Example 31 with MolecularTypePattern
use of org.vcell.model.rbm.MolecularTypePattern 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);
}
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)
ZoomShapeIcon(cbit.vcell.graph.gui.ZoomShapeIcon)
Icon(javax.swing.Icon)
JMenuItem(javax.swing.JMenuItem)
MolecularTypePattern(org.vcell.model.rbm.MolecularTypePattern)
Bond(org.vcell.model.rbm.SpeciesPattern.Bond)
JMenu(javax.swing.JMenu)
Example 32 with MolecularTypePattern
use of org.vcell.model.rbm.MolecularTypePattern in project vcell by virtualcell.
the class SpeciesPropertiesTreeModel 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;
}
// if (userObject instanceof SeedSpecies) {
// ((SeedSpecies) userObject).setSpeciesPattern(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);
// TODO: what's correct here ?
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);
speciesContext.getSpeciesPattern().resolveBonds();
} else {
}
}
}
} catch (Exception ex) {
DialogUtils.showErrorDialog(ownerTree, ex.getMessage());
}
}
Also used :
BondType(org.vcell.model.rbm.MolecularComponentPattern.BondType)
MolecularComponentPattern(org.vcell.model.rbm.MolecularComponentPattern)
MolecularComponent(org.vcell.model.rbm.MolecularComponent)
BioModelNode(cbit.vcell.desktop.BioModelNode)
MolecularTypePattern(org.vcell.model.rbm.MolecularTypePattern)
Example 33 with MolecularTypePattern
use of org.vcell.model.rbm.MolecularTypePattern in project vcell by virtualcell.
the class SpeciesContextSpecPanel method initialize.
private void initialize() {
try {
shapePanel = new // glyph (shape) panel
LargeShapePanel() {
@Override
public void paintComponent(Graphics g) {
super.paintComponent(g);
if (spls != null) {
spls.paintSelf(g);
}
}
@Override
public DisplayMode getDisplayMode() {
return DisplayMode.other;
}
@Override
public RuleAnalysisChanged hasStateChanged(String reactionRuleName, MolecularComponentPattern molecularComponentPattern) {
return RuleAnalysisChanged.UNCHANGED;
}
@Override
public RuleAnalysisChanged hasStateChanged(MolecularComponentPattern molecularComponentPattern) {
return RuleAnalysisChanged.UNCHANGED;
}
@Override
public RuleAnalysisChanged hasBondChanged(String reactionRuleName, MolecularComponentPattern molecularComponentPattern) {
return RuleAnalysisChanged.UNCHANGED;
}
@Override
public RuleAnalysisChanged hasBondChanged(MolecularComponentPattern molecularComponentPattern) {
return RuleAnalysisChanged.UNCHANGED;
}
@Override
public RuleAnalysisChanged hasNoMatch(String reactionRuleName, MolecularTypePattern mtp) {
return RuleAnalysisChanged.UNCHANGED;
}
@Override
public RuleAnalysisChanged hasNoMatch(MolecularTypePattern molecularTypePattern) {
return RuleAnalysisChanged.UNCHANGED;
}
@Override
public RuleParticipantSignature getSignature() {
return null;
}
@Override
public GroupingCriteria getCriteria() {
return null;
}
@Override
public boolean isViewSingleRow() {
return true;
}
};
shapePanel.addMouseMotionListener(new MouseMotionAdapter() {
public void mouseMoved(MouseEvent e) {
Point overWhat = e.getPoint();
PointLocationInShapeContext locationContext = new PointLocationInShapeContext(overWhat);
spls.contains(locationContext);
shapePanel.setToolTipText("View-Only panel");
}
});
shapePanel.setBackground(new Color(0xe0e0e0));
shapePanel.setZoomFactor(-2);
shapePanel.setEditable(false);
shapePanel.setShowMoleculeColor(false);
shapePanel.setShowNonTrivialOnly(false);
// --------------------------------------------------------------
JPanel upperPanel = new JPanel();
upperPanel.setLayout(new java.awt.BorderLayout());
upperPanel.add(getScrollPaneTable().getEnclosingScrollPane(), BorderLayout.CENTER);
getScrollPaneTable().setModel(getSpeciesContextSpecParameterTableModel());
scrollPane = new JScrollPane(shapePanel);
scrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
scrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);
JPanel optionsPanel = new JPanel();
optionsPanel.setLayout(new GridBagLayout());
getZoomSmallerButton().setEnabled(true);
getZoomLargerButton().setEnabled(true);
GridBagConstraints gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = 0;
gbc.insets = new Insets(4, 4, 0, 10);
gbc.anchor = GridBagConstraints.WEST;
optionsPanel.add(getZoomLargerButton(), gbc);
gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = 1;
gbc.insets = new Insets(4, 4, 4, 10);
gbc.anchor = GridBagConstraints.WEST;
optionsPanel.add(getZoomSmallerButton(), gbc);
gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = 2;
gbc.weightx = 1;
// fake cell used for filling all the vertical empty space
gbc.weighty = 1;
gbc.anchor = GridBagConstraints.WEST;
gbc.insets = new Insets(4, 4, 4, 10);
optionsPanel.add(new JLabel(""), gbc);
JPanel containerOfScrollPanel = new JPanel();
containerOfScrollPanel.setLayout(new BorderLayout());
containerOfScrollPanel.add(optionsPanel, BorderLayout.WEST);
containerOfScrollPanel.add(scrollPane, BorderLayout.CENTER);
// ------------------------------------------------
splitPaneHorizontal.setTopComponent(upperPanel);
splitPaneHorizontal.setBottomComponent(containerOfScrollPanel);
splitPaneHorizontal.setOneTouchExpandable(true);
// upper panel is 165 pixel height
splitPaneHorizontal.setDividerLocation(165);
splitPaneHorizontal.setResizeWeight(1);
setLayout(new BorderLayout());
add(splitPaneHorizontal, BorderLayout.CENTER);
setBackground(Color.white);
setName("SpeciesContextSpecPanel");
} catch (java.lang.Throwable ivjExc) {
handleException(ivjExc);
}
}
Also used :
JPanel(javax.swing.JPanel)
RuleParticipantSignature(cbit.vcell.model.RuleParticipantSignature)
GridBagConstraints(java.awt.GridBagConstraints)
Insets(java.awt.Insets)
GridBagLayout(java.awt.GridBagLayout)
BorderLayout(java.awt.BorderLayout)
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)
Color(java.awt.Color)
JLabel(javax.swing.JLabel)
Point(java.awt.Point)
PointLocationInShapeContext(cbit.vcell.graph.PointLocationInShapeContext)
Graphics(java.awt.Graphics)
MouseMotionAdapter(java.awt.event.MouseMotionAdapter)
MolecularTypePattern(org.vcell.model.rbm.MolecularTypePattern)
Example 34 with MolecularTypePattern
use of org.vcell.model.rbm.MolecularTypePattern in project vcell by virtualcell.
the class GeneratedSpeciesTableModel2 method getComparator.
public Comparator<GeneratedSpeciesTableRow> getComparator(final int col, final boolean ascending) {
final int scale = ascending ? 1 : -1;
return new Comparator<GeneratedSpeciesTableRow>() {
public int compare(GeneratedSpeciesTableRow o1, GeneratedSpeciesTableRow o2) {
switch(col) {
case iColMultiplier:
return scale * o1.getMultiplier().compareTo(o2.getMultiplier());
case iColOriginalName:
return scale * o1.getOriginalName().compareToIgnoreCase(o2.getOriginalName());
case iColStructure:
// String n1 = es1.substring(1, es1.indexOf(":"));
return // all generated species must belong to the same structure - the one of the observable
0;
case // sort just by the expression, doesn't matter if the structure is mentioned or not because
iColDefinition:
// all the generated species for this observable are in the same structure anyway
return scale * o1.getExpression().compareToIgnoreCase(o2.getExpression());
case iColDepiction:
if (o1.getSpecies() != null && o1.getSpecies().hasSpeciesPattern() && o2.getSpecies() != null && o2.getSpecies().hasSpeciesPattern()) {
Integer i1 = o1.getSpecies().getSpeciesPattern().getMolecularTypePatterns().size();
Integer i2 = o2.getSpecies().getSpeciesPattern().getMolecularTypePatterns().size();
if (scale * i1.compareTo(i2) == 0) {
// if same number of molecule we try to sort by number of sites of the mt
i1 = 0;
i2 = 0;
for (MolecularTypePattern mtp : o1.getSpecies().getSpeciesPattern().getMolecularTypePatterns()) {
i1 += mtp.getMolecularType().getComponentList().size();
}
for (MolecularTypePattern mtp : o2.getSpecies().getSpeciesPattern().getMolecularTypePatterns()) {
i2 += mtp.getMolecularType().getComponentList().size();
}
if (i1 == i2) {
// equal number of molecules and sites, sort by name as a last resort
return scale * o1.getOriginalName().compareToIgnoreCase(o2.getOriginalName());
}
return scale * i1.compareTo(i2);
} else {
return scale * i1.compareTo(i2);
}
}
return 0;
default:
return 0;
}
}
};
}
Also used :
MolecularTypePattern(org.vcell.model.rbm.MolecularTypePattern)
Comparator(java.util.Comparator)
Example 35 with MolecularTypePattern
use of org.vcell.model.rbm.MolecularTypePattern in project vcell by virtualcell.
the class ObservablesGroupTableModel method getComparator.
public Comparator<ObservablesGroupTableRow> getComparator(final int col, final boolean ascending) {
final int scale = ascending ? 1 : -1;
return new Comparator<ObservablesGroupTableRow>() {
public int compare(ObservablesGroupTableRow o1, ObservablesGroupTableRow o2) {
String n1 = o1.getObservableGroupObject().getObservableGroupName();
String n2 = o2.getObservableGroupObject().getObservableGroupName();
RbmObservable ob1 = o1.getObservable(n1);
RbmObservable ob2 = o2.getObservable(n2);
switch(col) {
case iColOriginalName:
return scale * n1.compareToIgnoreCase(n2);
case iColStructure:
String es1 = ObservablesGroupTableRow.toBnglString(o1.getObservable(n1));
String es2 = ObservablesGroupTableRow.toBnglString(o2.getObservable(n2));
if (es1.startsWith("@") && es1.contains(":")) {
// no point to check es2 as well
String sn1 = es1.substring(1, es1.indexOf(":"));
String sn2 = es2.substring(1, es2.indexOf(":"));
return scale * sn1.compareToIgnoreCase(sn2);
} else {
// we should be here only if we have one single structure, so nothing to sort
return 0;
}
case iColDepiction:
if (ob1 == null && ob2 == null) {
return 0;
}
// the sp list is always allocated even though it may be empty
Integer s1 = ob1.getSpeciesPatternList().size();
Integer s2 = ob2.getSpeciesPatternList().size();
if (s1 != s2) {
// different number of species patterns, sort by number of patterns
return scale * s1.compareTo(s2);
// this includes the case when one list is empty
}
if (s1 > 1 && s2 > 1) {
// same number of species patterns, more than one - we don't bother to sort
return 0;
// TODO: add functionality to sort by total number of molecules / sites
}
// one pattern each, sort by number of molecules, if that equal sort by total number of sites
if (s1 == 1 && s2 == 1) {
Integer i1 = ob1.getSpeciesPattern(0).getMolecularTypePatterns().size();
Integer i2 = ob2.getSpeciesPattern(0).getMolecularTypePatterns().size();
if (scale * i1.compareTo(i2) == 0) {
// if same number of molecule we try to sort by number of sites of the mt
i1 = 0;
i2 = 0;
for (MolecularTypePattern mtp : ob1.getSpeciesPattern(0).getMolecularTypePatterns()) {
i1 += mtp.getMolecularType().getComponentList().size();
}
for (MolecularTypePattern mtp : ob2.getSpeciesPattern(0).getMolecularTypePatterns()) {
i2 += mtp.getMolecularType().getComponentList().size();
}
return scale * i1.compareTo(i2);
} else {
return scale * i1.compareTo(i2);
}
}
return 0;
case iColDefinition:
es1 = ObservablesGroupTableRow.toBnglString(o1.getObservable(n1));
es2 = ObservablesGroupTableRow.toBnglString(o2.getObservable(n2));
if (es1.startsWith("@") && es1.contains(":")) {
// multi-structure; no point to check es2 as well
String sn1 = es1.substring(es1.indexOf(":") + 1);
String sn2 = es2.substring(es2.indexOf(":") + 1);
return scale * sn1.compareToIgnoreCase(sn2);
} else {
// single structure
return scale * es1.compareToIgnoreCase(es2);
}
case iColCount:
return scale * ob1.getType().name().compareTo(ob2.getType().name());
default:
return 0;
}
}
};
}
Also used :
RbmObservable(cbit.vcell.model.RbmObservable)
MolecularTypePattern(org.vcell.model.rbm.MolecularTypePattern)
Comparator(java.util.Comparator)
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
