Example usage for java.io StringWriter getBuffer

List of usage examples for java.io StringWriter getBuffer

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Introduction

In this page you can find the example usage for java.io StringWriter getBuffer.

Prototype

public StringBuffer getBuffer()

Source Link

Document

Return the string buffer itself.

Usage

From source file:edu.cornell.med.icb.goby.modes.TestDiscoverSVMethylationRatesMode.java

@Test
public void testMethylationFormatGenomicContext() throws IOException, JSAPException {
    final MethylationRateVCFOutputFormat outputFormat = new MethylationRateVCFOutputFormat();

    DiscoverVariantIterateSortedAlignments iterator = new DiscoverVariantIterateSortedAlignments(outputFormat) {
        @Override/*from w  ww .ja  v  a2 s  .  c  o m*/
        public CharSequence getReferenceId(int targetIndex) {
            return Integer.toString(targetIndex);
        }
    };
    DiscoverSequenceVariantsMode mode = new DiscoverSequenceVariantsMode() {
        @Override
        public String[] getSamples() {
            return new String[] { "methylated", "not-so" };
        }

        @Override
        public String[] getGroups() {
            return new String[] { "methylated", "not-so" };
        }

        @Override
        public int[] getReaderIndexToGroupIndex() {
            return new int[] { 0, 1 }; // sample index is group index;
        }

        @Override
        public ArrayList<GroupComparison> getGroupComparisons() {
            ArrayList<GroupComparison> list = new ArrayList<GroupComparison>();
            list.add(new GroupComparison("methylated", "not-so", 0, 1, 0));
            return list;
        }
    };
    outputFormat.setGenome(genome);

    StringWriter writer = new StringWriter();
    outputFormat.allocateStorage(2, 2);
    outputFormat.defineColumns(new PrintWriter(writer), mode);
    outputFormat.setMinimumEventThreshold(0);
    outputFormat.writeRecord(iterator, makeTwoSampleCounts(), 1, 6, list1(), 0, 1);
    writer.flush();

    String stringB = writer.getBuffer().toString();
    assertTrue(stringB, stringB.contains("Context=CpG"));

    writer = new StringWriter();
    outputFormat.allocateStorage(2, 2);
    outputFormat.defineColumns(new PrintWriter(writer), mode);
    outputFormat.setMinimumEventThreshold(0);

    final int referenceIndex = 2;
    outputFormat.setGenomeReferenceIndex(referenceIndex);
    outputFormat.writeRecord(iterator, makeTwoSampleCounts(), referenceIndex, 1, list1(), 0, 1);
    writer.flush();

    String stringC = writer.getBuffer().toString();
    assertTrue(stringC, stringC.contains("Context=CpT"));

    writer = new StringWriter();
    outputFormat.allocateStorage(2, 2);
    outputFormat.defineColumns(new PrintWriter(writer), mode);
    outputFormat.setMinimumEventThreshold(0);
    final int referenceIndex1 = 1;
    outputFormat.setGenomeReferenceIndex(referenceIndex1);
    outputFormat.writeRecord(iterator, makeTwoSampleCounts(), referenceIndex1, 2, list1(), 0, 1);
    stringB = writer.getBuffer().toString();
    assertTrue(stringB, stringB.contains("CpT"));

    writer = new StringWriter();
    outputFormat.allocateStorage(2, 2);
    outputFormat.defineColumns(new PrintWriter(writer), mode);
    outputFormat.setMinimumEventThreshold(0);
    final int referenceIndex4 = 4;
    outputFormat.setGenomeReferenceIndex(referenceIndex4);
    outputFormat.writeRecord(iterator, makeTwoSampleCounts(), referenceIndex4, 7, list1(), 0, 1);
    stringB = writer.getBuffer().toString();
    assertTrue(stringB, stringB.contains("CpC"));

}

From source file:com.evon.injectTemplate.InjectTemplateFilter.java

@Override
public void doFilter(ServletRequest request, ServletResponse response, FilterChain chain)
        throws IOException, ServletException {

    HttpServletRequest httpRequest = (HttpServletRequest) request;
    HttpServletResponse httpResponse = (HttpServletResponse) response;

    StringWriter writer = new StringWriter();
    BufferedResponseWrapper wrapper = new BufferedResponseWrapper((HttpServletResponse) response, writer);
    chain.doFilter(request, wrapper);//from   w w  w .j ava2  s.  co  m

    String contentType = null;
    String uri = httpRequest.getRequestURI();

    contentType = httpResponse.getContentType();

    if (contentTypes.containsKey(uri)) {
        contentType = contentTypes.get(uri);
    } else if (contentType != null) {
        contentTypes.put(uri, contentType);
    }
    contentType = (contentType == null) ? "none" : contentType;

    String out = writer.getBuffer().toString();

    boolean requestedURIIsTheTemplate = false;

    requestedURIIsTheTemplate = InjectUtils.isTemplate(uri);

    boolean contentTypeIsText = !wrapper.isBinary() && contentType != null && !contentType.equals("none");

    if (requestedURIIsTheTemplate || !contentTypeIsText) {
        if (contentTypeIsText) {
            response.getWriter().print(out);
        }
        return;
    }

    if (!templateLodaded && !templateLodadedStarted) {
        loadTemplates(httpRequest);
    }

    TemplateBean template = getTemplatePathByURI(uri);

    if (template == null) {
        response.getWriter().print(out);
        return;
    }

    String key = null;

    if (template.cache.equals("SESSION")) {
        String cookiesNames = getCookieHashs(httpRequest);
        key = template.path + cookiesNames;
    } else if (template.cache.equals("ON"))

    {
        key = template.path;

    }

    if (!templates.containsKey("/" + template.path)) {
        throw new ServletException("Template [" + template.path + "] not founded");
    }

    boolean needRefresh = template.refreshInSeconds > 0
            && ((System.currentTimeMillis() - template.lastUpdate) / 1000) > template.refreshInSeconds;

    boolean replaceTemplate = template.cache.equals("OFF") || !htmlContents.containsKey(key) || needRefresh;

    /*   pra investigar erro de nulo,    
          boolean notExist = key==null || !htmlContents.containsKey(key);
     * if(!notExist)
          {
             notExist=!notExist;
             //throw new ServletException("content not exist");
          }
       */

    if (replaceTemplate) {
        if (needRefresh) {
            template.lastUpdate = System.currentTimeMillis();
        }

        try {
            loadContentTemplate(template, request.getServerName(), request.getServerPort(),
                    request.getProtocol().contains("HTTPS"), httpRequest);
        } catch (Exception e) {
            throw new ServletException(e.getMessage(), e);
        }
    }

    HTMLInfoBean templateHTML = templates.get("/" + template.path);

    String contentTemplate = htmlContents.get(key).getContent();
    IDocument docOut = HTMLParser.parse(out);

    for (String selector : templateHTML.getSelectors()) {
        IElements elements = docOut.select(selector);
        if (elements.size() == 0) {
            System.out.println("WARNING: Selector [" + selector + "] in template [" + templateHTML.getUri()
                    + "] not founded in [" + httpRequest.getRequestURI() + "]");
            continue;
        }
        if (elements.size() != 1) {
            System.out.println(
                    "WARNING: Selector get many elements. Choosed the first to URI: " + templateHTML.getUri());
        }
        IElement element = elements.get(0);
        String innerHTML = element.html();

        contentTemplate = contentTemplate.replace("<INJECT selector='" + selector + "'/>", innerHTML);
    }

    response.getWriter().print(contentTemplate);
}

From source file:isl.FIMS.servlet.imports.ImportXML.java

protected void processRequest(HttpServletRequest request, HttpServletResponse response)
        throws ServletException, IOException {

    this.initVars(request);
    String username = getUsername(request);

    Config conf = new Config("EisagwghXML_RDF");
    String xsl = ApplicationConfig.SYSTEM_ROOT + "formating/xsl/import/ImportXML.xsl";
    String displayMsg = "";
    response.setContentType("text/html;charset=UTF-8");
    PrintWriter out = response.getWriter();
    StringBuilder xml = new StringBuilder(
            this.xmlStart(this.topmenu, username, this.pageTitle, this.lang, "", request));
    //  ArrayList<String> notValidMXL = new ArrayList<String>();
    HashMap<String, ArrayList> notValidMXL = new <String, ArrayList>HashMap();
    if (!ServletFileUpload.isMultipartContent(request)) {
        displayMsg = "form";
    } else {//  w ww . j a va2s.  c  om
        // configures some settings
        String filePath = this.export_import_Folder;
        java.util.Date date = new java.util.Date();
        Timestamp t = new Timestamp(date.getTime());
        String currentDir = filePath + t.toString().replaceAll(":", "");
        File saveDir = new File(currentDir);
        if (!saveDir.exists()) {
            saveDir.mkdir();
        }
        DiskFileItemFactory factory = new DiskFileItemFactory();
        factory.setSizeThreshold(DiskFileItemFactory.DEFAULT_SIZE_THRESHOLD);
        factory.setRepository(saveDir);
        ArrayList<String> savedIDs = new ArrayList<String>();

        ServletFileUpload upload = new ServletFileUpload(factory);
        upload.setSizeMax(REQUEST_SIZE);
        // constructs the directory path to store upload file
        String uploadPath = currentDir;
        int xmlCount = 0;
        String[] id = null;
        try {
            // parses the request's content to extract file data
            List formItems = upload.parseRequest(request);
            Iterator iter = formItems.iterator();
            // iterates over form's fields
            File storeFile = null;
            while (iter.hasNext()) {
                FileItem item = (FileItem) iter.next();
                // processes only fields that are not form fields
                if (!item.isFormField()) {
                    String fileName = new File(item.getName()).getName();
                    filePath = uploadPath + File.separator + fileName;
                    storeFile = new File(filePath);
                    item.write(storeFile);
                    Utils.unzip(fileName, uploadPath);
                    File dir = new File(uploadPath);

                    String[] extensions = new String[] { "xml", "x3ml" };
                    List<File> files = (List<File>) FileUtils.listFiles(dir, extensions, true);
                    xmlCount = files.size();
                    for (File file : files) {
                        // saves the file on disk
                        Document doc = ParseXMLFile.parseFile(file.getPath());
                        String xmlContent = doc.getDocumentElement().getTextContent();
                        String uri_name = "";
                        try {
                            uri_name = DMSTag.valueOf("uri_name", "target", type, this.conf)[0];
                        } catch (DMSException ex) {
                            ex.printStackTrace();
                        }
                        String uriValue = this.URI_Reference_Path + uri_name + "/";
                        boolean insertEntity = false;
                        if (xmlContent.contains(uriValue) || file.getName().contains(type)) {
                            insertEntity = true;
                        }
                        Element root = doc.getDocumentElement();
                        Node admin = Utils.removeNode(root, "admin", true);

                        //  File rename = new File(uploadPath + File.separator + id[0] + ".xml");
                        //  boolean isRename = storeFile.renameTo(rename);
                        //   ParseXMLFile.saveXMLDocument(rename.getPath(), doc);
                        String schemaFilename = "";
                        schemaFilename = type;

                        SchemaFile sch = new SchemaFile(schemaFolder + schemaFilename + ".xsd");
                        TransformerFactory tf = TransformerFactory.newInstance();
                        Transformer transformer = tf.newTransformer();
                        transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
                        StringWriter writer = new StringWriter();
                        transformer.transform(new DOMSource(doc), new StreamResult(writer));
                        String xmlString = writer.getBuffer().toString().replaceAll("\r", "");

                        //without admin
                        boolean isValid = sch.validate(xmlString);
                        if ((!isValid && insertEntity)) {
                            notValidMXL.put(file.getName(), null);
                        } else if (insertEntity) {
                            id = initInsertFile(type, false);
                            doc = createAdminPart(id[0], type, doc, username);
                            writer = new StringWriter();
                            transformer.transform(new DOMSource(doc), new StreamResult(writer));
                            xmlString = writer.getBuffer().toString().replaceAll("\r", "");
                            DBCollection col = new DBCollection(this.DBURI, id[1], this.DBuser,
                                    this.DBpassword);
                            DBFile dbF = col.createFile(id[0] + ".xml", "XMLDBFile");
                            dbF.setXMLAsString(xmlString);
                            dbF.store();
                            ArrayList<String> externalFiles = new <String>ArrayList();
                            ArrayList<String> externalDBFiles = new <String>ArrayList();

                            String q = "//*[";
                            for (String attrSet : this.uploadAttributes) {
                                String[] temp = attrSet.split("#");
                                String func = temp[0];
                                String attr = temp[1];
                                if (func.contains("text")) {
                                    q += "@" + attr + "]/text()";
                                } else {
                                    q = "data(//*[@" + attr + "]/@" + attr + ")";
                                }
                                String[] res = dbF.queryString(q);
                                for (String extFile : res) {
                                    externalFiles.add(extFile + "#" + attr);
                                }
                            }
                            q = "//";
                            if (!dbSchemaPath[0].equals("")) {
                                for (String attrSet : this.dbSchemaPath) {
                                    String[] temp = attrSet.split("#");
                                    String func = temp[0];
                                    String path = temp[1];
                                    if (func.contains("text")) {
                                        q += path + "//text()";
                                    } else {
                                        q = "data(//" + path + ")";
                                    }
                                    String[] res = dbF.queryString(q);
                                    for (String extFile : res) {
                                        externalDBFiles.add(extFile);
                                    }
                                }
                            }
                            ArrayList<String> missingExternalFiles = new <String>ArrayList();
                            for (String extFile : externalFiles) {
                                extFile = extFile.substring(0, extFile.lastIndexOf("#"));

                                List<File> f = (List<File>) FileUtils.listFiles(dir,
                                        FileFilterUtils.nameFileFilter(extFile), TrueFileFilter.INSTANCE);
                                if (f.size() == 0) {
                                    missingExternalFiles.add(extFile);
                                }
                            }
                            if (missingExternalFiles.size() > 0) {
                                notValidMXL.put(file.getName(), missingExternalFiles);
                            }

                            XMLEntity xmlNew = new XMLEntity(this.DBURI, this.systemDbCollection + type,
                                    this.DBuser, this.DBpassword, type, id[0]);

                            ArrayList<String> worngFiles = Utils.checkReference(xmlNew, this.DBURI, id[0], type,
                                    this.DBuser, this.DBpassword);
                            if (worngFiles.size() > 0) {
                                //dbF.remove();
                                notValidMXL.put(file.getName(), worngFiles);
                            }
                            //remove duplicates from externalFiles if any
                            HashSet hs = new HashSet();
                            hs.addAll(missingExternalFiles);
                            missingExternalFiles.clear();
                            missingExternalFiles.addAll(hs);
                            if (missingExternalFiles.isEmpty() && worngFiles.isEmpty()) {

                                for (String extFile : externalFiles) {
                                    String attr = extFile.substring(extFile.lastIndexOf("#") + 1,
                                            extFile.length());
                                    extFile = extFile.substring(0, extFile.lastIndexOf("#"));

                                    List<File> f = (List<File>) FileUtils.listFiles(dir,
                                            FileFilterUtils.nameFileFilter(extFile), TrueFileFilter.INSTANCE);
                                    File uploadFile = f.iterator().next();
                                    String content = FileUtils.readFileToString(uploadFile);

                                    DBFile uploadsDBFile = new DBFile(this.DBURI, this.adminDbCollection,
                                            "Uploads.xml", this.DBuser, this.DBpassword);
                                    String mime = Utils.findMime(uploadsDBFile, uploadFile.getName(), attr);
                                    String uniqueName = Utils.createUniqueFilename(uploadFile.getName());
                                    File uploadFileUnique = new File(uploadFile.getPath().substring(0,
                                            uploadFile.getPath().lastIndexOf(File.separator)) + File.separator
                                            + uniqueName);
                                    uploadFile.renameTo(uploadFileUnique);
                                    xmlString = xmlString.replaceAll(uploadFile.getName(), uniqueName);
                                    String upload_path = this.systemUploads + type;
                                    File upload_dir = null;
                                    ;
                                    if (mime.equals("Photos")) {
                                        upload_path += File.separator + mime + File.separator + "original"
                                                + File.separator;
                                        upload_dir = new File(upload_path + uniqueName);
                                        FileUtils.copyFile(uploadFileUnique, upload_dir);
                                        Utils.resizeImage(uniqueName, upload_path,
                                                upload_path.replaceAll("original", "thumbs"), thumbSize);
                                        Utils.resizeImage(uniqueName, upload_path,
                                                upload_path.replaceAll("original", "normal"), normalSize);
                                        xmlString = xmlString.replace("</versions>",
                                                "</versions>" + "\n" + "<type>Photos</type>");
                                    } else {
                                        upload_path += File.separator + mime + File.separator;
                                        upload_dir = new File(upload_path + uniqueName);
                                        FileUtils.copyFile(uploadFileUnique, upload_dir);
                                    }
                                    if (!dbSchemaFolder.equals("")) {
                                        if (externalDBFiles.contains(extFile)) {
                                            try {
                                                DBCollection colSchema = new DBCollection(this.DBURI,
                                                        dbSchemaFolder, this.DBuser, this.DBpassword);
                                                DBFile dbFSchema = colSchema.createFile(uniqueName,
                                                        "XMLDBFile");
                                                dbFSchema.setXMLAsString(content);
                                                dbFSchema.store();
                                            } catch (Exception e) {
                                            }
                                        }
                                    }
                                    uploadFileUnique.renameTo(uploadFile);

                                }
                                dbF.setXMLAsString(xmlString);
                                dbF.store();
                                Utils.updateReferences(xmlNew, this.DBURI, id[0].split(type)[1], type,
                                        this.DBpassword, this.DBuser);
                                Utils.updateVocabularies(xmlNew, this.DBURI, id[0].split(type)[1], type,
                                        this.DBpassword, this.DBuser, lang);
                                savedIDs.add(id[0]);
                            } else {
                                dbF.remove();
                            }

                        }
                    }

                }
            }
            Document doc = ParseXMLFile.parseFile(ApplicationConfig.SYSTEM_ROOT + "formating/multi_lang.xml");
            Element root = doc.getDocumentElement();
            Element contextTag = (Element) root.getElementsByTagName("context").item(0);
            String uri_name = "";
            try {
                uri_name = DMSTag.valueOf("uri_name", "target", type, this.conf)[0];
            } catch (DMSException ex) {
            }
            if (notValidMXL.size() == 0) {
                xsl = conf.DISPLAY_XSL;
                displayMsg = Messages.ACTION_SUCCESS;
                displayMsg += Messages.NL + Messages.NL + Messages.URI_ID;
                String uriValue = "";
                xml.append("<Display>").append(displayMsg).append("</Display>\n");
                xml.append("<backPages>").append('2').append("</backPages>\n");

                for (String saveId : savedIDs) {
                    uriValue = this.URI_Reference_Path + uri_name + "/" + saveId + Messages.NL;
                    xml.append("<codeValue>").append(uriValue).append("</codeValue>\n");

                }

            } else if (notValidMXL.size() >= 1) {
                xsl = ApplicationConfig.SYSTEM_ROOT + "formating/xsl/import/ImportXML.xsl";

                Iterator it = notValidMXL.keySet().iterator();
                while (it.hasNext()) {

                    String key = (String) it.next();
                    ArrayList<String> value = notValidMXL.get(key);

                    if (value != null) {
                        displayMsg += "<line>";
                        Element select = (Element) contextTag.getElementsByTagName("missingReferences").item(0);
                        displayMsg += select.getElementsByTagName(lang).item(0).getTextContent();
                        displayMsg = displayMsg.replace("?", key);
                        for (String mis_res : value) {

                            displayMsg += mis_res + ",";
                        }
                        displayMsg = displayMsg.substring(0, displayMsg.length() - 1);
                        displayMsg += ".";
                        displayMsg += "</line>";

                    } else {
                        displayMsg += "<line>";
                        Element select = (Element) contextTag.getElementsByTagName("NOT_VALID_XML").item(0);
                        displayMsg += select.getElementsByTagName(lang).item(0).getTextContent();
                        displayMsg = displayMsg.replace(";", key);
                        displayMsg += "</line>";
                    }
                    displayMsg += "<line>";
                    displayMsg += "</line>";
                }
                if (notValidMXL.size() < xmlCount) {
                    displayMsg += "<line>";
                    Element select = (Element) contextTag.getElementsByTagName("rest_valid").item(0);
                    displayMsg += select.getElementsByTagName(lang).item(0).getTextContent();
                    displayMsg += "</line>";
                    for (String saveId : savedIDs) {
                        displayMsg += "<line>";
                        String uriValue = this.URI_Reference_Path + uri_name + "/" + saveId;
                        select = (Element) contextTag.getElementsByTagName("URI_ID").item(0);
                        displayMsg += select.getElementsByTagName(lang).item(0).getTextContent() + ": "
                                + uriValue;
                        displayMsg += "</line>";
                    }
                }
            }
            Utils.deleteDir(currentDir);
        } catch (Exception ex) {
            ex.printStackTrace();
            displayMsg += Messages.NOT_VALID_IMPORT;
        }

    }
    xml.append("<Display>").append(displayMsg).append("</Display>\n");
    xml.append("<EntityType>").append(type).append("</EntityType>\n");
    xml.append(this.xmlEnd());
    try {
        XMLTransform xmlTrans = new XMLTransform(xml.toString());
        xmlTrans.transform(out, xsl);
    } catch (DMSException e) {
        e.printStackTrace();
    }
    out.close();
}

From source file:com.flexive.war.beans.admin.main.ScriptBean.java

/**
 * Runs the given script code in the console
 *//*from  ww  w .  j  av  a  2  s  . c  om*/
public void runScriptInConsole() {
    FxScriptInfoEdit sinfo = currentData.sinfo;
    if (StringUtils.isBlank(sinfo.getCode())) {
        new FxFacesMsgErr("Script.err.noCodeProvided").addToContext();
    } else {
        long start = System.currentTimeMillis();
        try {
            result = ScriptConsoleBean.runScript(sinfo.getCode(), sinfo.getName(), false);
        } catch (Exception e) {
            final StringWriter writer = new StringWriter();
            e.printStackTrace(new PrintWriter(writer));
            final String msg = e.getCause() != null ? e.getCause().getMessage() : e.getMessage();
            result = new Formatter().format("Exception caught: %s%n%s", msg, writer.getBuffer());
        } finally {
            currentData.executionTime = System.currentTimeMillis() - start;
        }
    }
}

From source file:com.twinsoft.convertigo.engine.util.XMLUtils.java

public static String prettyPrintElement(Element elt, boolean omitXMLDeclaration, boolean bIndent) {
    Node firstChild = elt;/* w w w  .  java2  s  . co m*/
    String encoding = "ISO-8859-1"; // default Encoding char set if non is
    // found in the PI

    if (omitXMLDeclaration && (firstChild.getNodeType() == Document.PROCESSING_INSTRUCTION_NODE)
            && (firstChild.getNodeName().equals("xml"))) {
        String piValue = firstChild.getNodeValue();
        // extract from PI the encoding Char Set
        int encodingOffset = piValue.indexOf("encoding=\"");
        if (encodingOffset != -1) {
            encoding = piValue.substring(encodingOffset + 10);
            // remove the last "
            encoding = encoding.substring(0, encoding.length() - 1);
        }
    }
    StringWriter strWtr = new StringWriter();
    try {
        Transformer t = getNewTransformer();
        t.setOutputProperty(OutputKeys.ENCODING, encoding);
        t.setOutputProperty(OutputKeys.INDENT, bIndent ? "yes" : "no");
        t.setOutputProperty(OutputKeys.METHOD, "xml"); // xml, html, text
        t.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "4");
        t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, omitXMLDeclaration ? "yes" : "no");
        t.transform(new DOMSource(elt), new StreamResult(strWtr));
        return strWtr.getBuffer().toString();
    } catch (Exception e) {
        System.err.println("XML.toString(Document): " + e);
        Engine.logEngine.error("Unexpected exception", e);
        return e.getMessage();
    }
}

From source file:net.sf.jabref.gui.plaintextimport.TextInputDialog.java

private void updateSourceView() {
    StringWriter sw = new StringWriter(200);
    try {//from   ww  w.  jav  a 2  s .c  o  m
        new BibEntryWriter(
                new LatexFieldFormatter(LatexFieldFormatterPreferences.fromPreferences(Globals.prefs)), false)
                        .write(entry, sw, frame.getCurrentBasePanel().getBibDatabaseContext().getMode());
        sourcePreview.setText(sw.getBuffer().toString());
    } catch (IOException ex) {
        LOGGER.error("Error in entry" + ": " + ex.getMessage(), ex);
    }

    fieldList.clearSelection();
}

From source file:edu.cornell.med.icb.goby.modes.TestDiscoverSVMethylationRatesMode.java

@Test
public void testMethylationFormat() throws IOException, JSAPException {
    final MethylationRateVCFOutputFormat outputFormat = new MethylationRateVCFOutputFormat();
    DiscoverVariantIterateSortedAlignments iterator = new DiscoverVariantIterateSortedAlignments(outputFormat) {
        @Override/*from w  w  w. ja  v  a  2  s .co  m*/
        public CharSequence getReferenceId(int targetIndex) {
            return "ref-id";
        }
    };
    DiscoverSequenceVariantsMode mode = new DiscoverSequenceVariantsMode() {
        @Override
        public String[] getSamples() {
            return new String[] { "methylated", "not-so" };
        }

        @Override
        public String[] getGroups() {
            return new String[] { "methylated", "not-so" };
        }

        @Override
        public int[] getReaderIndexToGroupIndex() {
            return new int[] { 0, 1 }; // sample index is group index;
        }

        @Override
        public ArrayList<GroupComparison> getGroupComparisons() {
            ArrayList<GroupComparison> list = new ArrayList<GroupComparison>();
            list.add(new GroupComparison("methylated", "not-so", 0, 1, 0));
            return list;
        }
    };
    StringWriter writer = new StringWriter();
    outputFormat.allocateStorage(2, 2);
    outputFormat.setGenome(genome);
    outputFormat.defineColumns(new PrintWriter(writer), mode);
    outputFormat.setMinimumEventThreshold(0);
    outputFormat.writeRecord(iterator, makeTwoSampleCounts(), 0, 0, list1(), 0, 1);
    writer.flush();

    String stringB = writer.getBuffer().toString();
    assertTrue(stringB, stringB.contains("#Cm_Group[methylated]=1;"));
    assertTrue(stringB, stringB.contains("#Cm_Group[not-so]=0;"));

    writer = new StringWriter();
    outputFormat.allocateStorage(2, 2);
    outputFormat.defineColumns(new PrintWriter(writer), mode);

    final SampleCountInfo[] sampleCounts = makeTwoSampleCounts();
    sampleCounts[0].referenceBase = 'G';
    outputFormat.writeRecord(iterator, sampleCounts, 0, 0, list2(), 0, 1);
    writer.flush();
    stringB = writer.getBuffer().toString();
    assertTrue(stringB, stringB.contains("#Cm_Group[methylated]=1;"));
    assertTrue(stringB, stringB.contains("#Cm_Group[not-so]=0;"));
    assertTrue(stringB, stringB.contains("MR[methylated]=100.0;"));
    assertTrue(stringB, stringB.contains("MR[not-so]=NaN;"));

    writer = new StringWriter();

    outputFormat.allocateStorage(2, 2);
    outputFormat.defineColumns(new PrintWriter(writer), mode);

    outputFormat.writeRecord(iterator, makeTwoSampleCounts(), 0, 0, list3(), 0, 1);
    stringB = writer.getBuffer().toString();
    assertTrue(stringB, stringB.contains("#Cm_Group[methylated]=1;"));
    assertTrue(stringB, stringB.contains("#C_Group[methylated]=1;"));
    assertTrue(stringB, stringB.contains("#Cm_Group[not-so]=0;"));
    assertTrue(stringB, stringB.contains("#C_Group[not-so]=0;"));

    /*  org.junit.Assert.assertEquals("content must match", header+
        "ref-id\t1\t\tC\tA,T,N\t\t\tBIOMART_COORDS=ref-id:1:1;Strand=+;LOD[methylated/not-so]=NaN;LOD_SE[methylated/not-so]=NaN;LOD_Z[methylated/not-so]=NaN;FisherP[methylated/not-so]=NaN;#C Group[methylated]=0;#Cm Group[methylated]=1;#C Group[not-so]=0;#Cm Group[not-so]=0;DP=1\tMR:GT:BC:GB:FB\t100:0/1/2/3:A=5,T=1,C=9,G=0,N=1:16:0\t0:1/2/3:A=10,T=4,C=0,G=0,N=2:16:0",
        buffer.toString());
    */
}

From source file:org.apache.hadoop.hdfs.server.namenode.INode.java

/**
 * Dump the subtree starting from this inode.
 * @return a text representation of the tree.
 *//*from ww  w.j a  va2s  . c o m*/
@VisibleForTesting
public final StringBuffer dumpTreeRecursively() {
    final StringWriter out = new StringWriter();
    dumpTreeRecursively(new PrintWriter(out, true), new StringBuilder(), Snapshot.CURRENT_STATE_ID);
    return out.getBuffer();
}

From source file:ddf.compression.exi.EXIEncoderTest.java

/**
 * Tests that the encode method converts xml into exi-compressed xml.
 *
 * @throws Exception/*from  w w w  . ja v a2  s  . com*/
 */
@Test
public void testEncode() throws Exception {

    ByteArrayOutputStream exiStream = new ByteArrayOutputStream();

    InputStream xmlStream = getClass().getResourceAsStream(TEST_FILE);

    EXIEncoder.encode(xmlStream, exiStream);

    StringWriter stringWriter = new StringWriter();

    GrammarCache grammarCache;

    SAXTransformerFactory saxTransformerFactory = (SAXTransformerFactory) SAXTransformerFactory.newInstance();
    SAXParserFactory saxParserFactory = SAXParserFactory.newInstance();
    saxParserFactory.setNamespaceAware(true);
    TransformerHandler transformerHandler = saxTransformerFactory.newTransformerHandler();

    EXIReader reader = new EXIReader();

    grammarCache = new GrammarCache(null, GrammarOptions.DEFAULT_OPTIONS);

    reader.setGrammarCache(grammarCache);

    transformerHandler.setResult(new StreamResult(stringWriter));

    reader.setContentHandler(transformerHandler);

    reader.parse(new InputSource(new ByteArrayInputStream(exiStream.toByteArray())));
    XMLUnit.setNormalize(true);
    XMLUnit.setNormalizeWhitespace(true);
    InputStream stream = getClass().getResourceAsStream(TEST_FILE);
    Diff diff = XMLUnit.compareXML(IOUtils.toString(stream), stringWriter.getBuffer().toString());
    IOUtils.closeQuietly(stream);
    assertTrue("The XML input file (" + TEST_FILE + ") did not match the EXI-decoded output", diff.similar());
}

From source file:com.sshtools.sshvnc.SshVncSessionPanel.java

/**
 *
 *
 * @param application//from  w  w  w  .  jav a2 s .  co  m
 *
 * @throws SshToolsApplicationException
 */
public void init(SshToolsApplication application) throws SshToolsApplicationException {
    super.init(application);

    setLayout(new BorderLayout());
    sendTimer = new javax.swing.Timer(500, this);
    sendTimer.setRepeats(false);
    receiveTimer = new javax.swing.Timer(500, this);
    receiveTimer.setRepeats(false);

    statusBar = new StatusBar();
    statusBar.setUser("");
    statusBar.setHost("");
    statusBar.setStatusText("Disconnected");
    statusBar.setConnected(false);
    setLayout(new BorderLayout());

    // Create our terminal emulation object
    try {
        emulation = createEmulation();
    } catch (IOException ioe) {
        throw new SshToolsApplicationException(ioe);
    }

    // Set a scrollbar for the terminal - doesn't seem to be as simple as this
    emulation.setBufferSize(1000);

    // Create our swing terminal and add it to the main frame
    terminal = new TerminalPanel(emulation);

    terminal.requestFocus();

    //
    try {
        vnc = new SshVNCViewer();

        //  Additional connection tabs
        additionalTabs = new SshToolsConnectionTab[] { new VNCTab(), new VNCAdvancedTab() };
        add(vnc, BorderLayout.CENTER);
        initActions();
    } catch (Throwable t) {
        StringWriter sw = new StringWriter();
        t.printStackTrace(new PrintWriter(sw));

        IconWrapperPanel p = new IconWrapperPanel(UIManager.getIcon("OptionPane.errorIcon"),
                new ErrorTextBox(((t.getMessage() == null) ? "<no message supplied>" : t.getMessage())
                        + (debug ? ("\n\n" + sw.getBuffer().toString()) : "")));
        p.setBorder(BorderFactory.createEmptyBorder(8, 8, 8, 8));
        add(p, BorderLayout.CENTER);
        throw new SshToolsApplicationException("Failed to start SshVNC. ", t);
    }
}