Example 6 with RbmKineticLaw
use of cbit.vcell.model.RbmKineticLaw in project vcell by virtualcell.
the class BioModelEditorModelPanel method initialize.
private void initialize() {
newButton = new JButton("New");
newButton2 = new JButton("New Rule");
newMemButton = new JButton("New Membrane");
deleteButton = new JButton("Delete");
duplicateButton = new JButton("Duplicate");
pathwayButton = new JButton("Pathway Links", new DownArrowIcon());
pathwayButton.setHorizontalTextPosition(SwingConstants.LEFT);
textFieldSearch = new JTextField();
textFieldSearch.putClientProperty("JTextField.variant", "search");
structuresTable = new EditorScrollTable();
reactionsTable = new EditorScrollTable();
speciesTable = new EditorScrollTable();
molecularTypeTable = new EditorScrollTable();
observablesTable = new EditorScrollTable();
structureTableModel = new BioModelEditorStructureTableModel(structuresTable);
reactionTableModel = new BioModelEditorReactionTableModel(reactionsTable);
speciesTableModel = new BioModelEditorSpeciesTableModel(speciesTable);
molecularTypeTableModel = new MolecularTypeTableModel(molecularTypeTable);
observableTableModel = new ObservableTableModel(observablesTable);
structuresTable.setModel(structureTableModel);
reactionsTable.setModel(reactionTableModel);
speciesTable.setModel(speciesTableModel);
molecularTypeTable.setModel(molecularTypeTableModel);
observablesTable.setModel(observableTableModel);
reactionCartoonEditorPanel = new ReactionCartoonEditorPanel();
reactionCartoonEditorPanel.addPropertyChangeListener(eventHandler);
reactionCartoonEditorPanel.getReactionCartoonFull().addPropertyChangeListener(eventHandler);
reactionCartoonEditorPanel.getReactionCartoonMolecule().addPropertyChangeListener(eventHandler);
reactionCartoonEditorPanel.getReactionCartoonRule().addPropertyChangeListener(eventHandler);
// cartoonEditorPanel = new CartoonEditorPanelFixed();
// cartoonEditorPanel.getStructureCartoon().addPropertyChangeListener(eventHandler);
/* button panel */
buttonPanel = new JPanel();
buttonPanel.setLayout(new GridBagLayout());
GridBagConstraints gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = 0;
gbc.insets = new Insets(4, 4, 4, 4);
gbc.anchor = GridBagConstraints.LINE_END;
buttonPanel.add(newButton, gbc);
gbc = new GridBagConstraints();
gbc.gridx = 1;
gbc.gridy = 0;
gbc.insets = new Insets(4, 4, 4, 4);
gbc.anchor = GridBagConstraints.LINE_END;
buttonPanel.add(newButton2, gbc);
gbc = new GridBagConstraints();
gbc.gridx = 2;
gbc.gridy = 0;
gbc.insets = new Insets(4, 4, 4, 4);
gbc.anchor = GridBagConstraints.LINE_END;
buttonPanel.add(newMemButton, gbc);
gbc = new GridBagConstraints();
gbc.gridx = 3;
gbc.insets = new Insets(4, 4, 4, 4);
gbc.gridy = 0;
gbc.anchor = GridBagConstraints.LINE_END;
buttonPanel.add(duplicateButton, gbc);
gbc = new GridBagConstraints();
gbc.gridx = 4;
gbc.insets = new Insets(4, 4, 4, 4);
gbc.gridy = 0;
gbc.anchor = GridBagConstraints.LINE_END;
buttonPanel.add(deleteButton, gbc);
gbc = new GridBagConstraints();
gbc.gridx = 5;
gbc.insets = new Insets(4, 4, 4, 4);
gbc.gridy = 0;
gbc.anchor = GridBagConstraints.LINE_END;
buttonPanel.add(pathwayButton, gbc);
gbc = new GridBagConstraints();
gbc.gridx = 6;
gbc.gridy = 0;
gbc.weightx = 0.5;
gbc.fill = GridBagConstraints.HORIZONTAL;
gbc.insets = new Insets(4, 4, 4, 4);
buttonPanel.add(Box.createRigidArea(new Dimension(5, 5)), gbc);
gbc = new GridBagConstraints();
gbc.gridx = 7;
gbc.gridy = 0;
gbc.anchor = GridBagConstraints.LINE_END;
gbc.insets = new Insets(4, 4, 4, 4);
buttonPanel.add(new JLabel("Search "), gbc);
gbc = new GridBagConstraints();
gbc.gridx = 8;
gbc.gridy = 0;
gbc.weightx = 1.5;
gbc.anchor = GridBagConstraints.LINE_START;
gbc.fill = GridBagConstraints.HORIZONTAL;
gbc.insets = new Insets(4, 4, 4, 4);
buttonPanel.add(textFieldSearch, gbc);
/* button panel */
tabbedPane = new JTabbedPaneEnhanced();
tabbedPane.setTabLayoutPolicy(JTabbedPane.SCROLL_TAB_LAYOUT);
modelPanelTabs[ModelPanelTabID.reaction_diagram.ordinal()] = new ModelPanelTab(ModelPanelTabID.reaction_diagram, reactionCartoonEditorPanel, VCellIcons.diagramIcon);
// modelPanelTabs[ModelPanelTabID.structure_diagram.ordinal()] = new ModelPanelTab(ModelPanelTabID.structure_diagram, cartoonEditorPanel, VCellIcons.structureIcon);
modelPanelTabs[ModelPanelTabID.reaction_table.ordinal()] = new ModelPanelTab(ModelPanelTabID.reaction_table, reactionsTable.getEnclosingScrollPane(), VCellIcons.tableIcon);
modelPanelTabs[ModelPanelTabID.structure_table.ordinal()] = new ModelPanelTab(ModelPanelTabID.structure_table, structuresTable.getEnclosingScrollPane(), VCellIcons.tableIcon);
modelPanelTabs[ModelPanelTabID.species_table.ordinal()] = new ModelPanelTab(ModelPanelTabID.species_table, speciesTable.getEnclosingScrollPane(), VCellIcons.tableIcon);
modelPanelTabs[ModelPanelTabID.species_definitions_table.ordinal()] = new ModelPanelTab(ModelPanelTabID.species_definitions_table, molecularTypeTable.getEnclosingScrollPane(), VCellIcons.tableIcon);
modelPanelTabs[ModelPanelTabID.observables_table.ordinal()] = new ModelPanelTab(ModelPanelTabID.observables_table, observablesTable.getEnclosingScrollPane(), VCellIcons.tableIcon);
tabbedPane.addChangeListener(eventHandler);
tabbedPane.addMouseListener(eventHandler);
for (ModelPanelTab tab : modelPanelTabs) {
tab.getComponent().setBorder(GuiConstants.TAB_PANEL_BORDER);
tabbedPane.addTab(tab.getName(), tab.getIcon(), tab.getComponent());
}
// tabbedPane.addChangeListener(changeListener);
setLayout(new BorderLayout());
add(tabbedPane, BorderLayout.CENTER);
add(buttonPanel, BorderLayout.SOUTH);
newButton.addActionListener(eventHandler);
newButton2.addActionListener(eventHandler);
newMemButton.addActionListener(eventHandler);
duplicateButton.addActionListener(eventHandler);
duplicateButton.setEnabled(false);
deleteButton.addActionListener(eventHandler);
deleteButton.setEnabled(false);
pathwayButton.addActionListener(eventHandler);
pathwayButton.setEnabled(false);
textFieldSearch.addActionListener(eventHandler);
textFieldSearch.getDocument().addDocumentListener(eventHandler);
structuresTable.getSelectionModel().addListSelectionListener(eventHandler);
reactionsTable.getSelectionModel().addListSelectionListener(eventHandler);
speciesTable.getSelectionModel().addListSelectionListener(eventHandler);
molecularTypeTable.getSelectionModel().addListSelectionListener(eventHandler);
observablesTable.getSelectionModel().addListSelectionListener(eventHandler);
DefaultScrollTableCellRenderer tableRenderer = 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 (value instanceof Structure) {
setText(((Structure) value).getName());
} else if (value instanceof Kinetics) {
setText(((Kinetics) value).getKineticsDescription().getDescription());
} else if (value instanceof RbmKineticLaw) {
setText(((RbmKineticLaw) value).getRateLawType().name());
}
return this;
}
};
RbmTableRenderer rbmTableRenderer = new RbmTableRenderer();
structuresTable.setDefaultRenderer(Structure.class, tableRenderer);
speciesTable.setDefaultRenderer(Structure.class, tableRenderer);
reactionsTable.setDefaultRenderer(Structure.class, tableRenderer);
reactionsTable.setDefaultRenderer(Kinetics.class, tableRenderer);
reactionsTable.setDefaultRenderer(RbmKineticLaw.class, tableRenderer);
reactionsTable.setDefaultRenderer(ModelProcessDynamics.class, tableRenderer);
DefaultScrollTableCellRenderer tableCellRenderer = 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);
BioModelEntityObject bioModelEntityObject = null;
if (table.getModel() instanceof VCellSortTableModel<?>) {
if (table.getModel() == reactionTableModel && reactionTableModel.getValueAt(row) instanceof BioModelEntityObject) {
bioModelEntityObject = (BioModelEntityObject) reactionTableModel.getValueAt(row);
} else if (table.getModel() == speciesTableModel) {
bioModelEntityObject = speciesTableModel.getValueAt(row);
} else if (table.getModel() == molecularTypeTableModel) {
bioModelEntityObject = molecularTypeTableModel.getValueAt(row);
}
if (bioModelEntityObject != null) {
Set<RelationshipObject> relationshipSet = bioModel.getRelationshipModel().getRelationshipObjects(bioModelEntityObject);
if (relationshipSet.size() > 0) {
StringBuilder tooltip = new StringBuilder("<html>Links to Pathway objects:<br>");
for (RelationshipObject ro : relationshipSet) {
tooltip.append("<li>" + ro.getBioPaxObject() + "</li>");
}
if (!isSelected) {
setForeground(Color.blue);
}
String finalName = null;
BioPaxObject bioPaxObject = relationshipSet.iterator().next().getBioPaxObject();
if (bioPaxObject instanceof EntityImpl && ((EntityImpl) bioPaxObject).getName() != null && ((EntityImpl) bioPaxObject).getName().size() > 0) {
finalName = ((EntityImpl) bioPaxObject).getName().get(0);
} else if (bioPaxObject instanceof Conversion) {
Conversion mp = (Conversion) bioPaxObject;
finalName = "[" + bioPaxObject.getIDShort() + "]";
} else {
finalName = bioModelEntityObject.getName();
}
final int LIMIT = 40;
final String DOTS = "...";
if (finalName != null && finalName.length() > LIMIT) {
finalName = finalName.substring(0, LIMIT - DOTS.length() - 1) + DOTS;
}
setText("<html><u>" + finalName + "</u></html>");
setToolTipText(tooltip.toString());
}
}
}
return this;
}
};
DefaultScrollTableCellRenderer rbmReactionExpressionCellRenderer = 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 VCellSortTableModel<?>) {
Object selectedObject = null;
if (table.getModel() == reactionTableModel) {
selectedObject = reactionTableModel.getValueAt(row);
}
if (selectedObject != null) {
if (selectedObject instanceof ReactionRule && value instanceof ModelProcessEquation) {
String text = "<html>";
text += "Reaction Rule";
text += "</html>";
setText(text);
} else {
// plain reaction, check if reactants have species pattern
ReactionStep rs = (ReactionStep) selectedObject;
String text = "<html>";
for (int i = 0; i < rs.getNumReactants(); i++) {
Reactant p = rs.getReactant(i);
if (p.getSpeciesContext().hasSpeciesPattern()) {
text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
// text += "<b>" + p.getName() + "</b>";
text += p.getName();
} else {
text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
text += p.getName();
}
if (i < rs.getNumReactants() - 1) {
text += " + ";
}
}
text += " -> ";
for (int i = 0; i < rs.getNumProducts(); i++) {
Product p = rs.getProduct(i);
if (p.getSpeciesContext().hasSpeciesPattern()) {
text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
// text += "<b>" + p.getName() + "</b>";
text += p.getName();
} else {
text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
text += p.getName();
}
if (i < rs.getNumProducts() - 1) {
text += " + ";
}
}
text += "</html>";
setText(text);
}
}
}
return this;
}
};
DefaultScrollTableCellRenderer rbmReactionDefinitionCellRenderer = 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 VCellSortTableModel<?>) {
Object selectedObject = null;
if (table.getModel() == reactionTableModel) {
selectedObject = reactionTableModel.getValueAt(row);
}
if (selectedObject != null) {
if (selectedObject instanceof ReactionRule && value instanceof ModelProcessEquation) {
ReactionRule rr = (ReactionRule) selectedObject;
String text = "<html>";
for (int i = 0; i < rr.getReactantPatterns().size(); i++) {
ReactantPattern rp = rr.getReactantPattern(i);
if (rp.getStructure() != null && !rp.getSpeciesPattern().getMolecularTypePatterns().isEmpty()) {
text += "@" + rp.getStructure().getName() + ":";
}
text += RbmUtils.toBnglString(rp.getSpeciesPattern(), null, CompartmentMode.hide, 0);
// text += RbmTableRenderer.toHtml(rp.getSpeciesPattern(), isSelected);
if (i < rr.getReactantPatterns().size() - 1) {
text += "+";
}
}
if (rr.isReversible()) {
// <-> <->
text += " <-> ";
} else {
text += " -> ";
}
for (int i = 0; i < rr.getProductPatterns().size(); i++) {
ProductPattern pp = rr.getProductPattern(i);
if (pp.getStructure() != null && !pp.getSpeciesPattern().getMolecularTypePatterns().isEmpty()) {
text += "@" + pp.getStructure().getName() + ":";
}
text += RbmUtils.toBnglString(pp.getSpeciesPattern(), null, CompartmentMode.hide, 0);
if (i < rr.getProductPatterns().size() - 1) {
text += "+";
}
}
text += "</html>";
setText(text);
} else {
// plain reaction, check if reactants have species pattern
ReactionStep rs = (ReactionStep) selectedObject;
String text = "<html>";
for (int i = 0; i < rs.getNumReactants(); i++) {
Reactant p = rs.getReactant(i);
if (p.getSpeciesContext().hasSpeciesPattern()) {
text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
text += p.getName();
} else {
text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
text += p.getName();
}
if (i < rs.getNumReactants() - 1) {
text += " + ";
}
}
if (rs.isReversible()) {
// <-> <->
text += " <-> ";
} else {
text += " -> ";
}
for (int i = 0; i < rs.getNumProducts(); i++) {
Product p = rs.getProduct(i);
if (p.getSpeciesContext().hasSpeciesPattern()) {
text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
text += p.getName();
} else {
text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
text += p.getName();
}
if (i < rs.getNumProducts() - 1) {
text += " + ";
}
}
text += "</html>";
setText(text);
}
}
}
return this;
}
};
DefaultScrollTableCellRenderer rbmObservablePatternCellRenderer = 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 VCellSortTableModel<?>) {
Object selectedObject = null;
if (table.getModel() == observableTableModel) {
selectedObject = observableTableModel.getValueAt(row);
}
if (selectedObject != null) {
if (selectedObject instanceof RbmObservable && value instanceof String) {
RbmObservable o = (RbmObservable) selectedObject;
String text = "<html>";
for (int i = 0; i < o.getSpeciesPatternList().size(); i++) {
SpeciesPattern sp = o.getSpeciesPattern(i);
text += RbmTableRenderer.toHtml(sp, isSelected);
if (i < o.getSpeciesPatternList().size() - 1) {
text += " ";
}
}
text = RbmUtils.appendSequence(text, o);
text += "</html>";
setText(text);
}
}
}
return this;
}
};
DefaultScrollTableCellRenderer rbmSpeciesNameCellRenderer = 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 VCellSortTableModel<?>) {
Object selectedObject = null;
if (table.getModel() == speciesTableModel) {
selectedObject = speciesTableModel.getValueAt(row);
}
if (selectedObject != null) {
if (selectedObject instanceof SpeciesContext) {
SpeciesContext sc = (SpeciesContext) selectedObject;
String text = "<html>";
if (sc.hasSpeciesPattern()) {
text += "<b>" + sc.getName() + "</b>";
} else {
text += sc.getName();
}
text += "</html>";
setText(text);
}
}
}
return this;
}
};
//
// this renderer only paints the molecular type small shape in the MolecularType Table
//
DefaultScrollTableCellRenderer rbmMolecularTypeShapeDepictionCellRenderer = new DefaultScrollTableCellRenderer() {
MolecularTypeSmallShape stls = 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() == molecularTypeTableModel) {
selectedObject = molecularTypeTableModel.getValueAt(row);
}
if (selectedObject != null) {
if (selectedObject instanceof MolecularType) {
MolecularType mt = (MolecularType) selectedObject;
Graphics cellContext = table.getGraphics();
if (mt != null) {
stls = new MolecularTypeSmallShape(4, 3, mt, null, cellContext, mt, null, issueManager);
}
}
} else {
stls = null;
}
}
return this;
}
@Override
public void paintComponent(Graphics g) {
super.paintComponent(g);
if (stls != null) {
stls.paintSelf(g);
}
}
};
// painting of species patterns small shapes inside the species context 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 SpeciesContext) {
SpeciesContext sc = (SpeciesContext) selectedObject;
// sp may be null for "plain" species contexts
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);
}
}
};
// ---------------------------------------------------------------------------------------------------------------------------------
DefaultScrollTableCellRenderer rbmReactionShapeDepictionCellRenderer = 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() == reactionTableModel) {
selectedObject = reactionTableModel.getValueAt(row);
}
if (selectedObject != null) {
if (selectedObject instanceof ReactionRule) {
ReactionRule rr = (ReactionRule) selectedObject;
Graphics panelContext = table.getGraphics();
spssList.clear();
List<ReactantPattern> rpList = rr.getReactantPatterns();
int xPos = 4;
for (int i = 0; i < rpList.size(); i++) {
SpeciesPattern sp = rr.getReactantPattern(i).getSpeciesPattern();
spss = new SpeciesPatternSmallShape(xPos, 2, sp, null, panelContext, rr, isSelected, issueManager);
if (i < rpList.size() - 1) {
spss.addEndText("+");
} else {
if (rr.isReversible()) {
spss.addEndText("<->");
xPos += 7;
} else {
spss.addEndText("->");
}
}
xPos += spss.getWidth() + 15;
spssList.add(spss);
}
List<ProductPattern> ppList = rr.getProductPatterns();
xPos += 7;
for (int i = 0; i < ppList.size(); i++) {
SpeciesPattern sp = rr.getProductPattern(i).getSpeciesPattern();
spss = new SpeciesPatternSmallShape(xPos, 2, sp, null, panelContext, rr, isSelected, issueManager);
if (i < ppList.size() - 1) {
spss.addEndText("+");
}
xPos += spss.getWidth() + 15;
spssList.add(spss);
}
} else {
ReactionStep rs = (ReactionStep) selectedObject;
Graphics panelContext = table.getGraphics();
spssList.clear();
int xPos = 4;
int extraSpace = 0;
for (int i = 0; i < rs.getNumReactants(); i++) {
SpeciesPattern sp = rs.getReactant(i).getSpeciesContext().getSpeciesPattern();
spss = new SpeciesPatternSmallShape(xPos, 2, sp, panelContext, rs, isSelected, issueManager);
if (i < rs.getNumReactants() - 1) {
spss.addEndText("+");
} else {
if (rs.isReversible()) {
spss.addEndText("<->");
extraSpace += 7;
} else {
spss.addEndText("->");
}
}
int offset = sp == null ? 17 : 15;
offset += extraSpace;
int w = spss.getWidth();
xPos += w + offset;
spssList.add(spss);
}
xPos += 8;
for (int i = 0; i < rs.getNumProducts(); i++) {
SpeciesPattern sp = rs.getProduct(i).getSpeciesContext().getSpeciesPattern();
if (i == 0 && rs.getNumReactants() == 0) {
xPos += 14;
}
spss = new SpeciesPatternSmallShape(xPos, 2, sp, panelContext, rs, isSelected, issueManager);
if (i == 0 && rs.getNumReactants() == 0) {
spss.addStartText("->");
}
if (i < rs.getNumProducts() - 1) {
spss.addEndText("+");
}
int offset = sp == null ? 17 : 15;
int w = spss.getWidth();
xPos += w + offset;
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);
}
}
};
// -------------------------------------------------------------------------------------------------------------------------------
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() == observableTableModel) {
selectedObject = observableTableModel.getValueAt(row);
}
if (selectedObject != null) {
if (selectedObject instanceof RbmObservable) {
RbmObservable observable = (RbmObservable) selectedObject;
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);
}
}
};
// TODO: here are the renderers associated with the columns
reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_LINK).setCellRenderer(tableCellRenderer);
reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_EQUATION).setCellRenderer(rbmReactionExpressionCellRenderer);
reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_DEFINITION).setCellRenderer(rbmReactionDefinitionCellRenderer);
speciesTable.getColumnModel().getColumn(BioModelEditorSpeciesTableModel.COLUMN_NAME).setCellRenderer(rbmSpeciesNameCellRenderer);
speciesTable.getColumnModel().getColumn(BioModelEditorSpeciesTableModel.COLUMN_LINK).setCellRenderer(tableCellRenderer);
molecularTypeTable.getColumnModel().getColumn(MolecularTypeTableModel.Column.link.ordinal()).setCellRenderer(tableCellRenderer);
observablesTable.getColumnModel().getColumn(ObservableTableModel.Column.species_pattern.ordinal()).setCellRenderer(rbmObservablePatternCellRenderer);
observablesTable.getColumnModel().getColumn(ObservableTableModel.Column.structure.ordinal()).setCellRenderer(tableRenderer);
// all "depictions" have their own renderer
molecularTypeTable.getColumnModel().getColumn(MolecularTypeTableModel.Column.depiction.ordinal()).setCellRenderer(rbmMolecularTypeShapeDepictionCellRenderer);
molecularTypeTable.getColumnModel().getColumn(MolecularTypeTableModel.Column.depiction.ordinal()).setMaxWidth(180);
speciesTable.getColumnModel().getColumn(BioModelEditorSpeciesTableModel.COLUMN_DEPICTION).setCellRenderer(rbmSpeciesShapeDepictionCellRenderer);
speciesTable.getColumnModel().getColumn(BioModelEditorSpeciesTableModel.COLUMN_DEFINITION).setCellRenderer(rbmTableRenderer);
observablesTable.getColumnModel().getColumn(ObservableTableModel.Column.depiction.ordinal()).setCellRenderer(rbmObservableShapeDepictionCellRenderer);
reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_DEPICTION).setCellRenderer(rbmReactionShapeDepictionCellRenderer);
reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_DEPICTION).setPreferredWidth(180);
observablesTable.getColumnModel().getColumn(ObservableTableModel.Column.type.ordinal()).setCellEditor(observableTableModel.getObservableTypeComboBoxEditor());
observableTableModel.updateObservableTypeComboBox();
reactionsTable.addMouseListener(eventHandler);
reactionsTable.addKeyListener(eventHandler);
speciesTable.addMouseListener(eventHandler);
speciesTable.addKeyListener(eventHandler);
molecularTypeTable.addMouseListener(eventHandler);
molecularTypeTable.addKeyListener(eventHandler);
observablesTable.addMouseListener(eventHandler);
observablesTable.addKeyListener(eventHandler);
structuresTable.addKeyListener(eventHandler);
}
Also used :
JPanel(javax.swing.JPanel)
GridBagConstraints(java.awt.GridBagConstraints)
Product(cbit.vcell.model.Product)
SpeciesContext(cbit.vcell.model.SpeciesContext)
RelationshipObject(org.vcell.relationship.RelationshipObject)
Reactant(cbit.vcell.model.Reactant)
JTabbedPaneEnhanced(org.vcell.util.gui.JTabbedPaneEnhanced)
BorderLayout(java.awt.BorderLayout)
ArrayList(java.util.ArrayList)
List(java.util.List)
JList(javax.swing.JList)
EntityImpl(org.vcell.pathway.EntityImpl)
RbmObservable(cbit.vcell.model.RbmObservable)
BioModelEntityObject(cbit.vcell.model.BioModelEntityObject)
Conversion(org.vcell.pathway.Conversion)
ReactionCartoonEditorPanel(cbit.vcell.graph.gui.ReactionCartoonEditorPanel)
MolecularType(org.vcell.model.rbm.MolecularType)
JTable(javax.swing.JTable)
ReactionStep(cbit.vcell.model.ReactionStep)
RelationshipObject(org.vcell.relationship.RelationshipObject)
BioModelEntityObject(cbit.vcell.model.BioModelEntityObject)
BioPaxObject(org.vcell.pathway.BioPaxObject)
EditorScrollTable(org.vcell.util.gui.EditorScrollTable)
Kinetics(cbit.vcell.model.Kinetics)
Insets(java.awt.Insets)
GridBagLayout(java.awt.GridBagLayout)
SpeciesPatternSmallShape(cbit.vcell.graph.SpeciesPatternSmallShape)
BioPaxObject(org.vcell.pathway.BioPaxObject)
JButton(javax.swing.JButton)
JTextField(javax.swing.JTextField)
SpeciesPattern(org.vcell.model.rbm.SpeciesPattern)
Structure(cbit.vcell.model.Structure)
ReactantPattern(cbit.vcell.model.ReactantPattern)
ReactionRule(cbit.vcell.model.ReactionRule)
ProductPattern(cbit.vcell.model.ProductPattern)
JLabel(javax.swing.JLabel)
Dimension(java.awt.Dimension)
RbmKineticLaw(cbit.vcell.model.RbmKineticLaw)
Graphics(java.awt.Graphics)
MolecularTypeSmallShape(cbit.vcell.graph.MolecularTypeSmallShape)
DownArrowIcon(org.vcell.util.gui.DownArrowIcon)
ModelProcessEquation(cbit.gui.ModelProcessEquation)
DefaultScrollTableCellRenderer(org.vcell.util.gui.DefaultScrollTableCellRenderer)
Example 7 with RbmKineticLaw
use of cbit.vcell.model.RbmKineticLaw in project vcell by virtualcell.
the class RbmNetworkGenerator method writeBngl_internal.
public static void writeBngl_internal(SimulationContext simulationContext, PrintWriter writer, Map<FakeReactionRuleRateParameter, LocalParameter> kineticsParameterMap, Map<FakeSeedSpeciesInitialConditionsParameter, Pair<SpeciesContext, Expression>> speciesEquivalenceMap, NetworkGenerationRequirements networkGenerationRequirements, CompartmentMode compartmentMode) {
String callerClassName = new Exception().getStackTrace()[1].getClassName();
String networkTransformerClassName = NetworkTransformer.class.getName();
String rulebasedTransformerClassName = RulebasedTransformer.class.getName();
if (!callerClassName.equals(networkTransformerClassName) && !callerClassName.equals(rulebasedTransformerClassName)) {
throw new UnsupportedOperationException("This method may only be called from within a " + networkTransformerClassName + " or " + rulebasedTransformerClassName + " instance.");
}
Model model = simulationContext.getModel();
RbmModelContainer rbmModelContainer = model.getRbmModelContainer();
checkConsistency(model);
// first we prepare the fake parameters we need to maintain the relationship between the species context and the seed species
List<FakeSeedSpeciesInitialConditionsParameter> fakeParameterList = new ArrayList<FakeSeedSpeciesInitialConditionsParameter>();
List<String> seedSpeciesList = new ArrayList<String>();
SpeciesContext[] speciesContexts = model.getSpeciesContexts();
for (int i = 0; i < speciesContexts.length; i++) {
SpeciesContext sc = speciesContexts[i];
if (!sc.hasSpeciesPattern()) {
continue;
}
SpeciesContextSpec scs = simulationContext.getReactionContext().getSpeciesContextSpec(sc);
Expression initialConcentration = scs.getParameter(SpeciesContextSpec.ROLE_InitialConcentration).getExpression();
// fake initial values for the seed species, we need to present them to bngl as parameters
FakeSeedSpeciesInitialConditionsParameter fakeSeedSpeciesParam = new FakeSeedSpeciesInitialConditionsParameter(sc.getName());
Pair<SpeciesContext, Expression> p = new Pair<SpeciesContext, Expression>(sc, initialConcentration);
speciesEquivalenceMap.put(fakeSeedSpeciesParam, p);
String modified;
if (compartmentMode == CompartmentMode.show) {
modified = RbmUtils.toBnglString(sc.getSpeciesPattern(), null, CompartmentMode.hide, 0);
modified = "@" + sc.getStructure().getName() + ":" + modified;
} else if (compartmentMode == CompartmentMode.asSite) {
modified = RbmUtils.toBnglString(sc.getSpeciesPattern(), sc.getStructure(), CompartmentMode.asSite, 0);
} else {
// CompartmentMode.hide
modified = RbmUtils.toBnglString(sc.getSpeciesPattern(), null, CompartmentMode.hide, 0);
}
modified += " " + fakeSeedSpeciesParam.fakeParameterName;
// we label the seed species with the index
modified = (i + 1) + " " + modified;
// we build the seed species list now, we write it later (in the BEGIN SPECIES block)
seedSpeciesList.add(modified);
fakeParameterList.add(fakeSeedSpeciesParam);
}
// second we produce the bngl file
writer.println(BEGIN_MODEL);
writer.println();
for (ReactionRuleSpec rrs : simulationContext.getReactionContext().getReactionRuleSpecs()) {
if (!rrs.isExcluded()) {
ReactionRule reactionRule = rrs.getReactionRule();
RbmKineticLaw kineticLaw = reactionRule.getKineticLaw();
switch(kineticLaw.getRateLawType()) {
case MassAction:
{
FakeReactionRuleRateParameter fakeRateParameterForward = new FakeReactionRuleRateParameter(reactionRule, RbmKineticLawParameterType.MassActionForwardRate);
LocalParameter origForwardRateParameter = kineticLaw.getLocalParameter(RbmKineticLawParameterType.MassActionForwardRate);
kineticsParameterMap.put(fakeRateParameterForward, origForwardRateParameter);
if (reactionRule.isReversible()) {
FakeReactionRuleRateParameter fakeRateParameterReverse = new FakeReactionRuleRateParameter(reactionRule, RbmKineticLawParameterType.MassActionReverseRate);
LocalParameter origReverseRateParameter = kineticLaw.getLocalParameter(RbmKineticLawParameterType.MassActionReverseRate);
kineticsParameterMap.put(fakeRateParameterReverse, origReverseRateParameter);
}
break;
}
default:
{
throw new RuntimeException("kinetic law type " + kineticLaw.getRateLawType().name() + " not yet implemented");
}
}
}
}
if (compartmentMode == CompartmentMode.show) {
RbmNetworkGenerator.writeCompartments(writer, model, simulationContext);
}
writer.println(BEGIN_PARAMETERS);
// the fake parameters used for reaction rule kinetics
for (FakeReactionRuleRateParameter p : kineticsParameterMap.keySet()) {
writer.println(p.fakeParameterName + "\t\t1");
}
// the fake parameters used at initial values for the seed species
for (FakeSeedSpeciesInitialConditionsParameter s : fakeParameterList) {
writer.println(s.fakeParameterName + "\t\t1");
}
writer.println(END_PARAMETERS);
writer.println();
RbmNetworkGenerator.writeMolecularTypes(writer, model, compartmentMode);
// write modified version of seed species while maintaining the connection between the species context and the real seed species
writer.println(BEGIN_SPECIES);
for (String s : seedSpeciesList) {
writer.println(s);
}
writer.println(END_SPECIES);
writer.println();
RbmNetworkGenerator.writeObservables(writer, rbmModelContainer, compartmentMode);
RbmNetworkGenerator.writeReactions_internal(writer, simulationContext, compartmentMode);
writer.println(END_MODEL);
writer.println();
if (callerClassName.equals(networkTransformerClassName)) {
RbmNetworkGenerator.writeNetworkConstraints(writer, rbmModelContainer, simulationContext, networkGenerationRequirements);
} else if (callerClassName.equals(rulebasedTransformerClassName)) {
writer.println();
writer.println("writeXML()");
}
writer.println();
}
Also used :
ReactionRule(cbit.vcell.model.ReactionRule)
ReactionRuleSpec(cbit.vcell.mapping.ReactionRuleSpec)
ArrayList(java.util.ArrayList)
SpeciesContext(cbit.vcell.model.SpeciesContext)
RbmKineticLaw(cbit.vcell.model.RbmKineticLaw)
SpeciesContextSpec(cbit.vcell.mapping.SpeciesContextSpec)
LocalParameter(cbit.vcell.mapping.ParameterContext.LocalParameter)
RbmModelContainer(cbit.vcell.model.Model.RbmModelContainer)
Expression(cbit.vcell.parser.Expression)
BioModel(cbit.vcell.biomodel.BioModel)
Model(cbit.vcell.model.Model)
Pair(org.vcell.util.Pair)
Example 8 with RbmKineticLaw
use of cbit.vcell.model.RbmKineticLaw in project vcell by virtualcell.
the class ReactionRulePropertiesTableModel method propertyChange.
/**
* This method gets called when a bound property is changed.
* @param evt A PropertyChangeEvent object describing the event source
* and the property that has changed.
*/
public void propertyChange(java.beans.PropertyChangeEvent evt) {
if (evt.getSource() == this && evt.getPropertyName().equals("reactionRule")) {
ReactionRule oldValue = (ReactionRule) evt.getOldValue();
if (oldValue != null) {
oldValue.removePropertyChangeListener(this);
oldValue.getKineticLaw().removePropertyChangeListener(this);
for (int i = 0; i < oldValue.getKineticLaw().getLocalParameters().length; i++) {
oldValue.getKineticLaw().getLocalParameters()[i].removePropertyChangeListener(this);
}
for (int i = 0; i < oldValue.getKineticLaw().getProxyParameters().length; i++) {
oldValue.getKineticLaw().getProxyParameters()[i].removePropertyChangeListener(this);
}
}
ReactionRule newValue = (ReactionRule) evt.getNewValue();
if (newValue != null) {
newValue.addPropertyChangeListener(this);
newValue.getKineticLaw().addPropertyChangeListener(this);
for (int i = 0; i < newValue.getKineticLaw().getLocalParameters().length; i++) {
newValue.getKineticLaw().getLocalParameters()[i].addPropertyChangeListener(this);
}
for (int i = 0; i < newValue.getKineticLaw().getProxyParameters().length; i++) {
newValue.getKineticLaw().getProxyParameters()[i].addPropertyChangeListener(this);
}
autoCompleteSymbolFilter = reactionRule.getAutoCompleteSymbolFilter();
}
refreshData();
}
if (evt.getSource() == reactionRule && evt.getPropertyName().equals(ReactionRule.PROPERTY_NAME_KINETICLAW)) {
RbmKineticLaw oldValue = (RbmKineticLaw) evt.getOldValue();
if (oldValue != null) {
oldValue.removePropertyChangeListener(this);
for (int i = 0; i < oldValue.getLocalParameters().length; i++) {
oldValue.getLocalParameters()[i].removePropertyChangeListener(this);
}
for (int i = 0; i < oldValue.getProxyParameters().length; i++) {
oldValue.getProxyParameters()[i].removePropertyChangeListener(this);
}
}
RbmKineticLaw newValue = (RbmKineticLaw) evt.getNewValue();
if (newValue != null) {
newValue.addPropertyChangeListener(this);
for (int i = 0; i < newValue.getLocalParameters().length; i++) {
newValue.getLocalParameters()[i].addPropertyChangeListener(this);
}
for (int i = 0; i < newValue.getProxyParameters().length; i++) {
newValue.getProxyParameters()[i].addPropertyChangeListener(this);
}
}
refreshData();
}
if (evt.getSource() instanceof RbmKineticLaw && (evt.getPropertyName().equals("localParameters") || evt.getPropertyName().equals("proxyParameters"))) {
Parameter[] oldParams = (Parameter[]) evt.getOldValue();
Parameter[] newParams = (Parameter[]) evt.getNewValue();
for (int i = 0; oldParams != null && i < oldParams.length; i++) {
oldParams[i].removePropertyChangeListener(this);
}
for (int i = 0; newParams != null && i < newParams.length; i++) {
newParams[i].addPropertyChangeListener(this);
}
refreshData();
}
if (evt.getSource() instanceof LocalParameter || evt.getSource() instanceof LocalProxyParameter) {
refreshData();
}
if (evt.getSource() instanceof Parameter) {
fireTableRowsUpdated(0, getRowCount() - 1);
}
}
Also used :
LocalParameter(cbit.vcell.mapping.ParameterContext.LocalParameter)
LocalProxyParameter(cbit.vcell.mapping.ParameterContext.LocalProxyParameter)
ReactionRule(cbit.vcell.model.ReactionRule)
LocalParameter(cbit.vcell.mapping.ParameterContext.LocalParameter)
ModelParameter(cbit.vcell.model.Model.ModelParameter)
Parameter(cbit.vcell.model.Parameter)
LocalProxyParameter(cbit.vcell.mapping.ParameterContext.LocalProxyParameter)
UnresolvedParameter(cbit.vcell.mapping.ParameterContext.UnresolvedParameter)
RbmKineticLaw(cbit.vcell.model.RbmKineticLaw)
Aggregations
RbmKineticLaw (cbit.vcell.model.RbmKineticLaw)8
ReactionRule (cbit.vcell.model.ReactionRule)8
LocalParameter (cbit.vcell.mapping.ParameterContext.LocalParameter)5
Expression (cbit.vcell.parser.Expression)5
ModelParameter (cbit.vcell.model.Model.ModelParameter)4
ProductPattern (cbit.vcell.model.ProductPattern)4
ReactantPattern (cbit.vcell.model.ReactantPattern)4
ArrayList (java.util.ArrayList)4
UnresolvedParameter (cbit.vcell.mapping.ParameterContext.UnresolvedParameter)3
Model (cbit.vcell.model.Model)3
Parameter (cbit.vcell.model.Parameter)3
SpeciesContext (cbit.vcell.model.SpeciesContext)3
ExpressionException (cbit.vcell.parser.ExpressionException)3
PropertyVetoException (java.beans.PropertyVetoException)3
LocalProxyParameter (cbit.vcell.mapping.ParameterContext.LocalProxyParameter)2
Kinetics (cbit.vcell.model.Kinetics)2
Product (cbit.vcell.model.Product)2
RateLawType (cbit.vcell.model.RbmKineticLaw.RateLawType)2
RbmObservable (cbit.vcell.model.RbmObservable)2
Reactant (cbit.vcell.model.Reactant)2
