Example usage for org.jdom2 Document Document

List of usage examples for org.jdom2 Document Document

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Introduction

In this page you can find the example usage for org.jdom2 Document Document.

Prototype

public Document()

Source Link

Document

Creates a new empty document.

Usage

From source file:es.uvigo.ei.sing.rubioseq.gui.view.models.experiments.SingleNucleotideVariantExperiment.java

License:Open Source License

public void generateXMLConfigurationFile(File output) throws IOException {
    Document configurationFile = new Document();
    Element configData = new Element(CONFIG_DATA);
    configurationFile.setRootElement(configData);
    configData.setAttribute(ExperimentUtils.BRANCH, ExperimentUtils.BRANCH_SNV);

    Element genRef = new Element(GENREF);
    genRef.addContent(this.getGenRefPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(genRef);

    Element dbSnpAnnot = new Element(DBSNPANNOT);
    dbSnpAnnot.addContent(this.getDbSnpAnnotPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(dbSnpAnnot);

    Element genomes1000Annot = new Element(GENOMES1000ANNOT);
    genomes1000Annot.addContent(this.getGenomes1000AnnotPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(genomes1000Annot);

    Element indelAnnot = new Element(INDELANNOT);
    indelAnnot.addContent(this.getIndelAnnotPath().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(indelAnnot);

    if (this.getIntervalsPath() != getIntervalsPath_DV()) {
        Element intervals = new Element(INTERVALS);
        intervals.addContent(this.getIntervalsPath().getFile().getAbsolutePath());
        configurationFile.getRootElement().addContent(intervals);
    }/*from ww w .j  a v  a  2  s.  co m*/

    if (this.getKnownIndels().size() > 0) {
        for (KnownIndels kI : this.getKnownIndels()) {
            Element knownIndels = new Element(KNOWNINDELS);
            knownIndels.addContent(kI.getFile().getFile().getAbsolutePath());
            configurationFile.getRootElement().addContent(knownIndels);
        }
    }

    Element plattform = new Element(PLATTFORM);
    plattform.addContent(this.getPlattform().getDisplayName());
    configurationFile.getRootElement().addContent(plattform);

    if (!this.getCheckCasava().equals(checkCasava_DV)) {
        Element checkCasava = new Element(CHECKCASAVA);
        checkCasava.addContent(this.getCheckCasava().toString());
        configurationFile.getRootElement().addContent(checkCasava);
    }

    Element dirOutBase = new Element(DIROUTBASE);
    dirOutBase.addContent(this.getDirOutBase().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(dirOutBase);

    Element projectId = new Element(PROJECTID);
    projectId.addContent(this.getProjectId());
    configurationFile.getRootElement().addContent(projectId);

    if (!this.getUserName().equals(userName_DV)) {
        Element userName = new Element(USERNAME);
        userName.addContent(this.getUserName());
        configurationFile.getRootElement().addContent(userName);
    }

    Element dataInDirpreProcess = new Element(INDIRPREPROCESS);
    dataInDirpreProcess.addContent(this.getDataInDirpreProcess().getFile().getAbsolutePath());
    configurationFile.getRootElement().addContent(dataInDirpreProcess);

    for (Sample s : this.getSamples()) {
        Element sample = new Element(SAMPLE);

        Element sampleName = new Element(SAMPLE_NAME);
        sampleName.addContent(s.getSampleName());
        sample.addContent(sampleName);

        Element sampleFiles = new Element(SAMPLE_FILES);
        sampleFiles.addContent(s.getSampleFiles());
        sample.addContent(sampleFiles);

        Element sampleSuffix = new Element(SAMPLE_SUFFIX);
        sampleSuffix.addContent(s.getSampleSuffix());
        sample.addContent(sampleSuffix);

        Element sampleType = new Element(SAMPLE_TYPE);
        sampleType.addContent(s.getSampleType().getDisplayName());
        sample.addContent(sampleType);

        configurationFile.getRootElement().addContent(sample);
    }

    if (!this.getCallingType().equals(callingType_DV)) {
        Element callingType = new Element(CALLYING_TYPE);
        callingType.addContent(this.getCallingType().toString());
        configurationFile.getRootElement().addContent(callingType);
    }

    if (!this.getgATKoutputMode().equals(gATKoutputMode_DV)) {
        Element gATKoutputModeoutputMode = new Element(GATKOUTPUTMODE);
        gATKoutputModeoutputMode.addContent(this.getgATKoutputMode().toString());
        configurationFile.getRootElement().addContent(gATKoutputModeoutputMode);
    }

    if (!this.getRsFilter().equals(rsFilter_DV)) {
        Element rsFilter = new Element(RSFILTER);
        rsFilter.addContent(this.getRsFilter().toString());
        configurationFile.getRootElement().addContent(rsFilter);
    }

    if (!this.getrUbioSeqMode().equals(rUbioSeqMode_DV)) {
        Element rUbioSeq_Mode = new Element(RUBIOSEQMODE);
        rUbioSeq_Mode.addContent(this.getrUbioSeqMode().toString());
        configurationFile.getRootElement().addContent(rUbioSeq_Mode);
    }

    if (!this.getFastqc().equals(fastqc_DV)) {
        Element fastqc = new Element(FASTQC);
        fastqc.addContent(this.getFastqc().toString());
        configurationFile.getRootElement().addContent(fastqc);
    }

    if (!this.getvEPFlag().equals(vEPFlag_DV)) {
        Element vEPFlag = new Element(VEPFLAG);
        vEPFlag.addContent(this.getvEPFlag().toString());
        configurationFile.getRootElement().addContent(vEPFlag);
    }

    if (!this.gettCFlag().equals(tCFlag_DV)) {
        Element tCFlag = new Element(TCFLAG);
        tCFlag.addContent(this.gettCFlag().toString());
        configurationFile.getRootElement().addContent(tCFlag);
    }

    if (!this.getmDFlag().equals(mDFlag_DV)) {
        Element mDFlag = new Element(MDFLAG);
        mDFlag.addContent(this.getmDFlag().toString());
        configurationFile.getRootElement().addContent(mDFlag);
    }

    if (!this.getStandCallConf().equals(standCallConf_DV)) {
        Element standCallConf = new Element(STANDCALLCONF);
        standCallConf.addContent(this.getStandCallConf().toString());
        configurationFile.getRootElement().addContent(standCallConf);
    }

    if (!this.getStandEmitConf().equals(standEmitConf_DV)) {
        Element standEmitConf = new Element(STANDEMITCONF);
        standEmitConf.addContent(this.getStandEmitConf().toString());
        configurationFile.getRootElement().addContent(standEmitConf);
    }

    if (!this.getQueueSGEProject().equals(queueSGEProject_DV)) {
        Element queueSGEProject = new Element(QUEUESGEPROJECT);
        queueSGEProject.addContent(this.getQueueSGEProject().toString());
        configurationFile.getRootElement().addContent(queueSGEProject);
    }

    if (this.getChoiceVqrsHardFilters().equals(VQRSHardFiltersChoice.VQRS)
            && this.getvQSRblockMills() != VQSRblockMills_DV && this.getvQSRblockHapMAp() != VQSRblockHapMAp_DV
            && this.getvQSRblockThousandG() != VQSRblockThousandG_DV) {

        Element vQSR_block = new Element(VQSRBLOCK);

        Element mills = new Element(MILLS);
        mills.addContent(this.getvQSRblockMills().getFile().getAbsolutePath());
        vQSR_block.addContent(mills);

        Element hapmap = new Element(HAPMAP);
        hapmap.addContent(this.getvQSRblockHapMAp().getFile().getAbsolutePath());
        vQSR_block.addContent(hapmap);

        Element thousandg = new Element(THOUSANDG);
        thousandg.addContent(this.getvQSRblockThousandG().getFile().getAbsolutePath());
        vQSR_block.addContent(thousandg);

        configurationFile.getRootElement().addContent(vQSR_block);
    }

    if (this.getChoiceVqrsHardFilters().equals(VQRSHardFiltersChoice.HARDFILTERS)
            && (!this.getminQual().equals(minQual_DV) || !this.getdPmin().equals(DPmin_DV)
                    || this.getHardFilters().size() > 0)) {

        Element hardFiltersBlock = new Element(HFILTERS);

        if (!this.getdPmin().equals(DPmin_DV)) {
            Element dpMin = new Element(DPMIN);
            dpMin.addContent(this.getdPmin().toString());
            hardFiltersBlock.addContent(dpMin);
        }

        if (!this.getminQual().equals(minQual_DV)) {
            Element minQual = new Element(MINQUAL);
            minQual.addContent(this.getminQual().toString());
            hardFiltersBlock.addContent(minQual);
        }

        for (HardFilter hF : this.getHardFilters()) {
            Element name = hF.getType().equals(HardFilter.HFilterType.SNP) ? new Element(HFILTER_NAME_SNP)
                    : new Element(HFILTER_NAME_INDEL);
            name.addContent(hF.getName());
            Element rule = hF.getType().equals(HardFilter.HFilterType.SNP) ? new Element(HFILTER_RULE_SNP)
                    : new Element(HFILTER_RULE_INDEL);
            rule.addContent(hF.getRule());
            hardFiltersBlock.addContent(name);
            hardFiltersBlock.addContent(rule);
        }

        configurationFile.getRootElement().addContent(hardFiltersBlock);
    }

    XMLOutputter xmlOutput = new XMLOutputter();
    xmlOutput.setFormat(Format.getPrettyFormat());
    xmlOutput.output(configurationFile, new FileWriter(output));
}

From source file:facturacion.xml.FacturaXml.java

public void crearFacturaAutorizadaXml(facturacion.model.beans.RespuestaComprobante autorizaciones) {
    Element root = new Element("autorizacion");
    //root.setAttribute("id", "comprobante");
    //root.setAttribute("version","1.0.0");
    doc = new Document();

    this.doc.setRootElement(root);

    for (facturacion.model.beans.Comprobante autorizacion : autorizaciones.getComprobantes()) {
        root.addContent(new Element("estado").setText(autorizacion.getEstado()));
        root.addContent(new Element("numeroAutorizacion").setText(autorizacion.getNumeroAutorizacion()));
        root.addContent(new Element("fechaAutorizacion").setText("" + autorizacion.getFechaAutorizacion()));
        String cad = "<![CDATA[" + autorizacion.getComprobante() + "]]>";
        byte ptext[] = cad.getBytes();
        //System.out.println("--------------------------------------------===");
        //System.out.println(cad);
        //System.out.println("--------------------------------------------===");

        try {//from  w ww.  j  a va2 s  . com
            cad = (new String(ptext, "UTF-8"));
            //System.out.println(cad);
            //System.out.println("--------------------------------------------===");
            root.addContent(new Element("comprobante").setText(cad));
        } catch (UnsupportedEncodingException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }

        Element mensajes = new Element("mensajes");
        Element mensaje1 = new Element("mensaje");
        for (facturacion.model.beans.Mensaje mensaje : autorizacion.getMensajes()) {
            Element mensaje2 = new Element("mensaje");
            mensaje2.addContent(new Element("identificador").setText(mensaje.getIdentificador()));
            mensaje2.addContent(new Element("informacionAdicional").setText(mensaje.getInformacionAdicional()));
            mensaje2.addContent(new Element("mensaje").setText(mensaje.getMensaje()));
            mensaje2.addContent(new Element("tipo").setText(mensaje.getTipo()));

            mensaje1.addContent(mensaje2);
            break;
        }

        mensajes.addContent(mensaje1);

        root.addContent(mensajes);
        break;
    }
}

From source file:facturacion.xml.FacturaXml.java

private void initXml() throws ParserConfigurationException {
    /*// w  ww  . ja  va 2  s  .c o  m
    DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
    dbf.setNamespaceAware(true);
    dbf.setCoalescing(true);
    dbf.setIgnoringElementContentWhitespace(true);
    dbf.setIgnoringComments(true);
    DocumentBuilder db = dbf.newDocumentBuilder();
    */
    Element root = new Element("factura");
    root.setAttribute("id", "comprobante");
    root.setAttribute("version", "1.0.0");
    doc = new Document();
    this.doc.setRootElement(root);
}

From source file:ilarkesto.feeds.Feed.java

License:Open Source License

public Document createRssJDom() {
    Document document = new Document();
    Element eRoot = new Element("rss");
    eRoot.setAttribute("version", "2.0");
    document.setRootElement(eRoot);//  w w w.j a v  a2  s . c  o  m

    Element eChannel = JDom.addElement(eRoot, "channel");
    JDom.addTextElement(eChannel, "title", title);
    JDom.addTextElement(eChannel, "link", link);
    JDom.addTextElement(eChannel, "description", description);
    if (language != null)
        JDom.addTextElement(eChannel, "language", language);
    if (pubDate != null)
        JDom.addTextElement(eChannel, "pubDate", pubDate);
    if (lastBuildDate != null)
        JDom.addTextElement(eChannel, "lastBuildDate", lastBuildDate);

    for (FeedItem item : items) {
        item.appendTo(eChannel);
    }

    return document;
}

From source file:ilarkesto.rss.Rss20Builder.java

License:Open Source License

public Document createXmlDocument() {
    Document doc = new Document();

    Element eRss = new Element("rss");
    doc.setRootElement(eRss);//from   ww  w  .j a va 2 s. c o  m
    eRss.setAttribute("version", "2.0");

    Element eChannel = JDom.addElement(eRss, "channel");
    if (title != null)
        JDom.addTextElement(eChannel, "title", title);
    if (link != null)
        JDom.addTextElement(eChannel, "link", link);
    if (description != null)
        JDom.addTextElement(eChannel, "description", description);
    if (language != null)
        JDom.addTextElement(eChannel, "language", language);
    if (pubDate != null)
        JDom.addTextElement(eChannel, "pubDate", Tm.FORMAT_RFC822.format(pubDate));
    if (image != null) {
        Element eImage = JDom.addElement(eChannel, "image");
        JDom.addTextElement(eImage, "url", image);
        JDom.addTextElement(eImage, "title", "Logo");
    }

    for (Item item : items) {
        Element eItem = JDom.addElement(eChannel, "item");
        item.appendTo(eItem);
    }

    return doc;
}

From source file:interfacermi.Traza.java

public void insertarTraza(String hora, String actor, String accion) {

    Document document = null;//from w w w.  ja  va  2s .c om
    Element root = null;
    File xmlFile = new File("Traza.xml");
    //Se comprueba si el archivo XML ya existe o no.
    if (xmlFile.exists()) {
        FileInputStream fis;
        try {
            fis = new FileInputStream(xmlFile);
            SAXBuilder sb = new SAXBuilder();
            document = sb.build(fis);
            //Si existe se obtiene su nodo raiz.
            root = document.getRootElement();
            fis.close();
        } catch (JDOMException | IOException e) {
            e.printStackTrace();
        }
    } else {
        //Si no existe se crea su nodo raz.
        document = new Document();
        root = new Element("Traza");
    }

    //Se crea un nodo Hecho para insertar la informacin.
    Element nodohecho = new Element("Hecho");
    //Se crea un nodo hora para insertar la informacin correspondiente a la hora.
    Element nodohora = new Element("Hora");
    //Se crea un nodo actor para insertar la informacin correspondiente al actor.
    Element nodoactor = new Element("Actor");
    //Se crea un nodo accion para insertar la informacin correspondiente a la accin.
    Element nodoaccion = new Element("Accion");

    //Se asignan los valores enviados para cada nodo.
    nodohora.setText(hora);
    nodoactor.setText(actor);
    nodoaccion.setText(accion);
    //Se aade el contenido al nodo Hecho.  
    nodohecho.addContent(nodohora);
    nodohecho.addContent(nodoactor);
    nodohecho.addContent(nodoaccion);
    //Se aade el nodo Hecho al nodo raz.
    root.addContent(nodohecho);
    document.setContent(root);

    //Se procede a exportar el nuevo o actualizado archivo de traza XML   
    XMLOutputter xmlOutput = new XMLOutputter();
    xmlOutput.setFormat(Format.getPrettyFormat());

    try {
        xmlOutput.output(document, new FileWriter("Traza.xml"));
    } catch (IOException e) {
        e.printStackTrace();
    }

}

From source file:io.LoadSave.java

License:Open Source License

/**
 * loads a .oger file/*from  www  .  j a  v  a  2s.c o m*/
 */
public static void load() {

    ParticipantTableModel tableModel = ParticipantTableModel.getInstance();
    RoomTreeModel slotModel = RoomTreeModel.getInstance();

    if (!Main.isSaved()) {

        // current game must be saved
        int saveResult = JOptionPane.showOptionDialog(null, "Mchten Sie vorher speichern?", "Speichern?",
                JOptionPane.YES_NO_OPTION, JOptionPane.INFORMATION_MESSAGE, null, null, null);
        if (saveResult == JOptionPane.YES_OPTION) {
            save();
        }
    }

    Document document = new Document();
    Element root = new Element("root");

    SAXBuilder saxBuilder = new SAXBuilder();

    // Dialog to choose the oger file to parse
    JFileChooser fileChoser = new JFileChooser(".xml");
    fileChoser.setFileFilter(new OgerDialogFilter());

    int result = fileChoser.showOpenDialog(null);
    switch (result) {

    case JFileChooser.APPROVE_OPTION:
        try {
            // clear models
            tableModel.clear();
            slotModel.clear();

            // Create a new JDOM document from a oger file
            File file = fileChoser.getSelectedFile();
            document = saxBuilder.build(file);
        } catch (Exception e) {
            JOptionPane.showMessageDialog(null, "Fehler beim Parsen der Datei!");
        }

        // Initialize the root Element with the document root Element
        try {
            root = document.getRootElement();
        } catch (NullPointerException e) {
            JOptionPane.showMessageDialog(null, "Fehler beim Parsen der Datei!");
        }

        // participants
        Element participantsElement = root.getChild("allParticipants");

        for (Element participant : participantsElement.getChildren("participant")) {
            String firstName = participant.getAttributeValue("firstName");
            String lastName = participant.getAttributeValue("lastName");
            String mail = participant.getAttributeValue("mail");
            int group = Integer.parseInt(participant.getAttributeValue("group"));

            Participant newParticipant = new Participant(firstName, lastName, mail, group);
            tableModel.addParticipant(newParticipant);
        }

        // slots
        final DateFormat dateFormat = new SimpleDateFormat("dd.MM.yy");
        final DateFormat timeFormat = new SimpleDateFormat("HH:mm");
        boolean parseFailed = false;

        Element slotsElement = root.getChild("Slots");
        for (Element slotElement : slotsElement.getChildren("Slot")) {
            Date date = null;
            Date beginTime = null;
            Date endTime = null;

            try {
                date = dateFormat.parse(slotElement.getAttributeValue("Date"));
            } catch (ParseException e) {
                JOptionPane.showMessageDialog(null, "Konnte Slot-Datum nicht parsen", "Datum nicht erkannt",
                        JOptionPane.ERROR_MESSAGE);
                parseFailed = true;
            }

            try {
                beginTime = timeFormat.parse(slotElement.getAttributeValue("Begin"));
            } catch (ParseException e) {
                JOptionPane.showMessageDialog(null, "Konnte Slot-Angfangszeit nicht parsen",
                        "Anfangszeit nicht erkannt", JOptionPane.ERROR_MESSAGE);
                parseFailed = true;
            }

            try {
                endTime = timeFormat.parse(slotElement.getAttributeValue("End"));
            } catch (ParseException e) {
                JOptionPane.showMessageDialog(null, "Konnte Slot-Endzeit nicht parsen", "Endzeit nicht erkannt",
                        JOptionPane.ERROR_MESSAGE);
                parseFailed = true;
            }

            if (!parseFailed) {
                Slot slot = new Slot(date, beginTime, endTime);
                SlotNode newSlotNode = new SlotNode();
                newSlotNode.setUserObject(slot);
                ((DefaultMutableTreeNode) RoomTreeModel.getInstance().getRoot()).add(newSlotNode);

                // Rooms
                Element roomsElement = slotElement.getChild("AllRooms");
                for (Element roomElement : roomsElement.getChildren("Room")) {
                    parseFailed = false;

                    String roomString = roomElement.getAttributeValue("ID");
                    Date roomBeginTime = null;
                    Date roomEndTime = null;

                    Boolean hasBeamer = false;
                    String hasBeamerString = roomElement.getAttributeValue("Beamer");
                    if (hasBeamerString.equals("false")) {
                        hasBeamer = false;
                    } else if (hasBeamerString.equals("true")) {
                        hasBeamer = true;
                    } else {
                        JOptionPane.showMessageDialog(null, "Beamer nicht erkannt", "Beamer nicht erkannt",
                                JOptionPane.ERROR_MESSAGE);
                        parseFailed = true;
                    }

                    try {
                        roomBeginTime = timeFormat.parse(roomElement.getAttributeValue("Begin"));
                    } catch (ParseException e) {
                        JOptionPane.showMessageDialog(null, "Konnte Slot-Angfangszeit nicht parsen",
                                "Anfangszeit nicht erkannt", JOptionPane.ERROR_MESSAGE);
                        parseFailed = true;
                    }

                    try {
                        roomEndTime = timeFormat.parse(roomElement.getAttributeValue("End"));
                    } catch (ParseException e) {
                        JOptionPane.showMessageDialog(null, "Konnte Slot-Endzeit nicht parsen",
                                "Endzeit nicht erkannt", JOptionPane.ERROR_MESSAGE);
                        parseFailed = true;
                    }

                    if (!parseFailed) {
                        Room room = new Room(roomString, hasBeamer, roomBeginTime, roomEndTime);

                        RoomNode newRoomNode = new RoomNode();
                        newRoomNode.setUserObject(room);

                        newSlotNode.add(newRoomNode);
                        Gui.getRoomTree().updateUI();
                    }
                }

                Gui.getRoomTree().updateUI();
            }
        }

    }

}

From source file:io.wcm.maven.plugins.i18n.SlingI18nMap.java

License:Apache License

private Document getMixLanguageXmlDocument() {
    Document doc = new Document();
    Element root = new Element("root", NAMESPACE_JCR);
    root.addNamespaceDeclaration(NAMESPACE_JCR);
    root.addNamespaceDeclaration(NAMESPACE_MIX);
    root.addNamespaceDeclaration(NAMESPACE_NT);
    root.addNamespaceDeclaration(NAMESPACE_SLING);
    doc.setRootElement(root);/*from  w w w .  j a  v a  2s . co  m*/

    // add boiler plate
    root.setAttribute(JCR_PRIMARY_TYPE, JCR_NODETYPE_FOLDER, NAMESPACE_JCR);
    root.setAttribute(JCR_MIXIN_TYPES, "[" + StringUtils.join(JCR_MIX_LANGUAGE, ",") + "]", NAMESPACE_JCR);

    // add language
    root.setAttribute(JCR_LANGUAGE, languageKey, NAMESPACE_JCR);

    return doc;
}

From source file:lu.list.itis.dkd.assess.cloze.template.Template.java

License:Apache License

public Document getTemplateDocument() {
    Document doc = new Document();
    Element template = new Element("template");
    doc.addContent(template);/*from   w  w w . ja v  a 2 s. c  o m*/

    template.addContent(metaData());
    template.addContent(layer());

    return doc;
}

From source file:lu.list.itis.dkd.assess.cloze.template.Template.java

License:Apache License

public void save(String path, String name) {
    Document doc = new Document();
    Element template = new Element("template");
    template.addContent(metaData());/*  ww  w .j a v  a2  s  .c  o  m*/
    template.addContent(layer());
    doc.addContent(template);

    XMLOutputter xmlOutput = new XMLOutputter();
    xmlOutput.setFormat(Format.getPrettyFormat());
    try {
        xmlOutput.output(doc, new FileWriter(path + name + ".xml"));
    } catch (IOException e) {
        logger.log(Level.SEVERE, "Problem saving template", e);
        e.printStackTrace();
    }

    logger.log(Level.INFO, "File saved to " + path + name + ".xml.");
}