Example 6 with MolecularTypePattern
use of org.vcell.model.rbm.MolecularTypePattern in project vcell by virtualcell.
the class BioModelEditorSpeciesTableModel method checkInputValue.
public String checkInputValue(String inputValue, int row, int column) {
SpeciesContext speciesContext = getValueAt(row);
String errMsg = null;
switch(column) {
case COLUMN_NAME:
if (speciesContext == null || !speciesContext.getName().equals(inputValue)) {
if (getModel().getSpeciesContext(inputValue) != null) {
errMsg = "Species '" + inputValue + "' already exists!";
errMsg += VCellErrorMessages.PressEscToUndo;
errMsg = "<html>" + errMsg + "</html>";
return errMsg;
}
}
break;
case COLUMN_STRUCTURE:
if (getModel().getStructure(inputValue) == null) {
errMsg = "Structure '" + inputValue + "' does not exist!";
errMsg += VCellErrorMessages.PressEscToUndo;
errMsg = "<html>" + errMsg + "</html>";
return errMsg;
}
break;
case COLUMN_DEFINITION:
try {
inputValue = inputValue.trim();
if (inputValue.length() > 0) {
// parsing will throw appropriate exception if molecular type or component don't exist
// our change
SpeciesPattern spThis = RbmUtils.parseSpeciesPattern(inputValue, bioModel.getModel());
// here we can restrict what the user can do
for (MolecularTypePattern mtpThis : spThis.getMolecularTypePatterns()) {
MolecularType mtThis = mtpThis.getMolecularType();
for (MolecularComponent mcThis : mtThis.getComponentList()) {
// we check that each component is present in the molecular type pattern (as component pattern)
if (mtpThis.getMolecularComponentPattern(mcThis) == null) {
// not found
errMsg = "All " + MolecularComponent.typeName + "s in the " + mtThis.getDisplayType() + " definition must be present. Missing: " + mcThis.getName();
errMsg += VCellErrorMessages.PressEscToUndo;
errMsg = "<html>" + errMsg + "</html>";
return errMsg;
} else if (mtpThis.getMolecularComponentPattern(mcThis).isImplied()) {
errMsg = "All " + MolecularComponent.typeName + "s in the " + mtThis.getDisplayType() + " definition must be present. Missing: " + mcThis.getName();
errMsg += VCellErrorMessages.PressEscToUndo;
errMsg = "<html>" + errMsg + "</html>";
return errMsg;
} else {
// now need to also check the states
if (mcThis.getComponentStateDefinitions().size() == 0) {
// nothing to do if the molecular component has no component state definition
continue;
// note that we raise exception in parseSpeciesPattern() if we attempt to use an undefined state
// so no need to check that here
}
boolean found = false;
for (ComponentStateDefinition csThis : mcThis.getComponentStateDefinitions()) {
MolecularComponentPattern mcpThis = mtpThis.getMolecularComponentPattern(mcThis);
if ((mcpThis.getComponentStatePattern() == null) || mcpThis.getComponentStatePattern().isAny()) {
// no component state pattern means no state, there's no point to check for this component again
break;
// we get out of the for and complain that we found no matching state
}
if (csThis.getName().equals(mcpThis.getComponentStatePattern().getComponentStateDefinition().getName())) {
found = true;
}
}
if (found == false) {
// we should have found a matching state for the molecular component pattern
errMsg = MolecularComponent.typeName + " " + mcThis.getDisplayName() + " of " + mtThis.getDisplayType() + " " + mtThis.getDisplayName() + " must be in one of the following states: ";
for (int i = 0; i < mcThis.getComponentStateDefinitions().size(); i++) {
ComponentStateDefinition csThis = mcThis.getComponentStateDefinitions().get(i);
errMsg += csThis.getName();
if (i < mcThis.getComponentStateDefinitions().size() - 1) {
errMsg += ", ";
}
}
errMsg += VCellErrorMessages.PressEscToUndo;
errMsg = "<html>" + errMsg + "</html>";
return errMsg;
}
}
}
}
}
} catch (Exception ex) {
errMsg = ex.getMessage();
errMsg += VCellErrorMessages.PressEscToUndo;
errMsg = "<html>" + errMsg + "</html>";
return errMsg;
}
break;
}
return null;
}
Also used :
MolecularType(org.vcell.model.rbm.MolecularType)
MolecularComponent(org.vcell.model.rbm.MolecularComponent)
MolecularComponentPattern(org.vcell.model.rbm.MolecularComponentPattern)
SpeciesContext(cbit.vcell.model.SpeciesContext)
MolecularTypePattern(org.vcell.model.rbm.MolecularTypePattern)
SpeciesPattern(org.vcell.model.rbm.SpeciesPattern)
ComponentStateDefinition(org.vcell.model.rbm.ComponentStateDefinition)
Example 7 with MolecularTypePattern
use of org.vcell.model.rbm.MolecularTypePattern in project vcell by virtualcell.
the class ModelRuleFactory method createRuleEntry.
public ModelRuleEntry createRuleEntry(ReactionRule reactionRule, int reactionRuleIndex, ReactionRuleDirection direction) {
ModelRuleEntry rule = new ModelRuleEntry(reactionRule, reactionRuleIndex);
//
// for each molecular type in reactant, find all possible matches in products (without regard for consistency).
//
int participantIndex = 0;
for (ReactantPattern rp : reactionRule.getReactantPatterns()) {
ModelParticipantEntry reactantEntry = new ModelParticipantEntry(rule, participantIndex, rp);
rule.reactantEntries.add(reactantEntry);
int moleculeIndex = 0;
for (MolecularTypePattern mtp : rp.getSpeciesPattern().getMolecularTypePatterns()) {
ModelMolecularTypeEntry molecularTypeEntry = new ModelMolecularTypeEntry(reactantEntry, moleculeIndex, mtp);
rule.reactantMolecularTypeEntries.add(molecularTypeEntry);
int componentIndex = 0;
for (MolecularComponentPattern mcp : mtp.getComponentPatternList()) {
// TODO: divergence point vs. MathRuleFactory
// we need to look at all components when we compare reactants to products looking for changes
// if(mcp.getBondType() == BondType.Possible && (mcp.getComponentStatePattern() == null || mcp.getComponentStatePattern().isAny())) {
// continue;
// }
ModelMolecularComponentEntry mce = new ModelMolecularComponentEntry(molecularTypeEntry, componentIndex, mcp);
rule.reactantMolecularComponentEntries.add(mce);
//
// if this reactant component has a bond, find partner already in list (will always find second binding site where first one is in the list already).
//
Bond bond = mcp.getBond();
if (bond != null) {
ReactantBondEntry bondEntry = null;
for (MolecularComponentEntry otherMCE : rule.reactantMolecularComponentEntries) {
if (((ModelMolecularComponentEntry) otherMCE).molecularComponentPattern == bond.molecularComponentPattern) {
bondEntry = new ReactantBondEntry(otherMCE, mce);
break;
}
}
if (bondEntry != null) {
rule.reactantBondEntries.add(bondEntry);
}
}
componentIndex++;
}
moleculeIndex++;
}
participantIndex++;
}
participantIndex = 0;
for (ProductPattern pp : reactionRule.getProductPatterns()) {
ModelParticipantEntry productEntry = new ModelParticipantEntry(rule, participantIndex, pp);
rule.productEntries.add(productEntry);
int moleculeIndex = 0;
for (MolecularTypePattern mtp : pp.getSpeciesPattern().getMolecularTypePatterns()) {
ModelMolecularTypeEntry molecularTypeEntry = new ModelMolecularTypeEntry(productEntry, moleculeIndex, mtp);
rule.productMolecularTypeEntries.add(molecularTypeEntry);
int componentIndex = 0;
for (MolecularComponentPattern mcp : mtp.getComponentPatternList()) {
// TODO: divergence point vs. MathRuleFactory
// we need to look at all components when we compare reactants to products looking for changes
// if(mcp.getBondType() == BondType.Possible && (mcp.getComponentStatePattern() == null || mcp.getComponentStatePattern().isAny())) {
// continue;
// }
ModelMolecularComponentEntry mce = new ModelMolecularComponentEntry(molecularTypeEntry, componentIndex, mcp);
rule.productMolecularComponentEntries.add(mce);
//
// if this product component has a bond, find partner already in list (will always find second binding site where first one is in the list already).
//
Bond bond = mcp.getBond();
if (bond != null) {
ProductBondEntry bondEntry = null;
for (MolecularComponentEntry otherMCE : rule.productMolecularComponentEntries) {
if (((ModelMolecularComponentEntry) otherMCE).molecularComponentPattern == bond.molecularComponentPattern) {
bondEntry = new ProductBondEntry(otherMCE, mce);
break;
}
}
if (bondEntry != null) {
rule.productBondEntries.add(bondEntry);
}
}
componentIndex++;
}
moleculeIndex++;
}
participantIndex++;
}
return rule;
}
Also used :
MolecularComponentPattern(org.vcell.model.rbm.MolecularComponentPattern)
ProductBondEntry(org.vcell.model.rbm.RuleAnalysis.ProductBondEntry)
ReactantBondEntry(org.vcell.model.rbm.RuleAnalysis.ReactantBondEntry)
MolecularComponentEntry(org.vcell.model.rbm.RuleAnalysis.MolecularComponentEntry)
MolecularTypePattern(org.vcell.model.rbm.MolecularTypePattern)
Bond(org.vcell.model.rbm.SpeciesPattern.Bond)
Example 8 with MolecularTypePattern
use of org.vcell.model.rbm.MolecularTypePattern in project vcell by virtualcell.
the class OutputSpeciesResultsPanel 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 OutputSpeciesResultsTableModel();
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);
// 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);
gridy++;
gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = gridy;
gbc.weightx = 1.0;
gbc.gridwidth = 2;
gbc.anchor = GridBagConstraints.WEST;
gbc.fill = java.awt.GridBagConstraints.HORIZONTAL;
gbc.insets = new Insets(4, 4, 4, 4);
add(getSpeciesFileLocationPanel(), gbc);
// // button to copy to clipboard the content of the JTextField.
// // TODO: do not delete! this is how it's done
// JButton buttonCopy = new JButton("Copy");
// buttonCopy.setToolTipText("Copy to clipboard the species file path");
// buttonCopy.addActionListener(new ActionListener() {
// public void actionPerformed(ActionEvent le) {
// if(speciesFileLocationTextField.getSelectionStart() == speciesFileLocationTextField.getSelectionEnd()) {
// speciesFileLocationTextField.setSelectionStart(0);
// speciesFileLocationTextField.setSelectionEnd(speciesFileLocationTextField.getText().length());
// }
// speciesFileLocationTextField.copy();
// speciesFileLocationTextField.setSelectionStart(0);
// speciesFileLocationTextField.setSelectionEnd(0);
// }
// });
// gbc = new GridBagConstraints();
// gbc.gridx = 4;
// gbc.gridy = gridy;
// gbc.fill = java.awt.GridBagConstraints.HORIZONTAL;
// gbc.insets = new Insets(4,4,4,4);
// add(buttonCopy, gbc);
// rendering the small shapes of the flattened species in the Depiction column of this viewer 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).species;
if (sc == null || sc.getSpeciesPattern() == null) {
spss = null;
} else {
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(OutputSpeciesResultsTableModel.iColDepiction).setCellRenderer(rbmSpeciesShapeDepictionCellRenderer);
table.getColumnModel().getColumn(OutputSpeciesResultsTableModel.iColDepiction).setPreferredWidth(400);
table.getColumnModel().getColumn(OutputSpeciesResultsTableModel.iColDepiction).setMinWidth(400);
table.getColumnModel().getColumn(OutputSpeciesResultsTableModel.iColDefinition).setPreferredWidth(30);
table.setAutoResizeMode(JTable.AUTO_RESIZE_LAST_COLUMN);
} catch (java.lang.Throwable ivjExc) {
handleException(ivjExc);
}
}
Also used :
GeneratedSpeciesTableRow(org.vcell.model.rbm.gui.GeneratedSpeciesTableRow)
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)
ASTSpeciesPattern(org.vcell.model.bngl.ASTSpeciesPattern)
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 9 with MolecularTypePattern
use of org.vcell.model.rbm.MolecularTypePattern in project vcell by virtualcell.
the class MolecularTypePropertiesPanel method initialize.
private void initialize() {
JPanel leftPanel = new JPanel();
leftPanel.setLayout(new GridBagLayout());
// leftPanel.setBackground(Color.white);
anchorPanel = new JAnchorPanel();
anchorScrollPanel = new JScrollPane(anchorPanel);
molecularTypeTree = new BioModelNodeEditableTree();
molecularTypeTreeModel = new MolecularTypeTreeModel(molecularTypeTree);
molecularTypeTree.setModel(molecularTypeTreeModel);
molecularTypeTree.setEditable(true);
molecularTypeTree.setCellRenderer(new RbmMolecularTypeTreeCellRenderer(molecularTypeTree, issueManager));
molecularTypeTree.setCellEditor(new RbmMolecularTypeTreeCellEditor(molecularTypeTree));
int rowHeight = molecularTypeTree.getRowHeight();
if (rowHeight < 10) {
rowHeight = 20;
}
molecularTypeTree.setRowHeight(rowHeight + 2);
molecularTypeTree.getSelectionModel().setSelectionMode(TreeSelectionModel.SINGLE_TREE_SELECTION);
ToolTipManager.sharedInstance().registerComponent(molecularTypeTree);
molecularTypeTree.addTreeSelectionListener(eventHandler);
molecularTypeTree.addTreeWillExpandListener(eventHandler);
molecularTypeTree.addMouseListener(eventHandler);
molecularTypeTree.setLargeModel(true);
molecularTypeTree.setRootVisible(true);
setLayout(new GridBagLayout());
int gridy = 0;
GridBagConstraints gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = gridy;
gbc.weightx = 1.0;
gbc.insets = new Insets(4, 4, 4, 4);
titleLabel = new JLabel("Construct Solid Geometry");
titleLabel.setFont(titleLabel.getFont().deriveFont(Font.BOLD));
leftPanel.add(titleLabel, gbc);
ButtonGroup bg = new ButtonGroup();
bg.add(getAnchorAllButton());
bg.add(getAnchorOnlyButton());
gridy++;
gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = gridy;
gbc.insets = new Insets(4, 4, 4, 4);
gbc.fill = GridBagConstraints.HORIZONTAL;
leftPanel.add(getAnchorAllButton(), gbc);
gridy++;
gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = gridy;
gbc.insets = new Insets(4, 4, 4, 4);
gbc.fill = GridBagConstraints.HORIZONTAL;
leftPanel.add(getAnchorOnlyButton(), gbc);
gridy++;
gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = gridy;
gbc.weightx = 1.0;
gbc.weighty = 1.0;
gbc.insets = new Insets(4, 4, 4, 4);
gbc.fill = GridBagConstraints.BOTH;
leftPanel.add(anchorScrollPanel, gbc);
// ------------------------------------------------------------------------------
splitPaneHorizontal.setOneTouchExpandable(true);
splitPaneHorizontal.setDividerLocation(120);
splitPaneHorizontal.setResizeWeight(0.1);
Border border = BorderFactory.createLineBorder(Color.gray);
Border loweredEtchedBorder = BorderFactory.createEtchedBorder(EtchedBorder.LOWERED);
Border loweredBevelBorder = BorderFactory.createLoweredBevelBorder();
TitledBorder annotationBorder = BorderFactory.createTitledBorder(loweredEtchedBorder, " Annotation and Pathway Links ");
annotationBorder.setTitleJustification(TitledBorder.LEFT);
annotationBorder.setTitlePosition(TitledBorder.TOP);
annotationBorder.setTitleFont(getFont().deriveFont(Font.BOLD));
shapePanel = new LargeShapePanel() {
@Override
public void paintComponent(Graphics g) {
super.paintComponent(g);
for (LargeShape stls : molecularTypeShapeList) {
stls.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 boolean isViewSingleRow() {
return true;
}
@Override
public RuleParticipantSignature getSignature() {
return null;
}
@Override
public GroupingCriteria getCriteria() {
return null;
}
};
shapePanel.setBorder(border);
shapePanel.setLayout(null);
shapePanel.setBackground(Color.white);
shapePanel.setEditable(true);
shapePanel.setShowMoleculeColor(true);
shapePanel.setShowNonTrivialOnly(true);
shapePanel.addMouseListener(new MouseAdapter() {
@Override
public void mouseClicked(MouseEvent e) {
super.mouseClicked(e);
stopEditing();
if (e.getButton() == 1) {
// left click selects the object (we highlight it)
Point whereClicked = e.getPoint();
PointLocationInShapeContext locationContext = new PointLocationInShapeContext(whereClicked);
manageMouseActivity(locationContext);
} else if (e.getButton() == 3) {
// right click invokes popup menu (only if the object is highlighted)
Point whereClicked = e.getPoint();
PointLocationInShapeContext locationContext = new PointLocationInShapeContext(whereClicked);
manageMouseActivity(locationContext);
if (locationContext.getDeepestShape() != null && !locationContext.getDeepestShape().isHighlighted()) {
// TODO: (maybe) add code here to highlight the shape if it's not highlighted already but don't show the menu
// return;
}
showPopupMenu(e, locationContext);
}
}
private void manageMouseActivity(PointLocationInShapeContext locationContext) {
Graphics g = shapePanel.getGraphics();
for (MolecularTypeLargeShape mtls : molecularTypeShapeList) {
mtls.turnHighlightOffRecursive(g);
}
for (MolecularTypeLargeShape mtls : molecularTypeShapeList) {
if (mtls.contains(locationContext)) {
// check if mouse is inside shape
break;
}
}
locationContext.highlightDeepestShape();
locationContext.paintDeepestShape(g);
}
});
shapePanel.addMouseMotionListener(new MouseMotionAdapter() {
public void mouseMoved(MouseEvent e) {
Point overWhat = e.getPoint();
PointLocationInShapeContext locationContext = new PointLocationInShapeContext(overWhat);
for (MolecularTypeLargeShape mtls : molecularTypeShapeList) {
if (mtls.contains(locationContext)) {
break;
}
}
HighlightableShapeInterface hsi = locationContext.getDeepestShape();
if (hsi == null) {
shapePanel.setToolTipText(null);
} else {
shapePanel.setToolTipText("Right click for " + hsi.getDisplayType() + " menus");
}
for (MolecularTypeLargeShape mtls : molecularTypeShapeList) {
Rectangle r = mtls.getAnchorHotspot();
if (r != null && r.contains(overWhat)) {
mtls.getMolecularType();
shapePanel.setToolTipText(mtls.getAnchorsHTML());
break;
}
}
}
});
// -------------------------------------------------------------------------------------------
// right bottom panel, contains just the annotation
JPanel generalPanel = new JPanel();
generalPanel.setBorder(annotationBorder);
generalPanel.setLayout(new GridBagLayout());
gridy = 0;
gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = 0;
gbc.anchor = GridBagConstraints.LINE_START;
JLabel pathwayLink = new JLabel("Linked Pathway Object(s): ");
generalPanel.add(pathwayLink, gbc);
linkedPOScrollPane = new JScrollPane();
gbc = new java.awt.GridBagConstraints();
gbc.gridx = 1;
gbc.gridy = gridy;
gbc.weightx = 1.0;
gbc.gridwidth = GridBagConstraints.REMAINDER;
gbc.fill = java.awt.GridBagConstraints.HORIZONTAL;
gbc.insets = new Insets(4, 4, 4, 4);
generalPanel.add(linkedPOScrollPane, gbc);
gridy++;
// annotationTextArea = new javax.swing.JTextArea("", 1, 30);
// annotationTextArea.setLineWrap(true);
// annotationTextArea.setWrapStyleWord(true);
// annotationTextArea.setFont(new Font("monospaced", Font.PLAIN, 11));
annotationTextArea = new JTextPane();
annotationTextArea.setContentType("text/html");
annotationTextArea.setEditable(false);
javax.swing.JScrollPane jsp = new javax.swing.JScrollPane(annotationTextArea);
gbc = new java.awt.GridBagConstraints();
gbc.weightx = 1.0;
gbc.weighty = 1.0;
gbc.gridx = 0;
gbc.gridy = gridy;
gbc.gridwidth = 2;
gbc.weightx = 1.0;
gbc.weighty = 1.0;
gbc.anchor = GridBagConstraints.LINE_START;
gbc.fill = java.awt.GridBagConstraints.BOTH;
gbc.insets = new Insets(4, 4, 4, 4);
generalPanel.add(jsp, gbc);
scrollPane = new JScrollPane(shapePanel);
scrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
scrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);
splitPaneHorizontal.setTopComponent(scrollPane);
splitPaneHorizontal.setBottomComponent(generalPanel);
// -----------------------------------------------------------------------------
splitPane.setOneTouchExpandable(true);
splitPane.setLeftComponent(leftPanel);
splitPane.setRightComponent(splitPaneHorizontal);
splitPane.setResizeWeight(0.0);
splitPane.getLeftComponent().setMaximumSize(new Dimension(120, 200));
splitPane.getLeftComponent().setPreferredSize(new Dimension(120, 200));
// splitPane.setDividerLocation(0.0d); // completely hides the left component
// attempt to use the preferred size
splitPane.setDividerLocation(-1);
setName("MolecularTypePropertiesPanel");
setLayout(new BorderLayout());
add(splitPane, BorderLayout.CENTER);
setBackground(Color.white);
annotationTextArea.addFocusListener(eventHandler);
annotationTextArea.addMouseListener(eventHandler);
}
Also used :
JPanel(javax.swing.JPanel)
GridBagConstraints(java.awt.GridBagConstraints)
RuleParticipantSignature(cbit.vcell.model.RuleParticipantSignature)
Insets(java.awt.Insets)
GridBagLayout(java.awt.GridBagLayout)
Rectangle(java.awt.Rectangle)
TitledBorder(javax.swing.border.TitledBorder)
LargeShapePanel(cbit.vcell.graph.gui.LargeShapePanel)
JTextPane(javax.swing.JTextPane)
MolecularTypeLargeShape(cbit.vcell.graph.MolecularTypeLargeShape)
BorderLayout(java.awt.BorderLayout)
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)
MouseAdapter(java.awt.event.MouseAdapter)
JLabel(javax.swing.JLabel)
HighlightableShapeInterface(cbit.vcell.graph.HighlightableShapeInterface)
Point(java.awt.Point)
Dimension(java.awt.Dimension)
PointLocationInShapeContext(cbit.vcell.graph.PointLocationInShapeContext)
GridBagConstraints(java.awt.GridBagConstraints)
Point(java.awt.Point)
Graphics(java.awt.Graphics)
JScrollPane(javax.swing.JScrollPane)
MouseMotionAdapter(java.awt.event.MouseMotionAdapter)
ButtonGroup(javax.swing.ButtonGroup)
MolecularTypeLargeShape(cbit.vcell.graph.MolecularTypeLargeShape)
SpeciesPatternLargeShape(cbit.vcell.graph.SpeciesPatternLargeShape)
ComponentStateLargeShape(cbit.vcell.graph.MolecularComponentLargeShape.ComponentStateLargeShape)
LargeShape(cbit.vcell.graph.LargeShape)
MolecularComponentLargeShape(cbit.vcell.graph.MolecularComponentLargeShape)
MolecularTypePattern(org.vcell.model.rbm.MolecularTypePattern)
Border(javax.swing.border.Border)
TitledBorder(javax.swing.border.TitledBorder)
EtchedBorder(javax.swing.border.EtchedBorder)
Example 10 with MolecularTypePattern
use of org.vcell.model.rbm.MolecularTypePattern in project vcell by virtualcell.
the class ObservablePropertiesPanel method manageComponentPatternFromShape.
public void manageComponentPatternFromShape(final RbmElementAbstract selectedObject, PointLocationInShapeContext locationContext, ShowWhat showWhat) {
final MolecularComponentPattern mcp = (MolecularComponentPattern) selectedObject;
final MolecularComponent mc = mcp.getMolecularComponent();
popupFromShapeMenu.removeAll();
// ------------------------------------------------------------------- State
if (showWhat == ShowWhat.ShowState && mc.getComponentStateDefinitions().size() != 0) {
String prefix = "State: ";
String csdCurrentName = "";
final Map<String, String> itemMap = new LinkedHashMap<String, String>();
if (mcp.getComponentStatePattern() == null || mcp.getComponentStatePattern().isAny()) {
csdCurrentName = "<html>" + prefix + "<b>" + ComponentStatePattern.strAny + "</b></html>";
} else {
csdCurrentName = "<html>" + prefix + ComponentStatePattern.strAny + "</html>";
}
itemMap.put(csdCurrentName, ComponentStatePattern.strAny);
for (final ComponentStateDefinition csd : mc.getComponentStateDefinitions()) {
csdCurrentName = "";
if (mcp.getComponentStatePattern() != null && !mcp.getComponentStatePattern().isAny()) {
ComponentStateDefinition csdCurrent = mcp.getComponentStatePattern().getComponentStateDefinition();
csdCurrentName = csdCurrent.getName();
}
String name = csd.getName();
if (name.equals(csdCurrentName)) {
// currently selected menu item is shown in bold
name = "<html>" + prefix + "<b>" + name + "</b></html>";
} else {
name = "<html>" + prefix + name + "</html>";
}
itemMap.put(name, csd.getName());
}
for (String name : itemMap.keySet()) {
JMenuItem menuItem = new JMenuItem(name);
popupFromShapeMenu.add(menuItem);
menuItem.setIcon(VCellIcons.rbmComponentStateIcon);
menuItem.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
String key = e.getActionCommand();
String name = itemMap.get(key);
if (name.equals(ComponentStatePattern.strAny)) {
ComponentStatePattern csp = new ComponentStatePattern();
mcp.setComponentStatePattern(csp);
} else {
ComponentStateDefinition csd = mcp.getMolecularComponent().getComponentStateDefinition(name);
if (csd == null) {
throw new RuntimeException("Missing ComponentStateDefinition " + name + " for Component " + mcp.getMolecularComponent().getName());
}
ComponentStatePattern csp = new ComponentStatePattern(csd);
mcp.setComponentStatePattern(csp);
}
}
});
}
}
if (showWhat == ShowWhat.ShowState) {
return;
}
// ------------------------------------------------------------------------------------------- Bonds
final MolecularTypePattern mtp = locationContext.getMolecularTypePattern();
final SpeciesPattern sp = locationContext.getSpeciesPattern();
JMenu editBondMenu = new JMenu();
final String specifiedString = mcp.getBondType() == BondType.Specified ? "<html><b>" + "Site bond specified" + "</b></html>" : "<html>" + "Site bond specified" + "</html>";
editBondMenu.setText(specifiedString);
editBondMenu.setToolTipText("Specified");
editBondMenu.removeAll();
final Map<String, Bond> itemMap = new LinkedHashMap<String, Bond>();
// String noneString = "<html>Bond: <b>" + BondType.None.symbol + "</b> " + BondType.None.name() + "</html>";
// String existsString = "<html>Bond: <b>" + BondType.Exists.symbol + "</b> " + BondType.Exists.name() + "</html>";
// String possibleString = "<html>Bond: <b>" + BondType.Possible.symbol + "</b> " + BondType.Possible.name() + "</html>";
String noneString = mcp.getBondType() == BondType.None ? "<html><b>" + "Site is unbound" + "</b></html>" : "<html>" + "Site is unbound" + "</html>";
// Site is bound
String existsString = mcp.getBondType() == BondType.Exists ? "<html><b>" + "Site has external bond" + "</b></html>" : "<html>" + "Site has external bond" + "</html>";
String possibleString = mcp.getBondType() == BondType.Possible ? "<html><b>" + "Site may be bound" + "</b></html>" : "<html>" + "Site may be bound" + "</html>";
itemMap.put(noneString, null);
itemMap.put(existsString, null);
itemMap.put(possibleString, null);
if (mtp != null && sp != null) {
List<Bond> bondPartnerChoices = sp.getAllBondPartnerChoices(mtp, mc);
for (Bond b : bondPartnerChoices) {
// if(b.equals(mcp.getBond())) {
// continue; // if the mcp has a bond already we don't offer it
// }
int index = 0;
if (mcp.getBondType() == BondType.Specified) {
index = mcp.getBondId();
} else {
index = sp.nextBondId();
}
// itemMap.put(b.toHtmlStringLong(mtp, mc, sp, index), b);
itemMap.put(b.toHtmlStringLong(sp, mtp, mc, index), b);
// itemMap.put(b.toHtmlStringLong(sp, index), b);
}
}
int index = 0;
Graphics gc = splitPaneHorizontal.getGraphics();
for (String name : itemMap.keySet()) {
JMenuItem menuItem = new JMenuItem(name);
if (index == 0) {
menuItem.setIcon(VCellIcons.rbmBondNoneIcon);
menuItem.setToolTipText("None");
popupFromShapeMenu.add(menuItem);
} else if (index == 1) {
menuItem.setIcon(VCellIcons.rbmBondExistsIcon);
menuItem.setToolTipText("Exists");
popupFromShapeMenu.add(menuItem);
} else if (index == 2) {
menuItem.setIcon(VCellIcons.rbmBondPossibleIcon);
menuItem.setToolTipText("Possible");
popupFromShapeMenu.add(menuItem);
} else if (index > 2) {
Bond b = itemMap.get(name);
// clone of the sp, with only the bond of interest
SpeciesPattern spBond = new SpeciesPattern(bioModel.getModel(), sp);
spBond.resetBonds();
spBond.resetStates();
MolecularTypePattern mtpFrom = spBond.getMolecularTypePattern(mtp.getMolecularType().getName(), mtp.getIndex());
MolecularComponentPattern mcpFrom = mtpFrom.getMolecularComponentPattern(mc);
MolecularTypePattern mtpTo = spBond.getMolecularTypePattern(b.molecularTypePattern.getMolecularType().getName(), b.molecularTypePattern.getIndex());
MolecularComponentPattern mcpTo = mtpTo.getMolecularComponentPattern(b.molecularComponentPattern.getMolecularComponent());
spBond.setBond(mtpTo, mcpTo, mtpFrom, mcpFrom);
Icon icon = new SpeciesPatternSmallShape(3, 4, spBond, gc, observable, false, issueManager);
((SpeciesPatternSmallShape) icon).setDisplayRequirements(DisplayRequirements.highlightBonds);
menuItem.setIcon(icon);
editBondMenu.add(menuItem);
// } else {
// if(index == 0) {
// menuItem.setForeground(Color.blue);
// }
// popupFromShapeMenu.add(menuItem);
}
menuItem.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
String name = e.getActionCommand();
BondType btBefore = mcp.getBondType();
if (name.equals(noneString)) {
if (btBefore == BondType.Specified) {
// specified -> not specified
// change the partner to possible
mcp.getBond().molecularComponentPattern.setBondType(BondType.Possible);
mcp.getBond().molecularComponentPattern.setBond(null);
}
mcp.setBondType(BondType.None);
mcp.setBond(null);
SwingUtilities.invokeLater(new Runnable() {
public void run() {
observableTreeModel.populateTree();
}
});
} else if (name.equals(existsString)) {
if (btBefore == BondType.Specified) {
// specified -> exists
// change the partner to possible
mcp.getBond().molecularComponentPattern.setBondType(BondType.Possible);
mcp.getBond().molecularComponentPattern.setBond(null);
}
mcp.setBondType(BondType.Exists);
mcp.setBond(null);
SwingUtilities.invokeLater(new Runnable() {
public void run() {
observableTreeModel.populateTree();
}
});
} else if (name.equals(possibleString)) {
if (btBefore == BondType.Specified) {
// specified -> possible
// change the partner to possible
mcp.getBond().molecularComponentPattern.setBondType(BondType.Possible);
mcp.getBond().molecularComponentPattern.setBond(null);
}
mcp.setBondType(BondType.Possible);
mcp.setBond(null);
SwingUtilities.invokeLater(new Runnable() {
public void run() {
observableTreeModel.populateTree();
}
});
} else {
if (btBefore != BondType.Specified) {
// if we go from a non-specified to a specified we need to find the next available
// bond id, so that we can choose the color for displaying the bond
// a bad bond id, like -1, will crash badly when trying to choose the color
int bondId = sp.nextBondId();
mcp.setBondId(bondId);
} else {
// specified -> specified
// change the old partner to possible, continue using the bond id
mcp.getBond().molecularComponentPattern.setBondType(BondType.Possible);
mcp.getBond().molecularComponentPattern.setBond(null);
}
mcp.setBondType(BondType.Specified);
Bond b = itemMap.get(name);
mcp.setBond(b);
mcp.getBond().molecularComponentPattern.setBondId(mcp.getBondId());
sp.resolveBonds();
SwingUtilities.invokeLater(new Runnable() {
public void run() {
observableTreeModel.populateTree();
}
});
}
}
});
index++;
}
popupFromShapeMenu.add(editBondMenu);
}
Also used :
BondType(org.vcell.model.rbm.MolecularComponentPattern.BondType)
MolecularComponentPattern(org.vcell.model.rbm.MolecularComponentPattern)
SpeciesPatternSmallShape(cbit.vcell.graph.SpeciesPatternSmallShape)
ActionEvent(java.awt.event.ActionEvent)
ComponentStatePattern(org.vcell.model.rbm.ComponentStatePattern)
SpeciesPattern(org.vcell.model.rbm.SpeciesPattern)
Point(java.awt.Point)
LinkedHashMap(java.util.LinkedHashMap)
ComponentStateDefinition(org.vcell.model.rbm.ComponentStateDefinition)
Graphics(java.awt.Graphics)
ActionListener(java.awt.event.ActionListener)
MolecularComponent(org.vcell.model.rbm.MolecularComponent)
Icon(javax.swing.Icon)
ZoomShapeIcon(cbit.vcell.graph.gui.ZoomShapeIcon)
JMenuItem(javax.swing.JMenuItem)
MolecularTypePattern(org.vcell.model.rbm.MolecularTypePattern)
Bond(org.vcell.model.rbm.SpeciesPattern.Bond)
JMenu(javax.swing.JMenu)
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
