/** * Marshall an array of Genes to an XML Element representation. * * @param a_geneValues the genes to represent as an XML element * @param a_xmlDocument a Document instance that will be used to create the Element instance. Note * that the element will NOT be added to the document by this method * @return an Element object representing the given genes * @author Neil Rotstan * @author Klaus Meffert * @since 1.0 * @deprecated use XMLDocumentBuilder instead */ public static Element representGenesAsElement( final Gene[] a_geneValues, final Document a_xmlDocument) { // Create the parent genes element. // -------------------------------- Element genesElement = a_xmlDocument.createElement(GENES_TAG); // Now add gene sub-elements for each gene in the given array. // ----------------------------------------------------------- Element geneElement; for (int i = 0; i < a_geneValues.length; i++) { // Create the allele element for this gene. // ---------------------------------------- geneElement = a_xmlDocument.createElement(GENE_TAG); // Add the class attribute and set its value to the class // name of the concrete class representing the current Gene. // --------------------------------------------------------- geneElement.setAttribute(CLASS_ATTRIBUTE, a_geneValues[i].getClass().getName()); // Create a text node to contain the string representation of // the gene's value (allele). // ---------------------------------------------------------- Element alleleRepresentation = representAlleleAsElement(a_geneValues[i], a_xmlDocument); // And now add the text node to the gene element, and then // add the gene element to the genes element. // ------------------------------------------------------- geneElement.appendChild(alleleRepresentation); genesElement.appendChild(geneElement); } return genesElement; }
public void saveToXml(String fileName) throws ParserConfigurationException, FileNotFoundException, TransformerException, TransformerConfigurationException { System.out.println("Saving network topology to file " + fileName); DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); DocumentBuilder parser = factory.newDocumentBuilder(); Document doc = parser.newDocument(); Element root = doc.createElement("neuralNetwork"); root.setAttribute("dateOfExport", new Date().toString()); Element layers = doc.createElement("structure"); layers.setAttribute("numberOfLayers", Integer.toString(this.numberOfLayers())); for (int il = 0; il < this.numberOfLayers(); il++) { Element layer = doc.createElement("layer"); layer.setAttribute("index", Integer.toString(il)); layer.setAttribute("numberOfNeurons", Integer.toString(this.getLayer(il).numberOfNeurons())); for (int in = 0; in < this.getLayer(il).numberOfNeurons(); in++) { Element neuron = doc.createElement("neuron"); neuron.setAttribute("index", Integer.toString(in)); neuron.setAttribute( "NumberOfInputs", Integer.toString(this.getLayer(il).getNeuron(in).numberOfInputs())); neuron.setAttribute( "threshold", Double.toString(this.getLayer(il).getNeuron(in).threshold)); for (int ii = 0; ii < this.getLayer(il).getNeuron(in).numberOfInputs(); ii++) { Element input = doc.createElement("input"); input.setAttribute("index", Integer.toString(ii)); input.setAttribute( "weight", Double.toString(this.getLayer(il).getNeuron(in).getInput(ii).weight)); neuron.appendChild(input); } layer.appendChild(neuron); } layers.appendChild(layer); } root.appendChild(layers); doc.appendChild(root); // save File xmlOutputFile = new File(fileName); FileOutputStream fos; Transformer transformer; fos = new FileOutputStream(xmlOutputFile); // Use a Transformer for output TransformerFactory transformerFactory = TransformerFactory.newInstance(); transformer = transformerFactory.newTransformer(); DOMSource source = new DOMSource(doc); StreamResult result = new StreamResult(fos); // transform source into result will do save transformer.setOutputProperty("encoding", "iso-8859-2"); transformer.setOutputProperty("indent", "yes"); transformer.transform(source, result); }
public void toWrite(int size, String[] mycontent) { Element root = document.createElement("WorkShop"); document.appendChild(root); Element title = document.createElement("Size"); title.appendChild(document.createTextNode(size + "")); root.appendChild(title); for (int i = 0; i < size; i++) { Element content = document.createElement("Content" + i); content.appendChild(document.createTextNode(mycontent[i])); root.appendChild(content); } }
private void addChannel(Document doc, Element root, Integer channel, HashSet<Integer> values) { Element el = doc.createElement(_channel); Attr attr = doc.createAttribute(_number); attr.setValue(Integer.toString(channel + 1)); el.setAttributeNode(attr); Text txt; for (Integer x : values) { txt = doc.createTextNode(x.toString()); el.appendChild(txt); } root.appendChild(el); }
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); } }
/** * Create an event that can be populated using its reference. * * @param type The event's type. * @param t The event's time stamp. * @return The pointer to the event. */ public Element newEvent(String source, String type, int t) { Element event = m_document.createElement("event"); event.setAttribute("id", m_id + ""); event.setAttribute("source", source); event.setAttribute("date", t + ""); m_id++; Element ty = m_document.createElement("type"); ty.setTextContent(type); event.appendChild(ty); m_sequence.appendChild(event); return event; }
/** Turns a List<CubicCurve2D.Float> into a SVG Element representing a sketch of that spline. */ Element splineToSketch(SVGDocument document, List<CubicCurve2D.Float> spline) { String svgNS = SVGDOMImplementation.SVG_NAMESPACE_URI; // <g> is an SVG group // TODO: add a random(ish) rotation to the group Element group = document.createElementNS(svgNS, "g"); // For each curve in the path, draw along it using a "brush". In // our case the brush is a simple circle, but this could be changed // to something more advanced. for (CubicCurve2D.Float curve : spline) { // TODO: magic number & step in loop guard for (double i = 0.0; i <= 1.0; i += 0.01) { Point2D result = evalParametric(curve, i); // Add random jitter at some random positive or negative // distance along the unit normal to the tangent of the // curve Point2D n = vectorUnitNormal(evalParametricTangent(curve, i)); float dx = (float) ((Math.random() - 0.5) * n.getX()); float dy = (float) ((Math.random() - 0.5) * n.getY()); Element brush = document.createElementNS(svgNS, "circle"); brush.setAttribute("cx", Double.toString(result.getX() + dx)); brush.setAttribute("cy", Double.toString(result.getY() + dy)); // TODO: magic number for circle radius brush.setAttribute("r", Double.toString(1.0)); brush.setAttribute("fill", "green"); brush.setAttributeNS(null, "z-index", Integer.toString(zOrder.CONTOUR.ordinal())); group.appendChild(brush); } } return group; }
/** * Writes a table to a XML-file * * @param t - Output Model * @param destination - File Destination */ public static void writeXML(Model t, String destination) { try { // Create the XML document builder, and document that will be used DocumentBuilderFactory xmlBuilder = DocumentBuilderFactory.newInstance(); DocumentBuilder Builder = xmlBuilder.newDocumentBuilder(); Document xmldoc = Builder.newDocument(); // create Document node, and get it into the file Element Documentnode = xmldoc.createElement("SPREADSHEET"); xmldoc.appendChild(Documentnode); // create element nodes, and their attributes (Cells, and row/column // data) and their content for (int row = 1; row < t.getRows(); row++) { for (int col = 1; col < t.getCols(col); col++) { Element cell = xmldoc.createElement("CELL"); // set attributes cell.setAttribute("column", Integer.toString(col)); cell.setAttribute("row", Integer.toString(col)); // set content cell.appendChild(xmldoc.createTextNode((String) t.getContent(row, col))); // append node to document node Documentnode.appendChild(cell); } } // Creating a datastream for the DOM tree TransformerFactory transformerFactory = TransformerFactory.newInstance(); Transformer transformer = transformerFactory.newTransformer(); // Indentation to make the XML file look better transformer.setOutputProperty(OutputKeys.METHOD, "xml"); transformer.setOutputProperty(OutputKeys.INDENT, "yes"); // remove the java version transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes"); DOMSource stream = new DOMSource(xmldoc); StreamResult target = new StreamResult(new File(destination)); // write the file transformer.transform(stream, target); } catch (ParserConfigurationException e) { System.out.println("Can't create the XML document builder"); } catch (TransformerConfigurationException e) { System.out.println("Can't create transformer"); } catch (TransformerException e) { System.out.println("Can't write to file"); } }
private Element addSubelementImpl(Element element, String name, String textContent) { if (element != null) { Element subElement = m_document.createElement(name); subElement.setTextContent(textContent); element.appendChild(subElement); return subElement; } else return null; }
private Element addEventElementImpl(String name, String textContent) { if (m_currentEvent != null) { Element element = m_document.createElement(name); element.setTextContent(textContent); m_currentEvent.appendChild(element); return element; } else return null; }
public XMLHelper createSubNode(String subnode) { int pos = subnode.lastIndexOf(DELIM); if (pos >= 0) { XMLHelper helper = getSubNode(subnode.substring(0, pos)); return helper.createSubNode(subnode.substring(pos + 1)); } else { return new XMLHelper( (Element) element.appendChild(element.getOwnerDocument().createElement(subnode)), true); } }
/** * Create a new event that can be populated with elements later. * * @param t the time stamp */ public void startNewEvent(int t) { m_currentEvent = m_document.createElement("event"); m_id++; m_currentEvent.setAttribute("id", m_id + ""); m_currentEvent.setAttribute("source", "Ernest"); m_currentEvent.setAttribute("date", t + ""); m_sequence.appendChild(m_currentEvent); }
private Node getTextNode() { NodeList list = element.getChildNodes(); int length = list.getLength(); for (int i = 0; i < length; i++) { Node node = list.item(i); if (node.getNodeType() == Node.TEXT_NODE) { return node; } } return element.appendChild(element.getOwnerDocument().createTextNode("")); }
public Element reportDtElem() { StringBuffer sb = new StringBuffer(255); sb.append(shortTypeName); sb.append(" [ dataSourceName: "); sb.append(pds.getDataSourceName()); sb.append("; identityToken: "); sb.append(pds.getIdentityToken()); sb.append(" ]"); Element dtElem = doc.createElement("dt"); dtElem.appendChild(doc.createTextNode(sb.toString())); return dtElem; }
public XMLHelper getSubNode(String subnode) { String nodes[] = subnode.split(REGEX); Element sub = element; boolean isnew = false; for (int i = 0; i < nodes.length; i++) { NodeList list = getImediateElementsByTagName(sub, nodes[i]); if (list.getLength() > 0) { sub = (Element) list.item(0); } else { sub = (Element) sub.appendChild(element.getOwnerDocument().createElement(nodes[i])); isnew = true; } } return new XMLHelper(sub, isnew); }
/** * Marshall a Chromosome instance to an XML Element representation, including its contained Genes * as sub-elements. This may be useful in scenarios where representation as an entire Document is * undesirable, such as when the representation of this Chromosome is to be combined with other * elements in a single Document. * * @param a_subject the chromosome to represent as an XML element * @param a_xmlDocument a Document instance that will be used to create the Element instance. Note * that the element will NOT be added to the document by this method * @return an Element object representing the given Chromosome * @author Neil Rotstan * @since 1.0 * @deprecated use XMLDocumentBuilder instead */ public static Element representChromosomeAsElement( final IChromosome a_subject, final Document a_xmlDocument) { // Start by creating an element for the chromosome and its size // attribute, which represents the number of genes in the chromosome. // ------------------------------------------------------------------ Element chromosomeElement = a_xmlDocument.createElement(CHROMOSOME_TAG); chromosomeElement.setAttribute(SIZE_ATTRIBUTE, Integer.toString(a_subject.size())); // Next create the genes element with its nested gene elements, // which will contain string representations of the alleles. // -------------------------------------------------------------- Element genesElement = representGenesAsElement(a_subject.getGenes(), a_xmlDocument); // Add the new genes element to the chromosome element and then // return the chromosome element. // ------------------------------------------------------------- chromosomeElement.appendChild(genesElement); return chromosomeElement; }
/** * Gets the string of an XML document containing multiple words for saving purposes. * * @param words The words to save. * @return String containing XML containing all words. */ public static String getMultipleWordXML(Word[] words) { try { DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); DocumentBuilder db = dbf.newDocumentBuilder(); Document doc = db.newDocument(); Element root = doc.createElement("Root"); for (int i = 0; i < words.length; i++) { root.appendChild(words[i].getWordXMLNode(doc)); } doc.appendChild(root); return getStringFromDocument(doc); } catch (Exception ex) { ex.printStackTrace(); return null; } }
private void addFade(Document doc, Element root, FadeData fade) { Element el = doc.createElement(_cue); Attr attr; attr = doc.createAttribute(_number); attr.setValue(Integer.toString(fade.getCueNumber())); el.setAttributeNode(attr); attr = doc.createAttribute(_uptime); attr.setValue(Integer.toString(fade.getUpTime())); el.setAttributeNode(attr); attr = doc.createAttribute(_downTime); attr.setValue(Integer.toString(fade.getDownTime())); el.setAttributeNode(attr); attr = doc.createAttribute(_upTimeDelay); attr.setValue(Integer.toString(fade.getDelayUpTime())); el.setAttributeNode(attr); attr = doc.createAttribute(_downTimeDelay); attr.setValue(Integer.toString(fade.getDelayDownTime())); el.setAttributeNode(attr); if (fade.getFollowTime() >= 0) { attr = doc.createAttribute(_followtime); attr.setValue(Integer.toString(fade.getFollowTime())); el.setAttributeNode(attr); } if (fade.getNextCue() > 0) { attr = doc.createAttribute(_nextCue); attr.setValue(Integer.toString(fade.getNextCue())); el.setAttributeNode(attr); } CueData cue = fade.getCue(); attr = doc.createAttribute(_discription); attr.setValue(cue.getDescription()); el.setAttributeNode(attr); for (Integer chan : cue.keySet()) addChannel(doc, el, chan, cue.get(chan)); root.appendChild(el); }
/** * Marshall a Genotype instance into an XML Element representation, including its population of * Chromosome instances as sub-elements. This may be useful in scenarios where representation as * an entire Document is undesirable, such as when the representation of this Genotype is to be * combined with other elements in a single Document. * * @param a_subject the genotype to represent as an XML element * @param a_xmlDocument a Document instance that will be used to create the Element instance. Note * that the element will NOT be added to the document by this method * @return an Element object representing the given Genotype * @author Neil Rotstan * @since 1.0 * @deprecated use XMLDocumentBuilder instead */ public static Element representGenotypeAsElement( final Genotype a_subject, final Document a_xmlDocument) { Population population = a_subject.getPopulation(); // Start by creating the genotype element and its size attribute, // which represents the number of chromosomes present in the // genotype. // -------------------------------------------------------------- Element genotypeTag = a_xmlDocument.createElement(GENOTYPE_TAG); genotypeTag.setAttribute(SIZE_ATTRIBUTE, Integer.toString(population.size())); // Next, add nested elements for each of the chromosomes in the // genotype. // ------------------------------------------------------------ for (int i = 0; i < population.size(); i++) { Element chromosomeElement = representChromosomeAsElement(population.getChromosome(i), a_xmlDocument); genotypeTag.appendChild(chromosomeElement); } return genotypeTag; }
public static boolean saveTombstones(List<Tombstone> deathChests, String chestsPath) { long timestamp = System.currentTimeMillis(); try { DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); DocumentBuilder builder = factory.newDocumentBuilder(); // Create the writer Document xmlDoc = builder.newDocument(); Element rootNode = xmlDoc.createElement("deathchestList"); // String pluginName = Settings.getPluginName(); String version = Settings.getVersion(); rootNode.setAttribute("version", version); xmlDoc.appendChild(rootNode); for (Tombstone tombstone : deathChests) { rootNode.appendChild( tombstone.createXmlNode( xmlDoc.createElement(Utils.DEATHCHEST_XML_TAG), xmlDoc, timestamp)); } // Put the XML file into domSource DOMSource domSource = new DOMSource(xmlDoc); // PrintStream will be responsible for writing // the text data to the file PrintStream ps = new PrintStream(chestsPath); StreamResult fileWriter = new StreamResult(ps); TransformerFactory transformerFactory = TransformerFactory.newInstance(); Transformer transformer = transformerFactory.newTransformer(); // Finally save the file transformer.transform(domSource, fileWriter); return true; } catch (ParserConfigurationException | TransformerException | FileNotFoundException ex) { System.err.println("Error while writing deathchest data:"); ex.printStackTrace(); } return false; }
private void addMagicChannel(Document doc, Element root, int channel, double x, double y) { Element el = doc.createElement(_channel); // Element xel = doc.createElement(_x); // Element yel = doc.createElement(_y); Attr attr = doc.createAttribute(_number); attr.setValue(Integer.toString(channel + 1)); el.setAttributeNode(attr); attr = doc.createAttribute(_x); attr.setValue(Double.toString(x)); el.setAttributeNode(attr); attr = doc.createAttribute(_y); attr.setValue(Double.toString(y)); el.setAttributeNode(attr); // xel.appendChild(doc.createTextNode(Integer.toString(x))); // yel.appendChild(doc.createTextNode(Integer.toString(y))); // el.appendChild(xel); // el.appendChild(yel); root.appendChild(el); }
/** * Gets XML string for this definition so that it may be printed. * * @return XML node that can be saved of this word. */ public Element getWordXMLNode(Document doc) { try { Element rootWordElement = doc.createElement("WordDefinitions"); rootWordElement.setAttribute("word", this.word); rootWordElement.setAttribute("mainDefinition", this.getMainDefinition()); if (this.otherDefinitions == null) { this.getDefinitions(); } for (int i = 0; i < this.otherDefinitions.length; i++) { // main definition node Element definition = doc.createElement("Definition"); // word Element word = doc.createElement("Word"); word.setTextContent(otherDefinitions[i].getWord()); // dictionary Element dictionary = doc.createElement("Dictionary"); Element id = doc.createElement("Id"); id.setTextContent(otherDefinitions[i].getId()); Element source = doc.createElement("Name"); source.setTextContent(otherDefinitions[i].getSource()); dictionary.appendChild(id); dictionary.appendChild(source); // definition Element wordDefinition = doc.createElement("WordDefinition"); wordDefinition.setTextContent(otherDefinitions[i].getDefinition()); // append all the children definition.appendChild(word); definition.appendChild(dictionary); definition.appendChild(wordDefinition); rootWordElement.appendChild(definition); } return rootWordElement; } catch (Exception ex) { ex.printStackTrace(); return null; } }
public boolean runTest(Test test) throws Exception { String filename = test.file.toString(); if (this.verbose) { System.out.println( "Running " + filename + " against " + this.host + ":" + this.port + " with " + this.browser); } this.document = parseDocument(filename); if (this.baseUrl == null) { NodeList links = this.document.getElementsByTagName("link"); if (links.getLength() != 0) { Element link = (Element) links.item(0); setBaseUrl(link.getAttribute("href")); } } if (this.verbose) { System.out.println("Base URL=" + this.baseUrl); } Node body = this.document.getElementsByTagName("body").item(0); Element resultContainer = document.createElement("div"); resultContainer.setTextContent("Result: "); Element resultElt = document.createElement("span"); resultElt.setAttribute("id", "result"); resultElt.setIdAttribute("id", true); resultContainer.appendChild(resultElt); body.insertBefore(resultContainer, body.getFirstChild()); Element executionLogContainer = document.createElement("div"); executionLogContainer.setTextContent("Execution Log:"); Element executionLog = document.createElement("div"); executionLog.setAttribute("id", "log"); executionLog.setIdAttribute("id", true); executionLog.setAttribute("style", "white-space: pre;"); executionLogContainer.appendChild(executionLog); body.appendChild(executionLogContainer); NodeList tableRows = document.getElementsByTagName("tr"); Element theadRow = (Element) tableRows.item(0); test.name = theadRow.getTextContent(); appendCellToRow(theadRow, "Result"); this.commandProcessor = new HtmlCommandProcessor(this.host, this.port, this.browser, this.baseUrl); String resultState; String resultLog; test.result = true; try { this.commandProcessor.start(); test.commands = new Command[tableRows.getLength() - 1]; for (int i = 1; i < tableRows.getLength(); i++) { Element stepRow = (Element) tableRows.item(i); Command command = executeStep(stepRow); appendCellToRow(stepRow, command.result); test.commands[i - 1] = command; if (command.error) { test.result = false; } if (command.failure) { test.result = false; // break; } } resultState = test.result ? "PASSED" : "FAILED"; resultLog = (test.result ? "Test Complete" : "Error"); this.commandProcessor.stop(); } catch (Exception e) { test.result = false; resultState = "ERROR"; resultLog = "Failed to initialize session\n" + e; e.printStackTrace(); } document.getElementById("result").setTextContent(resultState); Element log = document.getElementById("log"); log.setTextContent(log.getTextContent() + resultLog + "\n"); return test.result; }
/** @param args the command line arguments */ public static void main(String[] args) { // TODO code application logic here Model model; String insertstmt; String insertmodel = "", insertspecies = "", insertcompartment = "", insertfunction = "", insertunitdef = "", insertunits = "", insertreaction = "", insertreactant = "", insertproduct = ""; String insertmodifier = "", insertklaw = "", insertrules = "", insertconstraint = "", insertdelay = "", inserttrigger = "", insertevent = "", inserteventassign = "", insertparameter = ""; String insertstatement = ""; String server, user, password, dbname, filepath; String Filedata = ""; String cwd = System.getProperty("user.dir"); if (args.length == 0) { server = "localhost"; user = "******"; password = "******"; dbname = "sbmldb2"; /** * Path to extract the SBML files from database, where cwd is * "github\db2sbml\dbtosbml_standalone_Project\dbtosbml" so add a folder in this directory and * mention folder name instead of extractedbm folder */ filepath = cwd + "\\extractedbm\\"; } else { server = args[0]; user = args[1]; password = args[2]; dbname = args[3]; filepath = args[4]; } try { Filedata = readFileAsString(cwd + "\\sbmldbschema.sql"); } catch (Exception e) { e.printStackTrace(); } Mysqlconn sql = new Mysqlconn(server, user, password, dbname); // String modelids.getId() = "MorrisonAllegra" ; ASTNode math = null; int level = 0, version = 0; ArrayList<modellist> modelidlist = sql.getmodels(); insertstatement = "LOCK TABLES `model` WRITE,`species` WRITE,`compartment` WRITE,`functiondefinition` WRITE,"; insertstatement = insertstatement + "`listofunitdefinitions` WRITE,`listofunits` WRITE,`reaction` WRITE,`simplespeciesreference` WRITE,"; insertstatement = insertstatement + "`modifierspeciesreference` WRITE,`kineticlaw` WRITE,`parameter` WRITE,`sbmlconstraint` WRITE,"; insertstatement = insertstatement + "`event` WRITE,`sbmltrigger` WRITE,`delay` WRITE,`eventassignment` WRITE,`rules` WRITE" + ";"; for (modellist modelids : modelidlist) { ArrayList<modellist> modellevel = sql.getmodeldetails(modelids.getId()); for (modellist modellv : modellevel) { level = modellv.getlevel(); version = modellv.getversion(); } SBMLDocument doc = new SBMLDocument(level, version); ArrayList<modellist> modellists = sql.getmodeldetails(modelids.getId()); if (!modellists.isEmpty()) insertmodel = insertmodel + "\nInsert Into model (id, name,SBML_level,version,notes,annotation) Values"; for (modellist models : modellists) { insertmodel = insertmodel + "(\'" + models.getId() + "\',\'" + models.getName() + "\'," + models.getlevel() + "," + models.getversion() + ",\'" + models.getnotes() + "\',\'" + models.getannotation().toString() + "\'),"; model = doc.createModel(models.getId()); model.setName(models.getName()); // System.out.println("model : " + models.getId()); // model.setNotes(models.getnotes()); // there is some null exception is command line run // but run perfectly from netbeans so ommented out if (!models.getannotation().equals("")) { Annotation annot = new Annotation(models.getannotation().toString()); model.setAnnotation(annot); } doc.setModel(model); } if (!modellists.isEmpty()) { insertmodel = insertmodel.substring(0, insertmodel.length() - 1); insertmodel = insertmodel + ';'; } // insertmodel = insertmodel + "\nUNLOCK TABLES;"; // System.out.println(insertmodel); ArrayList<SpeciesList> specieslist = sql.getspecies(modelids.getId()); if (!specieslist.isEmpty()) insertspecies = insertspecies + "\nInsert Into species (id, name, compartment, initialAmount, initialConcentration,substanceUnits,hasOnlySubstanceUnits,boundaryCondition,constant,conversionFactor,model_id,annotation) Values"; for (SpeciesList species : specieslist) { insertspecies = insertspecies + "(\'" + species.getId() + "\',\'" + species.getName() + "\',\'" + species.getcompartment() + "\'," + species.getia() + "," + species.getic() + ",\'" + species.getsu() + "\'," + species.gethosu() + "," + species.getbc() + "," + species.getconstant() + "," + species.getcf() + ",\'" + modelids.getId() + "\',\'" + species.getannotation() + "\'),"; Species sp = doc.getModel().createSpecies(species.getId()); sp.setName(species.getName()); sp.setCompartment(species.getcompartment()); sp.setConstant(species.getconstant()); sp.setInitialAmount(species.getia()); sp.setInitialConcentration(species.getic()); sp.setHasOnlySubstanceUnits(species.gethosu()); if (doc.getModel().getLevel() == 3) sp.setConversionFactor(species.getcf()); sp.setBoundaryCondition(species.getbc()); sp.setSubstanceUnits(species.getsu()); if (!species.getannotation().equals("")) { Annotation annot = new Annotation(species.getannotation().toString()); sp.setAnnotation(annot); } // doc.getModel().addSpecies(sp) ; } if (!specieslist.isEmpty()) { insertspecies = insertspecies.substring(0, insertspecies.length() - 1); insertspecies = insertspecies + ';'; } ArrayList<CompartmentList> complist = sql.getcompartments(modelids.getId()); if (!complist.isEmpty()) insertcompartment = insertcompartment + "\nInsert Into compartment (id, name,constant,model_id,spacialDimensions,size,units) Values"; for (CompartmentList comp : complist) { insertcompartment = insertcompartment + "(\'" + comp.getId() + "\',\'" + comp.getName() + "\'," + comp.getconstant() + ",\'" + modelids.getId() + "\'," + comp.getspatialdimensions() + "," + comp.getsize() + "," + comp.getunits() + "\'),"; Compartment c = doc.getModel().createCompartment(comp.getId()); c.setName(comp.getName()); c.setConstant(comp.getconstant()); c.setSize(comp.getsize()); c.setSpatialDimensions(comp.getspatialdimensions()); if (comp.getspatialdimensions() != 0) c.setUnits(comp.getunits()); // doc.getModel().addSpecies(sp) ; } if (!complist.isEmpty()) { insertcompartment = insertcompartment.substring(0, insertcompartment.length() - 1); insertcompartment = insertcompartment + ';'; } ArrayList<functionList> funclist = sql.getfunctions(modelids.getId()); if (!funclist.isEmpty()) insertfunction = insertfunction + "\nInsert Into functiondefinition (id, xmlns,model_id) Values"; for (functionList func : funclist) { insertfunction = insertfunction + "(\'" + func.getId() + "\',\'" + func.getxmlns() + "\',\'" + modelids.getId() + "\'),"; FunctionDefinition fd = doc.getModel().createFunctionDefinition(func.getId()); try { math = ASTNode.parseFormula(func.getxmlns()); fd.setMath(math); } catch (Exception e) { e.printStackTrace(); } } if (!funclist.isEmpty()) { insertfunction = insertfunction.substring(0, insertfunction.length() - 1); insertfunction = insertfunction + ';'; } ArrayList<unitList> unitlist = sql.getunitlist(modelids.getId()); if (!unitlist.isEmpty()) insertunitdef = insertunitdef + "\nInsert Into listofunitdefinitions (id,name,model_id) Values"; for (unitList units : unitlist) { insertunitdef = insertunitdef + "(\'" + units.getId() + "\',\'" + units.getName() + "\',\'" + modelids.getId() + "\'),"; UnitDefinition ud = doc.getModel().createUnitDefinition(units.getId()); ud.setName(units.getName()); ArrayList<unitList> unitdeflist = sql.getunitdef(units.getId()); if (!unitdeflist.isEmpty()) insertunits = insertunits + "\nInsert Into listofunits (listofunitdefinitions_id,kind, scale,exponent,multiplier) Values"; for (unitList unitdef : unitdeflist) { insertunits = insertunits + "(\'" + units.getId() + "\',\'" + unitdef.getkind() + "\'," + unitdef.getscale() + "," + unitdef.getexponent() + "," + unitdef.getmultiplier() + "),"; Unit u = ud.createUnit(Unit.Kind.valueOf(unitdef.getkind())); u.setScale(unitdef.getscale()); u.setExponent(unitdef.getexponent()); u.setMultiplier(unitdef.getmultiplier()); } // doc.getModel().addSpecies(sp) ; if (!unitdeflist.isEmpty()) { insertunits = insertunits.substring(0, insertunits.length() - 1); insertunits = insertunits + ';'; } } if (!unitlist.isEmpty()) { insertunitdef = insertunitdef.substring(0, insertunitdef.length() - 1); insertunitdef = insertunitdef + ';'; } ArrayList<reactionList> reactionlist = sql.getreactons(modelids.getId()); if (!reactionlist.isEmpty()) insertreaction = insertreaction + "\nInsert Into reaction (id,name, reversible,fast,model_id,compartment,annotation) Values"; for (reactionList reaction : reactionlist) { insertreaction = insertreaction + "(\'" + reaction.getId() + "\',\'" + reaction.getName() + "\'," + reaction.getreversible() + "," + reaction.getfast() + ",\'" + modelids.getId() + "\',\'" + reaction.getcompartment() + "\',\'" + reaction.getannotation() + "\'),"; Reaction rn = doc.getModel().createReaction(reaction.getId()); rn.setName(reaction.getName()); if (doc.getModel().getLevel() == 3) rn.setCompartment(reaction.getcompartment()); rn.setFast(reaction.getfast()); rn.setReversible(reaction.getreversible()); if (!reaction.getannotation().equals("")) { Annotation annot = new Annotation(reaction.getannotation().toString()); rn.setAnnotation(annot); } ArrayList<reactionList> reactantlist = sql.getreactants(reaction.getId()); if (!reactantlist.isEmpty()) insertreactant = insertreactant + "\nInsert Into simplespeciesreference (reaction_id,species, sboTerm,stoichiometry,speciestype,constant) Values"; for (reactionList reactant : reactantlist) { insertreactant = insertreactant + "(\'" + reaction.getId() + "\',\'" + reactant.getspecies() + "\',\'" + reactant.getsboTerm() + "\'," + reactant.getstoichometry() + "," + reactant.getconstant() + ",\'reactants\'),"; SpeciesReference rt = new SpeciesReference(); rt.setName(reactant.getspecies()); rt.setSpecies(reactant.getspecies()); // rt.setSBOTerm(reactant.getsboTerm()); rt.setStoichiometry(reactant.getstoichometry()); // rt.setConstant(reactant.getconstant()); rn.addReactant(rt); } if (!reactantlist.isEmpty()) { insertreactant = insertreactant.substring(0, insertreactant.length() - 1); insertreactant = insertreactant + ';'; } ArrayList<reactionList> productlist = sql.getproducts(reaction.getId()); if (!productlist.isEmpty()) insertproduct = insertproduct + "\nInsert Into simplespeciesreference (reaction_id,species, sboTerm,stoichiometry,constant,speciestype) Values"; for (reactionList product : productlist) { insertproduct = insertproduct + "(\'" + reaction.getId() + "\',\'" + product.getspecies() + "\',\'" + product.getsboTerm() + "\'," + product.getstoichometry() + "," + product.getconstant() + ",\'products\'),"; SpeciesReference pr = new SpeciesReference(); pr.setName(product.getspecies()); pr.setSpecies(product.getspecies()); // pr.setSBOTerm(product.getsboTerm()); pr.setStoichiometry(product.getstoichometry()); // pr.setConstant(product.getconstant()); rn.addProduct(pr); } if (!productlist.isEmpty()) { insertproduct = insertproduct.substring(0, insertproduct.length() - 1); insertproduct = insertproduct + ';'; } ArrayList<reactionList> modifierlist = sql.getmodifiers(reaction.getId()); if (!modifierlist.isEmpty()) insertmodifier = insertmodifier + "\nInsert Into modifierspeciesreference (reaction_id,species, sboTerm,speciestype) Values"; for (reactionList modifier : modifierlist) { insertmodifier = insertmodifier + "(\'" + reaction.getId() + "\',\'" + modifier.getspecies() + "\',\'" + modifier.getsboTerm() + "\',\'modifiers\'),"; ModifierSpeciesReference m = new ModifierSpeciesReference(); m.setName(modifier.getspecies()); m.setSpecies(modifier.getspecies()); // m.setSBOTerm(modifier.getsboTerm()); rn.addModifier(m); } if (!modifierlist.isEmpty()) { insertmodifier = insertmodifier.substring(0, insertmodifier.length() - 1); insertmodifier = insertmodifier + ';'; } ArrayList<reactionList> klawlist = sql.getkineticlaws(reaction.getId()); if (!klawlist.isEmpty()) insertklaw = insertklaw + "\nInsert Into kineticlaw (reaction_id,kid, math,annotation) Values"; for (reactionList klaw : klawlist) { insertklaw = insertklaw + "(\'" + reaction.getId() + "\',\'" + klaw.getId() + "\',\'" + klaw.getmath() + "\',\'" + klaw.getannotation() + "\'),"; KineticLaw kl = rn.createKineticLaw(); try { math = ASTNode.parseFormula(klaw.getmath()); kl.setMath(math); if (!klaw.getannotation().equals("")) { Annotation annot = new Annotation(klaw.getannotation().toString()); kl.setAnnotation(annot); } } catch (Exception e) { e.printStackTrace(); } } if (!klawlist.isEmpty()) { insertklaw = insertklaw.substring(0, insertklaw.length() - 1); insertklaw = insertklaw + ';'; } } if (!reactionlist.isEmpty()) { insertreaction = insertreaction.substring(0, insertreaction.length() - 1); insertreaction = insertreaction + ';'; } ArrayList<parameterList> paralist = sql.getparameters(modelids.getId()); if (!paralist.isEmpty()) insertparameter = insertparameter + "\nInsert Into parameter (id,name,value,units,constant,model_id) Values"; for (parameterList para : paralist) { insertparameter = insertparameter + "(\'" + para.getId() + "\',\'" + para.getName() + "\'," + para.getvalue() + "," + para.getunits() + "," + para.getconstant() + ",\'" + modelids.getId() + "\'),"; Parameter par = doc.getModel().createParameter(para.getId()); par.setName(para.getId()); par.setConstant(para.getconstant()); par.setUnits(para.getunits()); par.setValue(para.getvalue()); } if (!paralist.isEmpty()) { insertparameter = insertparameter.substring(0, insertparameter.length() - 1); insertparameter = insertparameter + ';'; } ArrayList<constraintList> conslist = sql.getconstraints(modelids.getId()); if (!conslist.isEmpty()) insertconstraint = insertconstraint + "\nInsert Into sbmlconstraint (math,message,model_id) Values"; for (constraintList constraint : conslist) { insertconstraint = insertconstraint + "(\'" + constraint.getmath() + "\',\'" + constraint.getmessage() + "\',\'" + modelids.getId() + "\'),"; Constraint cons = doc.getModel().createConstraint(); try { math = ASTNode.parseFormula(constraint.getmath()); cons.setMath(math); cons.setMessage(constraint.getmessage()); } catch (Exception e) { e.printStackTrace(); } } if (!conslist.isEmpty()) { insertconstraint = insertconstraint.substring(0, insertconstraint.length() - 1); insertconstraint = insertconstraint + ';'; } ArrayList<eventsList> eventlist = sql.getevents(modelids.getId()); if (!eventlist.isEmpty()) insertevent = insertevent + "\nInsert Into event (id,name,UseValuesFromTriggerTime,model_id) Values"; for (eventsList events : eventlist) { insertevent = insertevent + "(\'" + events.getId() + "\',\'" + events.getName() + "\'," + events.getuservalues() + ",\'" + modelids.getId() + "\'),"; Event ev = doc.getModel().createEvent(events.getId()); ev.setName(events.getName()); // ev.setUseValuesFromTriggerTime(events.getuservalues()); ArrayList<eventsList> triggerlist = sql.gettriggers(events.getId()); if (!triggerlist.isEmpty()) inserttrigger = inserttrigger + "\nInsert Into sbmltrigger (event_id,initialvalue,persisent,math) Values"; for (eventsList triggers : triggerlist) { Trigger tr = doc.getModel().createTrigger(); try { math = ASTNode.parseFormula(triggers.getmath()); tr.setMath(math); tr.setInitialValue(triggers.getinitialval()); tr.setPersistent(triggers.getpersistent()); } catch (Exception e) { e.printStackTrace(); } } if (!triggerlist.isEmpty()) { inserttrigger = inserttrigger.substring(0, insertmodel.length() - 1); inserttrigger = inserttrigger + ';'; } ArrayList<eventsList> delaylist = sql.getdelays(events.getId()); if (!delaylist.isEmpty()) insertdelay = insertdelay + "\nInsert Into delay (event_id,math) Values"; for (eventsList delays : delaylist) { Delay d = doc.getModel().createDelay(); try { math = ASTNode.parseFormula(delays.getmath()); d.setMath(math); } catch (Exception e) { e.printStackTrace(); } } if (!delaylist.isEmpty()) { insertdelay = insertdelay.substring(0, insertdelay.length() - 1); insertdelay = insertdelay + ';'; } ArrayList<eventsList> evasslist = sql.geteventassignments(events.getId()); if (!evasslist.isEmpty()) inserteventassign = inserteventassign + "\nInsert Into eventassignment (event_id,variable,math) Values"; for (eventsList evassign : evasslist) { EventAssignment ea = doc.getModel().createEventAssignment(); try { math = ASTNode.parseFormula(evassign.getmath()); ea.setMath(math); } catch (Exception e) { e.printStackTrace(); } } if (!evasslist.isEmpty()) { inserteventassign = inserteventassign.substring(0, inserteventassign.length() - 1); inserteventassign = inserteventassign + ';'; } } if (!eventlist.isEmpty()) { insertevent = insertevent.substring(0, insertevent.length() - 1); insertevent = insertevent + ';'; } ArrayList<ruleslist> rulelist = sql.getrules(modelids.getId()); if (!rulelist.isEmpty()) insertrules = insertrules + "\nInsert Into rules (id,math,ruletype,model_id) Values"; for (ruleslist rules : rulelist) { insertrules = insertrules + "(\'" + rules.getId() + "\',\'" + rules.getmath() + "\',\'" + rules.getruletype() + "\',\'" + modelids.getId() + "\'),"; if (rules.getruletype().equals("assignmentrule")) { Rule r = doc.getModel().createAssignmentRule(); r.setMetaId(rules.getId()); try { math = ASTNode.parseFormula(rules.getmath()); r.setMath(math); } catch (Exception e) { e.printStackTrace(); } } } if (!rulelist.isEmpty()) { insertrules = insertrules.substring(0, insertrules.length() - 1); insertrules = insertrules + ';'; } SBMLWriter writer = new SBMLWriter(); try { String Path = filepath + modelids.getId() + ".xml"; writer.write(doc, Path); DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance(); DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder(); Document document = documentBuilder.parse(Path); Element root = document.getDocumentElement(); Element newdataset = document.createElement("dataset"); root.appendChild(newdataset); ArrayList<dataset> datasetlist = sql.getdataset(modelids.getId()); for (dataset ds : datasetlist) { // System.out.println(ds.getexpcond()); Element name = document.createElement("experimentalcondition"); name.setAttribute("bioelement", ds.getbioel()); name.setAttribute("name", ds.getName()); name.setAttribute("descr", ds.getdescr()); name.setAttribute("expcond", ds.getexpcond()); name.setAttribute("value", String.valueOf(ds.getvalue())); name.setAttribute("type", ds.gettype()); name.setAttribute("uri", ds.geturi()); newdataset.appendChild(name); } root.appendChild(newdataset); DOMSource source = new DOMSource(document); TransformerFactory transformerFactory = TransformerFactory.newInstance(); Transformer transformer = transformerFactory.newTransformer(); transformer.setOutputProperty(OutputKeys.INDENT, "yes"); transformer.setOutputProperty(OutputKeys.METHOD, "xml"); transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "4"); StreamResult result = new StreamResult(filepath + modelids.getId() + "d.xml"); transformer.transform(source, result); System.out.println( "Files : " + modelids.getId() + ".xml and " + modelids.getId() + "d.xml have been generated successfully !!!"); } catch (Exception e) { e.printStackTrace(); } insertstatement = insertstatement + "\n\n" + insertmodel + "\n" + insertspecies + "\n" + insertcompartment + "\n" + insertfunction; insertstatement = insertstatement + "\n" + insertparameter + "\n" + insertreaction + "\n" + insertreactant + "\n" + insertproduct; insertstatement = insertstatement + "\n" + insertmodifier + "\n" + insertklaw + "\n" + insertunitdef + "\n" + insertunits; insertstatement = insertstatement + "\n" + insertrules + "\n" + insertconstraint + "\n" + insertevent + "\n" + inserttrigger + "\n" + insertdelay + "\n" + inserteventassign; insertcompartment = ""; insertmodel = ""; insertspecies = ""; // System.out.println("document : " + doc); } insertstatement = insertstatement + "\nUNLOCK TABLES;"; Filedata = Filedata + "\n\n\n" + insertstatement; try { wrtireStringToFile(Filedata, filepath + "sbmldb.sql"); } catch (IOException e) { e.printStackTrace(); } // System.out.println(insertstatement); }
/** * Draws a concreteDiagram as an SVG. * * <p>This approach is wholly declarative. It currently knows nothing about the on screen * rendering of the diagram. To make decisions based on the on screen rendering (such as better * label placement) we will, in future, have to build a GVT (from the Batik library) of the * SVGDocument. * * @returns An SVGDocument DOM structure representing the SVG. */ @Override public SVGDocument toSVG(ConcreteDiagram cd) { // Get a DOMImplementation. DOMImplementation domImpl = SVGDOMImplementation.getDOMImplementation(); // Create an instance of org.w3c.dom.Document. String svgNS = SVGDOMImplementation.SVG_NAMESPACE_URI; SVGDocument document = (SVGDocument) domImpl.createDocument(svgNS, "svg", null); // Get the root element (the 'svg' element). Element svgRoot = document.getDocumentElement(); // Set the width and height attributes on the root 'svg' element. svgRoot.setAttributeNS(null, "width", Integer.toString(cd.getSize())); svgRoot.setAttributeNS(null, "height", Integer.toString(cd.getSize())); // Draw the shaded zones for (ConcreteZone z : cd.getShadedZones()) { Element path = document.createElementNS(svgNS, "path"); path.setAttributeNS(null, "d", toSVGPath(z.getShape(cd.getBox()))); path.setAttributeNS(null, "fill", "#cccccc"); // grey path.setAttributeNS(null, "z-index", Integer.toString(zOrder.SHADING.ordinal())); svgRoot.appendChild(path); } // TODO: Concrete* should return themselves as DocumentFragments for (CircleContour c : cd.getCircles()) { // Draw the circle Element circle = document.createElementNS(svgNS, "circle"); circle.setAttributeNS(null, "cx", Double.toString(c.get_cx())); circle.setAttributeNS(null, "cy", Double.toString(c.get_cy())); circle.setAttributeNS(null, "r", Double.toString(c.get_radius())); circle.setAttributeNS(null, "z-index", Integer.toString(zOrder.CONTOUR.ordinal())); // Not pretty, but it works. Color strokeColor = c.color(); circle.setAttributeNS( null, "stroke", (null == strokeColor) ? "black" : "#" + toHexString(c.color())); circle.setAttributeNS(null, "stroke-width", "2"); circle.setAttributeNS(null, "fill", "none"); svgRoot.appendChild(circle); // TODO: Put this text in a path around the circle // alternatively come up with some better label placement // algorithm Element text = document.createElementNS(svgNS, "text"); text.setAttributeNS(null, "x", Double.toString(c.get_cx())); text.setAttributeNS(null, "y", Double.toString(c.get_cy() + c.get_radius())); text.setAttributeNS(null, "text-anchor", "middle"); text.setAttributeNS( null, "fill", (null == strokeColor) ? "black" : "#" + toHexString(c.color())); text.setAttributeNS(null, "z-index", Integer.toString(zOrder.LABEL.ordinal())); Text textNode = document.createTextNode(c.ac.getLabel().getLabel()); text.appendChild(textNode); svgRoot.appendChild(text); } for (ConcreteSpider cs : cd.getSpiders()) { for (ConcreteSpiderFoot f : cs.feet) { // Draw the foot Element circle = document.createElementNS(svgNS, "circle"); circle.setAttributeNS(null, "cx", Double.toString(f.getX())); circle.setAttributeNS(null, "cy", Double.toString(f.getY())); circle.setAttributeNS(null, "r", Double.toString(ConcreteSpiderFoot.FOOT_RADIUS)); circle.setAttributeNS(null, "z-index", Integer.toString(zOrder.SPIDER.ordinal())); circle.setAttributeNS(null, "stroke", "black"); circle.setAttributeNS(null, "stroke-width", "2"); circle.setAttributeNS(null, "fill", "black"); svgRoot.appendChild(circle); } for (ConcreteSpiderLeg l : cs.legs) { Element line = document.createElementNS(svgNS, "line"); line.setAttributeNS(null, "x1", Double.toString(l.from.getX())); line.setAttributeNS(null, "y1", Double.toString(l.from.getY())); line.setAttributeNS(null, "x2", Double.toString(l.to.getX())); line.setAttributeNS(null, "y2", Double.toString(l.to.getY())); line.setAttributeNS(null, "z-index", Integer.toString(zOrder.SPIDER.ordinal())); line.setAttributeNS(null, "stroke", "black"); line.setAttributeNS(null, "stroke-width", "2"); line.setAttributeNS(null, "fill", "black"); svgRoot.appendChild(line); } } return document; }
public void build_bricks() { ImagePlus imp; ImagePlus orgimp; ImageStack stack; FileInfo finfo; if (lvImgTitle.isEmpty()) return; orgimp = WindowManager.getImage(lvImgTitle.get(0)); imp = orgimp; finfo = imp.getFileInfo(); if (finfo == null) return; int[] dims = imp.getDimensions(); int imageW = dims[0]; int imageH = dims[1]; int nCh = dims[2]; int imageD = dims[3]; int nFrame = dims[4]; int bdepth = imp.getBitDepth(); double xspc = finfo.pixelWidth; double yspc = finfo.pixelHeight; double zspc = finfo.pixelDepth; double z_aspect = Math.max(xspc, yspc) / zspc; int orgW = imageW; int orgH = imageH; int orgD = imageD; double orgxspc = xspc; double orgyspc = yspc; double orgzspc = zspc; lv = lvImgTitle.size(); if (filetype == "JPEG") { for (int l = 0; l < lv; l++) { if (WindowManager.getImage(lvImgTitle.get(l)).getBitDepth() != 8) { IJ.error("A SOURCE IMAGE MUST BE 8BIT GLAYSCALE"); return; } } } // calculate levels /* int baseXY = 256; int baseZ = 256; if (z_aspect < 0.5) baseZ = 128; if (z_aspect > 2.0) baseXY = 128; if (z_aspect >= 0.5 && z_aspect < 1.0) baseZ = (int)(baseZ*z_aspect); if (z_aspect > 1.0 && z_aspect <= 2.0) baseXY = (int)(baseXY/z_aspect); IJ.log("Z_aspect: " + z_aspect); IJ.log("BaseXY: " + baseXY); IJ.log("BaseZ: " + baseZ); */ int baseXY = 256; int baseZ = 128; int dbXY = Math.max(orgW, orgH) / baseXY; if (Math.max(orgW, orgH) % baseXY > 0) dbXY *= 2; int dbZ = orgD / baseZ; if (orgD % baseZ > 0) dbZ *= 2; lv = Math.max(log2(dbXY), log2(dbZ)) + 1; int ww = orgW; int hh = orgH; int dd = orgD; for (int l = 0; l < lv; l++) { int bwnum = ww / baseXY; if (ww % baseXY > 0) bwnum++; int bhnum = hh / baseXY; if (hh % baseXY > 0) bhnum++; int bdnum = dd / baseZ; if (dd % baseZ > 0) bdnum++; if (bwnum % 2 == 0) bwnum++; if (bhnum % 2 == 0) bhnum++; if (bdnum % 2 == 0) bdnum++; int bw = (bwnum <= 1) ? ww : ww / bwnum + 1 + (ww % bwnum > 0 ? 1 : 0); int bh = (bhnum <= 1) ? hh : hh / bhnum + 1 + (hh % bhnum > 0 ? 1 : 0); int bd = (bdnum <= 1) ? dd : dd / bdnum + 1 + (dd % bdnum > 0 ? 1 : 0); bwlist.add(bw); bhlist.add(bh); bdlist.add(bd); IJ.log("LEVEL: " + l); IJ.log(" width: " + ww); IJ.log(" hight: " + hh); IJ.log(" depth: " + dd); IJ.log(" bw: " + bw); IJ.log(" bh: " + bh); IJ.log(" bd: " + bd); int xyl2 = Math.max(ww, hh) / baseXY; if (Math.max(ww, hh) % baseXY > 0) xyl2 *= 2; if (lv - 1 - log2(xyl2) <= l) { ww /= 2; hh /= 2; } IJ.log(" xyl2: " + (lv - 1 - log2(xyl2))); int zl2 = dd / baseZ; if (dd % baseZ > 0) zl2 *= 2; if (lv - 1 - log2(zl2) <= l) dd /= 2; IJ.log(" zl2: " + (lv - 1 - log2(zl2))); if (l < lv - 1) { lvImgTitle.add(lvImgTitle.get(0) + "_level" + (l + 1)); IJ.selectWindow(lvImgTitle.get(0)); IJ.run( "Scale...", "x=- y=- z=- width=" + ww + " height=" + hh + " depth=" + dd + " interpolation=Bicubic average process create title=" + lvImgTitle.get(l + 1)); } } for (int l = 0; l < lv; l++) { IJ.log(lvImgTitle.get(l)); } Document doc = newXMLDocument(); Element root = doc.createElement("BRK"); root.setAttribute("version", "1.0"); root.setAttribute("nLevel", String.valueOf(lv)); root.setAttribute("nChannel", String.valueOf(nCh)); root.setAttribute("nFrame", String.valueOf(nFrame)); doc.appendChild(root); for (int l = 0; l < lv; l++) { IJ.showProgress(0.0); int[] dims2 = imp.getDimensions(); IJ.log( "W: " + String.valueOf(dims2[0]) + " H: " + String.valueOf(dims2[1]) + " C: " + String.valueOf(dims2[2]) + " D: " + String.valueOf(dims2[3]) + " T: " + String.valueOf(dims2[4]) + " b: " + String.valueOf(bdepth)); bw = bwlist.get(l).intValue(); bh = bhlist.get(l).intValue(); bd = bdlist.get(l).intValue(); boolean force_pow2 = false; /* if(IsPowerOf2(bw) && IsPowerOf2(bh) && IsPowerOf2(bd)) force_pow2 = true; if(force_pow2){ //force pow2 if(Pow2(bw) > bw) bw = Pow2(bw)/2; if(Pow2(bh) > bh) bh = Pow2(bh)/2; if(Pow2(bd) > bd) bd = Pow2(bd)/2; } if(bw > imageW) bw = (Pow2(imageW) == imageW) ? imageW : Pow2(imageW)/2; if(bh > imageH) bh = (Pow2(imageH) == imageH) ? imageH : Pow2(imageH)/2; if(bd > imageD) bd = (Pow2(imageD) == imageD) ? imageD : Pow2(imageD)/2; */ if (bw > imageW) bw = imageW; if (bh > imageH) bh = imageH; if (bd > imageD) bd = imageD; if (bw <= 1 || bh <= 1 || bd <= 1) break; if (filetype == "JPEG" && (bw < 8 || bh < 8)) break; Element lvnode = doc.createElement("Level"); lvnode.setAttribute("lv", String.valueOf(l)); lvnode.setAttribute("imageW", String.valueOf(imageW)); lvnode.setAttribute("imageH", String.valueOf(imageH)); lvnode.setAttribute("imageD", String.valueOf(imageD)); lvnode.setAttribute("xspc", String.valueOf(xspc)); lvnode.setAttribute("yspc", String.valueOf(yspc)); lvnode.setAttribute("zspc", String.valueOf(zspc)); lvnode.setAttribute("bitDepth", String.valueOf(bdepth)); root.appendChild(lvnode); Element brksnode = doc.createElement("Bricks"); brksnode.setAttribute("brick_baseW", String.valueOf(bw)); brksnode.setAttribute("brick_baseH", String.valueOf(bh)); brksnode.setAttribute("brick_baseD", String.valueOf(bd)); lvnode.appendChild(brksnode); ArrayList<Brick> bricks = new ArrayList<Brick>(); int mw, mh, md, mw2, mh2, md2; double tx0, ty0, tz0, tx1, ty1, tz1; double bx0, by0, bz0, bx1, by1, bz1; for (int k = 0; k < imageD; k += bd) { if (k > 0) k--; for (int j = 0; j < imageH; j += bh) { if (j > 0) j--; for (int i = 0; i < imageW; i += bw) { if (i > 0) i--; mw = Math.min(bw, imageW - i); mh = Math.min(bh, imageH - j); md = Math.min(bd, imageD - k); if (force_pow2) { mw2 = Pow2(mw); mh2 = Pow2(mh); md2 = Pow2(md); } else { mw2 = mw; mh2 = mh; md2 = md; } if (filetype == "JPEG") { if (mw2 < 8) mw2 = 8; if (mh2 < 8) mh2 = 8; } tx0 = i == 0 ? 0.0d : ((mw2 - mw + 0.5d) / mw2); ty0 = j == 0 ? 0.0d : ((mh2 - mh + 0.5d) / mh2); tz0 = k == 0 ? 0.0d : ((md2 - md + 0.5d) / md2); tx1 = 1.0d - 0.5d / mw2; if (mw < bw) tx1 = 1.0d; if (imageW - i == bw) tx1 = 1.0d; ty1 = 1.0d - 0.5d / mh2; if (mh < bh) ty1 = 1.0d; if (imageH - j == bh) ty1 = 1.0d; tz1 = 1.0d - 0.5d / md2; if (md < bd) tz1 = 1.0d; if (imageD - k == bd) tz1 = 1.0d; bx0 = i == 0 ? 0.0d : (i + 0.5d) / (double) imageW; by0 = j == 0 ? 0.0d : (j + 0.5d) / (double) imageH; bz0 = k == 0 ? 0.0d : (k + 0.5d) / (double) imageD; bx1 = Math.min((i + bw - 0.5d) / (double) imageW, 1.0d); if (imageW - i == bw) bx1 = 1.0d; by1 = Math.min((j + bh - 0.5d) / (double) imageH, 1.0d); if (imageH - j == bh) by1 = 1.0d; bz1 = Math.min((k + bd - 0.5d) / (double) imageD, 1.0d); if (imageD - k == bd) bz1 = 1.0d; int x, y, z; x = i - (mw2 - mw); y = j - (mh2 - mh); z = k - (md2 - md); bricks.add( new Brick( x, y, z, mw2, mh2, md2, 0, 0, tx0, ty0, tz0, tx1, ty1, tz1, bx0, by0, bz0, bx1, by1, bz1)); } } } Element fsnode = doc.createElement("Files"); lvnode.appendChild(fsnode); stack = imp.getStack(); int totalbricknum = nFrame * nCh * bricks.size(); int curbricknum = 0; for (int f = 0; f < nFrame; f++) { for (int ch = 0; ch < nCh; ch++) { int sizelimit = bdsizelimit * 1024 * 1024; int bytecount = 0; int filecount = 0; int pd_bufsize = Math.max(sizelimit, bw * bh * bd * bdepth / 8); byte[] packed_data = new byte[pd_bufsize]; String base_dataname = basename + "_Lv" + String.valueOf(l) + "_Ch" + String.valueOf(ch) + "_Fr" + String.valueOf(f); String current_dataname = base_dataname + "_data" + filecount; Brick b_first = bricks.get(0); if (b_first.z_ != 0) IJ.log("warning"); int st_z = b_first.z_; int ed_z = b_first.z_ + b_first.d_; LinkedList<ImageProcessor> iplist = new LinkedList<ImageProcessor>(); for (int s = st_z; s < ed_z; s++) iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1))); // ImagePlus test; // ImageStack tsst; // test = NewImage.createByteImage("test", imageW, imageH, imageD, // NewImage.FILL_BLACK); // tsst = test.getStack(); for (int i = 0; i < bricks.size(); i++) { Brick b = bricks.get(i); if (ed_z > b.z_ || st_z < b.z_ + b.d_) { if (b.z_ > st_z) { for (int s = 0; s < b.z_ - st_z; s++) iplist.pollFirst(); st_z = b.z_; } else if (b.z_ < st_z) { IJ.log("warning"); for (int s = st_z - 1; s > b.z_; s--) iplist.addFirst(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1))); st_z = b.z_; } if (b.z_ + b.d_ > ed_z) { for (int s = ed_z; s < b.z_ + b.d_; s++) iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1))); ed_z = b.z_ + b.d_; } else if (b.z_ + b.d_ < ed_z) { IJ.log("warning"); for (int s = 0; s < ed_z - (b.z_ + b.d_); s++) iplist.pollLast(); ed_z = b.z_ + b.d_; } } else { IJ.log("warning"); iplist.clear(); st_z = b.z_; ed_z = b.z_ + b.d_; for (int s = st_z; s < ed_z; s++) iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1))); } if (iplist.size() != b.d_) { IJ.log("Stack Error"); return; } // int zz = st_z; int bsize = 0; byte[] bdata = new byte[b.w_ * b.h_ * b.d_ * bdepth / 8]; Iterator<ImageProcessor> ipite = iplist.iterator(); while (ipite.hasNext()) { // ImageProcessor tsip = tsst.getProcessor(zz+1); ImageProcessor ip = ipite.next(); ip.setRoi(b.x_, b.y_, b.w_, b.h_); if (bdepth == 8) { byte[] data = (byte[]) ip.crop().getPixels(); System.arraycopy(data, 0, bdata, bsize, data.length); bsize += data.length; } else if (bdepth == 16) { ByteBuffer buffer = ByteBuffer.allocate(b.w_ * b.h_ * bdepth / 8); buffer.order(ByteOrder.LITTLE_ENDIAN); short[] data = (short[]) ip.crop().getPixels(); for (short e : data) buffer.putShort(e); System.arraycopy(buffer.array(), 0, bdata, bsize, buffer.array().length); bsize += buffer.array().length; } else if (bdepth == 32) { ByteBuffer buffer = ByteBuffer.allocate(b.w_ * b.h_ * bdepth / 8); buffer.order(ByteOrder.LITTLE_ENDIAN); float[] data = (float[]) ip.crop().getPixels(); for (float e : data) buffer.putFloat(e); System.arraycopy(buffer.array(), 0, bdata, bsize, buffer.array().length); bsize += buffer.array().length; } } String filename = basename + "_Lv" + String.valueOf(l) + "_Ch" + String.valueOf(ch) + "_Fr" + String.valueOf(f) + "_ID" + String.valueOf(i); int offset = bytecount; int datasize = bdata.length; if (filetype == "RAW") { int dummy = -1; // do nothing } if (filetype == "JPEG" && bdepth == 8) { try { DataBufferByte db = new DataBufferByte(bdata, datasize); Raster raster = Raster.createPackedRaster(db, b.w_, b.h_ * b.d_, 8, null); BufferedImage img = new BufferedImage(b.w_, b.h_ * b.d_, BufferedImage.TYPE_BYTE_GRAY); img.setData(raster); ByteArrayOutputStream baos = new ByteArrayOutputStream(); ImageOutputStream ios = ImageIO.createImageOutputStream(baos); String format = "jpg"; Iterator<javax.imageio.ImageWriter> iter = ImageIO.getImageWritersByFormatName("jpeg"); javax.imageio.ImageWriter writer = iter.next(); ImageWriteParam iwp = writer.getDefaultWriteParam(); iwp.setCompressionMode(ImageWriteParam.MODE_EXPLICIT); iwp.setCompressionQuality((float) jpeg_quality * 0.01f); writer.setOutput(ios); writer.write(null, new IIOImage(img, null, null), iwp); // ImageIO.write(img, format, baos); bdata = baos.toByteArray(); datasize = bdata.length; } catch (IOException e) { e.printStackTrace(); return; } } if (filetype == "ZLIB") { byte[] tmpdata = new byte[b.w_ * b.h_ * b.d_ * bdepth / 8]; Deflater compresser = new Deflater(); compresser.setInput(bdata); compresser.setLevel(Deflater.DEFAULT_COMPRESSION); compresser.setStrategy(Deflater.DEFAULT_STRATEGY); compresser.finish(); datasize = compresser.deflate(tmpdata); bdata = tmpdata; compresser.end(); } if (bytecount + datasize > sizelimit && bytecount > 0) { BufferedOutputStream fis = null; try { File file = new File(directory + current_dataname); fis = new BufferedOutputStream(new FileOutputStream(file)); fis.write(packed_data, 0, bytecount); } catch (IOException e) { e.printStackTrace(); return; } finally { try { if (fis != null) fis.close(); } catch (IOException e) { e.printStackTrace(); return; } } filecount++; current_dataname = base_dataname + "_data" + filecount; bytecount = 0; offset = 0; System.arraycopy(bdata, 0, packed_data, bytecount, datasize); bytecount += datasize; } else { System.arraycopy(bdata, 0, packed_data, bytecount, datasize); bytecount += datasize; } Element filenode = doc.createElement("File"); filenode.setAttribute("filename", current_dataname); filenode.setAttribute("channel", String.valueOf(ch)); filenode.setAttribute("frame", String.valueOf(f)); filenode.setAttribute("brickID", String.valueOf(i)); filenode.setAttribute("offset", String.valueOf(offset)); filenode.setAttribute("datasize", String.valueOf(datasize)); filenode.setAttribute("filetype", String.valueOf(filetype)); fsnode.appendChild(filenode); curbricknum++; IJ.showProgress((double) (curbricknum) / (double) (totalbricknum)); } if (bytecount > 0) { BufferedOutputStream fis = null; try { File file = new File(directory + current_dataname); fis = new BufferedOutputStream(new FileOutputStream(file)); fis.write(packed_data, 0, bytecount); } catch (IOException e) { e.printStackTrace(); return; } finally { try { if (fis != null) fis.close(); } catch (IOException e) { e.printStackTrace(); return; } } } } } for (int i = 0; i < bricks.size(); i++) { Brick b = bricks.get(i); Element bricknode = doc.createElement("Brick"); bricknode.setAttribute("id", String.valueOf(i)); bricknode.setAttribute("st_x", String.valueOf(b.x_)); bricknode.setAttribute("st_y", String.valueOf(b.y_)); bricknode.setAttribute("st_z", String.valueOf(b.z_)); bricknode.setAttribute("width", String.valueOf(b.w_)); bricknode.setAttribute("height", String.valueOf(b.h_)); bricknode.setAttribute("depth", String.valueOf(b.d_)); brksnode.appendChild(bricknode); Element tboxnode = doc.createElement("tbox"); tboxnode.setAttribute("x0", String.valueOf(b.tx0_)); tboxnode.setAttribute("y0", String.valueOf(b.ty0_)); tboxnode.setAttribute("z0", String.valueOf(b.tz0_)); tboxnode.setAttribute("x1", String.valueOf(b.tx1_)); tboxnode.setAttribute("y1", String.valueOf(b.ty1_)); tboxnode.setAttribute("z1", String.valueOf(b.tz1_)); bricknode.appendChild(tboxnode); Element bboxnode = doc.createElement("bbox"); bboxnode.setAttribute("x0", String.valueOf(b.bx0_)); bboxnode.setAttribute("y0", String.valueOf(b.by0_)); bboxnode.setAttribute("z0", String.valueOf(b.bz0_)); bboxnode.setAttribute("x1", String.valueOf(b.bx1_)); bboxnode.setAttribute("y1", String.valueOf(b.by1_)); bboxnode.setAttribute("z1", String.valueOf(b.bz1_)); bricknode.appendChild(bboxnode); } if (l < lv - 1) { imp = WindowManager.getImage(lvImgTitle.get(l + 1)); int[] newdims = imp.getDimensions(); imageW = newdims[0]; imageH = newdims[1]; imageD = newdims[3]; xspc = orgxspc * ((double) orgW / (double) imageW); yspc = orgyspc * ((double) orgH / (double) imageH); zspc = orgzspc * ((double) orgD / (double) imageD); bdepth = imp.getBitDepth(); } } File newXMLfile = new File(directory + basename + ".vvd"); writeXML(newXMLfile, doc); for (int l = 1; l < lv; l++) { imp = WindowManager.getImage(lvImgTitle.get(l)); imp.changes = false; imp.close(); } }
private void addText(Document doc, Element root, String name, String value) { Element el = doc.createElement(name); Text txt = doc.createTextNode(value); el.appendChild(txt); root.appendChild(el); }
public String saveShow(String fn, ShowFileData showData) { _calendar = new GregorianCalendar(); String showName = showData.getSettings().get(_title) + "_" + _format.format(_calendar.getTime()) + ".show"; try { new File(fn).mkdirs(); FileWriter _fileWriter = new FileWriter(fn + "/" + showName); BufferedWriter _outputFile = new BufferedWriter(_fileWriter); // Create the document Document doc = _impl.createDocument(null, _fileType, null); Element root = doc.getDocumentElement(); Element settings = doc.createElement(_settings); Element patch = doc.createElement(_patch); Element cues = doc.createElement(_cues); Element magic = doc.createElement(_magicSheet); addText(doc, settings, _recordMode, showData.getSettings().get(_recordMode)); addText(doc, settings, _totalChannels, showData.getSettings().get(_totalChannels)); addText(doc, settings, _totalDimmers, showData.getSettings().get(_totalDimmers)); addText(doc, settings, _dUpTime, showData.getSettings().get(_dUpTime)); addText(doc, settings, _dDownTime, showData.getSettings().get(_dDownTime)); addText(doc, settings, _gotoCueTime, showData.getSettings().get(_gotoCueTime)); addText(doc, settings, _title, showData.getSettings().get(_title)); addText(doc, settings, _comment, showData.getSettings().get(_comment)); addText(doc, settings, _channelPerLine, showData.getSettings().get(_channelPerLine)); addText(doc, settings, _channelHGroup, showData.getSettings().get(_channelHGroup)); addText(doc, settings, _channelVGroup, showData.getSettings().get(_channelVGroup)); for (Integer chan : showData.getPatch().keySet()) if (showData.getPatch().get(chan).size() > 0) addChannel(doc, patch, chan, showData.getPatch().get(chan)); for (FadeData fade : showData.getCueList()) addFade(doc, cues, fade); Position p; for (Integer chan : showData.getMagicSheet().keySet()) { MagicChannelData mChan = showData.getMagicSheet().get(chan); if (!(mChan._x == 0 && mChan._x == 0)) addMagicChannel(doc, magic, chan, mChan._x, mChan._y); } root.appendChild(settings); root.appendChild(patch); root.appendChild(cues); root.appendChild(magic); // Serialize the document onto System.out TransformerFactory xformFactory = TransformerFactory.newInstance(); Transformer idTransform = xformFactory.newTransformer(); Source input = new DOMSource(doc); // Result output = new StreamResult(System.out); // idTransform.transform(input, output); Result output = new StreamResult(_outputFile); idTransform.transform(input, output); _outputFile.close(); _fileWriter.close(); } catch (FactoryConfigurationError e) { System.out.println("Could not locate a JAXP factory class"); } catch (DOMException e) { System.err.println(e); } catch (TransformerConfigurationException e) { System.err.println(e); } catch (TransformerException e) { System.err.println(e); } catch (IOException e) { System.err.println(e); } return showName; }
void appendCellToRow(Element tableRow, String content) { Element newCell = document.createElement("td"); newCell.setTextContent(content); tableRow.appendChild(newCell); }
public void CollectData(String link) { try { // Creating an empty XML Document DocumentBuilderFactory dbfac = DocumentBuilderFactory.newInstance(); DocumentBuilder docBuilder = dbfac.newDocumentBuilder(); Document doc = docBuilder.newDocument(); int flag = 0; // create the root element and add it to the document Element movie = doc.createElement("movie"); doc.appendChild(movie); movie.setAttribute("id", String.valueOf(n)); n++; // create sub elements Element genres = doc.createElement("genres"); Element actors = doc.createElement("actors"); Element reviews = doc.createElement("reviews"); URL movieUrl = new URL(link); URL reviewsURL = new URL(link + "reviews/#type=top_critics"); BufferedWriter bw3 = new BufferedWriter(new FileWriter("movies.xml", true)); int count = -1; String auth = ""; BufferedReader br3 = new BufferedReader(new InputStreamReader(movieUrl.openStream())); String str2 = ""; String info = ""; while (null != (str2 = br3.readLine())) { // start reading the html document if (str2.isEmpty()) continue; if (count == 14) break; if (count == 12) { if (!str2.contains("<h3>Cast</h3>")) continue; else count++; } if (count == 13) { if (str2.contains(">ADVERTISEMENT</p>")) { count++; movie.appendChild(actors); continue; } else { if (str2.contains("itemprop=\"name\">")) { Element actor = doc.createElement("actor"); actors.appendChild(actor); Text text = doc.createTextNode(Jsoup.parse(str2.toString()).text()); actor.appendChild(text); } else continue; } } if (count <= 11) { switch (count) { case -1: { if (!str2.contains("property=\"og:image\"")) continue; else { Pattern image = Pattern.compile("http://.*.jpg", Pattern.CASE_INSENSITIVE | Pattern.DOTALL); Matcher match = image.matcher(str2); while (match.find()) { Element imageLink = doc.createElement("imageLink"); movie.appendChild(imageLink); Text text = doc.createTextNode(match.group()); imageLink.appendChild(text); count++; } } break; } case 0: { if (str2.contains("<title>")) { Element name = doc.createElement("name"); movie.appendChild(name); Text text = doc.createTextNode( Jsoup.parse(str2.toString().replace(" - Rotten Tomatoes", "")).text()); name.appendChild(text); count++; } break; } case 1: { if (!str2.contains("itemprop=\"ratingValue\"")) break; else { Element score = doc.createElement("score"); movie.appendChild(score); Text text = doc.createTextNode(Jsoup.parse(str2.toString()).text()); score.appendChild(text); count++; } break; } case 2: { if (!str2.contains("itemprop=\"description\">")) continue; else count++; break; } case 3: { if (!str2.contains("itemprop=\"duration\"")) info = info.concat(str2); else { Element MovieInfo = doc.createElement("MovieInfo"); movie.appendChild(MovieInfo); Text text = doc.createTextNode(Jsoup.parse(info.toString()).text()); MovieInfo.appendChild(text); info = str2; count++; } break; } case 4: { if (!str2.contains("itemprop=\"genre\"")) info = info.concat(str2); else { Element duration = doc.createElement("duration"); movie.appendChild(duration); Text text = doc.createTextNode(Jsoup.parse(info.toString()).text()); duration.appendChild(text); info = str2; count++; } break; } case 5: { if (info.contains("itemprop=\"genre\"")) { Element genre = doc.createElement("genre"); genres.appendChild(genre); Text text = doc.createTextNode(Jsoup.parse(info.toString()).text()); genre.appendChild(text); info = ""; } if (str2.contains(">Directed By:<")) { count++; movie.appendChild(genres); continue; } else { if (str2.contains("itemprop=\"genre\"")) { Element genre = doc.createElement("genre"); genres.appendChild(genre); Text text = doc.createTextNode(Jsoup.parse(str2.toString()).text()); genre.appendChild(text); } else continue; } break; } case 6: { if (!str2.contains(">Written By:<")) { if (str2.contains(">In Theaters:<")) { Element director = doc.createElement("director"); movie.appendChild(director); Text text = doc.createTextNode( Jsoup.parse(info.toString().replace("Directed By: ", "")).text()); director.appendChild(text); info = str2; count += 2; break; } info = info.concat(str2); } else { Element director = doc.createElement("director"); movie.appendChild(director); Text text = doc.createTextNode( Jsoup.parse(info.toString().replace("Directed By: ", "")).text()); director.appendChild(text); info = ""; count++; } break; } case 7: { if (!str2.contains(">In Theaters:<")) { if (str2.contains(">On DVD:<")) { Element writer = doc.createElement("writer"); movie.appendChild(writer); Text text = doc.createTextNode(Jsoup.parse(info.toString()).text()); writer.appendChild(text); info = str2; count += 2; break; } info = info.concat(str2); } else { Element writer = doc.createElement("writer"); movie.appendChild(writer); Text text = doc.createTextNode(Jsoup.parse(info.toString()).text()); writer.appendChild(text); info = str2; count++; } break; } case 8: { if (!str2.contains(">On DVD:<")) info = info.concat(str2); else { Element TheatreRelease = doc.createElement("TheatreRelease"); movie.appendChild(TheatreRelease); Text text = doc.createTextNode( Jsoup.parse(info.toString().replace("In Theaters:", "")).text()); TheatreRelease.appendChild(text); info = str2; count++; } break; } case 9: { if (!str2.contains(">US Box Office:<")) { if (str2.contains("itemprop=\"productionCompany\"")) { Element DvdRelease = doc.createElement("DvdRelease"); movie.appendChild(DvdRelease); Text text = doc.createTextNode( Jsoup.parse(info.toString().replace("On DVD:", "")).text()); DvdRelease.appendChild(text); info = str2; count += 2; break; } info = info.concat(str2); } else { Element DvdRelease = doc.createElement("DvdRelease"); movie.appendChild(DvdRelease); Text text = doc.createTextNode( Jsoup.parse(info.toString().replace("On DVD:", "")).text()); DvdRelease.appendChild(text); info = str2; count++; } break; } case 10: { if (!str2.contains("itemprop=\"productionCompany\"")) info = info.concat(str2); else { Element BOCollection = doc.createElement("BOCollection"); movie.appendChild(BOCollection); Text text = doc.createTextNode( Jsoup.parse(info.toString().replace("US Box Office:", "")).text()); BOCollection.appendChild(text); info = str2; count++; } break; } case 11: { if (!str2.contains(">Official Site")) info = info.concat(str2); else { Element Production = doc.createElement("Production"); movie.appendChild(Production); Text text = doc.createTextNode(Jsoup.parse(info.toString()).text()); Production.appendChild(text); info = str2; count++; } break; } default: break; } } } BufferedReader br4 = new BufferedReader(new InputStreamReader(reviewsURL.openStream())); String str3 = ""; String info2 = ""; int count2 = 0; while (null != (str3 = br4.readLine())) { if (count2 == 0) { if (!str3.contains("<div class=\"reviewsnippet\">")) continue; else count2++; } if (count2 == 1) { if (!str3.contains("<p class=\"small subtle\">")) info2 = info2.concat(str3); else { Element review = doc.createElement("review"); reviews.appendChild(review); Text text = doc.createTextNode(Jsoup.parse(info2.toString()).text()); review.appendChild(text); info2 = ""; count2 = 0; } } } movie.appendChild(reviews); TransformerFactory transfac = TransformerFactory.newInstance(); Transformer trans = transfac.newTransformer(); trans.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes"); trans.setOutputProperty(OutputKeys.INDENT, "yes"); // create string from xml tree StringWriter sw = new StringWriter(); StreamResult result = new StreamResult(sw); DOMSource source = new DOMSource(doc); trans.transform(source, result); String xmlString = sw.toString(); bw3.write(xmlString); br3.close(); br4.close(); bw3.close(); } catch (Exception ex) { ex.printStackTrace(); } }