDefinition).setPreferredWidth(30);
        table.setAutoResizeMode(JTable.AUTO_RESIZE_LAST_COLUMN);
    } catch (java.lang.Throwable ivjExc) {
        handleException(ivjExc);
    }
}

Example 89 with SpeciesContext

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

the class ViewObservablesMapPanel method updateShapeSpecies.

public void updateShapeSpecies(int selectedRow) {
    GeneratedSpeciesTableRow speciesTableRow = speciesTableModel.getValueAt(selectedRow);
    String inputString = speciesTableRow.getExpression();
    // System.out.println(selectedRows[0] + ": " + inputString);
    Model tempModel = null;
    try {
        tempModel = new Model("MyTempModel");
        tempModel.addFeature("c0");
    } catch (ModelException | PropertyVetoException e1) {
        e1.printStackTrace();
    }
    if (owner != null && owner.getSimulationContext() != null) {
        List<MolecularType> mtList = owner.getSimulationContext().getModel().getRbmModelContainer().getMolecularTypeList();
        try {
            tempModel.getRbmModelContainer().setMolecularTypeList(mtList);
        } catch (PropertyVetoException e1) {
            e1.printStackTrace();
            throw new RuntimeException("Unexpected exception setting " + MolecularType.typeName + " list: " + e1.getMessage(), e1);
        }
    } else {
        System.out.println("something is wrong, we just do nothing rather than crash");
        return;
    }
    try {
        String strStructure = null;
        if (inputString.contains(RbmUtils.SiteStruct)) {
            // we are in the mode where we emulate compartments by adding the compartment name as a fake site
            Pair<List<String>, String> p = RbmUtils.extractCompartment(inputString);
            // we'll just assume there's only one, may want to throw exception if more
            strStructure = p.one.get(0);
            inputString = p.two;
        } else {
            // should be the normal @comp:expression format - if it's not it will return null
            strStructure = RbmUtils.parseCompartment(inputString, tempModel);
        }
        Structure structure;
        if (strStructure != null) {
            if (tempModel.getStructure(strStructure) == null) {
                if (owner.getSimulationContext().getModel().getStructure(strStructure).getTypeName().equals(Structure.TYPE_NAME_MEMBRANE)) {
                    tempModel.addMembrane(strStructure);
                } else {
                    tempModel.addFeature(strStructure);
                }
            }
            structure = tempModel.getStructure(strStructure);
        } else {
            structure = tempModel.getStructure(0);
        }
        SpeciesPattern sp = (SpeciesPattern) RbmUtils.parseSpeciesPattern(inputString, tempModel);
        sp.resolveBonds();
        SpeciesContext sc = new SpeciesContext(new Species("a", ""), structure, sp);
        spls = new SpeciesPatternLargeShape(20, 20, -1, sp, shapePanelSpecies, sc, issueManager);
    } catch (ParseException | PropertyVetoException | ModelException e1) {
        e1.printStackTrace();
        // error (red circle)
        spls = new SpeciesPatternLargeShape(20, 20, -1, shapePanelSpecies, true, issueManager);
        shapePanelSpecies.repaint();
    }
    int xOffset = spls.getRightEnd() + 45;
    Dimension preferredSize = new Dimension(xOffset + 90, 50);
    shapePanelSpecies.setPreferredSize(preferredSize);
    shapePanelSpecies.repaint();
}

Example 90 with SpeciesContext

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

the class SymbolTableEntryTableCellRenderer method getTableCellRendererComponent.

public java.awt.Component getTableCellRendererComponent(javax.swing.JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
    super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
    if (value == null) {
        setText("unmapped");
        return this;
    }
    SymbolTableEntry ste = (SymbolTableEntry) value;
    if (ste instanceof Model.ReservedSymbol) {
        setText(ste.getName());
    } else if (ste instanceof SpeciesContext) {
        setText("[" + ste.getName() + "]");
    } else if (ste instanceof KineticsParameter) {
        setText(ste.getNameScope().getName() + ":" + ste.getName());
    } else if (ste instanceof ModelParameter) {
        setText(ste.getName());
    } else if (ste instanceof ReservedVariable) {
        setText(ste.getName());
    } else {
        setText(ste.getNameScope().getAbsoluteScopePrefix() + ste.getName());
    }
    // setToolTipText("Kinetic parameter \""+ste.getName()+"\" in reaction "+);
    return this;
}