List of usage examples for org.apache.commons.io FilenameUtils getFullPath
public static String getFullPath(String filename)
From source file:com.haulmont.cuba.web.sys.CubaApplicationServlet.java
@Nullable protected String getLocalizedTemplateContent(Resources resources, String defaultTemplateName, String locale) { String localizedTemplate = FilenameUtils.getFullPath(defaultTemplateName) + FilenameUtils.getBaseName(defaultTemplateName) + "_" + locale + "." + FilenameUtils.getExtension(defaultTemplateName); return resources.getResourceAsString(localizedTemplate); }
From source file:ching.icecreaming.action.ViewAction.java
@Action(value = "view", results = { @Result(name = "login", location = "edit.jsp"), @Result(name = "input", location = "view.jsp"), @Result(name = "success", location = "view.jsp"), @Result(name = "error", location = "error.jsp") }) public String execute() throws Exception { Enumeration enumerator = null; String[] array1 = null, array2 = null; int int1 = -1, int2 = -1, int3 = -1; InputStream inputStream1 = null; OutputStream outputStream1 = null; java.io.File file1 = null, file2 = null, dir1 = null; List<File> files = null; HttpHost httpHost1 = null;/*from w ww . jav a 2s.c o m*/ HttpGet httpGet1 = null, httpGet2 = null; HttpPut httpPut1 = null; URI uri1 = null; URL url1 = null; DefaultHttpClient httpClient1 = null; URIBuilder uriBuilder1 = null, uriBuilder2 = null; HttpResponse httpResponse1 = null, httpResponse2 = null; HttpEntity httpEntity1 = null, httpEntity2 = null; List<NameValuePair> nameValuePair1 = null; String string1 = null, string2 = null, string3 = null, string4 = null, return1 = LOGIN; XMLConfiguration xmlConfiguration = null; List<HierarchicalConfiguration> list1 = null, list2 = null; HierarchicalConfiguration hierarchicalConfiguration2 = null; DataModel1 dataModel1 = null; DataModel2 dataModel2 = null; List<DataModel1> listObject1 = null, listObject3 = null; org.joda.time.DateTime dateTime1 = null, dateTime2 = null; org.joda.time.Period period1 = null; PeriodFormatter periodFormatter1 = new PeriodFormatterBuilder().appendYears() .appendSuffix(String.format(" %s", getText("year")), String.format(" %s", getText("years"))) .appendSeparator(" ").appendMonths() .appendSuffix(String.format(" %s", getText("month")), String.format(" %s", getText("months"))) .appendSeparator(" ").appendWeeks() .appendSuffix(String.format(" %s", getText("week")), String.format(" %s", getText("weeks"))) .appendSeparator(" ").appendDays() .appendSuffix(String.format(" %s", getText("day")), String.format(" %s", getText("days"))) .appendSeparator(" ").appendHours() .appendSuffix(String.format(" %s", getText("hour")), String.format(" %s", getText("hours"))) .appendSeparator(" ").appendMinutes() .appendSuffix(String.format(" %s", getText("minute")), String.format(" %s", getText("minutes"))) .appendSeparator(" ").appendSeconds().minimumPrintedDigits(2) .appendSuffix(String.format(" %s", getText("second")), String.format(" %s", getText("seconds"))) .printZeroNever().toFormatter(); if (StringUtils.isBlank(urlString) || StringUtils.isBlank(wsType)) { urlString = portletPreferences.getValue("urlString", "/"); wsType = portletPreferences.getValue("wsType", "folder"); } Configuration propertiesConfiguration1 = new PropertiesConfiguration("system.properties"); timeZone1 = portletPreferences.getValue("timeZone", TimeZone.getDefault().getID()); enumerator = portletPreferences.getNames(); if (enumerator.hasMoreElements()) { array1 = portletPreferences.getValues("server", null); if (array1 != null) { if (ArrayUtils.isNotEmpty(array1)) { for (int1 = 0; int1 < array1.length; int1++) { switch (int1) { case 0: sid = array1[int1]; break; case 1: uid = array1[int1]; break; case 2: pid = array1[int1]; break; case 3: alias1 = array1[int1]; break; default: break; } } sid = new String(Base64.decodeBase64(sid.getBytes())); uid = new String(Base64.decodeBase64(uid.getBytes())); pid = new String(Base64.decodeBase64(pid.getBytes())); } return1 = INPUT; } else { return1 = LOGIN; } } else { return1 = LOGIN; } if (StringUtils.equals(urlString, "/")) { if (listObject1 != null) { listObject1.clear(); } if (session.containsKey("breadcrumbs")) { session.remove("breadcrumbs"); } } else { array2 = StringUtils.split(urlString, "/"); listObject1 = (session.containsKey("breadcrumbs")) ? (List<DataModel1>) session.get("breadcrumbs") : new ArrayList<DataModel1>(); int2 = array2.length - listObject1.size(); if (int2 > 0) { listObject1.add(new DataModel1(urlString, label1)); } else { int2 += listObject1.size(); for (int1 = listObject1.size() - 1; int1 >= int2; int1--) { listObject1.remove(int1); } } session.put("breadcrumbs", listObject1); } switch (wsType) { case "folder": break; case "reportUnit": try { dateTime1 = new org.joda.time.DateTime(); return1 = INPUT; httpClient1 = new DefaultHttpClient(); if (StringUtils.equals(button1, getText("Print"))) { nameValuePair1 = new ArrayList<NameValuePair>(); if (listObject2 != null) { if (listObject2.size() > 0) { for (DataModel2 dataObject2 : listObject2) { listObject3 = dataObject2.getOptions(); if (listObject3 == null) { string2 = dataObject2.getValue1(); if (StringUtils.isNotBlank(string2)) nameValuePair1.add(new BasicNameValuePair(dataObject2.getId(), string2)); } else { for (int1 = listObject3.size() - 1; int1 >= 0; int1--) { dataModel1 = (DataModel1) listObject3.get(int1); string2 = dataModel1.getString2(); if (StringUtils.isNotBlank(string2)) nameValuePair1 .add(new BasicNameValuePair(dataObject2.getId(), string2)); } } } } } url1 = new URL(sid); uriBuilder1 = new URIBuilder(sid); uriBuilder1.setUserInfo(uid, pid); if (StringUtils.isBlank(format1)) format1 = "pdf"; uriBuilder1.setPath(url1.getPath() + "/rest_v2/reports" + urlString + "." + format1); if (StringUtils.isNotBlank(locale2)) { nameValuePair1.add(new BasicNameValuePair("userLocale", locale2)); } if (StringUtils.isNotBlank(page1)) { if (NumberUtils.isNumber(page1)) { nameValuePair1.add(new BasicNameValuePair("page", page1)); } } if (nameValuePair1.size() > 0) { uriBuilder1.setQuery(URLEncodedUtils.format(nameValuePair1, "UTF-8")); } uri1 = uriBuilder1.build(); httpGet1 = new HttpGet(uri1); httpResponse1 = httpClient1.execute(httpGet1); int1 = httpResponse1.getStatusLine().getStatusCode(); if (int1 == HttpStatus.SC_OK) { string3 = System.getProperty("java.io.tmpdir") + File.separator + httpServletRequest.getSession().getId(); dir1 = new File(string3); if (!dir1.exists()) { dir1.mkdir(); } httpEntity1 = httpResponse1.getEntity(); file1 = new File(string3, StringUtils.substringAfterLast(urlString, "/") + "." + format1); if (StringUtils.equalsIgnoreCase(format1, "html")) { result1 = EntityUtils.toString(httpEntity1); FileUtils.writeStringToFile(file1, result1); array1 = StringUtils.substringsBetween(result1, "<img src=\"", "\""); if (ArrayUtils.isNotEmpty(array1)) { dir1 = new File( string3 + File.separator + FilenameUtils.getBaseName(file1.getName())); if (dir1.exists()) { FileUtils.deleteDirectory(dir1); } file2 = new File(FilenameUtils.getFullPath(file1.getAbsolutePath()) + FilenameUtils.getBaseName(file1.getName()) + ".zip"); if (file2.exists()) { if (FileUtils.deleteQuietly(file2)) { } } for (int2 = 0; int2 < array1.length; int2++) { try { string2 = url1.getPath() + "/rest_v2/reports" + urlString + "/" + StringUtils.substringAfter(array1[int2], "/"); uriBuilder1.setPath(string2); uri1 = uriBuilder1.build(); httpGet1 = new HttpGet(uri1); httpResponse1 = httpClient1.execute(httpGet1); int1 = httpResponse1.getStatusLine().getStatusCode(); } finally { if (int1 == HttpStatus.SC_OK) { try { string2 = StringUtils.substringBeforeLast(array1[int2], "/"); dir1 = new File(string3 + File.separator + string2); if (!dir1.exists()) { dir1.mkdirs(); } httpEntity1 = httpResponse1.getEntity(); inputStream1 = httpEntity1.getContent(); } finally { string1 = StringUtils.substringAfterLast(array1[int2], "/"); file2 = new File(string3 + File.separator + string2, string1); outputStream1 = new FileOutputStream(file2); IOUtils.copy(inputStream1, outputStream1); } } } } outputStream1 = new FileOutputStream( FilenameUtils.getFullPath(file1.getAbsolutePath()) + FilenameUtils.getBaseName(file1.getName()) + ".zip"); ArchiveOutputStream archiveOutputStream1 = new ArchiveStreamFactory() .createArchiveOutputStream(ArchiveStreamFactory.ZIP, outputStream1); archiveOutputStream1.putArchiveEntry(new ZipArchiveEntry(file1, file1.getName())); IOUtils.copy(new FileInputStream(file1), archiveOutputStream1); archiveOutputStream1.closeArchiveEntry(); dir1 = new File(FilenameUtils.getFullPath(file1.getAbsolutePath()) + FilenameUtils.getBaseName(file1.getName())); files = (List<File>) FileUtils.listFiles(dir1, TrueFileFilter.INSTANCE, TrueFileFilter.INSTANCE); for (File file3 : files) { archiveOutputStream1.putArchiveEntry(new ZipArchiveEntry(file3, StringUtils .substringAfter(file3.getCanonicalPath(), string3 + File.separator))); IOUtils.copy(new FileInputStream(file3), archiveOutputStream1); archiveOutputStream1.closeArchiveEntry(); } archiveOutputStream1.close(); } bugfixGateIn = propertiesConfiguration1.getBoolean("bugfixGateIn", false); string4 = bugfixGateIn ? String.format("<img src=\"%s/namespace1/file-link?sessionId=%s&fileName=", portletRequest.getContextPath(), httpServletRequest.getSession().getId()) : String.format("<img src=\"%s/namespace1/file-link?fileName=", portletRequest.getContextPath()); result1 = StringUtils.replace(result1, "<img src=\"", string4); } else { inputStream1 = httpEntity1.getContent(); outputStream1 = new FileOutputStream(file1); IOUtils.copy(inputStream1, outputStream1); result1 = file1.getAbsolutePath(); } return1 = SUCCESS; } else { addActionError(String.format("%s %d: %s", getText("Error"), int1, getText(Integer.toString(int1)))); } dateTime2 = new org.joda.time.DateTime(); period1 = new Period(dateTime1, dateTime2.plusSeconds(1)); message1 = getText("Execution.time") + ": " + periodFormatter1.print(period1); } else { url1 = new URL(sid); uriBuilder1 = new URIBuilder(sid); uriBuilder1.setUserInfo(uid, pid); uriBuilder1.setPath(url1.getPath() + "/rest_v2/reports" + urlString + "/inputControls"); uri1 = uriBuilder1.build(); httpGet1 = new HttpGet(uri1); httpResponse1 = httpClient1.execute(httpGet1); int1 = httpResponse1.getStatusLine().getStatusCode(); switch (int1) { case HttpStatus.SC_NO_CONTENT: break; case HttpStatus.SC_OK: httpEntity1 = httpResponse1.getEntity(); if (httpEntity1 != null) { inputStream1 = httpEntity1.getContent(); if (inputStream1 != null) { xmlConfiguration = new XMLConfiguration(); xmlConfiguration.load(inputStream1); list1 = xmlConfiguration.configurationsAt("inputControl"); if (list1.size() > 0) { listObject2 = new ArrayList<DataModel2>(); for (HierarchicalConfiguration hierarchicalConfiguration1 : list1) { string2 = hierarchicalConfiguration1.getString("type"); dataModel2 = new DataModel2(); dataModel2.setId(hierarchicalConfiguration1.getString("id")); dataModel2.setLabel1(hierarchicalConfiguration1.getString("label")); dataModel2.setType1(string2); dataModel2.setMandatory(hierarchicalConfiguration1.getBoolean("mandatory")); dataModel2.setReadOnly(hierarchicalConfiguration1.getBoolean("readOnly")); dataModel2.setVisible(hierarchicalConfiguration1.getBoolean("visible")); switch (string2) { case "bool": case "singleValueText": case "singleValueNumber": case "singleValueDate": case "singleValueDatetime": hierarchicalConfiguration2 = hierarchicalConfiguration1 .configurationAt("state"); dataModel2.setValue1(hierarchicalConfiguration2.getString("value")); break; case "singleSelect": case "singleSelectRadio": case "multiSelect": case "multiSelectCheckbox": hierarchicalConfiguration2 = hierarchicalConfiguration1 .configurationAt("state"); list2 = hierarchicalConfiguration2.configurationsAt("options.option"); if (list2.size() > 0) { listObject3 = new ArrayList<DataModel1>(); for (HierarchicalConfiguration hierarchicalConfiguration3 : list2) { dataModel1 = new DataModel1( hierarchicalConfiguration3.getString("label"), hierarchicalConfiguration3.getString("value")); if (hierarchicalConfiguration3.getBoolean("selected")) { dataModel2.setValue1( hierarchicalConfiguration3.getString("value")); } listObject3.add(dataModel1); } dataModel2.setOptions(listObject3); } break; default: break; } listObject2.add(dataModel2); } } } } break; default: addActionError(String.format("%s %d: %s", getText("Error"), int1, getText(Integer.toString(int1)))); break; } if (httpEntity1 != null) { EntityUtils.consume(httpEntity1); } uriBuilder1.setPath(url1.getPath() + "/rest/resource" + urlString); uri1 = uriBuilder1.build(); httpGet1 = new HttpGet(uri1); httpResponse1 = httpClient1.execute(httpGet1); int2 = httpResponse1.getStatusLine().getStatusCode(); if (int2 == HttpStatus.SC_OK) { httpEntity1 = httpResponse1.getEntity(); inputStream1 = httpEntity1.getContent(); xmlConfiguration = new XMLConfiguration(); xmlConfiguration.load(inputStream1); list1 = xmlConfiguration.configurationsAt("resourceDescriptor"); for (HierarchicalConfiguration hierarchicalConfiguration4 : list1) { if (StringUtils.equalsIgnoreCase( StringUtils.trim(hierarchicalConfiguration4.getString("[@wsType]")), "prop")) { if (map1 == null) map1 = new HashMap<String, String>(); string2 = StringUtils.substringBetween( StringUtils.substringAfter( hierarchicalConfiguration4.getString("[@uriString]"), "_files/"), "_", ".properties"); map1.put(string2, StringUtils.isBlank(string2) ? getText("Default") : getText(string2)); } } } if (httpEntity1 != null) { EntityUtils.consume(httpEntity1); } } } catch (IOException | ConfigurationException | URISyntaxException exception1) { exception1.printStackTrace(); addActionError(exception1.getLocalizedMessage()); httpGet1.abort(); return ERROR; } finally { httpClient1.getConnectionManager().shutdown(); IOUtils.closeQuietly(inputStream1); } break; default: addActionError(getText("This.file.type.is.not.supported")); break; } if (return1 != LOGIN) { sid = new String(Base64.encodeBase64(sid.getBytes())); uid = new String(Base64.encodeBase64(uid.getBytes())); pid = new String(Base64.encodeBase64(pid.getBytes())); } return return1; }
From source file:MSUmpire.PSMDataStructure.LCMSID.java
private void ExportPepIonCSV(String folder) throws IOException { if (folder == null | "".equals(folder)) { folder = FilenameUtils.getFullPath(mzXMLFileName); }// w w w . java 2 s . co m Logger.getRootLogger().info("Writing PepIon result to file:" + folder + FilenameUtils.getBaseName(mzXMLFileName) + "_PepIonIDs.csv..."); FileWriter writer = new FileWriter(folder + FilenameUtils.getBaseName(mzXMLFileName) + "_PepIonIDs.csv"); writer.write( "PepIndex,Sequence,ModSeq,TPPModSeq,IsNonDegenerate,Charge,mz,IDRT,PeakRT,NoPSMs,MS1ClusIndex,MS2ClusIndex,PeakScore,PeakHeight1,PeakHeight2,PeakHeight3,PeakArea1,PeakArea2,PeakArea3\n"); for (PepIonID pepion : PepIonList.values()) { writer.write(pepion.Index + "," + pepion.Sequence + "," + pepion.ModSequence + "," + pepion.TPPModSeq + "," + (pepion.Is_NonDegenerate ? 1 : 0) + "," + pepion.Charge + "," + pepion.NeutralPrecursorMz() + "," + pepion.GetIDRT() + "," + pepion.PeakRT + "," + pepion.GetSpectralCount() + "," + pepion.GetMS1ClusIndex() + "," + pepion.GetMS2ClusIndex() + "," + pepion.PeakClusterScore + "," + pepion.PeakHeight[0] + "," + pepion.PeakHeight[1] + "," + pepion.PeakHeight[2] + "," + pepion.PeakArea[0] + "," + pepion.PeakArea[1] + "," + pepion.PeakArea[2] + "\n"); } writer.close(); }
From source file:net.pms.util.SubtitleUtils.java
/** * Converts ASS/SSA subtitles to 3D ASS/SSA subtitles. * Based on https://bitbucket.org/r3pek/srt2ass3d * * @param tempSubs Subtitles file to convert * @param media Information about video/* w w w . j av a 2 s .com*/ * @return Converted subtitles file * @throws IOException */ public static File convertASSToASS3D(File tempSubs, DLNAMediaInfo media, OutputParams params) throws IOException, NullPointerException { File outputSubs = new File(FilenameUtils.getFullPath(tempSubs.getPath()), FilenameUtils.getBaseName(tempSubs.getName()) + "_3D.ass"); StringBuilder outputString = new StringBuilder(); Charset subsFileCharset = FileUtil.getFileCharset(tempSubs); if (subsFileCharset == null) { subsFileCharset = StandardCharsets.UTF_8; } BufferedWriter output; Mode3D mode3D = media.get3DLayout(); boolean isOU = mode3D == Mode3D.OUL || mode3D == Mode3D.OUR || mode3D == Mode3D.HOUL; boolean isSBS = mode3D == Mode3D.SBSL || mode3D == Mode3D.SBSR || mode3D == Mode3D.HSBSL; if (mode3D == null) { LOGGER.debug("The 3D layout not recognized for the 3D video"); throw new NullPointerException("The 3D layout not recognized for the 3D video"); } int depth3D = configuration.getDepth3D(); Pattern timePattern = Pattern.compile("[0-9]:[0-9]{2}:[0-9]{2}.[0-9]{2},[0-9]:[0-9]{2}:[0-9]{2}.[0-9]{2},"); try (BufferedReader input = new BufferedReader( new InputStreamReader(new FileInputStream(tempSubs), subsFileCharset))) { output = new BufferedWriter( new OutputStreamWriter(new FileOutputStream(outputSubs), Charset.forName(CHARSET_UTF_8))); String line; outputString.append("[Script Info]\n"); outputString.append("ScriptType: v4.00+\n"); outputString.append("Collisions: Normal\n"); outputString.append("PlayResX: ").append("384\n"); outputString.append("PlayResY: ").append("288\n"); outputString.append("ScaledBorderAndShadow: yes\n"); outputString.append("PlayDepth: 0\n"); outputString.append("Timer: 100.0\n"); outputString.append("WrapStyle: 0\n\n"); outputString.append("[V4+ Styles]\n"); outputString.append( "Format: Name, Fontname, Fontsize, PrimaryColour, SecondaryColour, OutlineColour, BackColour, Bold, Italic, Underline, StrikeOut, ScaleX, ScaleY, Spacing, Angle, BorderStyle, Outline, Shadow, Alignment, MarginL, MarginR, MarginV, Encoding\n"); String fontScaleX = "1"; String fontScaleY = "1"; if (isOU) { fontScaleX = Double.toString(100 * Double.parseDouble(configuration.getAssScale())); fontScaleY = Double.toString((100 * Double.parseDouble(configuration.getAssScale())) / 2); } else if (isSBS) { fontScaleX = Double.toString((100 * Double.parseDouble(configuration.getAssScale())) / 2); fontScaleY = Double.toString(100 * Double.parseDouble(configuration.getAssScale())); } String primaryColour = convertColourToASSColourString(configuration.getSubsColor()); String outline = configuration.getAssOutline(); String shadow = configuration.getAssShadow(); outputString.append("Style: Default,Arial,").append("15").append(",").append(primaryColour) .append(",&H000000FF,&H00000000,&H00000000,0,0,0,0,").append(fontScaleX).append(",") .append(fontScaleY).append(",0,0,1,").append(outline).append(",").append(shadow); if (isOU) { outputString.append(",2,15,15,15,0\n\n"); } else if (isSBS) { outputString.append(",2,0,0,15,0\n\n"); } outputString.append("[Events]\n"); outputString .append("Format: Layer, Start, End, Style, Name, MarginL, MarginR, MarginV, Effect, Text\n\n"); output.write(outputString.toString()); int textPosition = 0; while ((line = input.readLine()) != null) { if (line.startsWith("[Events]")) { line = input.readLine(); if (line != null && line.startsWith("Format:")) { String[] formatPattern = line.split(","); int i = 0; for (String component : formatPattern) { if (component.trim().equals("Text")) { textPosition = i; } i++; } } } outputString.setLength(0); if (line != null && line.startsWith("Dialogue:") && line.contains("Default")) { // TODO: For now convert only Default style. For other styles must be position and font size recalculated String[] dialogPattern = line.split(","); String text = StringUtils.join(dialogPattern, ",", textPosition, dialogPattern.length); Matcher timeMatcher = timePattern.matcher(line); if (timeMatcher.find()) { if (isOU) { outputString.append("Dialogue: 0,").append(timeMatcher.group()).append("Default,,"); if (depth3D > 0) { outputString.append("0000,").append(String.format("%04d,", depth3D)); } else if (depth3D < 0) { outputString.append(String.format("%04d,", -depth3D)).append("0000,"); } else { outputString.append("0000,0000,"); } outputString.append(String.format("%04d,,", 159)).append(text).append("\n") .append("Dialogue: 0,").append(timeMatcher.group()) .append("Default,,0000,0000,0000,,").append(text).append("\n"); } else if (isSBS) { outputString.append("Dialogue: 0,").append(timeMatcher.group()).append("Default,,") .append("0000,").append(String.format("%04d,", 192 - depth3D)).append("0000,") .append(text).append("\n").append("Dialogue: 0,").append(timeMatcher.group()) .append("Default,,").append(String.format("%04d,", 192 - depth3D)) .append("0000,0000,").append(text).append("\n"); } } output.write(outputString.toString()); } } } LOGGER.debug("Subtitles converted to 3DASS format and stored in the file: " + outputSubs.getName()); output.flush(); output.close(); tempSubs.deleteOnExit(); return outputSubs; }
From source file:de.tudarmstadt.ukp.dkpro.core.api.io.ResourceCollectionReaderBase.java
/** * Initialize the {@link DocumentMetaData}. This must be called before setting the document * text, otherwise the end feature of this annotation will not be set correctly. *//* w w w. j a v a 2s . c o m*/ protected void initCas(CAS aCas, Resource aResource, String aQualifier) { boolean singleLocation = patterns == null; String qualifier = aQualifier != null ? "#" + aQualifier : ""; try { // Set the document metadata DocumentMetaData docMetaData = DocumentMetaData.create(aCas); docMetaData.setDocumentTitle(new File(aResource.getPath()).getName()); docMetaData.setDocumentUri(aResource.getResolvedUri().toString() + qualifier); docMetaData.setDocumentId(aResource.getPath() + qualifier); if (aResource.getBase() != null) { if (singleLocation) { // If it was a single location, then use the parent folder as base String base = FilenameUtils.getFullPath(aResource.getResolvedBase()); docMetaData.setDocumentBaseUri(base); docMetaData.setCollectionId(base); } else { docMetaData.setDocumentBaseUri(aResource.getResolvedBase()); docMetaData.setCollectionId(aResource.getResolvedBase()); } } // Set the document language aCas.setDocumentLanguage(language); } catch (CASException e) { // This should not happen. throw new RuntimeException(e); } }
From source file:MSUmpire.LCMSPeakStructure.LCMSPeakBase.java
public void ExportPeakClusterRegionTXT() throws IOException { FileWriter writer = new FileWriter(FilenameUtils.getFullPath(ScanCollectionName) + FilenameUtils.getBaseName(ScanCollectionName) + "_PeakClusterRange.txt"); for (PeakCluster cluster : PeakClusters) { writer.write(cluster.startRT + "\t" + cluster.endRT + "\t" + (cluster.mz[0] + 1f) + "\t" + (cluster.mz[0]) + "\n"); }//from w ww. j av a 2 s . co m writer.close(); }
From source file:net.sourceforge.jencrypt.FileEncrypter.java
/** * Cipher the file or folder [sourceFileOrFolder] with the key [keyFile] and * store the ciphered files in the optional [targetFolder]. */// www. j a v a 2 s . c o m public boolean cipherFileOrFolder() throws Exception { final String sourceFileOrFolder = commandline.getSourceFileOrFolder(); long fileCounter = 0; File sourcePath = new File(sourceFileOrFolder); String targetFileOrFolder = commandline.getTargetFolder(); OutputStream os = null; System.out.println(); try { if (commandline.getCipherMode() == Cipher.ENCRYPT_MODE) { /* * Create one wrapper for file names, sizes and permissions, and * one wrapper for the file contents. If no IV and salt are * given they will be generated using the SecureRandom class. */ createCryptoWrappers(null /* initializationVector */, null /* salt */); if (sourcePath.isDirectory()) { // Get complete tree of all files and folders in sourcePath FolderList folderList = new FolderList(sourcePath.getPath()); Collection<String> fileTree = folderList.getFilesAsString(); Collection<String> folderTree = folderList.getFoldersAsString(); if (fileTree.isEmpty()) { logger.severe("Directory '" + sourcePath.getName() + "' is empty", true); return false; } os = openArchiveFileAndWriteHeader(targetFileOrFolder); // Walk through all directories and store directory // structure in archive. for (String relativePath : folderTree) { // Encrypt file and add to archive encryptAndArchivePath(folderList.getArchiveTopFolder(), relativePath + File.separator, os); } // Walk through all files for (String relativePath : fileTree) { // Encrypt file and add to archive encryptAndArchivePath(folderList.getArchiveTopFolder(), relativePath, os); System.out.println(); ++fileCounter; } } else { os = openArchiveFileAndWriteHeader(targetFileOrFolder); String fullPath = FilenameUtils.getFullPath(sourcePath.getAbsolutePath()); encryptAndArchivePath(fullPath, sourcePath.getName(), os); System.out.println(); ++fileCounter; } os.close(); } else if (sourcePath.isFile()) { fileCounter = decryptArchive(sourcePath.getAbsolutePath(), targetFileOrFolder); } } catch (Exception e) { logger.warning("File ciphering operation failed: " + e.getMessage(), true); e.printStackTrace(); return false; } finally { if (os != null) os.close(); } System.out.println(); String endText = (commandline.getCipherMode() == Cipher.ENCRYPT_MODE) ? "encrypted" : "decrypted"; logger.info(fileCounter + " file(s) " + endText, true); return true; }
From source file:MSUmpire.PSMDataStructure.LCMSID.java
private void ExportProtIDCSV(String folder) throws IOException { if (folder == null | "".equals(folder)) { folder = FilenameUtils.getFullPath(mzXMLFileName); }// w ww.j av a 2 s . c om Logger.getRootLogger().info("Writing ProteinID result to file:" + folder + FilenameUtils.getBaseName(mzXMLFileName) + "_ProtIDs.csv..."); FileWriter writer = new FileWriter(folder + FilenameUtils.getBaseName(mzXMLFileName) + "_ProtIDs.csv"); writer.write( "AccNo,UniProtID,ProteinLength,ProteinGroup,IndisProt,Description,Mass,Score,Peptides,Sequence\n"); for (ProtID protein : ProteinList.values()) { String pepstring = ""; for (PepIonID pep : protein.PeptideID.values()) { pepstring += pep.GetKey() + ";"; } String IndisProt = ""; for (String indisprot : protein.IndisProteins) { IndisProt += indisprot + ";"; } writer.write(protein.getAccNo() + "," + protein.UniProtID + "," + protein.ProteinLength + "," + protein.ProteinGroup + "," + IndisProt + "," + protein.Description + "," + protein.Mass + "," + protein.Probability + "," + pepstring + "," + protein.Sequence + "\n"); } writer.close(); }
From source file:edu.wustl.lookingglass.community.CommunityRepository.java
private void resolveMerge() throws NoWorkTreeException, GitAPIException, IOException { assert this.username != null; assert this.email != null; Status status = this.git.status().call(); Map<String, StageState> conflicting = status.getConflictingStageState(); for (String path : conflicting.keySet()) { StageState stageState = conflicting.get(path); switch (stageState) { case BOTH_MODIFIED: // UU case BOTH_ADDED: // AA case ADDED_BY_US: // AU case ADDED_BY_THEM: // UA // Both the local and server version have been modified File conflictingFile = new File(this.repoDir, path); String fullPath = conflictingFile.getAbsolutePath(); // Since the local copy was modified it probably makes sense to leave it // since that's the copy the user has been working on. Here's my assumption... // a sync didn't happen, so the user opens their project and sees it's not their // latest changes, they accept the failure and start to fix it... finally a sync // happens... at this point they are probably editing this world, so when they save // they wouldn't even load the new file, so we should just keep the old file. // TODO: we should really prompt the user to resolve this conflict. // but that's kinda hard with the singletons... because you probably just want // to open both files in two different windows (editors) but we can't do that. :( // Recover server version this.git.checkout().setStage(Stage.THEIRS).addPath(path).call(); // Append a timestamp LocalDateTime date = LocalDateTime.now(); DateTimeFormatter formatter = DateTimeFormatter.ofPattern("YYYY-mm-dd+HH'h'MM'm'"); String timestamp = date.format(formatter); File theirFile = new File(FilenameUtils.getFullPath(fullPath), FilenameUtils.getBaseName(path) + " (" + timestamp + ")." + FilenameUtils.getExtension(path)); if (conflictingFile.exists() && !theirFile.exists()) { Files.move(conflictingFile.toPath(), theirFile.toPath()); String relativePath = this.repoDir.toURI().relativize(theirFile.toURI()).getPath(); this.git.add().addFilepattern(relativePath).call(); }/*w ww . j av a 2 s . c o m*/ // Recover local version this.git.checkout().setStage(Stage.OURS).addPath(path).call(); this.git.add().addFilepattern(path).call(); break; case DELETED_BY_US: // DU // The modified local version is already in the checkout, so it just needs to be added. // We need to specifically mention the file, so we can't reuse the Add () method this.git.add().addFilepattern(path).call(); break; case DELETED_BY_THEM: // UD // Recover server version this.git.checkout().setStage(Stage.THEIRS).addPath(path).call(); this.git.add().addFilepattern(path).call(); break; case BOTH_DELETED: // DD break; default: throw new IllegalArgumentException("Unknown StageState: " + stageState); } } RepositoryState resolvedState = this.git.getRepository().getRepositoryState(); assert resolvedState == RepositoryState.MERGING_RESOLVED; // we are done resolving the merge! this.git.commit().setAuthor(this.username, this.email).call(); RepositoryState safeState = this.git.getRepository().getRepositoryState(); assert safeState == RepositoryState.SAFE; }
From source file:MSUmpire.PSMDataStructure.LCMSID.java
private void ExportMappedPepFragmentCSV() throws IOException { Logger.getRootLogger().info("Writing PepFragment result to file:" + FilenameUtils.getFullPath(mzXMLFileName) + FilenameUtils.getBaseName(mzXMLFileName) + "_MappedPepFragments.csv..."); FileWriter writer = new FileWriter(FilenameUtils.getFullPath(mzXMLFileName) + FilenameUtils.getBaseName(mzXMLFileName) + "_MappedPepFragments.csv"); writer.write("PepIndex,IonType,fragMZ,ObservedMZ,Charge,Intensity,Correlation,PPM,ApexDelta,RTOverlapP\n"); for (PepIonID pepion : MappedPepIonList.values()) { for (FragmentPeak frag : pepion.FragmentPeaks) { writer.write(pepion.Index + "," + frag.IonType + "," + frag.FragMZ + "," + frag.ObservedMZ + "," + frag.Charge + "," + frag.intensity + "," + frag.corr + "," + frag.ppm + "," + frag.ApexDelta + "," + frag.RTOverlapP + "\n"); }//from ww w. ja v a 2s . c o m } writer.close(); }