void setTileContent(TileEntity entity, int level, boolean undo) {
if (!isFlat()) {
return;
}
if (entity instanceof Roof) {
for (TileEntity e : entities.values()) {
if (e instanceof Roof) {
return;
}
}
}
final EntityData entityData = new EntityData(level, EntityType.FLOORROOF);
if (entity != entities.get(entityData)) {
Tile oldTile = new Tile(this);
if (entity != null) {
entities.put(entityData, entity);
} else {
entities.remove(entityData);
}
if (undo) {
map.addUndo(this, oldTile);
}
}
}
void setGameObject(GameObjectData data, ObjectLocation location, int floor, boolean undo) {
Tile oldTile = new Tile(this);
if (data != null) {
entities.put(new ObjectEntityData(floor, location), new GameObject(data));
} else {
entities.remove(new ObjectEntityData(floor, location));
}
if (undo) {
map.addUndo(this, oldTile);
}
}
/*
* 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;
}
void setVerticalBorder(BorderData border, boolean undo) {
final EntityData entityData = new EntityData(0, EntityType.VBORDER);
if (border != entities.get(entityData)) {
Tile oldTile = new Tile(this);
if (border != null) {
entities.put(entityData, border);
} else {
entities.remove(entityData);
}
if (undo) {
map.addUndo(this, oldTile);
}
}
}
void setVerticalWall(WallData wall, int level, boolean undo) {
if (wall != null && wall.houseWall) {
if (!(isFlat() || map.getTile(this, -1, 0).isFlat())) {
return;
}
}
final EntityData entityData;
if (wall != null && wall.houseWall) {
entityData = new EntityData(level, EntityType.VWALL);
} else if (wall != null) {
entityData = new EntityData(level, EntityType.VFENCE);
} else {
entityData = null;
}
final EntityData wallEntity = new EntityData(level, EntityType.VWALL);
final EntityData fenceEntity = new EntityData(level, EntityType.VFENCE);
final Wall currentWall = (Wall) entities.get(wallEntity);
final Wall currentFence = (Wall) entities.get(fenceEntity);
boolean reversed;
if (wall != null && wall.houseWall) {
if (Globals.autoReverseWall) {
reversed =
getTileContent(level) == null && map.getTile(this, -1, 0).getTileContent(level) != null;
if (reversed == false) {
reversed = Globals.reverseWall;
}
} else {
reversed = Globals.reverseWall;
}
} else {
reversed = false;
}
if (!(new Wall(wall, reversed).equals(entities.get(entityData)))) {
Tile oldTile = new Tile(this);
if (wall != null) {
entities.put(entityData, new Wall(wall, reversed));
if (wall.houseWall
&& !(wall.arch && currentFence != null && currentFence.data.archBuildable)) {
entities.remove(fenceEntity);
} else if (!wall.houseWall
&& !(wall.archBuildable && currentWall != null && currentWall.data.arch)) {
entities.remove(wallEntity);
}
} else {
entities.remove(wallEntity);
entities.remove(fenceEntity);
}
if (undo) {
map.addUndo(this, oldTile);
}
}
}
public static void traverseAMLforObjectNames(
HashMap partialMap, Node currentNode, HashMap ObjDef_LinkId, HashMap ModelId_ModelType) {
if (currentNode.hasChildNodes()) {
for (int i = 0; i < currentNode.getChildNodes().getLength(); i++) {
Node currentChild = currentNode.getChildNodes().item(i);
if (currentChild.getNodeName().equals("Group")) {
traverseAMLforObjectNames(partialMap, currentChild, ObjDef_LinkId, ModelId_ModelType);
}
if (currentChild.getNodeName().equals("Model")) {
if (currentChild.hasAttributes()) {
String mid = currentChild.getAttributes().getNamedItem("Model.ID").getNodeValue();
String type = currentChild.getAttributes().getNamedItem("Model.Type").getNodeValue();
ModelId_ModelType.put(mid, type);
}
// traverseAMLforObjectNames(partialMap, currentChild,
// ObjDef_LinkId);
}
if (currentChild.getNodeName().equals("ObjDef")) {
String id = currentChild.getAttributes().getNamedItem("ObjDef.ID").getNodeValue();
NodeList currentChildren = currentChild.getChildNodes();
String ObjName = "";
for (int k = 0; k < currentChildren.getLength(); k++) {
Node Child = currentChildren.item(k);
if (!Child.getNodeName().equals("AttrDef")) {
continue;
} else if (!Child.getAttributes()
.getNamedItem("AttrDef.Type")
.getNodeValue()
.equals("AT_NAME")) {
continue;
} else if (Child.hasChildNodes()) {
for (int l = 0; l < Child.getChildNodes().getLength(); l++) {
if (!(Child.getChildNodes().item(l).getNodeName().equals("AttrValue"))) {
continue;
} else {
ObjName = getTextContent(Child.getChildNodes().item(l));
ObjName = ObjName.replaceAll("\n", "\\\\n");
break;
}
}
}
}
partialMap.put(id, ObjName);
for (int j = 0; j < currentChild.getAttributes().getLength(); j++) {
if (currentChild.getAttributes().item(j).getNodeName().equals("LinkedModels.IdRefs")) {
String links =
currentChild.getAttributes().getNamedItem("LinkedModels.IdRefs").getNodeValue();
/*
* if (links.indexOf(" ") > -1) {
* Message.add("yes, yes, yes"); links =
* links.substring(0, links.indexOf(" ")); }
*/
ObjDef_LinkId.put(id, links);
}
}
}
}
}
}
void declare(Namespace n) {
if (map.get(n.prefix) == null) {
map.put(n.prefix, n.uri);
}
// TODO I think this is analogous to the other way, but have not really thought it
// through ... should local scope
// matter more than outer scope?
if (uriToPrefix.get(n.uri) == null) {
uriToPrefix.put(n.uri, n.prefix);
}
}
/**
* Returns a HashSet with the operations that have data element 'data' as output element.
*
* @param data PDMDataElement
* @return HashSet
*/
public HashSet getOperationsWithOutputElement(PDMDataElement data) {
HashSet opso = new HashSet();
Object[] ops = operations.values().toArray();
for (int i = 0; i < ops.length; i++) {
PDMOperation op = (PDMOperation) ops[i];
HashMap outputs = op.getOutputElements();
if (outputs.containsValue(data)) {
opso.add(op);
}
}
return opso;
}
Namespace[] getNamespaces() {
Iterator i = map.keySet().iterator();
ArrayList rv = new ArrayList();
while (i.hasNext()) {
String prefix = (String) i.next();
String uri = (String) map.get(prefix);
Namespace n = Namespace.create(prefix, uri);
if (!n.isEmpty()) {
rv.add(n);
}
}
return (Namespace[]) rv.toArray(new Namespace[0]);
}
private void processFilter(Session session, Element element, HashMap additionalInformation) {
String match = getAttribute(element, SessionAttribute.FILTER_MATCH.getText());
String showAllTracks = getAttribute(element, SessionAttribute.FILTER_SHOW_ALL_TRACKS.getText());
String filterName = getAttribute(element, SessionAttribute.NAME.getText());
TrackFilter filter = new TrackFilter(filterName, null);
additionalInformation.put(SessionElement.FILTER, filter);
NodeList elements = element.getChildNodes();
process(session, elements, additionalInformation);
// Save the filter
session.setFilter(filter);
// Set filter properties
if ("all".equalsIgnoreCase(match)) {
IGV.getInstance().setFilterMatchAll(true);
} else if ("any".equalsIgnoreCase(match)) {
IGV.getInstance().setFilterMatchAll(false);
}
if ("true".equalsIgnoreCase(showAllTracks)) {
IGV.getInstance().setFilterShowAllTracks(true);
} else {
IGV.getInstance().setFilterShowAllTracks(false);
}
}
/**
* 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");
}
/**
* Returns a HashMap with the preceeding data elements of data element 'data'
*
* @param data PDMDataElement
* @return HashMap
*/
public HashMap getPrecedingElements(PDMDataElement data) {
HashMap precs = new HashMap();
Object[] ops = operations.values().toArray();
for (int i = 0; i < ops.length; i++) {
PDMOperation op = (PDMOperation) ops[i];
if (op.getOutputElements().containsValue(data)) {
HashMap ins = op.getInputElements();
Object[] inputs = ins.values().toArray();
for (int j = 0; j < inputs.length; j++) {
PDMDataElement el = (PDMDataElement) inputs[j];
precs.put(el.getID(), el);
}
}
}
return precs;
}
public void render2d(GL2 g) {
for (Entry<EntityData, TileEntity> e : entities.entrySet()) {
EntityData key = e.getKey();
TileEntity entity = e.getValue();
g.glPushMatrix();
switch (key.getType()) {
case VBORDER:
g.glRotatef(90, 0, 0, 1);
BorderData vBorder = (BorderData) entity;
if (Globals.upCamera) {
vBorder.render(g, this);
}
g.glColor3f(1, 1, 1);
break;
case HBORDER:
BorderData hBorder = (BorderData) entity;
if (Globals.upCamera) {
hBorder.render(g, this);
}
g.glColor3f(1, 1, 1);
break;
}
g.glPopMatrix();
g.glColor3f(1, 1, 1);
}
}
public Materials getMaterials(boolean withRight, boolean withTop) {
Materials materials = new Materials();
entities
.values()
.stream()
.forEach(
(entity) -> {
materials.put(entity.getMaterials());
});
if (withRight) {
for (int i = 0; i < Constants.FLOORS_LIMIT; i++) {
Wall wall = map.getTile(this, 1, 0).getVerticalWall(i);
Wall fence = map.getTile(this, 1, 0).getVerticalFence(i);
if (wall != null) {
materials.put(wall.getMaterials());
}
if (fence != null) {
materials.put(fence.getMaterials());
}
}
}
if (withTop) {
for (int i = 0; i < Constants.FLOORS_LIMIT; i++) {
Wall wall = map.getTile(this, 0, 1).getHorizontalWall(i);
Wall fence = map.getTile(this, 0, 1).getHorizontalFence(i);
if (wall != null) {
materials.put(wall.getMaterials());
}
if (fence != null) {
materials.put(fence.getMaterials());
}
}
}
return materials;
}
public Tile(Map map, Tile tile, int x, int y) {
this.map = map;
this.x = x;
this.y = y;
this.height = tile.height;
this.ground = tile.ground;
this.cave = tile.cave;
this.label = tile.label;
HashMap<EntityData, TileEntity> entities = new HashMap<>();
for (Entry<EntityData, TileEntity> entrySet : tile.entities.entrySet()) {
EntityData key = entrySet.getKey();
TileEntity value = entrySet.getValue();
entities.put(key, value.deepCopy());
}
this.entities = new HashMap(tile.entities);
}
/** extracts attachments from PDF File */
@SuppressWarnings("unchecked")
protected Map extractAttachments(PdfReader reader) throws IOException {
Map fileMap = new HashMap();
PdfDictionary catalog = reader.getCatalog();
PdfDictionary names = (PdfDictionary) PdfReader.getPdfObject(catalog.get(PdfName.NAMES));
if (names != null) {
PdfDictionary embFiles =
(PdfDictionary) PdfReader.getPdfObject(names.get(new PdfName("EmbeddedFiles")));
if (embFiles != null) {
HashMap embMap = PdfNameTree.readTree(embFiles);
for (Iterator i = embMap.values().iterator(); i.hasNext(); ) {
PdfDictionary filespec = (PdfDictionary) PdfReader.getPdfObject((PdfObject) i.next());
Object fileInfo[] = unpackFile(reader, filespec);
if (fileMap.containsKey(fileInfo[0])) {
throw new RuntimeException(DUPLICATE_FILE_NAMES);
}
fileMap.put(fileInfo[0], fileInfo[1]);
}
}
}
for (int k = 1; k <= reader.getNumberOfPages(); ++k) {
PdfArray annots = (PdfArray) PdfReader.getPdfObject(reader.getPageN(k).get(PdfName.ANNOTS));
if (annots == null) {
continue;
}
for (Iterator i = annots.getArrayList().listIterator(); i.hasNext(); ) {
PdfDictionary annot = (PdfDictionary) PdfReader.getPdfObject((PdfObject) i.next());
PdfName subType = (PdfName) PdfReader.getPdfObject(annot.get(PdfName.SUBTYPE));
if (!PdfName.FILEATTACHMENT.equals(subType)) {
continue;
}
PdfDictionary filespec = (PdfDictionary) PdfReader.getPdfObject(annot.get(PdfName.FS));
Object fileInfo[] = unpackFile(reader, filespec);
if (fileMap.containsKey(fileInfo[0])) {
throw new RuntimeException(DUPLICATE_FILE_NAMES);
}
fileMap.put(fileInfo[0], fileInfo[1]);
}
}
return fileMap;
}
public boolean addNodeLayout(String pid, String id, String c, double x, double y) {
/*if(idToNode.containsKey(pid + id)){
return false;
} */
NodeLayout newNode = new NodeLayout(pid, id, c, x, y);
nodes.add(newNode);
idToNode.put(pid + id, newNode);
return true;
}
public HashSet getLeafOperations() {
HashSet result = new HashSet();
Object[] ops = operations.values().toArray();
for (int i = 0; i < ops.length; i++) {
PDMOperation op = (PDMOperation) ops[i];
if ((op.getInputElements().isEmpty())) {
result.add(op);
}
}
return result;
}
/**
* @param inputStream
* @param session
* @param sessionName @return
* @throws RuntimeException
*/
public void loadSession(InputStream inputStream, Session session, String sessionName) {
log.debug("Load session");
Document document = null;
try {
document = Utilities.createDOMDocumentFromXmlStream(inputStream);
} catch (Exception e) {
log.error("Load session error", e);
throw new RuntimeException(e);
}
NodeList tracks = document.getElementsByTagName("Track");
hasTrackElments = tracks.getLength() > 0;
HashMap additionalInformation = new HashMap();
additionalInformation.put(INPUT_FILE_KEY, sessionName);
NodeList nodes = document.getElementsByTagName(SessionElement.GLOBAL.getText());
if (nodes == null || nodes.getLength() == 0) {
nodes = document.getElementsByTagName(SessionElement.SESSION.getText());
}
processRootNode(session, nodes.item(0), additionalInformation);
// Add tracks not explicitly allocated to panels. It is legal to define sessions with the
// Resources
// section only (no Panel or Track elements).
addLeftoverTracks(trackDictionary.values());
if (session.getGroupTracksBy() != null && session.getGroupTracksBy().length() > 0) {
igv.setGroupByAttribute(session.getGroupTracksBy());
}
if (session.isRemoveEmptyPanels()) {
igv.getMainPanel().removeEmptyDataPanels();
}
igv.resetOverlayTracks();
}
/**
* Retrieves default values from xml.
*
* @param list the configuration list
*/
private static void parseDefaults(NodeList list) {
for (int i = 0; i < list.getLength(); ++i) {
NamedNodeMap mapping = list.item(i).getAttributes();
String attribute = mapping.getNamedItem("attribute").getNodeValue();
String value = mapping.getNamedItem("value").getNodeValue();
try {
Default field = Default.fromString(attribute);
DEFAULTS.put(field, value);
} catch (IllegalArgumentException exc) {
logger.warn("Unrecognized default attribute: " + attribute);
}
}
}
/**
* Export to PDM file.
*
* @param bw Writer
* @throws IOException If writing fails
*/
public void writeToPDM(Writer bw) throws IOException {
bw.write("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
bw.write("<PDM\n");
bw.write("\txmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"\n");
bw.write(
"\txsi:noNamespaceSchemaLocation=\"C:/Documents and Settings/ivdfeest/My Documents/Implementatie/PDM.xsd\"\n");
bw.write(">\n");
Iterator it = dataElements.values().iterator();
while (it.hasNext()) {
PDMDataElement dataElement = (PDMDataElement) it.next();
dataElement.writeToPDM(bw);
}
Iterator it2 = resources.values().iterator();
while (it2.hasNext()) {
PDMResource resource = (PDMResource) it.next();
resource.writeToPDM(bw);
}
Iterator it3 = operations.values().iterator();
while (it3.hasNext()) {
PDMOperation operation = (PDMOperation) it.next();
operation.writeToPDM(bw);
}
bw.write("</PDM>\n");
}
/**
* TDTEngine - constructor for a new Tag Data Translation engine
*
* @param confdir the string value of the path to a configuration directory consisting of two
* subdirectories, <code>schemes</code> and <code>auxiliary</code>.
* <p>When the class TDTEngine is constructed, the path to a local directory must be
* specified, by passing it as a single string parameter to the constructor method (without
* any trailing slash or file separator). e.g. <code>
* <pre>TDTEngine engine = new TDTEngine("/opt/TDT");</pre></code>
* <p>The specified directory must contain two subdirectories named auxiliary and schemes. The
* Tag Data Translation definition files for the various coding schemes should be located
* inside the subdirectory called <code>schemes</code>. Any auxiliary lookup files (such as
* <code>ManagerTranslation.xml</code>) should be located inside the subdirectory called
* <code>auxiliary</code>.
* <p>Files within the schemes directory ending in <code>.xml</code> are read in and
* unmarshalled using <a href = "http://www.castor.org">Castor</a>.
*/
public TDTEngine(String confdir)
throws FileNotFoundException, MarshalException, ValidationException, TDTException {
xmldir = confdir;
long t = System.currentTimeMillis();
File[] dir =
new java.io.File(confdir + File.separator + "schemes").listFiles(new XMLFilenameFilter());
// java.util.Arrays.sort(dir); // Sort it
if (dir == null) throw new TDTException("Cannot find schemes in " + confdir);
Unmarshaller unmar = new Unmarshaller();
for (File f : dir) {
EpcTagDataTranslation tdt =
(EpcTagDataTranslation) unmar.unmarshal(EpcTagDataTranslation.class, new FileReader(f));
initFromTDT(tdt);
}
// need to populate the hashmap gs1cpi from the ManagerTranslation.xml table in auxiliary.
// Unmarshaller unmar = new Unmarshaller();
GEPC64Table cpilookup =
(GEPC64Table)
unmar.unmarshal(
GEPC64Table.class,
new FileReader(
confdir
+ File.separator
+ "auxiliary"
+ File.separator
+ "ManagerTranslation.xml"));
for (Enumeration e = cpilookup.enumerateEntry(); e.hasMoreElements(); ) {
Entry entry = (Entry) e.nextElement();
String comp = entry.getCompanyPrefix();
String indx = Integer.toString(entry.getIndex());
gs1cpi.put(indx, comp);
gs1cpi.put(comp, indx);
}
// System.out.println("Loaded schemas in " +
// (System.currentTimeMillis() - t)
// + " millisecs");
}
private void processFilterElement(
Session session, Element element, HashMap additionalInformation) {
TrackFilter filter = (TrackFilter) additionalInformation.get(SessionElement.FILTER);
String item = getAttribute(element, SessionAttribute.ITEM.getText());
String operator = getAttribute(element, SessionAttribute.OPERATOR.getText());
String value = getAttribute(element, SessionAttribute.VALUE.getText());
String booleanOperator = getAttribute(element, SessionAttribute.BOOLEAN_OPERATOR.getText());
TrackFilterElement trackFilterElement =
new TrackFilterElement(
filter,
item,
Operator.findEnum(operator),
value,
BooleanOperator.findEnum(booleanOperator));
filter.add(trackFilterElement);
NodeList elements = element.getChildNodes();
process(session, elements, additionalInformation);
}
public static MiningResult importFile(InputStream input) throws IOException {
try {
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
Document doc;
// NodeList netNodes;
dbf.setValidating(false);
dbf.setIgnoringComments(true);
dbf.setIgnoringElementContentWhitespace(true);
// dbf.setExpandEntityReferences(false);
// dbf.setNamespaceAware(false);
DocumentBuilder db = dbf.newDocumentBuilder();
db.setEntityResolver(
new EntityResolver() {
public InputSource resolveEntity(String publicId, String systemId) {
if (systemId.indexOf("ARIS-Export") != -1) {
return new InputSource("file:" + About.EXTLIBLOCATION() + "ARIS-Export101.dtd");
} else {
return null;
}
}
});
InputSource inpStream = new InputSource(input);
inpStream.setSystemId("file:" + System.getProperty("user.dir", ""));
doc = db.parse(inpStream);
// check if root element is a aml tag
Message.add("parsing done" + doc, Message.DEBUG);
if (!(doc.getDocumentElement().getNodeName().equals("AML"))) {
Message.add("aml tag not found", Message.ERROR);
throw new Exception("aml tag not found");
} else {
Message.add("aml root element found");
}
EPCResult result = new EPCResult(null, (EPC) null);
HashMap ObjDef_LinkId = new HashMap();
HashMap modelid_net = new HashMap();
HashMap ObjDef_Name = new HashMap();
HashMap function_LinkId = new HashMap();
HashMap ModelId_ModelType = new HashMap();
traverseAMLforObjectNames(
ObjDef_Name, doc.getDocumentElement(), ObjDef_LinkId, ModelId_ModelType);
Iterator findLinkToEpc = ObjDef_LinkId.keySet().iterator();
while (findLinkToEpc.hasNext()) {
String currentObjDef = (String) findLinkToEpc.next();
String Links = (String) ObjDef_LinkId.get(currentObjDef);
StringTokenizer linkSet = new StringTokenizer(Links);
String realEpcLink = "";
while (linkSet.hasMoreTokens()) {
String currentLink = linkSet.nextToken();
if (ModelId_ModelType.get(currentLink).equals("MT_EEPC")) {
realEpcLink = currentLink;
break;
}
}
if (realEpcLink.equals(" ")) {
ObjDef_LinkId.remove(currentObjDef);
} else {
ObjDef_LinkId.put(currentObjDef, realEpcLink);
}
}
result =
traverseAML(
result,
doc.getDocumentElement(),
null,
ObjDef_Name,
ObjDef_LinkId,
modelid_net,
function_LinkId);
Iterator hierarchicalFunctions = function_LinkId.keySet().iterator();
while (hierarchicalFunctions.hasNext()) {
EPCSubstFunction f = (EPCSubstFunction) hierarchicalFunctions.next();
f.setSubstitutedEPC((EPC) modelid_net.get(function_LinkId.get(f)));
// Message.add(f.getSubstitutedEPC().getName());
}
return result;
} catch (Throwable x) {
Message.add(x.toString());
throw new IOException(x.getMessage());
}
}
public static PetriNet convert(ConfigurableEPC baseEPC) {
HashMap<EPCFunction, Transition> functionActivityMapping;
HashMap<EPCConnector, Place> xorconnectorChoiceMapping;
// HV: Initialize the mappings.
functionActivityMapping = new HashMap<EPCFunction, Transition>();
xorconnectorChoiceMapping = new HashMap<EPCConnector, Place>();
// Check to use the weights if necessary
// HV: Add both mappings. On completion, these will be filledd.
PetriNet petrinet =
EPCToPetriNetConverter.convert(
baseEPC, new HashMap(), functionActivityMapping, xorconnectorChoiceMapping);
HashSet visible = new HashSet();
// HV: The next block is taken care of by the functionActivityMapping
// below.
/*
* Iterator it = petrinet.getTransitions().iterator(); while
* (it.hasNext()) { Transition t = (Transition) it.next(); if (t.object
* instanceof EPCFunction) { // if (t.getLogEvent() != null) { // Add
* transitions with LogEvent (i.e. referring to functions)
* visible.add(t); } }
*/
// HV: Prevent the places mapped onto from being reduced.
visible.addAll(functionActivityMapping.values());
visible.addAll(xorconnectorChoiceMapping.values());
Message.add(visible.toString(), Message.DEBUG);
Iterator it = petrinet.getPlaces().iterator();
while (it.hasNext()) {
Place p = (Place) it.next();
if (p.inDegree() * p.outDegree() == 0) {
// Add Initial and final places to visible, i.e. places that
// refer to in and output events
visible.add(p);
}
}
// Reduce the PetriNet with Murata rules, while keeping the visible ones
PetriNetReduction pnred = new PetriNetReduction();
pnred.setNonReducableNodes(visible);
HashMap pnMap = new HashMap(); // Used to map pre-reduction nodes to
// post-reduction nodes.
PetriNet reduced = pnred.reduce(petrinet, pnMap);
if (reduced != petrinet) {
// Update both mappings from pre-reduction nodes to post-reduction
// nodes.
HashMap<EPCFunction, Transition> newFunctionActivityMapping =
new HashMap<EPCFunction, Transition>();
for (EPCFunction function : functionActivityMapping.keySet()) {
Transition transition = (Transition) functionActivityMapping.get(function);
if (pnMap.keySet().contains(transition)) {
newFunctionActivityMapping.put(function, (Transition) pnMap.get(transition));
}
}
functionActivityMapping = newFunctionActivityMapping;
HashMap<EPCConnector, Place> newXorconnectorChoiceMapping =
new HashMap<EPCConnector, Place>();
for (EPCConnector connector : xorconnectorChoiceMapping.keySet()) {
Place place = (Place) xorconnectorChoiceMapping.get(connector);
if (pnMap.keySet().contains(place)) {
newXorconnectorChoiceMapping.put(connector, (Place) pnMap.get(place));
}
}
xorconnectorChoiceMapping = newXorconnectorChoiceMapping;
}
reduced.makeClusters();
// filter the \nunknown:normal
ArrayList<Transition> alTrans = reduced.getVisibleTasks();
for (int i = 0; i < alTrans.size(); i++) {
Transition t = alTrans.get(i);
String id = t.getIdentifier();
int idx = id.indexOf("\\nunknown:normal");
if (idx > 0) {
id = id.substring(0, idx);
}
// �˴������ֵ��ѯ�滻���е�label
String mappedId = htDict.get(id);
if (mappedId != null) {
t.setIdentifier(mappedId);
} else {
t.setIdentifier(id);
}
}
return reduced;
}
private static void parseNet(
Node node,
EPC net,
HashMap ObjDef_Name,
HashMap ObjDef_LinkId,
HashMap function_LinkId,
String ModelName)
throws Exception {
HashMap mapping = new HashMap();
// read all nodes
NodeList nodes = node.getChildNodes();
net.setIdentifier(ModelName);
// Message.add("here I am still happy");
for (int i = 0; i < nodes.getLength(); i++) {
Node n = nodes.item(i);
if (!n.getNodeName().equals("ObjOcc")) {
continue;
}
if (n.getAttributes().getNamedItem("SymbolNum") == null) {
continue;
}
String symbolnum = n.getAttributes().getNamedItem("SymbolNum").getNodeValue();
if (!(symbolnum.equals("ST_FUNC")
|| symbolnum.equals("ST_EV")
|| symbolnum.equals("ST_OPR_AND_1")
|| symbolnum.equals("ST_OPR_OR_1")
|| symbolnum.equals("ST_OPR_XOR_1"))) {
continue;
}
String ObjDef = n.getAttributes().getNamedItem("ObjDef.IdRef").getNodeValue();
String ownName = (String) ObjDef_Name.get(ObjDef);
// Message.add("YES " +
// n.getAttributes().getNamedItem("ObjOcc.ID").getNodeValue());
String id = n.getAttributes().getNamedItem("ObjOcc.ID").getNodeValue();
// Message.add(id + " " + ownName);
if (ownName == null || ownName == "") {
ownName = id.substring(7, 11);
}
if (symbolnum.equals("ST_FUNC")) {
if (ObjDef_LinkId.containsKey(ObjDef)) {
EPCSubstFunction sf =
(EPCSubstFunction)
net.addFunction(
new EPCSubstFunction(new LogEvent(ownName, "unknown:normal"), net, null));
sf.setIdentifier(ownName);
mapping.put(id, sf);
function_LinkId.put(sf, ObjDef_LinkId.get(ObjDef));
} else {
EPCFunction f =
net.addFunction(new EPCFunction(new LogEvent(ownName, "unknown:normal"), net));
f.setIdentifier(ownName);
mapping.put(id, f);
}
} else if (symbolnum.equals("ST_EV")) {
EPCEvent e = net.addEvent(new EPCEvent(ownName, net));
e.setIdentifier(ownName);
mapping.put(id, e);
} else if (symbolnum.equals("ST_OPR_AND_1")) {
EPCConnector c = net.addConnector(new EPCConnector(EPCConnector.AND, net));
mapping.put(id, c);
} else if (symbolnum.equals("ST_OPR_OR_1")) {
// EPCConnector c = net.addConnector(new
// EPCConnector(EPCConnector.OR, net));
EPCConnector c = net.addConnector(new EPCConnector(EPCConnector.AND, net));
mapping.put(id, c);
} else if (symbolnum.equals("ST_OPR_XOR_1")) {
EPCConnector c = net.addConnector(new EPCConnector(EPCConnector.XOR, net));
mapping.put(id, c);
}
}
for (int i = 0; i < nodes.getLength(); i++) {
Node n = nodes.item(i);
if (!n.getNodeName().equals("ObjOcc")) {
continue;
}
if (n.getAttributes().getNamedItem("SymbolNum") == null) {
continue;
}
String symbolnum = n.getAttributes().getNamedItem("SymbolNum").getNodeValue();
if (!(symbolnum.equals("ST_FUNC")
|| symbolnum.equals("ST_EV")
|| symbolnum.equals("ST_OPR_AND_1")
|| symbolnum.equals("ST_OPR_OR_1")
|| symbolnum.equals("ST_OPR_XOR_1"))) {
continue;
}
String source = n.getAttributes().getNamedItem("ObjOcc.ID").getNodeValue();
if (n.hasChildNodes()) {
for (int j = 0; j < n.getChildNodes().getLength(); j++) {
if (n.getChildNodes().item(j).getNodeName().equals("CxnOcc")) {
Node CxnOcc = n.getChildNodes().item(j);
String dest = CxnOcc.getAttributes().getNamedItem("ToObjOcc.IdRef").getNodeValue();
if (mapping.get(dest) == null) {
continue;
}
if (net.addEdge((EPCObject) mapping.get(source), (EPCObject) mapping.get(dest))
== null) {
throw (new Exception(
"<html>Structural properties of EPCs are violated in input file.<br>"
+ "The following edge could not be added:<br><br>"
+ mapping.get(source).toString()
+ " ==> "
+ mapping.get(dest).toString()
+ "<br><br>Import aborted.</html>"));
}
}
}
}
}
}
public static EPCResult traverseAML(
EPCResult partialResult,
Node currentNode,
Object parent,
HashMap ObjDef_Name,
HashMap ObjDef_LinkId,
HashMap modelid_net,
HashMap function_LinkId)
throws Exception {
if (currentNode.hasChildNodes()) {
for (int i = 0; i < currentNode.getChildNodes().getLength(); i++) {
Node currentChild = currentNode.getChildNodes().item(i);
if (currentChild.getNodeName().equals("Group")) {
String id = currentChild.getAttributes().getNamedItem("Group.ID").getNodeValue();
String GroupName = "";
if (currentChild.hasChildNodes()) {
NodeList currentChildren = currentChild.getChildNodes();
for (int j = 0; j < currentChildren.getLength(); j++) {
Node Child = currentChildren.item(j);
if (!(Child.getNodeName().equals("AttrDef"))) {
continue;
}
if (Child.getAttributes()
.getNamedItem("AttrDef.Type")
.getNodeValue()
.equals("AT_NAME")) {
if (Child.hasChildNodes()) {
for (int l = 0; l < Child.getChildNodes().getLength(); l++) {
if (!(Child.getChildNodes().item(l).getNodeName().equals("AttrValue"))) {
continue;
} else {
GroupName = getTextContent(Child.getChildNodes().item(l));
}
}
break;
}
}
}
if (GroupName.equals("")) {
GroupName = id;
}
}
ModelHierarchyDirectory dir = new ModelHierarchyDirectory(id, GroupName);
partialResult.addInHierarchy(dir, parent, GroupName);
partialResult =
traverseAML(
partialResult,
currentChild,
dir,
ObjDef_Name,
ObjDef_LinkId,
modelid_net,
function_LinkId);
}
if (currentChild.getNodeName().equals("Model")
&& currentChild
.getAttributes()
.getNamedItem("Model.Type")
.getNodeValue()
.equals("MT_EEPC")) {
String ModelName = "gaga";
if (currentChild.hasChildNodes()) {
NodeList currentChildren = currentChild.getChildNodes();
for (int j = 0; j < currentChildren.getLength(); j++) {
Node Child = currentChildren.item(j);
if (!(Child.getNodeName().equals("AttrDef"))) {
continue;
}
if (Child.getAttributes()
.getNamedItem("AttrDef.Type")
.getNodeValue()
.equals("AT_NAME")) {
if (Child.hasChildNodes()) {
for (int l = 0; l < Child.getChildNodes().getLength(); l++) {
if (!(Child.getChildNodes().item(l).getNodeName().equals("AttrValue"))) {
continue;
} else {
ModelName = getTextContent(Child.getChildNodes().item(l));
}
}
}
break;
}
}
}
try {
ModelName = ModelName.replaceAll("\n", " ");
EPC net = read(currentChild, ObjDef_Name, ObjDef_LinkId, function_LinkId, ModelName);
partialResult.addInHierarchy(net, parent, ModelName);
modelid_net.put(
currentChild.getAttributes().getNamedItem("Model.ID").getNodeValue(), net);
} catch (Throwable x) {
Message.add(x.getClass().getName());
// throw new IOException(x.getMessage());
}
}
}
}
return partialResult;
}
/**
* Process a track element. This should return a single track, but could return multiple tracks
* since the uniqueness of the track id is not enforced.
*
* @param session
* @param element
* @param additionalInformation
* @return
*/
private List<Track> processTrack(
Session session, Element element, HashMap additionalInformation) {
String id = getAttribute(element, SessionAttribute.ID.getText());
// TODo -- put in utility method, extacts attributes from element **Definitely need to do this
HashMap<String, String> tAttributes = new HashMap();
HashMap<String, String> drAttributes = null;
NamedNodeMap tNodeMap = element.getAttributes();
for (int i = 0; i < tNodeMap.getLength(); i++) {
Node node = tNodeMap.item(i);
String value = node.getNodeValue();
if (value != null && value.length() > 0) {
tAttributes.put(node.getNodeName(), value);
}
}
if (element.hasChildNodes()) {
drAttributes = new HashMap();
Node childNode = element.getFirstChild();
Node sibNode = childNode.getNextSibling();
String sibName = sibNode.getNodeName();
if (sibName.equals(SessionElement.DATA_RANGE.getText())) {
NamedNodeMap drNodeMap = sibNode.getAttributes();
for (int i = 0; i < drNodeMap.getLength(); i++) {
Node node = drNodeMap.item(i);
String value = node.getNodeValue();
if (value != null && value.length() > 0) {
drAttributes.put(node.getNodeName(), value);
}
}
}
}
// Get matching tracks.
List<Track> matchedTracks = trackDictionary.get(id);
if (matchedTracks == null) {
log.info("Warning. No tracks were found with id: " + id + " in session file");
} else {
for (final Track track : matchedTracks) {
// Special case for sequence & gene tracks, they need to be removed before being placed.
if (version >= 4 && track == geneTrack || track == seqTrack) {
igv.removeTracks(Arrays.asList(track));
}
track.restorePersistentState(tAttributes);
if (drAttributes != null) {
DataRange dr = track.getDataRange();
dr.restorePersistentState(drAttributes);
track.setDataRange(dr);
}
}
trackDictionary.remove(id);
}
NodeList elements = element.getChildNodes();
process(session, elements, additionalInformation);
return matchedTracks;
}
Namespace getNamespaceByUri(String uri) {
if (uriToPrefix.get(uri) == null) return null;
return Namespace.create(uri, (String) uriToPrefix.get(uri));
}
Namespace getNamespace(String prefix) {
if (map.get(prefix) == null) return null;
return Namespace.create(prefix, (String) map.get(prefix));
}