List of usage examples for org.dom4j Node valueOf
String valueOf(String xpathExpression);
valueOf evaluates an XPath expression and returns the textual representation of the results the XPath string-value of this node.
From source file:net.bpfurtado.tas.runner.savegame.SaveGamePersister.java
License:Open Source License
public static SaveGame read(File saveGameFile) { try {//from ww w. j a v a2s . c o m SAXReader xmlReader = new SAXReader(); Document xml = xmlReader.read(saveGameFile); Element root = xml.getRootElement(); Node xmlPlayer = root.selectSingleNode("player"); Player player = new Player("noName", 0, integer(xmlPlayer, "stamina")); player.setDamage(integer(xmlPlayer, "damage")); List<Node> skills = xmlPlayer.selectNodes("skills/skill"); for (Node skill : skills) { player.addSkill(skill.valueOf("@name"), integer(skill, "level")); } List<Node> attributes = xmlPlayer.selectNodes("attributes/attribute"); for (Node attribute : attributes) { String key = attribute.valueOf("@key"); String val = attribute.valueOf("@value"); try { player.addAttribute(key, Integer.parseInt(val)); } catch (NumberFormatException e) { player.addAttribute(key, val); } } Workspace workspace = Workspace.loadFrom(root.valueOf("@workspaceId")); SaveGame saveGame = new SaveGame(workspace, player, integer(root, "sceneId"), root.valueOf("@creation")); saveGame.setFile(saveGameFile); return saveGame; } catch (DocumentException e) { throw new AdventureReaderException("Error reading XML document", e); } }
From source file:net.bpfurtado.tas.runner.savegame.SaveGamePersister.java
License:Open Source License
public static int integer(Node node, String attribute) { return Integer.parseInt(node.valueOf("@" + attribute)); }
From source file:net.form105.rm.server.ant.container.InboundConfiguration.java
License:Apache License
public void readXml(Node xmlNode) { List<Node> nodes; XPath xPath;/*from ww w. ja va 2 s . c o m*/ inboundType = xmlNode.valueOf("@type"); xPath = DocumentHelper.createXPath("//inbound/parameters/parameter"); nodes = (List<Node>) xPath.selectNodes(xmlNode); for (Node node : nodes) { logger.info(node); paramMap.addParameter(new ConfigParameter(node.valueOf("@key"), node.valueOf("@value"))); } xPath = DocumentHelper.createXPath("//inbound/validators/validator"); nodes = (List<Node>) xPath.selectNodes(xmlNode); for (Node node : nodes) { IInboundValidator validator = (IInboundValidator) Agent.getComponentById(node.getText()); validatorList.add(validator); } xPath = DocumentHelper.createXPath("//inbound/listeners/listener"); nodes = (List<Node>) xPath.selectNodes(xmlNode); for (Node node : nodes) { IInboundListener inboundListener = (IInboundListener) Agent.getComponentById(node.getText()); listenerList.add(inboundListener); } xPath = DocumentHelper.createXPath("//inbound/executor"); logger.info(xPath.selectSingleNode(xmlNode).getText()); command = (AbstractCallbackCommand) Agent.getComponentById(xPath.selectSingleNode(xmlNode).getText()); }
From source file:nl.architolk.ldt.processors.HttpClientProcessor.java
License:Open Source License
public void generateData(PipelineContext context, ContentHandler contentHandler) throws SAXException { try {//from www. j av a 2 s.co m CloseableHttpClient httpclient = HttpClientProperties.createHttpClient(); try { // Read content of config pipe Document configDocument = readInputAsDOM4J(context, INPUT_CONFIG); Node configNode = configDocument.selectSingleNode("//config"); URL theURL = new URL(configNode.valueOf("url")); if (configNode.valueOf("auth-method").equals("basic")) { HttpHost targetHost = new HttpHost(theURL.getHost(), theURL.getPort(), theURL.getProtocol()); //Authentication support CredentialsProvider credsProvider = new BasicCredentialsProvider(); credsProvider.setCredentials(AuthScope.ANY, new UsernamePasswordCredentials( configNode.valueOf("username"), configNode.valueOf("password"))); // logger.info("Credentials: "+configNode.valueOf("username")+"/"+configNode.valueOf("password")); // Create AuthCache instance AuthCache authCache = new BasicAuthCache(); authCache.put(targetHost, new BasicScheme()); // Add AuthCache to the execution context httpContext = HttpClientContext.create(); httpContext.setCredentialsProvider(credsProvider); httpContext.setAuthCache(authCache); } else if (configNode.valueOf("auth-method").equals("form")) { //Sign in. Cookie will be remembered bij httpclient HttpPost authpost = new HttpPost(configNode.valueOf("auth-url")); List<NameValuePair> nameValuePairs = new ArrayList<NameValuePair>(); nameValuePairs.add(new BasicNameValuePair("userName", configNode.valueOf("username"))); nameValuePairs.add(new BasicNameValuePair("password", configNode.valueOf("password"))); authpost.setEntity(new UrlEncodedFormEntity(nameValuePairs)); CloseableHttpResponse httpResponse = httpclient.execute(authpost); // logger.info("Signin response:"+Integer.toString(httpResponse.getStatusLine().getStatusCode())); } CloseableHttpResponse response; if (configNode.valueOf("method").equals("post")) { // POST HttpPost httpRequest = new HttpPost(configNode.valueOf("url")); setBody(httpRequest, context, configNode); response = executeRequest(httpRequest, httpclient); } else if (configNode.valueOf("method").equals("put")) { // PUT HttpPut httpRequest = new HttpPut(configNode.valueOf("url")); setBody(httpRequest, context, configNode); response = executeRequest(httpRequest, httpclient); } else if (configNode.valueOf("method").equals("delete")) { //DELETE HttpDelete httpRequest = new HttpDelete(configNode.valueOf("url")); response = executeRequest(httpRequest, httpclient); } else if (configNode.valueOf("method").equals("head")) { //HEAD HttpHead httpRequest = new HttpHead(configNode.valueOf("url")); response = executeRequest(httpRequest, httpclient); } else if (configNode.valueOf("method").equals("options")) { //OPTIONS HttpOptions httpRequest = new HttpOptions(configNode.valueOf("url")); response = executeRequest(httpRequest, httpclient); } else { //Default = GET HttpGet httpRequest = new HttpGet(configNode.valueOf("url")); String acceptHeader = configNode.valueOf("accept"); if (!acceptHeader.isEmpty()) { httpRequest.addHeader("accept", configNode.valueOf("accept")); } //Add proxy route if needed HttpClientProperties.setProxy(httpRequest, theURL.getHost()); response = executeRequest(httpRequest, httpclient); } try { contentHandler.startDocument(); int status = response.getStatusLine().getStatusCode(); AttributesImpl statusAttr = new AttributesImpl(); statusAttr.addAttribute("", "status", "status", "CDATA", Integer.toString(status)); contentHandler.startElement("", "response", "response", statusAttr); if (status >= 200 && status < 300) { HttpEntity entity = response.getEntity(); Header contentType = response.getFirstHeader("Content-Type"); if (entity != null && contentType != null) { //logger.info("Contenttype: " + contentType.getValue()); //Read content into inputstream InputStream inStream = entity.getContent(); // output-type = json means: response is json, convert to xml if (configNode.valueOf("output-type").equals("json")) { //TODO: net.sf.json.JSONObject might nog be the correct JSONObject. javax.json.JsonObject might be better!!! //javax.json contains readers to read from an inputstream StringWriter writer = new StringWriter(); IOUtils.copy(inStream, writer, "UTF-8"); JSONObject json = JSONObject.fromObject(writer.toString()); parseJSONObject(contentHandler, json); // output-type = xml means: response is xml, keep it } else if (configNode.valueOf("output-type").equals("xml")) { try { XMLReader saxParser = XMLParsing .newXMLReader(new XMLParsing.ParserConfiguration(false, false, false)); saxParser.setContentHandler(new ParseHandler(contentHandler)); saxParser.parse(new InputSource(inStream)); } catch (Exception e) { throw new OXFException(e); } // output-type = jsonld means: reponse is json-ld, (a) convert to nquads; (b) convert to xml } else if (configNode.valueOf("output-type").equals("jsonld")) { try { Object jsonObject = JsonUtils.fromInputStream(inStream, "UTF-8"); //TODO: UTF-8 should be read from response! Object nquads = JsonLdProcessor.toRDF(jsonObject, new NQuadTripleCallback()); Any23 runner = new Any23(); DocumentSource source = new StringDocumentSource((String) nquads, configNode.valueOf("url")); ByteArrayOutputStream out = new ByteArrayOutputStream(); TripleHandler handler = new RDFXMLWriter(out); try { runner.extract(source, handler); } finally { handler.close(); } ByteArrayInputStream inJsonStream = new ByteArrayInputStream(out.toByteArray()); XMLReader saxParser = XMLParsing .newXMLReader(new XMLParsing.ParserConfiguration(false, false, false)); saxParser.setContentHandler(new ParseHandler(contentHandler)); saxParser.parse(new InputSource(inJsonStream)); } catch (Exception e) { throw new OXFException(e); } // output-type = rdf means: response is some kind of rdf (except json-ld...), convert to xml } else if (configNode.valueOf("output-type").equals("rdf")) { try { Any23 runner = new Any23(); DocumentSource source; //If contentType = text/html than convert from html to xhtml to handle non-xml style html! logger.info("Contenttype: " + contentType.getValue()); if (configNode.valueOf("tidy").equals("yes") && contentType.getValue().startsWith("text/html")) { org.jsoup.nodes.Document doc = Jsoup.parse(inStream, "UTF-8", configNode.valueOf("url")); //TODO UTF-8 should be read from response! RDFCleaner cleaner = new RDFCleaner(); org.jsoup.nodes.Document cleandoc = cleaner.clean(doc); cleandoc.outputSettings().escapeMode(Entities.EscapeMode.xhtml); cleandoc.outputSettings() .syntax(org.jsoup.nodes.Document.OutputSettings.Syntax.xml); cleandoc.outputSettings().charset("UTF-8"); source = new StringDocumentSource(cleandoc.html(), configNode.valueOf("url"), contentType.getValue()); } else { source = new ByteArrayDocumentSource(inStream, configNode.valueOf("url"), contentType.getValue()); } ByteArrayOutputStream out = new ByteArrayOutputStream(); TripleHandler handler = new RDFXMLWriter(out); try { runner.extract(source, handler); } finally { handler.close(); } ByteArrayInputStream inAnyStream = new ByteArrayInputStream(out.toByteArray()); XMLReader saxParser = XMLParsing .newXMLReader(new XMLParsing.ParserConfiguration(false, false, false)); saxParser.setContentHandler(new ParseHandler(contentHandler)); saxParser.parse(new InputSource(inAnyStream)); } catch (Exception e) { throw new OXFException(e); } } else { CharArrayWriter writer = new CharArrayWriter(); IOUtils.copy(inStream, writer, "UTF-8"); contentHandler.characters(writer.toCharArray(), 0, writer.size()); } } } contentHandler.endElement("", "response", "response"); contentHandler.endDocument(); } finally { response.close(); } } finally { httpclient.close(); } } catch (Exception e) { throw new OXFException(e); } }
From source file:nl.architolk.ldt.processors.HttpClientProcessor.java
License:Open Source License
private void setBody(HttpEntityEnclosingRequestBase httpRequest, PipelineContext context, Node configNode) throws IOException { Document dataDocument = readInputAsDOM4J(context, INPUT_DATA); if (configNode.valueOf("input-type").equals("form")) { List<NameValuePair> nameValuePairs = new ArrayList<NameValuePair>(); Element rootElement = dataDocument.getRootElement(); Iterator<?> elit = rootElement.elementIterator(); while (elit.hasNext()) { Element child = (Element) elit.next(); nameValuePairs.add(new BasicNameValuePair(child.getQName().getName(), child.getText())); }//ww w. ja va 2 s . c om httpRequest.setEntity(new UrlEncodedFormEntity(nameValuePairs)); } else { String jsonstr; if (configNode.valueOf("input-type").equals("json")) { //Conversion of XML input to JSON JSONObject jsondata = new JSONObject(); populateJSONObject(jsondata, dataDocument); jsonstr = jsondata.toString(); } else { //No conversion, just use plain text in input jsonstr = dataDocument.getRootElement().getText(); } httpRequest.setEntity(new StringEntity(jsonstr)); } }
From source file:nl.architolk.ldt.processors.MarkDownConverter.java
License:Open Source License
public ProcessorOutput createOutput(String name) { final ProcessorOutput output = new ProcessorOutputImpl(MarkDownConverter.this, name) { public void readImpl(PipelineContext context, XMLReceiver xmlReceiver) { // Read content of config pipe Document configDocument = readInputAsDOM4J(context, INPUT_CONFIG); Node configNode = configDocument.selectSingleNode("//config"); String uri = configNode.valueOf("uri"); // Read en process content of input pipe readInputAsSAX(context, INPUT_DATA, new MarkDownXMLReceiver(xmlReceiver, uri)); }//from w w w .j av a2s. c om @Override public OutputCacheKey getKeyImpl(PipelineContext pipelineContext) { return getInputKey(pipelineContext, getInputByName(INPUT_DATA)); } @Override public Object getValidityImpl(PipelineContext pipelineContext) { return getInputValidity(pipelineContext, getInputByName(INPUT_DATA)); } }; addOutput(name, output); return output; }
From source file:nl.architolk.ldt.processors.RDF4JProcessor.java
License:Open Source License
public void generateData(PipelineContext context, ContentHandler contentHandler) throws SAXException { Document configDocument = readInputAsDOM4J(context, INPUT_CONFIG); Node configNode = configDocument.selectSingleNode("//config"); contentHandler.startDocument();//from w ww. j ava2 s. c om contentHandler.startElement("", "response", "response", new AttributesImpl()); String action = configNode.valueOf("action"); // The action to perform String cgraph = configNode.valueOf("cgraph"); // Container graph, the main graph String tgraph = configNode.valueOf("tgraph"); // The target graph String pgraph = configNode.valueOf("pgraph"); // The parent graph, for version information String postQuery = configNode.valueOf("postquery"); // Some post query, optional String uriPrefix = configNode.valueOf("uriprefix"); // The uri prefix for relative uri's String errorMsg = ""; db = RDF4JProperties.createRepository(); if (db == null) { errorMsg = "Unknown database. \n"; } else { conn = db.getConnection(); try { if (!(conn instanceof SPARQLConnection)) { conn.begin(IsolationLevels.NONE); } // Clear target graph, partially (all triples in original container) or completely if (action.equals("replace")) { String msg = "Target graph <" + tgraph + "> cleared"; try { IRI tgraphResource = db.getValueFactory().createIRI(tgraph); conn.clear(tgraphResource); } catch (Exception e) { // In case of an error, put the errormessage in the result, but don't throw the exception msg = e.toString(); errorMsg += e.getMessage() + ". \n"; } contentHandler.startElement("", "scene", "scene", new AttributesImpl()); contentHandler.characters(msg.toCharArray(), 0, msg.length()); contentHandler.endElement("", "scene", "scene"); } else if (action.equals("part")) { String msg = "Target graph <" + tgraph + "> partially cleared"; try { conn.prepareUpdate( "delete { graph <" + tgraph + "> {?s?p?o}} using <" + cgraph + "> where {?s?p?o}") .execute(); } catch (Exception e) { // In case of an error, put the errormessage in the result, but don't throw the exception msg = e.toString(); errorMsg += e.getMessage() + ". \n"; } contentHandler.startElement("", "scene", "scene", new AttributesImpl()); contentHandler.characters(msg.toCharArray(), 0, msg.length()); contentHandler.endElement("", "scene", "scene"); } // Clear container, except when action = insert if (!action.equals("insert")) { String msg = "Container <" + cgraph + "> cleared"; try { IRI cgraphResource = db.getValueFactory().createIRI(cgraph); conn.clear(cgraphResource); } catch (Exception e) { // In case of an error, put the errormessage in the result, but don't throw the exception msg = e.toString(); errorMsg += e.getMessage() + ". \n"; } contentHandler.startElement("", "scene", "scene", new AttributesImpl()); contentHandler.characters(msg.toCharArray(), 0, msg.length()); contentHandler.endElement("", "scene", "scene"); } // Insert documents into container graph Document dataDocument = readInputAsDOM4J(context, INPUT_DATA); List filelist = dataDocument.selectNodes("//filelist//file"); Iterator<?> elit = filelist.listIterator(); while (elit.hasNext()) { Node child = (Node) elit.next(); String msg = "file uploaded: " + child.valueOf("@name"); try { uploadFile(child.valueOf("@name"), child.getText(), cgraph, uriPrefix); } catch (Exception e) { // In case of an error, put the errormessage in the result, but don't throw the exception msg = "[" + child.valueOf("@name") + "] " + e.getMessage(); errorMsg += e.getMessage(); if (e.getCause() != null) { msg += " (" + e.getCause().getMessage() + ")"; errorMsg += " (" + e.getCause().getMessage() + ")"; } errorMsg += ". \n"; } contentHandler.startElement("", "scene", "scene", new AttributesImpl()); contentHandler.characters(msg.toCharArray(), 0, msg.length()); contentHandler.endElement("", "scene", "scene"); } // Remove existing properties in case of action = update if (action.equals("update")) { String msg = "Target graph cleared for update"; try { conn.prepareUpdate("delete {graph <" + tgraph + "> {?s?x?y}} using <" + cgraph + "> using <" + tgraph + "> where {graph <" + tgraph + "> {?s?x?y} graph <" + cgraph + "> {?s?p?o}}").execute(); // Remove orphant blank nodes (to third degree, beter option could be to count the number of deleted nodes and repeat when not equal to zero) conn.prepareUpdate("delete {graph <" + tgraph + "> {?bs?bp?bo}} using <" + tgraph + "> where {?bs?bp?bo FILTER(isblank(?bs)) FILTER NOT EXISTS {?s?p?bs}}").execute(); conn.prepareUpdate("delete {graph <" + tgraph + "> {?bs?bp?bo}} using <" + tgraph + "> where {?bs?bp?bo FILTER(isblank(?bs)) FILTER NOT EXISTS {?s?p?bs}}").execute(); conn.prepareUpdate("delete {graph <" + tgraph + "> {?bs?bp?bo}} using <" + tgraph + "> where {?bs?bp?bo FILTER(isblank(?bs)) FILTER NOT EXISTS {?s?p?bs}}").execute(); } catch (Exception e) { // In case of an error, put the errormessage in the result, but don't throw the exception msg = e.toString(); errorMsg += e.getMessage() + ". \n"; } contentHandler.startElement("", "scene", "scene", new AttributesImpl()); contentHandler.characters(msg.toCharArray(), 0, msg.length()); contentHandler.endElement("", "scene", "scene"); } // Populate target graph with content of the container-graph if (action.equals("part") || action.equals("replace") || action.equals("update")) { String msg = "Target graph <" + tgraph + "> populated from container <" + cgraph + ">"; try { conn.prepareUpdate( "insert { graph <" + tgraph + "> {?s?p?o}} using <" + cgraph + "> where {?s?p?o}") .execute(); } catch (Exception e) { // In case of an error, put the errormessage in the result, but don't throw the exception msg = e.toString(); errorMsg += e.getMessage() + ". \n"; } contentHandler.startElement("", "scene", "scene", new AttributesImpl()); contentHandler.characters(msg.toCharArray(), 0, msg.length()); contentHandler.endElement("", "scene", "scene"); } // Insert version-info into parent graph, if applicable if (!(cgraph.equals(pgraph) || pgraph.isEmpty())) { String msg = "Version metadata inserted into parent graph"; try { conn.prepareUpdate("insert data {graph <" + pgraph + "> {<" + pgraph + "> <http://purl.org/dc/terms/hasVersion> <" + cgraph + ">}}").execute(); } catch (Exception e) { // In case of an error, put the errormessage in the result, but don't throw the exception msg = e.toString(); errorMsg += e.getMessage() + ". \n"; } contentHandler.startElement("", "scene", "scene", new AttributesImpl()); contentHandler.characters(msg.toCharArray(), 0, msg.length()); contentHandler.endElement("", "scene", "scene"); } // Execute post query if (!postQuery.isEmpty()) { String msg = "Post query executed"; try { conn.prepareUpdate(postQuery).execute(); } catch (Exception e) { // In case of an error, put the errormessage in the result, but don't throw the exception msg = e.toString(); errorMsg += e.getMessage() + ". \n"; } contentHandler.startElement("", "scene", "scene", new AttributesImpl()); contentHandler.characters(msg.toCharArray(), 0, msg.length()); contentHandler.endElement("", "scene", "scene"); } if (!(conn instanceof SPARQLConnection)) { conn.commit(); } } finally { conn.close(); } } if (!errorMsg.isEmpty()) { contentHandler.startElement("", "error", "error", new AttributesImpl()); contentHandler.characters(errorMsg.toCharArray(), 0, errorMsg.length()); contentHandler.endElement("", "error", "error"); } contentHandler.endElement("", "response", "response"); contentHandler.endDocument(); }
From source file:nl.ru.cmbi.pisa.wrapper.PisaCachedWebDao.java
License:Apache License
/** * Gets the 3D rotation-translation biomolecule matrices from PISA. * <p>/* ww w.j a va 2 s . c o m*/ * These matrices detail how chains in the specified PDB entry should be manipulated to obtain desired the PISA * assembly. * * @param rawPdbId * the 4-letter PDB code we want the assembly of (e.g. "1crn") * @param setNr * the PISA assembly set. "1" is most stable in solution, higher numbers increasingly unstable. * @param assemblyNr * the substructure within an assembly. Note that structurally identical substructures get the * same assemblyNr. This DAO ignores all but the first substructure. Ignored chains (those chains not * needed to make this assembly) are listed in the {@link MatricesResult#ignoredChains} property of the * returned result. * @return A compound result of the transformation matrices to apply and the ignored chains (I.E. those * chains whose transformation lead to an identical substructure to the one returned). This result may be * empty. * @throws IOException * when web-fetching fails. */ @SuppressWarnings("unchecked") public MatricesResult getMatrices(final String rawPdbId, final int setNr, final int assemblyNr) throws IOException { final String pdbId = rawPdbId.trim().toLowerCase(); Document mmrInfo; try { mmrInfo = parseDocumentOf(getRawMultimerInfoSingle(pdbId)); } catch (final DocumentException docex) { log.error("Problem parsing Pisa raw multimer info for {}, see debug level for details", pdbId); log.debug("Exception: ", docex); throw new IOException("Problem parsing multimer XML document", docex); } final List<ChainTransform> output = new ArrayList<ChainTransform>(); final Set<String> ignoredChainIds = new HashSet<String>(); try { // Unfortunately, multiple assemblies share the same <ID> subnode if they are structurally identical // So, we need indexing ("[1]") to get only the first of an identical set of assemblies // ('identical' meaning "structurally identical except for ChainIDs") // Sigh... reusing IDs for different things! final String matricesXpath = String.format( "(/pisa_multimers/pdb_entry[ pdb_code='%s' ]/asm_set[ ser_no=%d ]/assembly[ id=%d ])[1]/molecule", pdbId, setNr, assemblyNr); final List<Node> matrices = mmrInfo.selectNodes(matricesXpath); for (final Node node : matrices) { final ChainTransform ct = new ChainTransform(node.valueOf("chain_id"), // X-row (Double) node.numberValueOf("rxx"), (Double) node.numberValueOf("rxy"), (Double) node.numberValueOf("rxz"), (Double) node.numberValueOf("tx"), // Y-row (Double) node.numberValueOf("ryx"), (Double) node.numberValueOf("ryy"), (Double) node.numberValueOf("ryz"), (Double) node.numberValueOf("ty"), // Z-row (Double) node.numberValueOf("rzx"), (Double) node.numberValueOf("rzy"), (Double) node.numberValueOf("rzz"), (Double) node.numberValueOf("tz")); if (ct.isUnity() && ct.isStationary()) { ct.setDuplication(false); } else { ct.setDuplication(true); } output.add(ct); } final String ignoredMatricesXpath = String.format( "(/pisa_multimers/pdb_entry[ pdb_code='%s' ]/asm_set[ ser_no=%d ]/assembly[ id=%d ])[position() > 1]/molecule/chain_id", pdbId, setNr, assemblyNr); final List<Node> ignoredChains = mmrInfo.selectNodes(ignoredMatricesXpath); for (final Node ignoredChain : ignoredChains) { ignoredChainIds.add(ignoredChain.getText()); } } catch (final ClassCastException ccex) { log.error( "malformed XML response from PISA when getting matrices for assembly {}:{}.{}: expected list of matrix nodes, but obtained something else", new Object[] { pdbId, setNr, assemblyNr }); throw new IOException("malformed XML response from PISA when getting matrices for assembly of " + pdbId + ": expected list of matrix nodes, but obtained something else", ccex); } return new MatricesResult(output, ignoredChainIds); }
From source file:nnga.NNGA.java
License:Open Source License
@Override public void continueOptimization(ProblemXMLData problemData, ComponentXMLData representationData, ComponentXMLData rankingData, Hashtable<String, XMLFieldEntry> properties, Document doc) { // load and calculate parameters parameters.initialize(getProperties()); if (!loadFromDoc(problemData, representationData, doc)) { return;//from ww w . ja v a2 s. c o m } // record the best fitness over the evolution Node dpopulations = doc.selectSingleNode("/frevo/populations"); double best_fitness = Double.parseDouble(dpopulations.valueOf("./@best_fitness")); int lastGeneration = Integer.parseInt(dpopulations.valueOf("./@generation")); createStatistics(); // Mutate all populations except when this is the last generation for (SimplePopulation population : pops) { try { population.evolve(lastGeneration, pops); } catch (Exception e) { e.printStackTrace(); return; } } try { NNGAStep step = new NNGAStep(problemData, rankingData); step.setBestFitness(best_fitness); // Iterate through generations for (int generation = lastGeneration + 1; generation < parameters.getGenerations(); generation++) { step.setGeneration(generation); if (!evolve(step)) { break; } } } catch (InstantiationException e1) { e1.printStackTrace(); } catch (Exception e) { e.printStackTrace(); } // finalize progress setProgress(1f); }
From source file:nnga.NNGA.java
License:Open Source License
@Override public ArrayList<ArrayList<AbstractRepresentation>> loadFromXML(Document doc) { // final list to be returned ArrayList<ArrayList<AbstractRepresentation>> populations = new ArrayList<ArrayList<AbstractRepresentation>>(); // get population root node Node dpopulations = doc.selectSingleNode("/frevo/populations"); // get number of populations int populationCount = Integer.parseInt(dpopulations.valueOf("./@count")); // get number of current generation int currentGeneration = Integer.parseInt(dpopulations.valueOf("./@generation")); // get population size @SuppressWarnings("unchecked") List<? extends Node> populationsNode = dpopulations.selectNodes(".//population"); int populationSize = populationsNode.get(0).selectNodes("*").size(); // calculate total representations int totalRepresentations = populationCount * populationSize; int currentPopulation = 0; int currentRepresentation = 0; // Iterate through the population nodes Iterator<?> populationIterator = populationsNode.iterator(); while (populationIterator.hasNext()) { Node populationNode = (Node) populationIterator.next(); // create list of candidate representations for this population ArrayList<AbstractRepresentation> result = new ArrayList<AbstractRepresentation>(); // track current progress currentRepresentation = 0;//from ww w . j av a 2 s. co m try { // Obtain an iterator over the representations List<?> representations = populationNode.selectNodes("./*"); Iterator<?> representationsIterator = representations.iterator(); while (representationsIterator.hasNext()) { // calculate current position for progress reporting int currentItem = currentPopulation * populationSize + currentRepresentation + 1; // report loading state FrevoMain.setLoadingProgress((float) currentItem / totalRepresentations); // step to next node Node net = (Node) representationsIterator.next(); // construct representation based on loaded representation // data ComponentXMLData representation = FrevoMain .getSelectedComponent(ComponentType.FREVO_REPRESENTATION); AbstractRepresentation member = representation.getNewRepresentationInstance(0, 0, null); // load representation data from the XML into the instance member.loadFromXML(net); // add data to current population list result.add(member); // increment tracker currentRepresentation++; } } catch (Exception e) { e.printStackTrace(); } populations.add(result); currentPopulation++; } // Load the number of generations XMLFieldEntry gensize = getProperties().get("generations"); if (gensize != null) { int generations = Integer.parseInt(gensize.getValue()); // TODO check max fitness also // set boolean value which shows possibility of continuation of experiment // if maximum number of generations hasn't been reached. setCanContinue(currentGeneration + 1 < generations); } return populations; }