Search in sources :

Example 36 with MolecularTypePattern

use of org.vcell.model.rbm.MolecularTypePattern 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);
    }
}
Also used : JPanel(javax.swing.JPanel) RuleParticipantSignature(cbit.vcell.model.RuleParticipantSignature) GridBagConstraints(java.awt.GridBagConstraints) Insets(java.awt.Insets) GridBagLayout(java.awt.GridBagLayout) SpeciesPatternSmallShape(cbit.vcell.graph.SpeciesPatternSmallShape) SpeciesContext(cbit.vcell.model.SpeciesContext) JTextField(javax.swing.JTextField) SpeciesPattern(org.vcell.model.rbm.SpeciesPattern) LargeShapePanel(cbit.vcell.graph.gui.LargeShapePanel) DefaultTableCellRenderer(javax.swing.table.DefaultTableCellRenderer) BorderLayout(java.awt.BorderLayout) VCellSortTableModel(cbit.vcell.client.desktop.biomodel.VCellSortTableModel) RuleAnalysisChanged(cbit.vcell.graph.ReactionCartoon.RuleAnalysisChanged) JScrollPane(javax.swing.JScrollPane) MouseEvent(java.awt.event.MouseEvent) MolecularComponentPattern(org.vcell.model.rbm.MolecularComponentPattern) GroupingCriteria(cbit.vcell.model.GroupingCriteria) JLabel(javax.swing.JLabel) Dimension(java.awt.Dimension) Point(java.awt.Point) GridBagConstraints(java.awt.GridBagConstraints) Point(java.awt.Point) Graphics(java.awt.Graphics) MouseMotionAdapter(java.awt.event.MouseMotionAdapter) JTable(javax.swing.JTable) DefaultScrollTableCellRenderer(org.vcell.util.gui.DefaultScrollTableCellRenderer) EditorScrollTable(org.vcell.util.gui.EditorScrollTable) MolecularTypePattern(org.vcell.model.rbm.MolecularTypePattern) Border(javax.swing.border.Border)

Example 37 with MolecularTypePattern

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

the class RulebasedTransformer method extractMolecules.

private void extractMolecules(SpeciesPattern sp, Model model, Element participantPatternElement) {
    List<MolecularTypePattern> mtpUsedAlreadyList = new ArrayList<MolecularTypePattern>();
    Element listOfMoleculesElement = participantPatternElement.getChild("ListOfMolecules", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
    List<Element> moleculeChildren = new ArrayList<Element>();
    moleculeChildren = listOfMoleculesElement.getChildren("Molecule", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
    for (Element moleculeElement : moleculeChildren) {
        String molecule_id_str = moleculeElement.getAttributeValue("id");
        String molecule_name_str = moleculeElement.getAttributeValue("name");
        List<MolecularTypePattern> mtpList = sp.getMolecularTypePatterns(molecule_name_str);
        if (mtpList.isEmpty())
            System.out.println("!!! Missing molecule " + molecule_name_str);
        MolecularTypePattern mtp = null;
        for (MolecularTypePattern mtpCandidate : mtpList) {
            if (mtpUsedAlreadyList.contains(mtpCandidate)) {
                continue;
            }
            // this mtp is the next in line unused, so we associate it with this id
            mtp = mtpCandidate;
            mtpUsedAlreadyList.add(mtpCandidate);
            break;
        }
        System.out.println("     molecule  id=" + molecule_id_str + ", name=" + molecule_name_str);
        keyMap.put(molecule_id_str, mtp);
        Element listOfComponentsElement = moleculeElement.getChild("ListOfComponents", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        if (listOfComponentsElement == null) {
            continue;
        }
        List<Element> componentChildren = new ArrayList<Element>();
        componentChildren = listOfComponentsElement.getChildren("Component", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        for (Element componentElement : componentChildren) {
            String component_id_str = componentElement.getAttributeValue("id");
            String component_name_str = componentElement.getAttributeValue("name");
            MolecularComponentPattern mcp = mtp.getMolecularComponentPattern(component_name_str);
            if (mcp == null)
                System.out.println("!!! Missing component " + component_name_str);
            System.out.println("        component  id=" + component_id_str + ", name=" + component_name_str);
            keyMap.put(component_id_str, mcp);
        }
    }
}
Also used : MolecularComponentPattern(org.vcell.model.rbm.MolecularComponentPattern) Element(org.jdom.Element) ArrayList(java.util.ArrayList) MolecularTypePattern(org.vcell.model.rbm.MolecularTypePattern)

Example 38 with MolecularTypePattern

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

the class XmlReader method getSpeciesPattern.

// private SeedSpecies getRbmSeedSpecies(Element e, Model newModel) {
// String s = e.getAttributeValue(XMLTags.RbmInitialConditionTag);
// if(s == null || s.isEmpty()) {
// System.out.println("XMLReader: getRbmSeedSpecies: initial condition is missing.");
// return null;
// }
// Expression exp = unMangleExpression(s);
// Element element = e.getChild(XMLTags.RbmSpeciesPatternTag, vcNamespace);
// SpeciesPattern sp = getSpeciesPattern(element, newModel);
// if(sp == null) {
// System.out.println("XMLReader: getRbmSeedSpecies: SpeciesPattern is missing.");
// return null;
// }
// SeedSpecies ss = new SeedSpecies(sp, exp);
// return ss;
// }
private SpeciesPattern getSpeciesPattern(Element e, Model newModel) {
    SpeciesPattern sp = new SpeciesPattern();
    List<Element> children = e.getChildren(XMLTags.RbmMolecularTypePatternTag, vcNamespace);
    for (Element element : children) {
        MolecularTypePattern tp = getRbmMolecularTypePattern(element, newModel);
        if (tp != null) {
            sp.addMolecularTypePattern(tp);
        }
    }
    return sp;
}
Also used : Element(org.jdom.Element) ParticleMolecularTypePattern(cbit.vcell.math.ParticleMolecularTypePattern) MolecularTypePattern(org.vcell.model.rbm.MolecularTypePattern) ParticleSpeciesPattern(cbit.vcell.math.ParticleSpeciesPattern) VolumeParticleSpeciesPattern(cbit.vcell.math.VolumeParticleSpeciesPattern) SpeciesPattern(org.vcell.model.rbm.SpeciesPattern)

Example 39 with MolecularTypePattern

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

the class SpeciesPropertiesTreeModel method propertyChange.

public void propertyChange(PropertyChangeEvent evt) {
    if (evt.getPropertyName().equals(PropertyConstants.PROPERTY_NAME_NAME)) {
        nodeChanged(rootNode);
    // } else if (evt.getSource() == seedSpecies && evt.getPropertyName().equals(SeedSpecies.PROPERTY_NAME_TYPE)){
    // nodeChanged(rootNode);
    } else if (evt.getPropertyName().equals("entityChange")) {
        nodeChanged(rootNode);
    } else {
        populateTree();
        Object source = evt.getSource();
        if (source == speciesContext) {
            if (evt.getPropertyName().equals(SeedSpecies.PROPERTY_NAME_SPECIES_PATTERN)) {
                SpeciesPattern oldValue = (SpeciesPattern) evt.getOldValue();
                if (oldValue != null) {
                    RbmUtils.removePropertyChangeListener(oldValue, this);
                }
                SpeciesPattern newValue = (SpeciesPattern) evt.getNewValue();
                if (newValue != null) {
                    // TODO
                    RbmUtils.addPropertyChangeListener(newValue, this);
                }
            }
        } else if (source instanceof SpeciesPattern) {
            if (evt.getPropertyName().equals(SpeciesPattern.PROPERTY_NAME_MOLECULAR_TYPE_PATTERNS)) {
                List<MolecularTypePattern> oldValue = (List<MolecularTypePattern>) evt.getOldValue();
                if (oldValue != null) {
                    for (MolecularTypePattern mtp : oldValue) {
                        RbmUtils.removePropertyChangeListener(mtp, this);
                    }
                }
                List<MolecularTypePattern> newValue = (List<MolecularTypePattern>) evt.getNewValue();
                if (newValue != null) {
                    for (MolecularTypePattern mtp : newValue) {
                        RbmUtils.addPropertyChangeListener(mtp, this);
                    }
                }
            }
        } else if (source instanceof MolecularTypePattern) {
            if (evt.getPropertyName().equals(MolecularTypePattern.PROPERTY_NAME_COMPONENT_PATTERN_LIST)) {
                List<MolecularComponentPattern> oldValue = (List<MolecularComponentPattern>) evt.getOldValue();
                if (oldValue != null) {
                    for (MolecularComponentPattern mcp : oldValue) {
                        RbmUtils.removePropertyChangeListener(mcp, this);
                    }
                }
                List<MolecularComponentPattern> newValue = (List<MolecularComponentPattern>) evt.getNewValue();
                if (newValue != null) {
                    for (MolecularComponentPattern mcp : newValue) {
                        RbmUtils.addPropertyChangeListener(mcp, this);
                    }
                }
            }
        } else if (source instanceof MolecularComponentPattern) {
            if (evt.getSource().equals(MolecularComponentPattern.PROPERTY_NAME_COMPONENT_STATE)) {
                // it's componentStatePattern
                ComponentStateDefinition oldValue = (ComponentStateDefinition) evt.getOldValue();
                if (oldValue != null) {
                    oldValue.removePropertyChangeListener(this);
                }
                ComponentStateDefinition newValue = (ComponentStateDefinition) evt.getNewValue();
                if (newValue != null) {
                    newValue.addPropertyChangeListener(this);
                }
            }
        }
    }
}
Also used : MolecularComponentPattern(org.vcell.model.rbm.MolecularComponentPattern) List(java.util.List) MolecularTypePattern(org.vcell.model.rbm.MolecularTypePattern) SpeciesPattern(org.vcell.model.rbm.SpeciesPattern) ComponentStateDefinition(org.vcell.model.rbm.ComponentStateDefinition)

Example 40 with MolecularTypePattern

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

the class RbmObservableTreeCellRenderer method getTreeCellRendererComponent.

@Override
public Component getTreeCellRendererComponent(JTree tree, Object value, boolean sel, boolean expanded, boolean leaf, int row, boolean hasFocus) {
    super.getTreeCellRendererComponent(tree, value, sel, expanded, leaf, row, hasFocus);
    setBorder(null);
    if (value instanceof BioModelNode) {
        BioModelNode node = (BioModelNode) value;
        Object userObject = node.getUserObject();
        obj = userObject;
        String text = null;
        Icon icon = null;
        String toolTip = null;
        if (userObject instanceof RbmObservable) {
            RbmObservable ob = (RbmObservable) userObject;
            text = toHtml(ob);
            toolTip = toHtmlWithTip(ob);
            icon = VCellIcons.rbmObservableIcon;
        } else if (userObject instanceof SpeciesPatternLocal) {
            SpeciesPatternLocal spl = (SpeciesPatternLocal) userObject;
            text = toHtml(spl, true);
            toolTip = toHtmlWithTip(spl, true);
            icon = VCellIcons.rbmProductIcon;
        } else if (userObject instanceof MolecularTypePattern) {
            MolecularTypePattern molecularTypePattern = (MolecularTypePattern) userObject;
            text = toHtml(molecularTypePattern, true);
            toolTip = toHtmlWithTip(molecularTypePattern, true);
            if (owner == null) {
                icon = VCellIcons.rbmMolecularTypeSimpleIcon;
                ;
            } else {
                Graphics gc = owner.getGraphics();
                icon = new MolecularTypeSmallShape(1, 5, molecularTypePattern.getMolecularType(), null, gc, molecularTypePattern.getMolecularType(), null, issueManager);
            }
        } else if (userObject instanceof MolecularComponentPattern) {
            MolecularComponentPattern mcp = (MolecularComponentPattern) userObject;
            text = toHtml(mcp, true);
            toolTip = toHtmlWithTip(mcp, true);
            icon = VCellIcons.rbmComponentGrayIcon;
            if (mcp.getMolecularComponent().getComponentStateDefinitions().size() > 0) {
                icon = VCellIcons.rbmComponentGrayStateIcon;
            }
            if (mcp.isbVisible()) {
                icon = VCellIcons.rbmComponentGreenIcon;
                if (mcp.getMolecularComponent().getComponentStateDefinitions().size() > 0) {
                    icon = VCellIcons.rbmComponentGreenStateIcon;
                }
            }
            ComponentStatePattern csp = mcp.getComponentStatePattern();
            if (csp != null && !csp.isAny()) {
                icon = VCellIcons.rbmComponentGreenIcon;
                if (mcp.getMolecularComponent().getComponentStateDefinitions().size() > 0) {
                    icon = VCellIcons.rbmComponentGreenStateIcon;
                }
            }
            BioModelNode parent = (BioModelNode) ((BioModelNode) value).getParent().getParent().getParent();
            if (parent == null) {
                icon = VCellIcons.rbmComponentErrorIcon;
                return this;
            }
            Object parentObject = parent.getUserObject();
            if (!(parentObject instanceof RbmObservable)) {
                icon = VCellIcons.rbmComponentErrorIcon;
                return this;
            }
            if (hasErrorIssues((RbmObservable) parentObject, mcp, mcp.getMolecularComponent())) {
                icon = VCellIcons.rbmComponentErrorIcon;
            }
        } else if (userObject instanceof StateLocal) {
            StateLocal sl = (StateLocal) userObject;
            text = toHtml(sl, true);
            toolTip = toHtmlWithTip(sl, true);
            icon = VCellIcons.rbmComponentStateIcon;
        } else if (userObject instanceof BondLocal) {
            BondLocal bl = (BondLocal) userObject;
            text = toHtml(bl, sel);
            toolTip = toHtmlWithTip(bl, true);
            icon = VCellIcons.rbmBondIcon;
        } else {
            if (userObject != null) {
                System.out.println(userObject.toString());
                text = userObject.toString();
            } else {
                text = "null user object";
            }
        }
        setText(text);
        setIcon(icon);
        setToolTipText(toolTip == null ? text : toolTip);
    }
    return this;
}
Also used : MolecularComponentPattern(org.vcell.model.rbm.MolecularComponentPattern) RbmObservable(cbit.vcell.model.RbmObservable) ComponentStatePattern(org.vcell.model.rbm.ComponentStatePattern) StateLocal(cbit.vcell.client.desktop.biomodel.RbmDefaultTreeModel.StateLocal) BioModelNode(cbit.vcell.desktop.BioModelNode) Graphics(java.awt.Graphics) MolecularTypeSmallShape(cbit.vcell.graph.MolecularTypeSmallShape) SpeciesPatternLocal(cbit.vcell.client.desktop.biomodel.RbmDefaultTreeModel.SpeciesPatternLocal) BondLocal(cbit.vcell.client.desktop.biomodel.RbmDefaultTreeModel.BondLocal) Icon(javax.swing.Icon) MolecularTypePattern(org.vcell.model.rbm.MolecularTypePattern)

Aggregations

MolecularTypePattern (org.vcell.model.rbm.MolecularTypePattern)72 MolecularComponentPattern (org.vcell.model.rbm.MolecularComponentPattern)49 SpeciesPattern (org.vcell.model.rbm.SpeciesPattern)39 ComponentStatePattern (org.vcell.model.rbm.ComponentStatePattern)19 Graphics (java.awt.Graphics)16 MolecularType (org.vcell.model.rbm.MolecularType)16 Point (java.awt.Point)14 BioModelNode (cbit.vcell.desktop.BioModelNode)11 RbmObservable (cbit.vcell.model.RbmObservable)10 SpeciesContext (cbit.vcell.model.SpeciesContext)10 Icon (javax.swing.Icon)10 ComponentStateDefinition (org.vcell.model.rbm.ComponentStateDefinition)10 MolecularComponent (org.vcell.model.rbm.MolecularComponent)10 ArrayList (java.util.ArrayList)9 SpeciesPatternLargeShape (cbit.vcell.graph.SpeciesPatternLargeShape)7 ReactionRule (cbit.vcell.model.ReactionRule)7 LinkedHashMap (java.util.LinkedHashMap)7 MolecularTypeLargeShape (cbit.vcell.graph.MolecularTypeLargeShape)6 MolecularTypeSmallShape (cbit.vcell.graph.MolecularTypeSmallShape)6 RuleAnalysisChanged (cbit.vcell.graph.ReactionCartoon.RuleAnalysisChanged)6