use of org.vcell.model.rbm.MolecularComponentPattern in project vcell by virtualcell.
the class SpeciesContextSpecPanel method initialize.
private void initialize() {
try {
shapePanel = new // glyph (shape) panel
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;
}
};
shapePanel.addMouseMotionListener(new MouseMotionAdapter() {
public void mouseMoved(MouseEvent e) {
Point overWhat = e.getPoint();
PointLocationInShapeContext locationContext = new PointLocationInShapeContext(overWhat);
spls.contains(locationContext);
shapePanel.setToolTipText("View-Only panel");
}
});
shapePanel.setBackground(new Color(0xe0e0e0));
shapePanel.setZoomFactor(-2);
shapePanel.setEditable(false);
shapePanel.setShowMoleculeColor(false);
shapePanel.setShowNonTrivialOnly(false);
// --------------------------------------------------------------
JPanel upperPanel = new JPanel();
upperPanel.setLayout(new java.awt.BorderLayout());
upperPanel.add(getScrollPaneTable().getEnclosingScrollPane(), BorderLayout.CENTER);
getScrollPaneTable().setModel(getSpeciesContextSpecParameterTableModel());
scrollPane = new JScrollPane(shapePanel);
scrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
scrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);
JPanel optionsPanel = new JPanel();
optionsPanel.setLayout(new GridBagLayout());
getZoomSmallerButton().setEnabled(true);
getZoomLargerButton().setEnabled(true);
GridBagConstraints gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = 0;
gbc.insets = new Insets(4, 4, 0, 10);
gbc.anchor = GridBagConstraints.WEST;
optionsPanel.add(getZoomLargerButton(), gbc);
gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = 1;
gbc.insets = new Insets(4, 4, 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);
// ------------------------------------------------
splitPaneHorizontal.setTopComponent(upperPanel);
splitPaneHorizontal.setBottomComponent(containerOfScrollPanel);
splitPaneHorizontal.setOneTouchExpandable(true);
// upper panel is 165 pixel height
splitPaneHorizontal.setDividerLocation(165);
splitPaneHorizontal.setResizeWeight(1);
setLayout(new BorderLayout());
add(splitPaneHorizontal, BorderLayout.CENTER);
setBackground(Color.white);
setName("SpeciesContextSpecPanel");
} catch (java.lang.Throwable ivjExc) {
handleException(ivjExc);
}
}
use of org.vcell.model.rbm.MolecularComponentPattern 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);
}
}
use of org.vcell.model.rbm.MolecularComponentPattern 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);
}
}
}
use of org.vcell.model.rbm.MolecularComponentPattern 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);
}
}
}
}
}
use of org.vcell.model.rbm.MolecularComponentPattern 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;
}
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