Examples with SpeciesPattern org.vcell.model.rbm.SpeciesPattern used on opensource projects

Example 46 with SpeciesPattern

use of org.vcell.model.rbm.SpeciesPattern 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 47 with SpeciesPattern

use of org.vcell.model.rbm.SpeciesPattern 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 48 with SpeciesPattern

use of org.vcell.model.rbm.SpeciesPattern in project vcell by virtualcell.

the class RulebasedMathMapping method addObservables.

private List<ParticleObservable> addObservables(GeometryClass geometryClass, Domain domain, HashMap<SpeciesPattern, VolumeParticleSpeciesPattern> speciesPatternMap) throws MappingException, MathException {
    ArrayList<ParticleObservable> observables = new ArrayList<>();
    // 
    for (MathMappingParameter mathMappingParameter : getMathMappingParameters()) {
        if (mathMappingParameter instanceof ObservableCountParameter) {
            ObservableCountParameter observableCountParameter = (ObservableCountParameter) mathMappingParameter;
            RbmObservable rbmObservable = observableCountParameter.getObservable();
            ParticleObservable.ObservableType particleObservableType = null;
            if (rbmObservable.getType() == RbmObservable.ObservableType.Molecules) {
                particleObservableType = ParticleObservable.ObservableType.Molecules;
            } else {
                particleObservableType = ParticleObservable.ObservableType.Species;
            }
            ParticleObservable particleObservable = new VolumeParticleObservable(getMathSymbol(observableCountParameter, geometryClass), domain, particleObservableType);
            switch(rbmObservable.getSequence()) {
                case Multimolecular:
                    {
                        particleObservable.setSequence(Sequence.Multimolecular);
                        break;
                    }
                case PolymerLengthEqual:
                    {
                        particleObservable.setSequence(Sequence.PolymerLengthEqual);
                        particleObservable.setQuantity(rbmObservable.getSequenceLength());
                        break;
                    }
                case PolymerLengthGreater:
                    {
                        particleObservable.setSequence(Sequence.PolymerLengthGreater);
                        particleObservable.setQuantity(rbmObservable.getSequenceLength());
                        break;
                    }
                default:
                    {
                        throw new RuntimeException("unexpected sequence " + rbmObservable.getSequence());
                    }
            }
            for (SpeciesPattern speciesPattern : rbmObservable.getSpeciesPatternList()) {
                VolumeParticleSpeciesPattern vpsp = speciesPatternMap.get(speciesPattern);
                particleObservable.addParticleSpeciesPattern(vpsp);
            }
            observables.add(particleObservable);
        }
        if (mathMappingParameter instanceof SpeciesCountParameter) {
            SpeciesCountParameter speciesCountParameter = (SpeciesCountParameter) mathMappingParameter;
            ParticleObservable.ObservableType particleObservableType = ParticleObservable.ObservableType.Species;
            ParticleObservable particleObservable = new VolumeParticleObservable(getMathSymbol(speciesCountParameter, geometryClass), domain, particleObservableType);
            particleObservable.setSequence(Sequence.Multimolecular);
            SpeciesPattern speciesPattern = speciesCountParameter.getSpeciesContext().getSpeciesPattern();
            VolumeParticleSpeciesPattern vpsp = speciesPatternMap.get(speciesPattern);
            particleObservable.addParticleSpeciesPattern(vpsp);
            observables.add(particleObservable);
        }
    }
    return observables;
}

Example 49 with SpeciesPattern

use of org.vcell.model.rbm.SpeciesPattern in project vcell by virtualcell.

the class BioModelEditorModelPanel method newButtonPressed.

private void newButtonPressed() throws ModelException, PropertyVetoException {
    newObject = null;
    computeCurrentSelectedTable();
    if (currentSelectedTable == speciesTable) {
        if (bioModel.getModel().getNumStructures() == 1) {
            newObject = bioModel.getModel().createSpeciesContext(bioModel.getModel().getStructures()[0]);
        } else if (bioModel.getModel().getNumStructures() > 1) {
            final JPopupMenu menu = new JPopupMenu("Choose compartment");
            for (int i = 0; i < bioModel.getModel().getNumStructures(); i++) {
                Structure s = bioModel.getModel().getStructure(i);
                String sName = s.getName();
                JMenuItem menuItem = new JMenuItem("In " + s.getTypeName() + " " + sName);
                menuItem.setIcon(new StructureToolShapeIcon(17));
                menu.add(menuItem);
                menuItem.addActionListener(new ActionListener() {

                    public void actionPerformed(ActionEvent e) {
                        newObject = bioModel.getModel().createSpeciesContext(s);
                    }
                });
            }
            menu.show(newButton, 0, newButton.getHeight());
        }
    } else if (currentSelectedTable == molecularTypeTable) {
        if (bioModel.getModel().getRbmModelContainer() != null) {
            MolecularType mt = bioModel.getModel().getRbmModelContainer().createMolecularType();
            bioModel.getModel().getRbmModelContainer().addMolecularType(mt, true);
            newObject = mt;
        }
    } else if (currentSelectedTable == observablesTable) {
        if (bioModel.getModel().getRbmModelContainer() != null) {
            if (bioModel.getModel().getRbmModelContainer().getMolecularTypeList().isEmpty()) {
                PopupGenerator.showInfoDialog(this, VCellErrorMessages.MustBeRuleBased);
                return;
            }
            if (bioModel.getModel().getNumStructures() == 1) {
                RbmObservable o = bioModel.getModel().getRbmModelContainer().createObservable(RbmObservable.ObservableType.Molecules);
                bioModel.getModel().getRbmModelContainer().addObservable(o);
                SpeciesPattern sp = new SpeciesPattern();
                o.addSpeciesPattern(sp);
                newObject = o;
            } else if (bioModel.getModel().getNumStructures() > 1) {
                final JPopupMenu menu = new JPopupMenu("Choose compartment");
                for (int i = 0; i < bioModel.getModel().getNumStructures(); i++) {
                    Structure s = bioModel.getModel().getStructure(i);
                    String sName = s.getName();
                    JMenuItem menuItem = new JMenuItem("In " + s.getTypeName() + " " + sName);
                    menuItem.setIcon(new StructureToolShapeIcon(17));
                    menu.add(menuItem);
                    menuItem.addActionListener(new ActionListener() {

                        public void actionPerformed(ActionEvent e) {
                            RbmObservable o = bioModel.getModel().getRbmModelContainer().createObservable(RbmObservable.ObservableType.Molecules, null, s);
                            o.setStructure(s);
                            try {
                                bioModel.getModel().getRbmModelContainer().addObservable(o);
                            } catch (ModelException | PropertyVetoException e1) {
                                e1.printStackTrace();
                                throw new RuntimeException(e1.getMessage(), e1);
                            }
                            SpeciesPattern sp = new SpeciesPattern();
                            o.addSpeciesPattern(sp);
                            newObject = o;
                            if (newObject != null) {
                                for (int i = 0; i < currentSelectedTableModel.getRowCount(); i++) {
                                    if (currentSelectedTableModel.getValueAt(i) == newObject) {
                                        currentSelectedTable.setRowSelectionInterval(i, i);
                                        break;
                                    }
                                }
                            }
                        }
                    });
                }
                menu.show(newButton, 0, newButton.getHeight());
            }
        }
    } else if (currentSelectedTable == structuresTable) {
        try {
            Feature feature = bioModel.getModel().createFeature();
            newObject = feature;
        } catch (Exception e) {
            e.printStackTrace();
            DialogUtils.showErrorDialog(this, e.getMessage(), e);
        }
    } else if (currentSelectedTable == reactionsTable) {
        if (bioModel.getModel().getNumStructures() == 1) {
            SimpleReaction reactionStep = bioModel.getModel().createSimpleReaction(bioModel.getModel().getStructures()[0]);
            newObject = reactionStep;
        } else {
            addNewReaction();
        }
    }
    if (newObject != null) {
        for (int i = 0; i < currentSelectedTableModel.getRowCount(); i++) {
            if (currentSelectedTableModel.getValueAt(i) == newObject) {
                currentSelectedTable.setRowSelectionInterval(i, i);
                break;
            }
        }
    }
}

Example 50 with SpeciesPattern

use of org.vcell.model.rbm.SpeciesPattern in project vcell by virtualcell.

the class BioModelEditorSpeciesTableModel method setValueAt.

public void setValueAt(Object value, int row, int column) {
    if (getModel() == null || value == null) {
        return;
    }
    try {
        SpeciesContext speciesContext = getValueAt(row);
        if (speciesContext != null) {
            // row with existing species
            switch(column) {
                case COLUMN_NAME:
                    {
                        String inputValue = ((String) value);
                        inputValue = inputValue.trim();
                        if (inputValue.length() == 0) {
                            return;
                        }
                        speciesContext.setName(inputValue);
                        break;
                    }
                case COLUMN_STRUCTURE:
                    {
                        // value might be null because no popup in JCombo editor ui.
                        // the first time.
                        Structure structure = (Structure) value;
                        speciesContext.setStructure(structure);
                        break;
                    }
                case COLUMN_DEFINITION:
                    String inputValue = ((String) value);
                    inputValue = inputValue.trim();
                    if (inputValue.length() == 0) {
                        speciesContext.setSpeciesPattern(null);
                        return;
                    }
                    SpeciesPattern sp = RbmUtils.parseSpeciesPattern(inputValue, bioModel.getModel());
                    speciesContext.setSpeciesPattern(sp);
                    break;
            }
        } else {
            // empty row being edited - Deprecated, we now must use the "New Species" button
            switch(column) {
                case // only "name" column is editable
                COLUMN_NAME:
                    String inputValue = ((String) value);
                    if (inputValue.length() == 0 || inputValue.equals(ADD_NEW_HERE_TEXT)) {
                        return;
                    }
                    inputValue = inputValue.trim();
                    SpeciesContext freeSpeciesContext = getModel().createSpeciesContext(getModel().getStructures()[0]);
                    freeSpeciesContext.setName(inputValue);
                    break;
            }
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
        DialogUtils.showErrorDialog(ownerTable, e.getMessage(), e);
    }
}