/** The finite branch points of the curve */
public Set<Point2D> getFiniteBranches() {
if (this.branches == null) return new HashSet<Point2D>();
Set<Point2D> branches = new HashSet<Point2D>(this.branches);
branches.remove(INFINITY);
return branches;
}
{
for (myjava.gui.syntax.Painter painter : myjava.gui.syntax.Painter.getPainters()) {
painterComboBox.addItem(painter);
EntryListPanel panel = new EntryListPanel(painter);
listPanelSet.add(panel);
centerPanel.add(panel, painter.getName());
}
componentSet.addAll(Arrays.asList(matchBracket, painterComboBox, centerPanel));
}
public void resetListOfExpandedNodes() {
expandedNodes.clear();
for (int i = 1; i < getTree().getRowCount(); i++) {
if (getTree().isExpanded(i)) {
Object o = getTree().getPathForRow(i).getLastPathComponent();
if (o instanceof Config) {
expandedNodes.add(o);
}
}
}
}
private void addPainter(myjava.gui.syntax.Painter painter) {
EntryListPanel newPanel = new EntryListPanel(painter);
listPanelSet.add(newPanel);
centerPanel.add(newPanel, painter.getName());
painterComboBox.removeItemListener(painterChangeListener);
painterComboBox.removeAllItems();
for (EntryListPanel p : listPanelSet) {
painterComboBox.addItem(p.getPainter());
}
removedPainters.remove(painter);
painterComboBox.addItemListener(painterChangeListener);
}
/**
* Load the volume data to the display
*
* @throws RemoteException problem loading remote data
* @throws VisADException problem loading the data
*/
private void loadVolumeData() throws VisADException, RemoteException {
Trace.call1("VRC.loadVolumeData");
FieldImpl grid = getGridDataInstance().getGrid();
FieldImpl newGrid = grid;
if (getSkipValue() > 0) {
grid = GridUtil.subset(grid, getSkipValue() + 1);
newGrid = grid;
}
if (!usePoints) {
// make sure the projection is correct before we start
// transforming the data
setProjectionInView(true, true);
CoordinateSystem cs = getNavigatedDisplay().getDisplayCoordinateSystem();
if ((cs != null) && (getNavigatedDisplay() instanceof MapProjectionDisplay)) {
try {
if (GridUtil.isConstantSpatialDomain(grid)) {
newGrid = makeLinearGrid(grid, cs);
} else {
Set timeSet = GridUtil.getTimeSet(grid);
for (int i = 0; i < timeSet.getLength(); i++) {
FieldImpl timeField = makeLinearGrid((FieldImpl) grid.getSample(i, false), cs);
if (i == 0) {
FunctionType ft =
new FunctionType(
((SetType) timeSet.getType()).getDomain(), timeField.getType());
newGrid = new FieldImpl(ft, timeSet);
}
newGrid.setSample(i, timeField, false);
}
}
} catch (VisADException ve) {
ve.printStackTrace();
userErrorMessage(
"Can't render volume for "
+ paramName
+ " in this projection. Try using the data projection");
newGrid = grid;
}
}
}
Trace.call1("VRC.loadVolumeData.loadData");
myDisplay.loadData(newGrid);
Trace.call2("VRC.loadVolumeData.loadData");
Trace.call2("loadVolumeData");
}
WordListModel(ASDGrammar grammar) {
Set entrySet = grammar.lexicon().entrySet();
ArrayList words = new ArrayList(entrySet.size());
for (Iterator it = entrySet.iterator(); it.hasNext(); ) {
Map.Entry e = (Map.Entry) it.next();
String word = (String) e.getKey();
words.add(word);
}
Object[] wordArray = words.toArray();
if (words.size() > 1)
// Arrays.sort(wordArray);
Arrays.sort(wordArray, new WordComparator());
for (int j = 0; j < wordArray.length; j++) {
this.addElement((String) wordArray[j]);
}
}
/**
* Goal-driven recursive (depth-first, exhaustive) search with backtracking
*
* @param problem
* @param algorithm
* @param subtaskRelsInPath
* @param depth
*/
private boolean subtaskPlanningImpl(
PlanningContext context,
Set<Rel> relsWithSubtasks,
EvaluationAlgorithm algorithm,
LinkedList<Rel> subtaskRelsInPath,
int depth) {
Set<Rel> relsWithSubtasksCopy = new LinkedHashSet<Rel>(relsWithSubtasks);
Set<Rel> relsWithSubtasksToRemove = new LinkedHashSet<Rel>();
boolean firstMLB = true;
// start building Maximal Linear Branch (MLB)
MLB:
while (!relsWithSubtasksCopy.isEmpty()) {
if (isSubtaskLoggingOn()) {
String print = p(depth) + "Starting new MLB with: ";
for (Rel rel : relsWithSubtasksCopy) {
print +=
"\n" + p(depth) + " " + rel.getParent().getFullName() + " : " + rel.getDeclaration();
}
/*
print += "\n" + p( depth ) + " All remaining rels in problem:";
for ( Rel rel : problem.getAllRels() ) {
print += "\n" + p( depth ) + " " + rel.getParentObjectName() + " : " + rel.getDeclaration();
}
print += "\n" + p( depth ) + "All found variables: ";
for ( Var var : problem.getFoundVars() ) {
print += "\n" + p( depth ) + " " + var.toString();
}
*/
logger.debug(print);
}
// if this is a first attempt to construct an MLB to solve a subtask(i.e. depth>0),
// do not invoke linear planning because it has already been done
if ((depth == 0) || !firstMLB) {
boolean solvedIntermediately = linearForwardSearch(context, algorithm, true);
// Having constructed some MLBs the (sub)problem may be solved
// and there is no need in wasting precious time planning unnecessary branches
if (solvedIntermediately
&& ( // on the top level optimize only if computing goals
(depth == 0 && !computeAll)
// otherwise (inside subtasks) always optimize
|| (depth != 0))) {
// If the problem is solved, optimize and return
if (!isOptDisabled) Optimizer.optimize(context, algorithm);
return true;
}
} else {
firstMLB = false;
}
// or children
OR:
for (Iterator<Rel> subtaskRelIterator = relsWithSubtasksCopy.iterator();
subtaskRelIterator.hasNext(); ) {
Rel subtaskRel = subtaskRelIterator.next();
if (isSubtaskLoggingOn())
logger.debug(
p(depth)
+ "OR: depth: "
+ (depth + 1)
+ " rel - "
+ subtaskRel.getParent().getFullName()
+ " : "
+ subtaskRel.getDeclaration());
if (subtaskRel.equals(subtaskRelsInPath.peekLast())
|| (!context.isRelReadyToUse(subtaskRel))
|| context.getFoundVars().containsAll(subtaskRel.getOutputs())
|| (!isSubtaskRepetitionAllowed && subtaskRelsInPath.contains(subtaskRel))) {
if (isSubtaskLoggingOn()) {
logger.debug(p(depth) + "skipped");
if (!context.isRelReadyToUse(subtaskRel)) {
logger.debug(p(depth) + "because it has unknown inputs"); // TODO print unknown
} else if (context.getFoundVars().containsAll(subtaskRel.getOutputs())) {
logger.debug(p(depth) + "because all outputs in FoundVars");
} else if (subtaskRel.equals(subtaskRelsInPath.peekLast())) {
logger.debug(p(depth) + "because it is nested in itself");
} else if (!isSubtaskRepetitionAllowed && subtaskRelsInPath.contains(subtaskRel)) {
logger.debug(
p(depth)
+ "This rel with subtasks is already in use, path: "
+ subtaskRelsInPath);
}
}
continue OR;
}
LinkedList<Rel> newPath = new LinkedList<Rel>(subtaskRelsInPath);
newPath.add(subtaskRel);
PlanningResult result = new PlanningResult(subtaskRel, true);
// this is true if all subtasks are solvable
boolean allSolved = true;
// and children
AND:
for (SubtaskRel subtask : subtaskRel.getSubtasks()) {
if (isSubtaskLoggingOn()) logger.debug(p(depth) + "AND: subtask - " + subtask);
EvaluationAlgorithm sbtAlgorithm = null;
////////////////////// INDEPENDENT SUBTASK////////////////////////////////////////
if (subtask.isIndependent()) {
if (isSubtaskLoggingOn()) logger.debug("Independent!!!");
if (subtask.isSolvable() == null) {
if (isSubtaskLoggingOn())
logger.debug("Start solving independent subtask " + subtask.getDeclaration());
// independent subtask is solved only once
Problem problemContext = subtask.getContext();
DepthFirstPlanner planner = new DepthFirstPlanner();
planner.indSubtasks = indSubtasks;
planner.nested = true;
sbtAlgorithm = planner.invokePlaning(problemContext, isOptDisabled);
PlanningContext indCntx = problemContext.getCurrentContext();
boolean solved = indCntx.getFoundVars().containsAll(indCntx.getAllGoals());
if (solved) {
subtask.setSolvable(Boolean.TRUE);
indSubtasks.put(subtask, sbtAlgorithm);
if (isSubtaskLoggingOn()) logger.debug("Solved " + subtask.getDeclaration());
} else {
subtask.setSolvable(Boolean.FALSE);
if (RuntimeProperties.isLogInfoEnabled()) {
logger.debug("Unable to solve " + subtask.getDeclaration());
}
}
allSolved &= solved;
} else if (subtask.isSolvable() == Boolean.TRUE) {
if (isSubtaskLoggingOn()) logger.debug("Already solved");
allSolved &= true;
sbtAlgorithm = indSubtasks.get(subtask);
} else {
if (isSubtaskLoggingOn()) logger.debug("Not solvable");
allSolved &= false;
}
if (isSubtaskLoggingOn()) logger.debug("End of independent subtask " + subtask);
if (!allSolved) {
continue OR;
}
assert sbtAlgorithm != null;
result.addSubtaskAlgorithm(subtask, sbtAlgorithm);
}
////////////////////// DEPENDENT SUBTASK//////////////////////////////////////
else {
// lets clone the environment
PlanningContext newContext = prepareNewContext(context, subtask);
sbtAlgorithm = new EvaluationAlgorithm();
// during linear planning, if some goals are found, they are removed from the set
// "goals"
boolean solved =
linearForwardSearch(
newContext,
sbtAlgorithm,
// do not optimize here, because the solution may require additional rels with
// subtasks
true);
if (solved) {
if (isSubtaskLoggingOn()) logger.debug(p(depth) + "SOLVED subtask: " + subtask);
if (!isOptDisabled) {
// if a subtask has been solved, optimize its algorithm
Optimizer.optimize(newContext, sbtAlgorithm);
}
result.addSubtaskAlgorithm(subtask, sbtAlgorithm);
allSolved &= solved;
continue AND;
} else if (!solved && (depth == maxDepth)) {
if (isSubtaskLoggingOn())
logger.debug(p(depth) + "NOT SOLVED and cannot go any deeper, subtask: " + subtask);
continue OR;
}
if (isSubtaskLoggingOn()) logger.debug(p(depth) + "Recursing deeper");
solved =
subtaskPlanningImpl(newContext, relsWithSubtasks, sbtAlgorithm, newPath, depth + 1);
if (isSubtaskLoggingOn()) logger.debug(p(depth) + "Back to depth " + (depth + 1));
// the linear planning has been performed at the end of MLB on the depth+1,
// if the problem was solved, there is no need to run linear planning again
if ((solved || (solved = linearForwardSearch(newContext, sbtAlgorithm, true)))
&& !isOptDisabled) {
// if solved, optimize here with full list of goals in order to get rid of
// unnecessary subtask instances and other relations
Optimizer.optimize(newContext, sbtAlgorithm);
}
if (isSubtaskLoggingOn())
logger.debug(p(depth) + (solved ? "" : "NOT") + " SOLVED subtask: " + subtask);
allSolved &= solved;
// if at least one subtask is not solvable, try another
// branch
if (!allSolved) {
continue OR;
}
result.addSubtaskAlgorithm(subtask, sbtAlgorithm);
}
} // AND
if (allSolved) {
algorithm.add(result);
Set<Var> newVars = new LinkedHashSet<Var>();
unfoldVarsToSet(subtaskRel.getOutputs(), newVars);
context.getKnownVars().addAll(newVars);
context.getFoundVars().addAll(newVars);
subtaskRelIterator.remove();
if (isSubtaskLoggingOn()) {
logger.debug(
p(depth)
+ "SOLVED ALL SUBTASKS for "
+ subtaskRel.getParent().getFullName()
+ " : "
+ subtaskRel.getDeclaration());
logger.debug(p(depth) + "Updating the problem graph and continuing building new MLB");
}
// this is used for incremental dfs
if (depth == 0) {
relsWithSubtasksToRemove.add(subtaskRel);
}
continue MLB;
}
if (isSubtaskLoggingOn())
logger.debug(
p(depth)
+ "NOT SOLVED ALL subtasks, removing from path "
+ subtaskRel.getParent().getFullName()
+ " : "
+ subtaskRel.getDeclaration());
newPath.remove(subtaskRel);
} // end OR
// exit loop because there are no more rels with subtasks to be
// applied
// (i.e. no more rels can introduce new variables into the
// algorithm)
if (isSubtaskLoggingOn()) logger.debug(p(depth) + "No more MLB can be constructed");
break MLB;
}
// incremental dfs, remove solved subtasks
if (depth == 0) {
relsWithSubtasks.removeAll(relsWithSubtasksToRemove);
}
return false;
}
/**
* Linear forward search algorithm
*
* @param p
* @param algorithm
* @param targetVars
* @param _computeAll
* @return
*/
private boolean linearForwardSearch(
PlanningContext context, EvaluationAlgorithm algorithm, boolean _computeAll) {
/*
* while iterating through hashset, items cant be removed from/added to
* that set. Theyre collected into these sets and added/removedall
* together after iteration is finished
*/
Set<Var> newVars = new LinkedHashSet<Var>();
Set<Var> relOutputs = new LinkedHashSet<Var>();
Set<Var> removableVars = new LinkedHashSet<Var>();
boolean changed = true;
if (isLinearLoggingOn())
logger.debug(
"------Starting linear planning with (sub)goals: "
+ context.getRemainingGoals()
+ "--------");
if (isLinearLoggingOn()) logger.debug("Algorithm " + algorithm);
int counter = 1;
while ((!_computeAll && changed && !context.getRemainingGoals().isEmpty())
|| (changed && _computeAll)) {
if (isLinearLoggingOn()) logger.debug("----Iteration " + counter + " ----");
counter++;
changed = false;
// iterate through all knownvars
if (isLinearLoggingOn()) logger.debug("Known:" + context.getKnownVars());
for (Var var : context.getKnownVars()) {
if (isLinearLoggingOn()) logger.debug("Current Known: " + var);
// Check the relations of all components
for (Rel rel : var.getRels()) {
if (isLinearLoggingOn()) logger.debug("And its rel: " + rel);
if (context.isAvailableRel(rel)) {
context.removeUnknownInput(rel, var);
if (isLinearLoggingOn()) logger.debug("problem contains it " + rel);
removableVars.add(var);
if (context.isRelReadyToUse(rel) && rel.getType() != RelType.TYPE_METHOD_WITH_SUBTASK) {
if (isLinearLoggingOn()) logger.debug("rel is ready to be used " + rel);
boolean relIsNeeded = false;
if (isLinearLoggingOn()) logger.debug("its outputs " + rel.getOutputs());
for (Var relVar : rel.getOutputs()) {
if (!context.getFoundVars().contains(relVar)) {
relIsNeeded = true;
}
}
if (rel.getOutputs().isEmpty()) {
relIsNeeded = true;
}
if (isLinearLoggingOn()) logger.debug("relIsNeeded " + relIsNeeded);
if (relIsNeeded) {
if (isLinearLoggingOn()) logger.debug("needed rel: " + rel);
if (!rel.getOutputs().isEmpty()) {
relOutputs.clear();
unfoldVarsToSet(rel.getOutputs(), relOutputs);
newVars.addAll(relOutputs);
context.getFoundVars().addAll(relOutputs);
}
algorithm.addRel(rel);
if (isLinearLoggingOn()) logger.debug("algorithm " + algorithm);
}
context.removeRel(rel);
changed = true;
}
}
}
}
// remove targets if they have already been found
for (Iterator<Var> targetIter = context.getRemainingGoals().iterator();
targetIter.hasNext(); ) {
Var targetVar = targetIter.next();
if (context.getFoundVars().contains(targetVar)) {
targetIter.remove();
}
}
if (isLinearLoggingOn()) logger.debug("foundvars " + context.getFoundVars());
context.getKnownVars().addAll(newVars);
context.getKnownVars().removeAll(removableVars);
newVars.clear();
}
if (isLinearLoggingOn()) logger.debug("algorithm " + algorithm);
if (!_computeAll) {
Optimizer.optimize(context, algorithm);
if (isLinearLoggingOn()) logger.debug("optimized algorithm " + algorithm);
}
if (isLinearLoggingOn()) logger.debug("\n---!!!Finished linear planning!!!---\n");
return context.getRemainingGoals().isEmpty()
|| context.getFoundVars().containsAll(context.getAllGoals());
}
/**
* Call when an expanded node has gone missing
*
* @param c The config that is gone
*/
void nodeRemoved(Config c) {
expandedNodes.remove(c);
}
@Override
public boolean isAlwaysLeaf(Object element) {
//noinspection SuspiciousMethodCalls
return myLeaves.contains(element);
}
public static void removeChangeListener(ChangeListener cl) {
if (changeListeners.contains(cl)) {
changeListeners.remove(cl);
}
}
public static void addChangeListener(ChangeListener cl) {
changeListeners.add(cl);
}
public boolean execute() {
if (CDState.getCycle() % period != 0) return false;
MycoCast mycocast = (MycoCast) Network.get(0).getProtocol(mycocastPid);
int bio = mycocast.countBiomass();
int ext = mycocast.countExtending();
int bra = mycocast.countBranching();
int imm = mycocast.countImmobile();
// Update vertices
Set<MycoNode> activeNodes = new HashSet<MycoNode>();
for (int i = 0; i < Network.size(); i++) {
MycoNode n = (MycoNode) Network.get(i);
activeNodes.add(n);
HyphaData data = n.getHyphaData();
// if (data.isBiomass()) { continue; }
if (graph.containsVertex(n)) {
graph.removeVertex(n);
}
if (!graph.containsVertex(n)) {
graph.addVertex(n);
}
}
Set<MycoNode> jungNodes = new HashSet<MycoNode>(graph.getVertices());
jungNodes.removeAll(activeNodes);
for (MycoNode n : jungNodes) {
graph.removeVertex(n);
}
// Update edges
for (int i = 0; i < Network.size(); i++) {
MycoNode n = (MycoNode) Network.get(i);
HyphaData data = n.getHyphaData();
HyphaLink link = n.getHyphaLink();
synchronized (graph) {
// We now add in all links and tune out display in Visualizer
java.util.List<MycoNode> neighbors = (java.util.List<MycoNode>) link.getNeighbors();
//// Adding only links to hypha thins out links to biomass
// (java.util.List<MycoNode>) link.getHyphae();
Collection<MycoNode> jungNeighbors = graph.getNeighbors(n);
// Remove edges from Jung graph that are not in peersim graph
for (MycoNode o : jungNeighbors) {
if (!neighbors.contains(o)) {
MycoEdge edge = graph.findEdge(n, o);
while (edge != null) {
graph.removeEdge(edge);
edge = graph.findEdge(n, o);
}
}
}
// Add missing edges to Jung graph that are in peersim graph
for (MycoNode o : neighbors) {
if (graph.findEdge(n, o) == null) {
MycoEdge edge = new MycoEdge();
graph.addEdge(edge, n, o, EdgeType.DIRECTED);
}
}
}
// log.finest("VERTICES: " + graph.getVertices());
// log.finest("EDGES: " + graph.getEdges());
}
for (ChangeListener cl : changeListeners) {
cl.stateChanged(new ChangeEvent(graph));
}
if (walking) {
try {
Thread.sleep(walkDelay);
} catch (InterruptedException e) {
}
stepBlocked = false;
}
try {
while (stepBlocked && !noBlock) {
synchronized (JungGraphObserver.class) {
JungGraphObserver.class.wait();
}
}
} catch (InterruptedException e) {
stepBlocked = true;
}
stepBlocked = true;
// System.out.println(graph.toString());
return false;
}
public void removeLeaf(NodeElement element) {
myLeaves.remove(element);
}
public void addLeaf(NodeElement element) {
myLeaves.add(element);
}
public SyntaxTab() {
super(new BorderLayout(), "Syntax highlighting");
/*
* upper checkboxes
*/
JPanel upper = new JPanel(new GridLayout(2, 1, 0, 0));
upper.setOpaque(false);
upper.add(MyPanel.wrap(highlightSyntax));
upper.add(MyPanel.wrap(matchBracket));
highlightSyntax.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent ev) {
SyntaxTab.this.updateComponentStatus();
}
});
this.add(upper, BorderLayout.PAGE_START);
/*
* upper panel (painters)
*/
painterComboBox.setSelectedItem(myjava.gui.syntax.Painter.getCurrentInstance());
painterComboBox.setFont(f13);
if (isMetal) painterComboBox.setBackground(Color.WHITE);
painterComboBox.addItemListener(this.painterChangeListener);
JButton addPainter =
new MyButton("+") {
{
if (isMetal) {
this.setPreferredSize(new Dimension(28, 28));
}
}
@Override
public void actionPerformed(ActionEvent ev) {
String name;
do {
name =
JOptionPane.showInputDialog(
SyntaxTab.this, "Enter a name:", "Name", JOptionPane.QUESTION_MESSAGE);
} while (!myjava.gui.syntax.Painter.isValidPrompt(name, SyntaxTab.this));
if ((name != null) && (!name.isEmpty())) {
// name is valid, neither cancelled nor pressed enter directly
myjava.gui.syntax.Painter newPainter =
((myjava.gui.syntax.Painter) (painterComboBox.getSelectedItem()))
.newInstance(name);
addPainter(newPainter);
System.out.println("now set, should call listener");
painterComboBox.setSelectedItem(newPainter); // auto-call ItemListener(s)
}
}
};
JButton removePainter =
new MyButton("-") {
{
if (isMetal) {
this.setPreferredSize(new Dimension(28, 28));
}
}
@Override
public void actionPerformed(ActionEvent ev) {
myjava.gui.syntax.Painter painter =
(myjava.gui.syntax.Painter) (painterComboBox.getSelectedItem());
if (painter.equals(myjava.gui.syntax.Painter.getDefaultInstance())) {
JOptionPane.showMessageDialog(
SyntaxTab.this,
"The default painter cannot be removed.",
"Error",
JOptionPane.ERROR_MESSAGE);
} else {
int option =
JOptionPane.showConfirmDialog(
SyntaxTab.this,
"Remove painter \"" + painter.getName() + "\"?",
"Confirm",
JOptionPane.YES_NO_OPTION);
if (option == JOptionPane.YES_OPTION) {
// remove "painter"
removedPainters.add(painter);
painterComboBox.removeItemListener(painterChangeListener);
painterComboBox.setSelectedItem(myjava.gui.syntax.Painter.getDefaultInstance());
painterComboBox.removeItem(painter);
for (Iterator<EntryListPanel> it = listPanelSet.iterator(); it.hasNext(); ) {
EntryListPanel panel = it.next();
if (panel.getPainter().getName().equals(painter.getName())) {
System.out.println("removing, then break");
it.remove();
centerPanel.remove(panel);
break;
}
}
painterComboBox.addItemListener(painterChangeListener);
cardLayout.show(
centerPanel, myjava.gui.syntax.Painter.getDefaultInstance().getName());
}
}
}
};
// lower part
JPanel center = new JPanel(new BorderLayout());
JLabel selectLabel = new MyLabel("Selected painter:");
center.add(
MyPanel.wrap(MyPanel.CENTER, selectLabel, painterComboBox, addPainter, removePainter),
BorderLayout.PAGE_START);
componentSet.addAll(Arrays.asList(selectLabel, addPainter, removePainter));
center.add(centerPanel, BorderLayout.CENTER);
this.add(center, BorderLayout.CENTER);
cardLayout.show(centerPanel, myjava.gui.syntax.Painter.getCurrentInstance().getName());
}
Iterator getExpandedNodes() {
return expandedNodes.iterator();
}
Config[] getCopyOfExpandedNodes() {
return (Config[]) expandedNodes.toArray(new Config[0]);
}
public void reInitRoot(Node root) {
myRoot = root;
myElement2Node.clear();
myLeaves.clear();
myElement2Node.put(root.myElement, root);
}
