/*
* public HashMap getLeafElements() { HashMap map = new HashMap(); Object[]
* elts = dataElements.values().toArray(); for (int j=0; j<elts.length; j++)
* { PDMDataElement data = (PDMDataElement) elts[j];
* map.put(data.getID(),data); } Object[] ops =
* operations.values().toArray(); for (int i=0; i<ops.length; i++){
* PDMOperation op = (PDMOperation) ops[i]; if
* (!(op.getInputElements().isEmpty())){ HashMap outs =
* op.getOutputElements(); Object[] outArray = outs.values().toArray(); for
* (int j=0; j<outArray.length; j++) { PDMDataElement d = (PDMDataElement)
* outArray[j]; map.remove(d.getID()); } } } return map; }
*/
public HashMap getLeafElements() {
HashMap result = new HashMap();
HashSet leafOps = getLeafOperations();
if (!(leafOps.isEmpty())) {
Iterator it = leafOps.iterator();
while (it.hasNext()) {
PDMOperation op = (PDMOperation) it.next();
PDMDataElement data = op.getOutputElement();
result.put(data.getID(), data);
}
} else {
Object[] elts = dataElements.values().toArray();
for (int j = 0; j < elts.length; j++) {
PDMDataElement data = (PDMDataElement) elts[j];
result.put(data.getID(), data);
}
Object[] ops = operations.values().toArray();
for (int i = 0; i < ops.length; i++) {
PDMOperation op = (PDMOperation) ops[i];
HashMap outs = op.getOutputElements();
Object[] outArray = outs.values().toArray();
for (int j = 0; j < outArray.length; j++) {
PDMDataElement d = (PDMDataElement) outArray[j];
result.remove(d.getID());
}
}
}
return result;
}
// ## operation writeChemkinSpecies(ReactionModel,SystemSnapshot)
public static String writeChemkinSpecies(
ReactionModel p_reactionModel, SystemSnapshot p_beginStatus) {
// #[ operation writeChemkinSpecies(ReactionModel,SystemSnapshot)
StringBuilder result = new StringBuilder();
result.append("SPECIES\n");
CoreEdgeReactionModel cerm = (CoreEdgeReactionModel) p_reactionModel;
// write inert gas
for (Iterator iter = p_beginStatus.getInertGas(); iter.hasNext(); ) {
String name = (String) iter.next();
result.append('\t' + name + '\n');
}
// write species
for (Iterator iter = cerm.getSpecies(); iter.hasNext(); ) {
Species spe = (Species) iter.next();
result.append('\t' + spe.getChemkinName() + '\n');
}
result.append("END\n");
return result.toString();
// #]
}
public void display(Graphics2D g, AffineTransform a_trans) {
Iterator i = createIterator();
while (i.hasNext()) {
GlyphObject object = (GlyphObject) i.next();
object.display(g, a_trans);
} // while
}
public void selectNext() {
Iterator i = new SelectionIterator(this);
if (m_actives.size() == 1) {
boolean isFound = false;
// loop the iterator in reverse order of drawing
while (i.hasNext()) {
GlyphObject object = (GlyphObject) i.next();
if (m_actives.isSelected(object)) {
isFound = true;
continue;
} // if
if (!isFound) {
continue;
} // if
m_actives.unselectAll();
m_actives.addActive(object);
return;
} // while i
} // if
i = new SelectionIterator(this);
if (i.hasNext()) {
GlyphObject object = (GlyphObject) i.next();
m_actives.unselectAll();
m_actives.addActive(object);
return;
} // if
}
private String unirMapeos(LinkedHashMap<String, String> mapa, Object[] descripciones) {
// mapa(llave,punto)
// descripciones en el mismo orden que el mapeo
String comillas = "\"";
StringBuilder builder = new StringBuilder();
Iterator<String> iterador = mapa.keySet().iterator();
int indice = 0;
while (iterador.hasNext()) {
String llave = iterador.next();
String puntaje = mapa.get(llave);
String descripcion =
descripciones[indice].toString().equals("null") ? "" : descripciones[indice].toString();
builder.append(comillas + descripcion + comillas + "," + comillas + puntaje + comillas + ",");
indice++;
}
return builder.toString();
}
// ## operation writeChemkinReactions(ReactionModel)
// 10/26/07 gmagoon: changed to take temperature as parameter (it doesn't seem like this method is
// currently used anywhere)
public static String writeChemkinReactions(
ReactionModel p_reactionModel, Temperature p_temperature) {
// #[ operation writeChemkinReactions(ReactionModel)
StringBuilder result = new StringBuilder();
result.append("REACTIONS KCAL/MOLE\n");
CoreEdgeReactionModel cerm = (CoreEdgeReactionModel) p_reactionModel;
LinkedHashSet all = cerm.getReactedReactionSet();
HashSet hs = new HashSet();
int numfor = 0;
int numrev = 0;
int numdup = 0;
int numnorev = 0;
for (Iterator iter = all.iterator(); iter.hasNext(); ) {
Reaction rxn = (Reaction) iter.next();
if (rxn.isForward()) {
result.append(
" "
+ rxn.toChemkinString(p_temperature)
+ "\n"); // 10/26/07 gmagoon: changed to avoid use of Global.temperature
// result.append(" " + rxn.toChemkinString(Global.temperature) + "\n");
}
}
result.append("END\n");
return result.toString();
// #]
}
/**
* Reload the composite nodes of the circuit, this is recursive
*
* @param g the graphics that will paint the node
* @throws CircuitLoadingException if the internal circuit can not be loaded
*/
public void reloadCompositeNodes(Graphics g) throws CircuitLoadingException {
for (iterNodes = this.nodes.iterator(); iterNodes.hasNext(); ) {
Node n = iterNodes.next();
if (n.getCategoryID() == Node.COMPOSITE) ((CompositeNode) n).reload(g);
}
}
/**
* Method filterResources filters the given resources using the given working set.
*
* @param current
* @param resources
* @return ICVSRemoteResource[]
*/
public ICVSRemoteResource[] filterResources(
IWorkingSet workingSet, ICVSRemoteResource[] resources) {
if (workingSet == null) return resources;
// get the projects associated with the working set
IAdaptable[] adaptables = workingSet.getElements();
Set projects = new HashSet();
for (int i = 0; i < adaptables.length; i++) {
IAdaptable adaptable = adaptables[i];
Object adapted = adaptable.getAdapter(IResource.class);
if (adapted != null) {
// Can this code be generalized?
IProject project = ((IResource) adapted).getProject();
projects.add(project);
}
}
List result = new ArrayList();
for (int i = 0; i < resources.length; i++) {
ICVSRemoteResource resource = resources[i];
for (Iterator iter = projects.iterator(); iter.hasNext(); ) {
IProject project = (IProject) iter.next();
if (project.getName().equals(resource.getName())) {
result.add(resource);
break;
}
}
}
return (ICVSRemoteResource[]) result.toArray(new ICVSRemoteResource[result.size()]);
}
/** A repository root has been added. Notify any listeners. */
public void rootAdded(ICVSRepositoryLocation root) {
Iterator it = listeners.iterator();
while (it.hasNext()) {
IRepositoryListener listener = (IRepositoryListener) it.next();
listener.repositoryAdded(root);
}
}
/**
* Writes the model to DOT.
*
* @param bw The writer
* @throws IOException If writing fails
*/
public void writeToDot(Writer bw) throws IOException {
// super.writeToDot(bw);
// Preamble of dot file
bw.write(
"digraph G {ranksep=\".3\"; fontsize=\"8\"; remincross=true; margin=\"0.0,0.0\"; rankdir=TB; ");
bw.write("fontname=\"Arial\"; \n");
bw.write("edge [arrowsize=\"0.5\"];\n");
bw.write("node [fontname=\"Arial\",fontsize=\"8\"];\n");
// Add the Data Element nodes
Iterator it = getVerticeList().iterator();
while (it.hasNext()) {
Object object = it.next();
if (object instanceof PDMDataElement) {
((PDMDataElement) object).writeToDot(bw, this);
}
}
// Add all edges
it = operations.values().iterator();
while (it.hasNext()) {
Object object = it.next();
if (object instanceof PDMOperation) {
((PDMOperation) object).writeToDot(bw, this);
}
}
bw.write("\n}\n");
}
public PDMState checkIfStateExists(
PDMStateSpace statespace, HashSet data, HashSet exec, HashSet failed) {
PDMState result = null;
boolean bool = false;
HashSet states = statespace.getStates();
Iterator it = states.iterator();
while (it.hasNext() && !bool) {
PDMState state2 = (PDMState) it.next();
boolean one = false;
boolean two = false;
boolean three = false;
HashSet data2 = state2.dataElements;
HashSet exec2 = state2.executedOperations;
HashSet failed2 = state2.failedOperations;
one = hashSetContainsSameDataElements(data, data2);
two = hashSetContainsSameOperations(exec, exec2);
three = hashSetContainsSameOperations(failed, failed2);
if (one && two && three) {
bool = true;
result = state2;
}
}
return result;
}
private void broadcastRepositoriesChanged(ICVSRepositoryLocation[] roots) {
if (roots.length == 0) return;
Iterator it = listeners.iterator();
while (it.hasNext()) {
IRepositoryListener listener = (IRepositoryListener) it.next();
listener.repositoriesChanged(roots);
}
}
private QueryResult gatherResultInfoForSelectQuery(
String queryString, int queryNr, boolean sorted, Document doc, String[] rows) {
Element root = doc.getRootElement();
// Get head information
Element child =
root.getChild("head", Namespace.getNamespace("http://www.w3.org/2005/sparql-results#"));
// Get result rows (<head>)
List headChildren =
child.getChildren(
"variable", Namespace.getNamespace("http://www.w3.org/2005/sparql-results#"));
Iterator it = headChildren.iterator();
ArrayList<String> headList = new ArrayList<String>();
while (it.hasNext()) {
headList.add(((Element) it.next()).getAttributeValue("name"));
}
List resultChildren =
root.getChild("results", Namespace.getNamespace("http://www.w3.org/2005/sparql-results#"))
.getChildren(
"result", Namespace.getNamespace("http://www.w3.org/2005/sparql-results#"));
int nrResults = resultChildren.size();
QueryResult queryResult = new QueryResult(queryNr, queryString, nrResults, sorted, headList);
it = resultChildren.iterator();
while (it.hasNext()) {
Element resultElement = (Element) it.next();
String result = "";
// get the row values and paste it together to one String
for (int i = 0; i < rows.length; i++) {
List bindings =
resultElement.getChildren(
"binding", Namespace.getNamespace("http://www.w3.org/2005/sparql-results#"));
String rowName = rows[i];
for (int j = 0; j < bindings.size(); j++) {
Element binding = (Element) bindings.get(j);
if (binding.getAttributeValue("name").equals(rowName))
if (result.equals(""))
result +=
rowName + ": " + ((Element) binding.getChildren().get(0)).getTextNormalize();
else
result +=
"\n"
+ rowName
+ ": "
+ ((Element) binding.getChildren().get(0)).getTextNormalize();
}
}
queryResult.addResult(result);
}
return queryResult;
}
private void addDefaultValues(Map attributes, Map mappings) {
if (mappings == null) return;
Iterator i = mappings.entrySet().iterator();
while (i.hasNext()) {
Map.Entry e = (Map.Entry) i.next();
TagMap.AttributeMapping m = (TagMap.AttributeMapping) e.getValue();
if (null != m && null != m.getDefaultValue() && null == attributes.get(m.getPropertyName()))
attributes.put(m.getPropertyName(), m.getDefaultValue());
}
}
public EdgeLayout getEdgeLayouts(String spid, String sid, String tpid, String tid) {
Iterator<EdgeLayout> ee = edges.iterator();
EdgeLayout el;
while (ee.hasNext()) {
el = ee.next();
if (el.sourceNode.equals(sid) && el.targetNode.equals(tid)) {
return el;
}
}
return null;
} // */
protected void doGet(HttpServletRequest req, HttpServletResponse res)
throws ServletException, IOException {
try {
DateFormat df = DateFormat.getDateTimeInstance();
String titleStr = "C3P0 Status - " + df.format(new Date());
DocumentBuilderFactory fact = DocumentBuilderFactory.newInstance();
DocumentBuilder db = fact.newDocumentBuilder();
Document doc = db.newDocument();
Element htmlElem = doc.createElement("html");
Element headElem = doc.createElement("head");
Element titleElem = doc.createElement("title");
titleElem.appendChild(doc.createTextNode(titleStr));
Element bodyElem = doc.createElement("body");
Element h1Elem = doc.createElement("h1");
h1Elem.appendChild(doc.createTextNode(titleStr));
Element h3Elem = doc.createElement("h3");
h3Elem.appendChild(doc.createTextNode("PooledDataSources"));
Element pdsDlElem = doc.createElement("dl");
pdsDlElem.setAttribute("class", "PooledDataSources");
for (Iterator ii = C3P0Registry.getPooledDataSources().iterator(); ii.hasNext(); ) {
PooledDataSource pds = (PooledDataSource) ii.next();
StatusReporter sr = findStatusReporter(pds, doc);
pdsDlElem.appendChild(sr.reportDtElem());
pdsDlElem.appendChild(sr.reportDdElem());
}
headElem.appendChild(titleElem);
htmlElem.appendChild(headElem);
bodyElem.appendChild(h1Elem);
bodyElem.appendChild(h3Elem);
bodyElem.appendChild(pdsDlElem);
htmlElem.appendChild(bodyElem);
res.setContentType("application/xhtml+xml");
TransformerFactory tf = TransformerFactory.newInstance();
Transformer transformer = tf.newTransformer();
Source src = new DOMSource(doc);
Result result = new StreamResult(res.getOutputStream());
transformer.transform(src, result);
} catch (IOException e) {
throw e;
} catch (Exception e) {
throw new ServletException(e);
}
}
/**
* Get the outputable nodes of the circuit
*
* @return an hashset of the outputable nodes of the circuit
*/
public HashSet<Outputable> getOutputables() {
HashSet<Outputable> outputs = new HashSet<Outputable>();
for (iterNodes = getNodesIterator(); iterNodes.hasNext(); ) {
Node n = iterNodes.next();
if (n.getCategoryID() == Node.OUTPUT) outputs.add((Outputable) n);
}
return outputs;
}
/**
* Get the inputable nodes of the circuit
*
* @return an hashset of the inputable nodes of the circuit
*/
public HashSet<Inputable> getInputables() {
HashSet<Inputable> inputs = new HashSet<Inputable>();
for (iterNodes = getNodesIterator(); iterNodes.hasNext(); ) {
Node n = iterNodes.next();
if (n.getCategoryID() == Node.INPUT) inputs.add((Inputable) n);
}
return inputs;
}
private void writeState(XMLWriter writer) {
writer.startTag(RepositoriesViewContentHandler.REPOSITORIES_VIEW_TAG, null, true);
// Write the repositories
Collection repos = Arrays.asList(getKnownRepositoryLocations());
Iterator it = repos.iterator();
while (it.hasNext()) {
CVSRepositoryLocation location = (CVSRepositoryLocation) it.next();
RepositoryRoot root = getRepositoryRootFor(location);
root.writeState(writer);
}
writer.endTag(RepositoriesViewContentHandler.REPOSITORIES_VIEW_TAG);
}
public String toString() {
StringBuffer sb = new StringBuffer();
sb.append(sourcepid + "," + sourceNode + "," + targetpid + "," + targetNode + ",");
Iterator<LayoutPoint> e = bends.iterator();
LayoutPoint b;
while (e.hasNext()) {
b = (LayoutPoint) e.next();
sb.append(b.x + "," + b.y + ",");
}
sb.append("\n");
return sb.toString();
}
/**
* Convert dom4j attributes to SAX attributes.
*
* @param element dom4j Element
* @return SAX Attributes
*/
public static Attributes getSAXAttributes(Element element) {
final AttributesImpl result = new AttributesImpl();
for (Iterator i = element.attributeIterator(); i.hasNext(); ) {
final org.dom4j.Attribute attribute = (org.dom4j.Attribute) i.next();
result.addAttribute(
attribute.getNamespaceURI(),
attribute.getName(),
attribute.getQualifiedName(),
ContentHandlerHelper.CDATA,
attribute.getValue());
}
return result;
}
public String toBeautifiedString() {
StringBuffer sb = new StringBuffer();
sb.append("sourcePID: " + sourcepid);
sb.append(" sourceNodeId: " + sourceNode + "\n");
sb.append(" targetPID: " + targetpid);
sb.append(" targetNodeId: " + targetNode + "\n");
Iterator<LayoutPoint> e = bends.iterator();
LayoutPoint b;
while (e.hasNext()) {
b = (LayoutPoint) e.next();
sb.append(" Bend Points: " + b.x + "," + b.y + " ");
}
sb.append("\n\n");
return sb.toString();
}
private void checkForRequiredAttributes(String tagName, Map attributes, Map mappings)
throws ParserException {
if (mappings == null) return;
Iterator i = mappings.entrySet().iterator();
while (i.hasNext()) {
Map.Entry e = (Map.Entry) i.next();
TagMap.AttributeMapping m = (TagMap.AttributeMapping) e.getValue();
if (null != m && m.getRequired())
if (null == mappings || null == attributes.get(m.getPropertyName()))
throw new ParserException(
"An attribute that maps to property name: "
+ m.getPropertyName()
+ " is required and was not specified for tag:"
+ tagName
+ "!");
}
}
/**
* converts this glyph into Shape. It could be called for root's preview mode or by include
* invoke. Pushing either this GlyphFile or DIncludeInvoke should be handled before this.
*/
public Shape toShape(AffineTransform a_trans) {
int ppem = k_defaultPixelSize;
GeneralPath retval = new GeneralPath();
Iterator i = createIterator();
while (i.hasNext()) {
GlyphObject object = (GlyphObject) i.next();
if (object instanceof EContourPoint || object instanceof EHint) {
continue;
} // if
retval.append(object.toShape(a_trans, ppem), false);
} // if
return retval;
}
private void nameLengthStatistics() {
Iterator i = Person.iterator();
Person p;
int l = Person.getMaxNameLength();
int lengthTable[] = new int[l + 1];
int j;
System.out.println();
// System.out.println("Name length: Number of persons");
while (i.hasNext()) {
p = (Person) i.next();
lengthTable[p.getName().length()]++;
}
for (j = 1; j <= l; j++) {
System.out.print(j + ": " + lengthTable[j] + " ");
if (j % 5 == 0) System.out.println();
}
System.out.println();
}
private static final Skeleton parseSkeleton(Node skel_node) {
Map name_to_bone_map = new HashMap();
Map initial_pose =
AnimationLoader.parseFrame(ConvertToBinary.getNodeByName("init_pose", skel_node));
NodeList bone_list = ConvertToBinary.getNodeByName("bones", skel_node).getChildNodes();
Map bone_parent_map = new HashMap();
for (int i = 0; i < bone_list.getLength(); i++) {
Node bone_node = bone_list.item(i);
if (bone_node.getNodeName().equals("bone")) {
String bone_name = bone_node.getAttributes().getNamedItem("name").getNodeValue();
String bone_parent_name = bone_node.getAttributes().getNamedItem("parent").getNodeValue();
// System.out.println("bone name = " + bone_name + " parent name = " + bone_parent_name);
bone_parent_map.put(bone_name, bone_parent_name);
}
}
Map bone_children_map = new HashMap();
Iterator it = bone_parent_map.keySet().iterator();
String root = null;
while (it.hasNext()) {
String name = (String) it.next();
String parent = (String) bone_parent_map.get(name);
if (bone_parent_map.get(parent) == null) {
if (root != null) {
System.out.println(
"WARNING: Multiple roots in skeleton, root = "
+ root
+ ", additional root = "
+ name);
parent = root;
bone_parent_map.put(name, parent);
} else root = name;
}
List parent_children = (List) bone_children_map.get(parent);
if (parent_children == null) {
parent_children = new ArrayList();
bone_children_map.put(parent, parent_children);
}
parent_children.add(name);
}
Bone bone_root = buildBone((byte) 0, bone_children_map, root, name_to_bone_map);
return new Skeleton(bone_root, initial_pose, name_to_bone_map);
}
/**
* Save the XML description of the circuit
*
* @param output an output stream to write in
* @return true if the dump was successful, false either
*/
public boolean dumpToXml(OutputStream output) {
Document doc;
Element root;
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder;
try {
builder = factory.newDocumentBuilder();
doc = builder.newDocument();
} catch (ParserConfigurationException pce) {
System.err.println("dumpToXmlFile: unable to write XML save file.");
return false;
}
root = doc.createElement("Circuit");
root.setAttribute("name", this.getName());
for (iterNodes = this.nodes.iterator(); iterNodes.hasNext(); )
iterNodes.next().dumpToXml(doc, root);
root.normalize();
doc.appendChild(root);
try {
TransformerFactory tffactory = TransformerFactory.newInstance();
Transformer transformer = tffactory.newTransformer();
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
DOMSource source = new DOMSource(doc);
StreamResult result = new StreamResult(output);
transformer.transform(source, result);
} catch (TransformerConfigurationException tce) {
System.err.println("dumpToXmlFile: Configuration Transformer exception.");
return false;
} catch (TransformerException te) {
System.err.println("dumpToXmlFile: Transformer exception.");
return false;
}
return true;
}
// convert coordinates to relative coordinates with the top-left one as (0,0)
public void convertToRelativePositions() {
LayoutBox box = getExactLayoutBox();
// System.out.println("Box
// ("+box.topleft.x+","+box.topleft.y+");("+(box.topleft.x+box.width)+","+(box.topleft.y+box.height));
Iterator<NodeLayout> e = nodes.iterator();
NodeLayout nl;
while (e.hasNext()) {
nl = e.next();
/* Debug code
if(nl.x<box.topleft.x || nl.y<box.topleft.y || nl.x>(box.topleft.x+box.width) || nl.y>(box.topleft.y+box.height)){
System.out.println("Invalid node "+nl.x+","+nl.y);
}
//*/
nl.x = nl.x - box.topleft.x;
nl.y = nl.y - box.topleft.y;
}
Iterator<EdgeLayout> e2 = edges.iterator();
EdgeLayout el;
while (e2.hasNext()) {
el = e2.next();
for (LayoutPoint lp : el.bends) {
lp.x = lp.x - box.topleft.x;
lp.y = lp.y - box.topleft.y;
}
}
}
public void flipLayoutLeftRight() {
LayoutBox box = getExactLayoutBox();
Iterator<NodeLayout> ne = nodes.iterator();
while (ne.hasNext()) {
NodeLayout nl = ne.next();
if (nl.processID.equals("null")) {
nl.x =
box.topleft.x
+ (box.width - (nl.x - box.topleft.x))
- 60; // minus 60 which is the width of process node's box, since using upperleft
// coor
} else if (isSecondary(nl)) {
nl.x = box.topleft.x + (box.width - (nl.x - box.topleft.x)) - 60;
} else {
nl.x = box.topleft.x + (box.width - (nl.x - box.topleft.x)) - 20;
}
}
Iterator<EdgeLayout> e2 = edges.iterator();
EdgeLayout el;
while (e2.hasNext()) {
el = e2.next();
for (LayoutPoint lp : el.bends) {
lp.x = box.topleft.x + (box.width - (lp.x - box.topleft.x));
}
}
}
private void publicationCountStatistics() {
Iterator i = Person.iterator();
Person p;
int l = Person.getMaxPublCount();
int countTable[] = new int[l + 1];
int j, n;
System.out.println();
System.out.println("Number of publications: Number of persons");
while (i.hasNext()) {
p = (Person) i.next();
countTable[p.getCount()]++;
}
n = 0;
for (j = 1; j <= l; j++) {
if (countTable[j] == 0) continue;
n++;
System.out.print(j + ": " + countTable[j] + " ");
if (n % 5 == 0) System.out.println();
}
System.out.println();
}
