use of org.vcell.model.rbm.MolecularComponentPattern.BondType in project vcell by virtualcell.
the class XmlReader method getRbmMolecularComponentPattern.
private MolecularComponentPattern getRbmMolecularComponentPattern(Element e, MolecularTypePattern mtp, MolecularType mt, Model newModel) {
RbmModelContainer mc = newModel.getRbmModelContainer();
String s = e.getAttributeValue(XMLTags.RbmMolecularComponentTag);
if (s == null || s.isEmpty()) {
System.out.println("XMLReader: getRbmMolecularComponentPattern: MolecularComponent name is missing.");
return null;
}
MolecularComponent c = mt.getMolecularComponent(s);
if (c == null) {
System.out.println("XMLReader: getRbmMolecularComponentPattern: encountered reference " + s + " to non-existing MolecularComponent.");
return null;
}
ComponentStatePattern csp = new ComponentStatePattern();
MolecularComponentPattern mcp = new MolecularComponentPattern(c);
s = e.getAttributeValue(XMLTags.RbmMolecularComponentStatePatternTag);
if (s != null && !s.isEmpty()) {
// state may be missing, we set it only if is present
ComponentStateDefinition cs = c.getComponentStateDefinition(s);
if (cs == null) {
System.out.println("XMLReader: getRbmMolecularComponentPattern: encountered reference " + s + " to non-existing MolecularComponentState.");
return null;
}
csp = new ComponentStatePattern(cs);
mcp.setComponentStatePattern(csp);
}
// s = e.getAttributeValue(XMLTags.RbmMolecularTypeAnyTag);
// if(s!=null && !s.isEmpty()) {
// boolean any = Boolean.parseBoolean(s);
// csp.setAny(any);
// }
s = e.getAttributeValue(XMLTags.RbmBondTypeAttrTag);
BondType bondType = BondType.fromSymbol(s);
if (bondType == BondType.Specified) {
int bondId = Integer.parseInt(s);
mcp.setBondId(bondId);
}
mcp.setBondType(bondType);
// sanity check, we only read the names here and make sure they make sense
Element bondElement = e.getChild(XMLTags.RbmBondTag, vcNamespace);
if (bondElement != null) {
// it's actually the name of the MolecularType inside this pattern
String molecularTypeName = bondElement.getAttributeValue(XMLTags.RbmMolecularTypePatternTag);
String molecularComponentName = bondElement.getAttributeValue(XMLTags.RbmMolecularComponentPatternTag);
if (molecularTypeName == null || molecularTypeName.isEmpty()) {
System.out.println("XMLReader: getRbmMolecularComponentPattern: Bond Attribute molecularTypeName missing.");
return mcp;
}
if (molecularComponentName == null || molecularComponentName.isEmpty()) {
System.out.println("XMLReader: getRbmMolecularComponentPattern: Bond Attribute molecularComponentName missing.");
return mcp;
}
// we'll have a bond here, it will be properly initialized during RbmObservable.resolveBonds() call !!!
Bond bond = new Bond();
mcp.setBond(bond);
}
return mcp;
}
use of org.vcell.model.rbm.MolecularComponentPattern.BondType 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);
}
use of org.vcell.model.rbm.MolecularComponentPattern.BondType in project vcell by virtualcell.
the class ObservableTreeModel method valueForPathChanged.
@Override
public void valueForPathChanged(TreePath path, Object newValue) {
Object obj = path.getLastPathComponent();
if (obj == null || !(obj instanceof BioModelNode)) {
return;
}
BioModelNode selectedNode = (BioModelNode) obj;
BioModelNode parentNode = (BioModelNode) selectedNode.getParent();
Object userObject = selectedNode.getUserObject();
try {
if (newValue instanceof String) {
String inputString = (String) newValue;
if (inputString == null || inputString.length() == 0) {
return;
}
String mangled = TokenMangler.fixTokenStrict(inputString);
if (!mangled.equals(inputString)) {
String errMsg = ((Displayable) userObject).getDisplayType() + " '" + inputString + "' not legal identifier, try '" + mangled + "'";
throw new RuntimeException(errMsg);
}
if (userObject instanceof RbmObservable) {
// TODO: untested!!!
((RbmObservable) userObject).setName(inputString);
}
} else if (newValue instanceof MolecularComponentPattern) {
MolecularComponentPattern newMcp = (MolecularComponentPattern) newValue;
Object parentObject = parentNode == null ? null : parentNode.getUserObject();
if (parentObject instanceof MolecularTypePattern) {
MolecularTypePattern mtp = (MolecularTypePattern) parentObject;
MolecularComponent mc = newMcp.getMolecularComponent();
MolecularComponentPattern mcp = mtp.getMolecularComponentPattern(mc);
mcp.setComponentStatePattern(newMcp.getComponentStatePattern());
BondType bp = mcp.getBondType();
BondType newbp = newMcp.getBondType();
mcp.setBondType(newbp);
// specified -> specified
if (bp == BondType.Specified && newbp == BondType.Specified) {
// bond didn't change
} else if (bp == BondType.Specified && newbp != BondType.Specified) {
// specified -> non specified
// change the partner to possible
mcp.getBond().molecularComponentPattern.setBondType(BondType.Possible);
mcp.setBond(null);
} else if (bp != BondType.Specified && newbp == BondType.Specified) {
// non specified -> specified
int newBondId = newMcp.getBondId();
mcp.setBondId(newBondId);
mcp.setBond(newMcp.getBond());
mcp.getBond().molecularComponentPattern.setBondId(newBondId);
for (SpeciesPattern sp : observable.getSpeciesPatternList()) {
sp.resolveBonds();
}
} else {
}
}
}
} catch (Exception ex) {
DialogUtils.showErrorDialog(ownerTree, ex.getMessage());
}
}
use of org.vcell.model.rbm.MolecularComponentPattern.BondType in project vcell by virtualcell.
the class RbmTreeCellRenderer method toHtmlWorkShort.
private static final String toHtmlWorkShort(BondLocal bl) {
// used for tooltips
MolecularComponentPattern mcp = bl.getMolecularComponentPattern();
String bondText = "";
String colorTextStart = "<font color=" + "\"rgb(" + GraphConstants.red.getRed() + "," + GraphConstants.red.getGreen() + "," + GraphConstants.red.getBlue() + ")\">";
String colorTextEnd = "</font>";
bondText = colorTextStart + "<b>" + "(unbound)" + "</b>" + colorTextEnd;
if (mcp != null) {
BondType bondType = mcp.getBondType();
if (bondType == BondType.Specified) {
Bond bond = mcp.getBond();
if (bond == null) {
colorTextStart = "<font color=" + "\"rgb(" + GraphConstants.red.getRed() + "," + GraphConstants.red.getGreen() + "," + GraphConstants.red.getBlue() + ")\">";
colorTextEnd = "</font>";
bondText = colorTextStart + "<b>" + "bond (missing)" + "</b>" + colorTextEnd;
} else {
int id = mcp.getBondId();
colorTextStart = "<font color=" + "\"rgb(" + GraphConstants.bondHtmlColors[id].getRed() + "," + GraphConstants.bondHtmlColors[id].getGreen() + "," + GraphConstants.bondHtmlColors[id].getBlue() + ")\">";
colorTextEnd = "</font>";
// <sub> </sub>
bondText = colorTextStart + "<b>" + "Bond<sub>" + id + "</sub></b>" + colorTextEnd;
}
} else if (bondType == BondType.None) {
bondText = "Unbound";
// bondText = "<b>" + "unbound" + "</b>";
} else if (bondType == BondType.Exists) {
Color c = AbstractComponentShape.plusSignGreen;
colorTextStart = "<font color=" + "\"rgb(" + c.getRed() + "," + c.getGreen() + "," + c.getBlue() + ")\">";
colorTextEnd = "</font>";
// green '+'
bondText = colorTextStart + "<b>" + mcp.getBondType().symbol + "</b>" + colorTextEnd;
bondText = "Bond: '" + bondText + "'";
} else if (bondType == BondType.Possible) {
Color c = Color.gray;
colorTextStart = "<font color=" + "\"rgb(" + c.getRed() + "," + c.getGreen() + "," + c.getBlue() + ")\">";
colorTextEnd = "</font>";
// gray '?'
bondText = colorTextStart + "<b>" + mcp.getBondType().symbol + "</b>" + colorTextEnd;
bondText = "Bond: '" + bondText + "'";
}
}
return bondText;
}
use of org.vcell.model.rbm.MolecularComponentPattern.BondType in project vcell by virtualcell.
the class SpeciesPropertiesPanel method manageComponentPatternFromShape.
public void manageComponentPatternFromShape(final RbmElementAbstract selectedObject, PointLocationInShapeContext locationContext, ShowWhat showWhat) {
popupFromShapeMenu.removeAll();
final MolecularComponentPattern mcp = (MolecularComponentPattern) selectedObject;
final MolecularComponent mc = mcp.getMolecularComponent();
// ------------------------------------------------------------------- State
if (showWhat == ShowWhat.ShowState && mc.getComponentStateDefinitions().size() != 0) {
String prefix = "State: ";
final Map<String, String> itemMap = new LinkedHashMap<String, String>();
// itemList.add(ComponentStatePattern.strAny); // any is not an option for state
String csdCurrentName;
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 = mcp.getBondType() == BondType.None ? "<html><b>" + "Site is unbound" + "</b></html>" : "<html>" + "Site is unbound" + "</html>";
itemMap.put(noneString, null);
// itemMap.put(possibleString, null); // not a valid option for species
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(sp, mtp, mc, index), b);
// itemMap.put(b.toHtmlStringLong(sp, index), b);
}
}
int index = 0;
Graphics gc = shapePanel.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 {
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, fieldSpeciesContext, false, issueManager);
((SpeciesPatternSmallShape) icon).setDisplayRequirements(DisplayRequirements.highlightBonds);
menuItem.setIcon(icon);
editBondMenu.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 none since this is the only option
mcp.getBond().molecularComponentPattern.setBondType(BondType.None);
mcp.getBond().molecularComponentPattern.setBond(null);
}
mcp.setBondType(BondType.None);
mcp.setBond(null);
SwingUtilities.invokeLater(new Runnable() {
public void run() {
speciesPropertiesTreeModel.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 none since it's the only available option, continue using the bond id
mcp.getBond().molecularComponentPattern.setBondType(BondType.None);
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() {
speciesPropertiesTreeModel.populateTree();
}
});
}
}
});
index++;
}
popupFromShapeMenu.add(editBondMenu);
}
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