Example usage for org.dom4j Element elementText

List of usage examples for org.dom4j Element elementText

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Introduction

In this page you can find the example usage for org.dom4j Element elementText.

Prototype

String elementText(QName qname);

Source Link

Usage

From source file:mesquite.minimal.Installer.Installer.java

License:Open Source License

void cleanUp(Element installElement) {
    String pathInMesquiteFolder = installElement.elementText("location");
    if (!StringUtil.blank(pathInMesquiteFolder))
        pathInMesquiteFolder = pathInMesquiteFolder + "/";
    String fileName = installElement.elementText("file");
    File tempPackage = new File(getRootPath() + pathInMesquiteFolder + fileName + "PREVIOUSVERSION");
    boolean hadExisted = tempPackage.exists();
    if (hadExisted) {
        logln("Deleting old version of " + fileName);
        if (tempPackage.isDirectory())
            MesquiteFile.deleteDirectory(getRootPath() + pathInMesquiteFolder + fileName + "PREVIOUSVERSION");
        else//w  ww.  j a  v  a  2 s .c om
            MesquiteFile.deleteFile(getRootPath() + pathInMesquiteFolder + fileName + "PREVIOUSVERSION");
    }
}

From source file:mesquite.minimal.Installer.Installer.java

License:Open Source License

void reverse(Element installElement) {
    String pathInMesquiteFolder = installElement.elementText("location");
    if (!StringUtil.blank(pathInMesquiteFolder))
        pathInMesquiteFolder = pathInMesquiteFolder + "/";
    String fileName = installElement.elementText("file");
    String prevPackagePath = getRootPath() + pathInMesquiteFolder + fileName;
    String tempPackagePath = getRootPath() + pathInMesquiteFolder + fileName + "PREVIOUSVERSION";
    File prevPackage = new File(prevPackagePath);

    File tempPackage = new File(tempPackagePath);
    boolean hadExisted = tempPackage.exists();
    if (hadExisted) {
        logln("Installation unsuccessful; attempting to recover old version of " + fileName);
        if (prevPackage.isDirectory())
            MesquiteFile.deleteDirectory(getRootPath() + pathInMesquiteFolder + fileName);
        else/*from w  w  w  .j  a  v a2 s. c  o m*/
            MesquiteFile.deleteFile(getRootPath() + pathInMesquiteFolder + fileName);
        MesquiteFile.rename(tempPackagePath, prevPackagePath);
    }
}

From source file:mesquite.minimal.Simplicity.Simplicity.java

License:Open Source License

StringArray importFile(String path, boolean isDefault) {
    if (!MesquiteFile.fileExists(path))
        return null;
    String settingsXML = MesquiteFile.getFileContentsAsString(path);
    Element root = XMLUtil.getRootXMLElementFromString("mesquite", settingsXML);
    if (root == null)
        return null;
    Element element = root.element("simplicitySettings");
    if (element != null) {
        Element versionElement = element.element("version");
        if (versionElement == null)
            return null;
        else {//  ww  w.j  a v a 2 s. co m
            int version = MesquiteInteger.fromString(element.elementText("version"));
            boolean acceptableVersion = version == 1;
            if (acceptableVersion) {
                String name = (element.elementText("name"));
                StringArray s = new StringArray(3);
                s.setName(name);
                s.setValue(XML, settingsXML);
                s.setValue(PATH, path);
                if (isDefault)
                    s.setValue(DEFAULTORNOT, "default");
                else
                    s.setValue(DEFAULTORNOT, "nonDefault");
                return s;
            }
        }
    }
    return null;
}

From source file:mesquite.minimal.Simplicity.Simplicity.java

License:Open Source License

public void renameSettingsFile(int i, String newName) {
    if (!MesquiteInteger.isCombinable(i) || i < 0 || i >= InterfaceManager.settingsFiles.size())
        return;/*from  ww w  .  j  av a2s  .  com*/
    StringArray s = (StringArray) InterfaceManager.settingsFiles.elementAt(i);
    String path = s.getValue(PATH);
    String settingsXML = s.getValue(XML);
    Element root = XMLUtil.getRootXMLElementFromString("mesquite", settingsXML);
    if (root == null)
        return;
    Element element = root.element("simplicitySettings");
    if (element != null) {
        Element versionElement = element.element("version");
        if (versionElement == null)
            return;
        else {
            int version = MesquiteInteger.fromString(element.elementText("version"));
            boolean acceptableVersion = version == 1;
            if (acceptableVersion) {
                Element name = element.element("name");

                Element settingsFile = DocumentHelper.createElement("mesquite");
                Document doc = DocumentHelper.createDocument(settingsFile);
                Element hidden = DocumentHelper.createElement("simplicitySettings");
                settingsFile.add(hidden);
                XMLUtil.addFilledElement(hidden, "version", "1");
                XMLUtil.addFilledElement(hidden, "name", newName);
                Element hp = element.element("hiddenPackages");
                element.remove(hp);
                hidden.add(hp);
                hp = element.element("hiddenMenuItems");
                element.remove(hp);
                hidden.add(hp);
                hp = element.element("hiddenTools");
                element.remove(hp);
                hidden.add(hp);
                s.setName(newName);
                MesquiteFile.putFileContents(path, XMLUtil.getDocumentAsXMLString(doc), false);
            }
        }
    }
}

From source file:mesquite.minimal.Simplicity.Simplicity.java

License:Open Source License

public void loadSettingsFile(StringArray s) {
    if (s == null)
        return;/* www . j  a  va  2s .  c o  m*/
    settingsLoaded = true;
    InterfaceManager.hiddenPackages.removeAllElements(false);
    InterfaceManager.hiddenMenuItems.removeAllElements(false);
    InterfaceManager.hiddenTools.removeAllElements(false);
    String settingsXML = s.getValue(XML);
    Element root = XMLUtil.getRootXMLElementFromString("mesquite", settingsXML);
    if (root == null)
        return;
    Element element = root.element("simplicitySettings");
    if (element != null) {
        Element versionElement = element.element("version");
        if (versionElement == null)
            return;
        else {
            int version = MesquiteInteger.fromString(element.elementText("version"));
            boolean acceptableVersion = version == 1;
            if (acceptableVersion) {
                String name = (element.elementText("name"));
                InterfaceManager.themeName = name;
                Element packages = element.element("hiddenPackages");
                if (packages != null) {
                    List packageElements = packages.elements("package");
                    for (Iterator iter = packageElements.iterator(); iter.hasNext();) { // this is going through all of the notices
                        Element hiddenPackage = (Element) iter.next();
                        String pkg = hiddenPackage.element("name").getText();
                        InterfaceManager.addPackageToHidden(pkg, false);
                    }
                }
                Element menuItems = element.element("hiddenMenuItems");
                if (menuItems != null) {
                    List menuElements = menuItems.elements("menuItem");
                    for (Iterator iter = menuElements.iterator(); iter.hasNext();) { // this is going through all of the notices
                        Element hiddenM = (Element) iter.next();
                        String label = XMLUtil.getTextFromElement(hiddenM, "label");
                        String arguments = XMLUtil.getTextFromElement(hiddenM, "arguments");
                        String command = XMLUtil.getTextFromElement(hiddenM, "command");
                        String commandableClass = XMLUtil.getTextFromElement(hiddenM, "commandableClass");
                        String dutyClass = XMLUtil.getTextFromElement(hiddenM, "dutyClass");
                        InterfaceManager.hiddenMenuItems.addElement(
                                new MenuVisibility(label, arguments, command, commandableClass, dutyClass),
                                false);
                    }
                }
                Element tools = element.element("hiddenTools");
                if (tools != null) {
                    List buttonElement = tools.elements("tool");
                    for (Iterator iter = buttonElement.iterator(); iter.hasNext();) { // this is going through all of the notices
                        Element hiddenT = (Element) iter.next();
                        String n = XMLUtil.getTextFromElement(hiddenT, "name");
                        String d = XMLUtil.getTextFromElement(hiddenT, "description");
                        InterfaceManager.hiddenTools.addElement(new MesquiteString(n, d), false);
                    }
                }
                storePreferences();
            }
        }
    }
    InterfaceManager.reset();

}

From source file:mesquite.molec.lib.NCBIUtil.java

License:Open Source License

public static String[] requestGenBankAccessions(String eSearchResponse, int number) {
    if (eSearchResponse == null)
        return null;
    String[] accessions = new String[number];
    Element gbSetElement = XMLUtil.getRootXMLElementFromString("GBSet", eSearchResponse);
    if (gbSetElement == null)
        return null;
    int count = 0;
    String s = "";
    List gbSeqList = gbSetElement.elements("GBSeq");
    for (Iterator iter = gbSeqList.iterator(); iter.hasNext();) { // this is going through all of the hits
        Element gbSeqElement = (Element) iter.next();
        if (gbSeqElement != null) {
            if (count < accessions.length) {
                accessions[count] = gbSeqElement.elementText("GBSeq_primary-accession");
            } else
                return accessions;
            count++;//from ww w  .  j  a v a 2s . c om
        }

    }
    return accessions;
}

From source file:mesquite.molec.lib.NCBIUtil.java

License:Open Source License

public static String getGenIDFromELinkResults(String response) {
    if (response == null)
        return null;
    Element eLinkResultElement = XMLUtil.getRootXMLElementFromString("eLinkResult", response);
    if (eLinkResultElement == null)
        return null;
    String s = "";
    Element LinkSetElement = eLinkResultElement.element("LinkSet");
    if (LinkSetElement != null) {
        //   Element LinkSetDBElement = LinkSetElement.element("LinkSetDb");
        List hitList = LinkSetElement.elements("LinkSetDb");
        for (Iterator iter = hitList.iterator(); iter.hasNext();) { // this is going through all of the hits
            Element hitElement = (Element) iter.next();
            if (hitElement != null) {
                String linkName = hitElement.elementText("LinkName");
                if ("protein_nuccore_mrna".equalsIgnoreCase(linkName)) {
                    Element LinkElement = hitElement.element("Link");
                    if (LinkElement != null) {
                        s = LinkElement.elementText("Id");
                        return s;
                    }//from w  w  w.j a v  a2  s  . c o m
                }
            }
        }
    }
    return null;
}

From source file:musite.io.xml.PredictionResultXMLReader.java

License:Open Source License

public PredictionResult read(InputStream is) throws IOException {
    if (is == null) {
        throw new IllegalArgumentException();
    }//from  w w w  .ja v a2 s.c  o m

    final PredictionResult result = data == null ? new PredictionResultImpl() : data;

    ProteinsXMLReader proteinsReader = ProteinsXMLReader.createReader(result, false);
    proteinsReader.setRoot(root);

    ProteinResidueAnnotationReader annReader = new ProteinResidueAnnotationReader();
    annReader.putAnnotationFieldReader(musite.prediction.PredictionResult.ANNOTATION_FIELD_SCORE,
            SimpleFieldXMLReader.createDoubleCollectionReader());
    proteinsReader.putProteinFieldReader(musite.ResidueAnnotationUtil.RESIDUE_ANNOTATION, annReader);

    String path = "/model-list/model";
    if (root != null)
        path = "/" + root + path;
    proteinsReader.addSaxReaderHandler(path, new ElementHandler() {
        public void onStart(ElementPath path) {
        }

        public void onEnd(ElementPath path) {
            Element elem = path.getCurrent();
            String name = StringEscapeUtils.unescapeXml(elem.attributeValue("name"));

            PTM ptm = null;
            String strPTM = StringEscapeUtils.unescapeXml(elem.elementText("ptm"));
            if (strPTM != null)
                ptm = PTM.valueOf(strPTM);

            Set<AminoAcid> aas = null;
            String strAAs = StringEscapeUtils.unescapeXml(elem.elementText("amino-acids"));
            if (strAAs != null) {
                String[] strs = strAAs.replaceAll("\n", "").split(";");
                int n = strs.length;
                aas = new HashSet(n);
                for (int i = 0; i < n; i++) {
                    String str = strs[i].trim();
                    aas.add(AminoAcid.valueOf(str));
                }
            }

            SpecificityEstimatorImpl si = null;
            String strSI = StringEscapeUtils.unescapeXml(elem.elementText("spec-estimate-data"));
            if (strSI != null) {
                String[] strs = strSI.replaceAll("\n", "").split(";");
                List<Double> train = new ArrayList();
                for (String str : strs) {
                    train.add(Double.valueOf(str.trim()));
                }
                si = new SpecificityEstimatorImpl(train);
            }

            String comment = StringEscapeUtils.unescapeXml(elem.elementText("comment"));
            if (comment != null)
                comment = comment.replaceAll("%EOL%", "\n");

            PredictionModelImpl model = new PredictionModelImpl.Builder().name(name).ptm(ptm).aminoAcids(aas)
                    .specEstimator(si).comment(comment).build();

            result.addModel(model);

            // prune the tree
            elem.detach();
        }
    });

    proteinsReader.read(is);

    return result;
}

From source file:net.sf.cpsolver.ifs.example.tt.TimetableModel.java

License:Open Source License

public static TimetableModel loadFromXML(File inFile, boolean assign) throws IOException, DocumentException {
    Document document = (new SAXReader()).read(inFile);
    Element root = document.getRootElement();
    if (!"Timetable".equals(root.getName())) {
        sLogger.error("Given XML file is not interactive timetabling problem.");
        return null;
    }/* ww w. j  a  v  a 2s . co m*/

    Element problem = root.element("Problem");
    Element problemGen = problem.element("General");
    TimetableModel m = new TimetableModel(Integer.parseInt(problemGen.elementText("DaysPerWeek")),
            Integer.parseInt(problemGen.elementText("SlotsPerDay")));

    Element resources = problem.element("Resources");

    HashMap<String, Resource> resTab = new HashMap<String, Resource>();

    Element resEl = resources.element("Classrooms");
    for (Iterator<?> i = resEl.elementIterator("Resource"); i.hasNext();) {
        Element el = (Element) i.next();
        Resource r = new Resource(el.attributeValue("id"), Resource.TYPE_ROOM, el.elementText("Name"));
        Element pref = el.element("TimePreferences");
        for (Iterator<?> j = pref.elementIterator("Soft"); j.hasNext();)
            r.addDiscouragedSlot(Integer.parseInt(((Element) j.next()).getText()));
        for (Iterator<?> j = pref.elementIterator("Hard"); j.hasNext();)
            r.addProhibitedSlot(Integer.parseInt(((Element) j.next()).getText()));
        m.addConstraint(r);
        resTab.put(r.getResourceId(), r);
    }

    resEl = resources.element("Teachers");
    for (Iterator<?> i = resEl.elementIterator("Resource"); i.hasNext();) {
        Element el = (Element) i.next();
        Resource r = new Resource(el.attributeValue("id"), Resource.TYPE_INSTRUCTOR, el.elementText("Name"));
        Element pref = el.element("TimePreferences");
        for (Iterator<?> j = pref.elementIterator("Soft"); j.hasNext();)
            r.addDiscouragedSlot(Integer.parseInt(((Element) j.next()).getText()));
        for (Iterator<?> j = pref.elementIterator("Hard"); j.hasNext();)
            r.addProhibitedSlot(Integer.parseInt(((Element) j.next()).getText()));
        m.addConstraint(r);
        resTab.put(r.getResourceId(), r);
    }

    resEl = resources.element("Classes");
    for (Iterator<?> i = resEl.elementIterator("Resource"); i.hasNext();) {
        Element el = (Element) i.next();
        Resource r = new Resource(el.attributeValue("id"), Resource.TYPE_CLASS, el.elementText("Name"));
        Element pref = el.element("TimePreferences");
        for (Iterator<?> j = pref.elementIterator("Soft"); j.hasNext();)
            r.addDiscouragedSlot(Integer.parseInt(((Element) j.next()).getText()));
        for (Iterator<?> j = pref.elementIterator("Hard"); j.hasNext();)
            r.addProhibitedSlot(Integer.parseInt(((Element) j.next()).getText()));
        m.addConstraint(r);
        resTab.put(r.getResourceId(), r);
    }

    resEl = resources.element("Special");
    for (Iterator<?> i = resEl.elementIterator("Resource"); i.hasNext();) {
        Element el = (Element) i.next();
        Resource r = new Resource(el.attributeValue("id"), Resource.TYPE_OTHER, el.elementText("Name"));
        Element pref = el.element("TimePreferences");
        for (Iterator<?> j = pref.elementIterator("Soft"); j.hasNext();)
            r.addDiscouragedSlot(Integer.parseInt(((Element) j.next()).getText()));
        for (Iterator<?> j = pref.elementIterator("Hard"); j.hasNext();)
            r.addProhibitedSlot(Integer.parseInt(((Element) j.next()).getText()));
        m.addConstraint(r);
        resTab.put(r.getResourceId(), r);
    }

    Element actEl = problem.element("Activities");
    HashMap<String, Activity> actTab = new HashMap<String, Activity>();
    for (Iterator<?> i = actEl.elementIterator("Activity"); i.hasNext();) {
        Element el = (Element) i.next();
        Activity a = new Activity(Integer.parseInt(el.elementText("Length")), el.attributeValue("id"),
                el.elementText("Name"));
        Element pref = el.element("TimePreferences");
        for (Iterator<?> j = pref.elementIterator("Soft"); j.hasNext();)
            a.addDiscouragedSlot(Integer.parseInt(((Element) j.next()).getText()));
        for (Iterator<?> j = pref.elementIterator("Hard"); j.hasNext();)
            a.addProhibitedSlot(Integer.parseInt(((Element) j.next()).getText()));
        Element req = el.element("RequiredResources");
        for (Iterator<?> j = req.elementIterator(); j.hasNext();) {
            Element rqEl = (Element) j.next();
            if ("Resource".equals(rqEl.getName())) {
                a.addResourceGroup(resTab.get(rqEl.getText()));
            } else if ("Group".equals(rqEl.getName())) {
                if ("no".equalsIgnoreCase(rqEl.attributeValue("conjunctive"))
                        || "false".equalsIgnoreCase(rqEl.attributeValue("conjunctive"))) {
                    List<Resource> gr = new ArrayList<Resource>();
                    for (Iterator<?> k = rqEl.elementIterator("Resource"); k.hasNext();)
                        gr.add(resTab.get(((Element) k.next()).getText()));
                    a.addResourceGroup(gr);
                } else {
                    for (Iterator<?> k = rqEl.elementIterator("Resource"); k.hasNext();)
                        a.addResourceGroup(resTab.get(((Element) k.next()).getText()));
                }
            }
        }
        m.addVariable(a);
        a.init();
        actTab.put(a.getActivityId(), a);
    }

    Element depEl = problem.element("Dependences");
    for (Iterator<?> i = depEl.elementIterator("Dependence"); i.hasNext();) {
        Element el = (Element) i.next();
        int type = Dependence.TYPE_NO_DEPENDENCE;
        String typeStr = el.elementText("Operator");
        if ("After".equals(typeStr))
            type = Dependence.TYPE_AFTER;
        else if ("Before".equals(typeStr))
            type = Dependence.TYPE_BEFORE;
        else if ("After".equals(typeStr))
            type = Dependence.TYPE_AFTER;
        else if ("Closely before".equals(typeStr))
            type = Dependence.TYPE_CLOSELY_BEFORE;
        else if ("Closely after".equals(typeStr))
            type = Dependence.TYPE_CLOSELY_AFTER;
        else if ("Concurrently".equals(typeStr))
            type = Dependence.TYPE_CONCURRENCY;
        Dependence d = new Dependence(el.attributeValue("id"), type);
        d.addVariable(actTab.get(el.elementText("FirstActivity")));
        d.addVariable(actTab.get(el.elementText("SecondActivity")));
        m.addConstraint(d);
    }

    Element solEl = root.element("Solution");
    if (solEl != null) {
        for (Iterator<?> i = solEl.elementIterator("Activity"); i.hasNext();) {
            Element el = (Element) i.next();
            Activity a = actTab.get(el.attributeValue("id"));
            if (a == null)
                continue;
            int slot = Integer.parseInt(el.elementText("StartTime"));
            Element usResEl = el.element("UsedResources");
            List<Resource> res = new ArrayList<Resource>();
            for (Iterator<?> j = usResEl.elementIterator("Resource"); j.hasNext();)
                res.add(resTab.get(((Element) j.next()).getText()));
            for (Location loc : a.values()) {
                if (loc.getSlot() != slot || loc.getResources().length != res.size())
                    continue;
                boolean same = true;
                for (int j = 0; j < loc.getResources().length && same; j++)
                    if (!res.get(j).equals(loc.getResources()[j]))
                        same = false;
                if (!same)
                    continue;
                a.setInitialAssignment(loc);
                if (assign)
                    a.assign(0, loc);
                break;
            }
        }
    }
    return m;
}

From source file:net.sf.jvifm.model.BookmarkManager.java

License:Open Source License

@SuppressWarnings("unchecked")
private void init() {

    storePath = HomeLocator.getConfigHome() + File.separator + "bookmarks.xml";
    SAXReader saxReader = new SAXReader();
    File file = new File(storePath);
    Document document = null;//from w  w  w .j av  a2  s.  co m

    try {

        if (file.exists()) {
            FileInputStream is = new FileInputStream(file);
            InputStreamReader reader = new InputStreamReader(is, "UTF-8");
            BufferedReader br = new BufferedReader(reader);
            document = saxReader.read(br);

            List elementList = document.selectNodes("//bookmark");

            for (Iterator it = elementList.iterator(); it.hasNext();) {

                Element bookmarkElement = (Element) it.next();
                String name = bookmarkElement.elementText("name");
                String path = bookmarkElement.elementText("path");
                String key = bookmarkElement.elementText("key");

                Bookmark bookmark = new Bookmark();
                bookmark.setPath(path);
                bookmark.setName(name);
                bookmark.setKey(key);

                if (key != null) {
                    bookmarkMap.put(key, bookmark);
                }

                bookmarkList.add(bookmark);
            }

            reader.close();
            is.close();
        }
    } catch (Exception e) {
        e.printStackTrace();
    }

}