use of cbit.vcell.graph.SpeciesPatternLargeShape in project vcell by virtualcell.
the class ObservablePropertiesPanel method initialize.
private void initialize() {
observableTree = new BioModelNodeEditableTree();
observableTreeModel = new ObservableTreeModel(observableTree);
observableTree.setModel(observableTreeModel);
setLayout(new GridBagLayout());
// --------------------------------------------------------------------------------------------------------
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 ");
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 (SpeciesPatternLargeShape sps : spsList) {
if (sps == null) {
continue;
}
sps.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.setBorder(border);
shapePanel.setBackground(Color.white);
shapePanel.setLayout(null);
shapePanel.setZoomFactor(-1);
shapePanel.setEditable(true);
shapePanel.setShowMoleculeColor(true);
shapePanel.setShowNonTrivialOnly(true);
shapePanel.addMouseListener(new MouseAdapter() {
@Override
public void mouseClicked(MouseEvent e) {
super.mouseClicked(e);
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 (SpeciesPatternLargeShape sps : spsList) {
sps.turnHighlightOffRecursive(g);
}
for (SpeciesPatternLargeShape sps : spsList) {
if (sps.contains(locationContext)) {
// check if mouse is inside shape
break;
}
}
locationContext.highlightDeepestShape();
locationContext.paintDeepestShape(g);
}
});
// shapePanel.addMouseListener(eventHandler); // alternately use this
shapePanel.addMouseMotionListener(new MouseMotionAdapter() {
public void mouseMoved(MouseEvent e) {
Point overWhat = e.getPoint();
PointLocationInShapeContext locationContext = new PointLocationInShapeContext(overWhat);
for (SpeciesPatternLargeShape sps : spsList) {
if (sps.contains(locationContext)) {
break;
}
}
HighlightableShapeInterface hsi = locationContext.getDeepestShape();
if (hsi == null) {
shapePanel.setToolTipText(null);
} else {
shapePanel.setToolTipText("Right click for " + hsi.getDisplayType() + " menus");
}
for (SpeciesPatternLargeShape sps : spsList) {
for (MolecularTypeLargeShape mtls : sps.getMolecularTypeLargeShapes()) {
Rectangle r = mtls.getAnchorHotspot();
if (r != null && r.contains(overWhat)) {
mtls.getMolecularType();
shapePanel.setToolTipText(mtls.getAnchorsHTML());
break;
}
}
}
}
});
JPanel optionsPanel = new JPanel();
// gray options panel
optionsPanel.setPreferredSize(new Dimension(140, 200));
optionsPanel.setLayout(new GridBagLayout());
getZoomSmallerButton().setEnabled(true);
getZoomLargerButton().setEnabled(true);
int gridy = 0;
GridBagConstraints gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = gridy;
gbc.gridwidth = 3;
// top, left bottom, right
gbc.insets = new Insets(4, 4, 2, 4);
gbc.fill = GridBagConstraints.HORIZONTAL;
gbc.anchor = GridBagConstraints.NORTHWEST;
optionsPanel.add(getAddSpeciesButton(), gbc);
ButtonGroup bg = new ButtonGroup();
bg.add(getSequenceMultimolecularButton());
bg.add(getSequencePolimerEqualButton());
bg.add(getSequencePolimerGreaterButton());
gridy++;
gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = gridy;
gbc.gridwidth = 2;
gbc.insets = new Insets(8, 4, 2, 4);
gbc.fill = GridBagConstraints.HORIZONTAL;
optionsPanel.add(getSequenceMultimolecularButton(), gbc);
gridy++;
gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = gridy;
gbc.insets = new Insets(4, 10, 2, 4);
gbc.fill = GridBagConstraints.HORIZONTAL;
JLabel label = new JLabel("Polymer of");
label.setToolTipText("Compact notation available below for single-Molecule polymers");
optionsPanel.add(label, gbc);
gridy++;
gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = gridy;
gbc.insets = new Insets(2, 4, 1, 2);
gbc.fill = GridBagConstraints.HORIZONTAL;
optionsPanel.add(getSequencePolimerEqualButton(), gbc);
gbc = new GridBagConstraints();
gbc.gridx = 1;
gbc.gridy = gridy;
gbc.gridwidth = 2;
gbc.insets = new Insets(2, 4, 1, 4);
gbc.fill = GridBagConstraints.HORIZONTAL;
optionsPanel.add(getLengthEqualTextField(), gbc);
gridy++;
gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = gridy;
gbc.insets = new Insets(1, 4, 4, 2);
gbc.fill = GridBagConstraints.HORIZONTAL;
optionsPanel.add(getSequencePolimerGreaterButton(), gbc);
gbc = new GridBagConstraints();
gbc.gridx = 1;
gbc.gridy = gridy;
gbc.gridwidth = 2;
gbc.insets = new Insets(1, 4, 4, 4);
gbc.fill = GridBagConstraints.HORIZONTAL;
optionsPanel.add(getLengthGreaterTextField(), gbc);
// --- zoom buttons in their own panel, for alignment ---
JPanel buttonPanel = new JPanel();
buttonPanel.setLayout(new GridBagLayout());
GridBagConstraints gbc2 = new GridBagConstraints();
gbc2.gridx = 0;
gbc2.gridy = 0;
gbc2.insets = new Insets(1, 1, 1, 1);
gbc2.anchor = GridBagConstraints.WEST;
buttonPanel.add(getZoomLargerButton(), gbc2);
gbc2 = new GridBagConstraints();
gbc2.gridx = 1;
gbc2.gridy = 0;
gbc2.insets = new Insets(1, 1, 1, 1);
gbc2.anchor = GridBagConstraints.WEST;
buttonPanel.add(getZoomSmallerButton(), gbc2);
// ---------------------------------------------------
gridy++;
gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = gridy;
gbc.anchor = GridBagConstraints.WEST;
gbc.insets = new Insets(1, 4, 4, 2);
gbc.fill = GridBagConstraints.HORIZONTAL;
// zoom buttons panel
optionsPanel.add(buttonPanel, gbc);
gridy++;
gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = gridy;
gbc.gridwidth = 3;
gbc.weightx = 1;
// fake cell used for filling all the vertical empty space
gbc.weighty = 1;
gbc.anchor = GridBagConstraints.WEST;
gbc.insets = new Insets(2, 1, 2, 10);
optionsPanel.add(new JLabel(""), gbc);
// -----------------------------------------------------------------------------------------
// right bottom panel, contains just the annotation
JPanel generalPanel = new JPanel();
generalPanel.setBorder(annotationBorder);
generalPanel.setLayout(new GridBagLayout());
gridy = 0;
annotationTextArea = new javax.swing.JTextArea("", 1, 30);
annotationTextArea.setLineWrap(true);
annotationTextArea.setWrapStyleWord(true);
annotationTextArea.setFont(new Font("monospaced", Font.PLAIN, 11));
annotationTextArea.setEditable(false);
javax.swing.JScrollPane jsp = new javax.swing.JScrollPane(annotationTextArea);
gbc = new java.awt.GridBagConstraints();
gbc.weightx = 1.0;
gbc.weighty = 0.1;
gbc.gridx = 0;
gbc.gridy = gridy;
gbc.anchor = GridBagConstraints.LINE_START;
gbc.fill = java.awt.GridBagConstraints.BOTH;
gbc.insets = new Insets(4, 4, 4, 4);
generalPanel.add(jsp, gbc);
// where we display the shapes
scrollPane = new JScrollPane(shapePanel);
scrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
scrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);
JPanel containerOfScrollPanel = new JPanel();
containerOfScrollPanel.setLayout(new BorderLayout());
containerOfScrollPanel.add(optionsPanel, BorderLayout.WEST);
containerOfScrollPanel.add(scrollPane, BorderLayout.CENTER);
splitPaneHorizontal.setTopComponent(containerOfScrollPanel);
splitPaneHorizontal.setBottomComponent(generalPanel);
splitPaneHorizontal.setResizeWeight(0.9d);
splitPaneHorizontal.setDividerLocation(0.8d);
setName("ObservablePropertiesPanel");
setLayout(new BorderLayout());
add(splitPaneHorizontal, BorderLayout.CENTER);
setBackground(Color.white);
annotationTextArea.addFocusListener(eventHandler);
annotationTextArea.addMouseListener(eventHandler);
}
use of cbit.vcell.graph.SpeciesPatternLargeShape in project vcell by virtualcell.
the class SpeciesPropertiesPanel method updateShape.
private void updateShape() {
if (fieldSpeciesContext != null) {
SpeciesPattern sp = fieldSpeciesContext.getSpeciesPattern();
spls = new SpeciesPatternLargeShape(xOffsetInitial, yOffsetInitial, -1, sp, shapePanel, fieldSpeciesContext, issueManager);
int maxXOffset = xOffsetInitial + spls.getWidth();
int maxYOffset = yOffsetInitial + 80;
Dimension preferredSize = new Dimension(maxXOffset + 120, maxYOffset + 20);
shapePanel.setPreferredSize(preferredSize);
shapePanel.repaint();
// scrollPane.repaint();
}
}
use of cbit.vcell.graph.SpeciesPatternLargeShape in project vcell by virtualcell.
the class SpeciesPropertiesPanel method showPopupMenu.
private void showPopupMenu(MouseEvent e, PointLocationInShapeContext locationContext) {
if (popupFromShapeMenu == null) {
popupFromShapeMenu = new JPopupMenu();
}
if (popupFromShapeMenu.isShowing()) {
return;
}
final Object deepestShape = locationContext.getDeepestShape();
final RbmElementAbstract selectedObject;
if (deepestShape == null) {
selectedObject = null;
// when cursor is outside any species pattern we offer to add a new one
System.out.println("outside");
// popupFromShapeMenu.add(getAddSpeciesPatternFromShapeMenuItem());
} else if (deepestShape instanceof ComponentStateLargeShape) {
System.out.println("inside state");
if (((ComponentStateLargeShape) deepestShape).isHighlighted()) {
selectedObject = ((ComponentStateLargeShape) deepestShape).getComponentStatePattern();
} else {
return;
}
} else if (deepestShape instanceof MolecularComponentLargeShape) {
System.out.println("inside component");
if (((MolecularComponentLargeShape) deepestShape).isHighlighted()) {
selectedObject = ((MolecularComponentLargeShape) deepestShape).getMolecularComponentPattern();
} else {
return;
}
} else if (deepestShape instanceof MolecularTypeLargeShape) {
System.out.println("inside molecule");
if (((MolecularTypeLargeShape) deepestShape).isHighlighted()) {
selectedObject = ((MolecularTypeLargeShape) deepestShape).getMolecularTypePattern();
} else {
return;
}
} else if (deepestShape instanceof SpeciesPatternLargeShape) {
System.out.println("inside species pattern");
if (((SpeciesPatternLargeShape) deepestShape).isHighlighted()) {
selectedObject = ((SpeciesPatternLargeShape) deepestShape).getSpeciesPattern();
} else {
if (!fieldSpeciesContext.hasSpeciesPattern()) {
selectedObject = new SpeciesPattern();
} else {
return;
}
}
} else {
selectedObject = null;
System.out.println("inside something else?");
return;
}
System.out.println(selectedObject);
popupFromShapeMenu.removeAll();
Point mousePoint = e.getPoint();
if (selectedObject instanceof SpeciesPattern) {
final SpeciesPattern sp = (SpeciesPattern) selectedObject;
JMenu addMenuItem = new JMenu(VCellErrorMessages.SpecifyMolecularTypes);
popupFromShapeMenu.add(addMenuItem);
addMenuItem.removeAll();
for (final MolecularType mt : bioModel.getModel().getRbmModelContainer().getMolecularTypeList()) {
JMenuItem menuItem = new JMenuItem(mt.getName());
Graphics gc = shapePanel.getGraphics();
Icon icon = new MolecularTypeSmallShape(1, 4, mt, null, gc, mt, null, issueManager);
menuItem.setIcon(icon);
addMenuItem.add(menuItem);
menuItem.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
MolecularTypePattern molecularTypePattern = new MolecularTypePattern(mt);
for (MolecularComponentPattern mcp : molecularTypePattern.getComponentPatternList()) {
mcp.setBondType(BondType.None);
}
if (!fieldSpeciesContext.hasSpeciesPattern()) {
fieldSpeciesContext.setSpeciesPattern(sp);
}
fieldSpeciesContext.getSpeciesPattern().addMolecularTypePattern(molecularTypePattern);
}
});
}
// JMenu compartmentMenuItem = new JMenu("Specify structure");
// popupFromShapeMenu.add(compartmentMenuItem);
// compartmentMenuItem.removeAll();
// for (final Structure struct : bioModel.getModel().getStructures()) {
// JMenuItem menuItem = new JMenuItem(struct.getName());
// compartmentMenuItem.add(menuItem);
// menuItem.addActionListener(new ActionListener() {
// public void actionPerformed(ActionEvent e) {
// String nameStruct = e.getActionCommand();
// Structure struct = bioModel.getModel().getStructure(nameStruct);
// fieldSpeciesContext.setStructure(struct);
// }
// });
// }
} else if (selectedObject instanceof MolecularTypePattern) {
MolecularTypePattern mtp = (MolecularTypePattern) selectedObject;
String moveRightMenuText = "Move <b>" + "right" + "</b>";
moveRightMenuText = "<html>" + moveRightMenuText + "</html>";
JMenuItem moveRightMenuItem = new JMenuItem(moveRightMenuText);
Icon icon = VCellIcons.moveRightIcon;
moveRightMenuItem.setIcon(icon);
moveRightMenuItem.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
MolecularTypePattern from = (MolecularTypePattern) selectedObject;
SpeciesPattern sp = locationContext.sps.getSpeciesPattern();
sp.shiftRight(from);
speciesPropertiesTreeModel.populateTree();
}
});
popupFromShapeMenu.add(moveRightMenuItem);
String moveLeftMenuText = "Move <b>" + "left" + "</b>";
moveLeftMenuText = "<html>" + moveLeftMenuText + "</html>";
JMenuItem moveLeftMenuItem = new JMenuItem(moveLeftMenuText);
icon = VCellIcons.moveLeftIcon;
moveLeftMenuItem.setIcon(icon);
moveLeftMenuItem.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
MolecularTypePattern from = (MolecularTypePattern) selectedObject;
SpeciesPattern sp = locationContext.sps.getSpeciesPattern();
sp.shiftLeft(from);
speciesPropertiesTreeModel.populateTree();
}
});
popupFromShapeMenu.add(moveLeftMenuItem);
popupFromShapeMenu.add(new JSeparator());
String deleteMenuText = "Delete <b>" + mtp.getMolecularType().getName() + "</b>";
deleteMenuText = "<html>" + deleteMenuText + "</html>";
JMenuItem deleteMenuItem = new JMenuItem(deleteMenuText);
deleteMenuItem.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
MolecularTypePattern mtp = (MolecularTypePattern) selectedObject;
SpeciesPattern sp = locationContext.sps.getSpeciesPattern();
sp.removeMolecularTypePattern(mtp);
if (sp.getMolecularTypePatterns().isEmpty()) {
fieldSpeciesContext.setSpeciesPattern(null);
}
}
});
popupFromShapeMenu.add(deleteMenuItem);
} else if (selectedObject instanceof MolecularComponentPattern) {
manageComponentPatternFromShape(selectedObject, locationContext, ShowWhat.ShowBond);
} else if (selectedObject instanceof ComponentStatePattern) {
MolecularComponentPattern mcp = ((ComponentStateLargeShape) deepestShape).getMolecularComponentPattern();
manageComponentPatternFromShape(mcp, locationContext, ShowWhat.ShowState);
} else {
System.out.println("Where am I ???");
}
popupFromShapeMenu.show(e.getComponent(), mousePoint.x, mousePoint.y);
}
use of cbit.vcell.graph.SpeciesPatternLargeShape in project vcell by virtualcell.
the class SpeciesContextSpecPanel method updateShape.
private void updateShape() {
if (speciesContext == null) {
return;
}
SpeciesPattern sp = speciesContext.getSpeciesPattern();
spls = new SpeciesPatternLargeShape(xOffsetInitial, yOffsetInitial, -1, sp, shapePanel, speciesContext, issueManager);
Dimension preferredSize = new Dimension(spls.getRightEnd() + 40, yOffsetInitial + 80);
shapePanel.setPreferredSize(preferredSize);
shapePanel.repaint();
}
use of cbit.vcell.graph.SpeciesPatternLargeShape in project vcell by virtualcell.
the class ViewGeneratedSpeciesPanel method updateShape.
public void updateShape(int selectedRow) {
GeneratedSpeciesTableRow speciesTableRow = tableModel.getValueAt(selectedRow);
String inputString = speciesTableRow.getExpression();
// System.out.println(selectedRows[0] + ": " + inputString);
Model tempModel = null;
try {
tempModel = new Model("MyTempModel");
tempModel.addFeature("c0");
} catch (ModelException | PropertyVetoException e1) {
e1.printStackTrace();
}
if (owner != null && owner.getSimulationContext() != null) {
List<MolecularType> mtList = owner.getSimulationContext().getModel().getRbmModelContainer().getMolecularTypeList();
try {
tempModel.getRbmModelContainer().setMolecularTypeList(mtList);
} catch (PropertyVetoException e1) {
e1.printStackTrace();
throw new RuntimeException("Unexpected exception setting " + MolecularType.typeName + " list: " + e1.getMessage(), e1);
}
} else {
System.out.println("something is wrong, we just do nothing rather than crash");
return;
}
try {
String strStructure = null;
if (inputString.contains(RbmUtils.SiteStruct)) {
// we are in the mode where we emulate compartments by adding the compartment name as a fake site
Pair<List<String>, String> p = RbmUtils.extractCompartment(inputString);
// we'll just assume there's only one, may want to throw exception if more
strStructure = p.one.get(0);
inputString = p.two;
} else {
// should be the normal @comp:expression format - if it's not it will return null
strStructure = RbmUtils.parseCompartment(inputString, tempModel);
}
Structure structure;
if (strStructure != null) {
if (tempModel.getStructure(strStructure) == null) {
if (owner.getSimulationContext().getModel().getStructure(strStructure).getTypeName().equals(Structure.TYPE_NAME_MEMBRANE)) {
tempModel.addMembrane(strStructure);
} else {
tempModel.addFeature(strStructure);
}
}
structure = tempModel.getStructure(strStructure);
} else {
structure = tempModel.getStructure(0);
}
SpeciesPattern sp = (SpeciesPattern) RbmUtils.parseSpeciesPattern(inputString, tempModel);
sp.resolveBonds();
SpeciesContext sc = new SpeciesContext(new Species("a", ""), structure, sp);
spls = new SpeciesPatternLargeShape(20, 20, -1, sp, shapePanel, sc, issueManager);
} catch (ParseException | PropertyVetoException | ModelException e1) {
e1.printStackTrace();
// error (red circle)
spls = new SpeciesPatternLargeShape(20, 20, -1, shapePanel, true, issueManager);
shapePanel.repaint();
}
int xOffset = spls.getRightEnd() + 45;
Dimension preferredSize = new Dimension(xOffset + 90, 50);
shapePanel.setPreferredSize(preferredSize);
shapePanel.repaint();
}
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