List of usage examples for org.apache.commons.io FilenameUtils getBaseName
public static String getBaseName(String filename)
From source file:MSUmpire.DIA.RTAlignedPepIonMapping.java
private void GenerateRTMapPNG(XYSeriesCollection xySeriesCollection, XYSeries series, float R2) throws IOException { new File(Workfolder + "/RT_Mapping/").mkdir(); String pngfile = Workfolder + "/RT_Mapping/" + FilenameUtils.getBaseName(LCMSA.mzXMLFileName).substring(0, Math.min(120, FilenameUtils.getBaseName(LCMSA.mzXMLFileName).length() - 1)) + "_" + FilenameUtils.getBaseName(LCMSB.mzXMLFileName).substring(0, Math.min(120, FilenameUtils.getBaseName(LCMSB.mzXMLFileName).length() - 1)) + "_RT.png"; XYSeries smoothline = new XYSeries("RT fitting curve"); for (XYZData data : regression.PredictYList) { smoothline.add(data.getX(), data.getY()); }//from w w w .j a va2 s . c o m xySeriesCollection.addSeries(smoothline); xySeriesCollection.addSeries(series); JFreeChart chart = ChartFactory.createScatterPlot("Retention time mapping: R2=" + R2, "RT:" + FilenameUtils.getBaseName(LCMSA.mzXMLFileName), "RT:" + FilenameUtils.getBaseName(LCMSB.mzXMLFileName), xySeriesCollection, PlotOrientation.VERTICAL, true, true, false); XYPlot xyPlot = (XYPlot) chart.getPlot(); xyPlot.setDomainCrosshairVisible(true); xyPlot.setRangeCrosshairVisible(true); XYItemRenderer renderer = xyPlot.getRenderer(); renderer.setSeriesPaint(1, Color.blue); renderer.setSeriesPaint(0, Color.BLACK); renderer.setSeriesShape(1, new Ellipse2D.Double(0, 0, 3, 3)); renderer.setSeriesStroke(1, new BasicStroke(3.0f)); renderer.setSeriesStroke(0, new BasicStroke(3.0f)); xyPlot.setBackgroundPaint(Color.white); ChartUtilities.saveChartAsPNG(new File(pngfile), chart, 1000, 600); }
From source file:net.chris54721.infinitycubed.workers.PackLoader.java
@Override public void run() { try {/*from w ww . j a v a 2s . c om*/ LogHelper.info("Loading and updating modpacks"); String publicJson = Utils.toString(new URL(Reference.FILES_URL + "public.json")); Type stringIntMap = new TypeToken<LinkedHashMap<String, Integer>>() { }.getType(); LinkedHashMap<String, Integer> publicObjects = Reference.DEFAULT_GSON.fromJson(publicJson, stringIntMap); File localJson = new File(Resources.getFolder(Reference.PACKS_FOLDER), "public.json"); List<String> updatePacks = new ArrayList<String>(); if (localJson.isFile()) { String localPublicJson = Files.toString(localJson, Charsets.UTF_8); LinkedHashMap<String, Integer> localPublicObjects = Reference.DEFAULT_GSON.fromJson(localPublicJson, stringIntMap); for (String pack : publicObjects.keySet()) { if (!localPublicObjects.containsKey(pack) || !localPublicObjects.get(pack).equals(publicObjects.get(pack))) { updatePacks.add(pack); } } } else updatePacks.addAll(publicObjects.keySet()); Files.write(publicJson, localJson, Charsets.UTF_8); if (updatePacks.size() > 0) { for (String pack : updatePacks) { LogHelper.info("Updating JSON file for modpack " + pack); URL packJsonURL = Resources.getUrl(Resources.ResourceType.PACK_JSON, pack + ".json"); File packJsonFile = Resources.getFile(Resources.ResourceType.PACK_JSON, pack + ".json"); if (packJsonFile.isFile()) packJsonFile.delete(); Downloadable packJsonDownloadable = new Downloadable(packJsonURL, packJsonFile); if (!packJsonDownloadable.download()) LogHelper.error("Failed updating JSON for modpack " + pack); } } Collection<File> packJsons = FileUtils.listFiles(Resources.getFolder(Reference.DATA_FOLDER), new String[] { "json" }, false); for (File packJsonFile : packJsons) loadPack(FilenameUtils.getBaseName(packJsonFile.getName())); } catch (Exception e) { LogHelper.fatal("Failed updating and loading public packs", e); } }
From source file:de.fau.cs.osr.hddiff.perfsuite.HDDiffTestUtils.java
public Wom3Document parse(File inputFile, ExpansionCallback callback) throws Exception { String fileTitle = FilenameUtils.getBaseName(inputFile.getName()); PageId pageId = getWtWom3Toolbox().makePageId(fileTitle); Wom3Document wom = getWtWom3Toolbox().wmToWom(inputFile, pageId, callback, "UTF8").womDoc; // We will modify this document in possibly illegal ways later wom.setStrictErrorChecking(false);// w ww .j a v a 2 s . c o m return wom; }
From source file:codes.thischwa.c5c.impl.JarFilemanagerMessageResolver.java
@Override public void setServletContext(ServletContext servletContext) { ObjectMapper mapper = new ObjectMapper(); try {/*from www . ja v a2 s . c o m*/ if (JarPathResolver.insideJar(getMessagesFolderPath())) { CodeSource src = JarFilemanagerMessageResolver.class.getProtectionDomain().getCodeSource(); URI uri = src.getLocation().toURI(); logger.info("Message folder is inside jar: {}", uri); try (FileSystem jarFS = FileSystems.newFileSystem(uri, new HashMap<String, String>())) { if (jarFS.getRootDirectories().iterator().hasNext()) { Path rootDirectory = jarFS.getRootDirectories().iterator().next(); Path langFolder = rootDirectory.resolve(getMessagesFolderPath()); if (langFolder != null) { try (DirectoryStream<Path> langFolderStream = Files.newDirectoryStream(langFolder, JS_FILE_MASK)) { for (Path langFile : langFolderStream) { String lang = langFile.getFileName().toString(); InputStream is = Files.newInputStream(langFile); Map<String, String> langData = mapper.readValue(is, new TypeReference<HashMap<String, String>>() { }); collectLangData(lang, langData); } } } else { throw new RuntimeException("Folder in jar " + langFolder + " does not exists."); } } } } else { File messageFolder = JarPathResolver.getFolder(getMessagesFolderPath()); logger.info("Message folder resolved to: {}", messageFolder); if (messageFolder == null || !messageFolder.exists()) { throw new RuntimeException("Folder " + getMessagesFolderPath() + " does not exist"); } for (File file : messageFolder.listFiles(jsFilter)) { String lang = FilenameUtils.getBaseName(file.getName()); Map<String, String> langData = mapper.readValue(file, new TypeReference<HashMap<String, String>>() { }); collectLangData(lang, langData); } } } catch (URISyntaxException | IOException e) { throw new RuntimeException(e); } }
From source file:ijfx.explorer.datamodel.wrappers.ImageRecordIconizer.java
public ImageRecordIconizer(Context context, ImageRecord imageRecord, int imageId) { this(context, imageRecord); series = true;//w w w . jav a2 s. c om this.imageId = imageId; set.putGeneric(MetaData.SERIE, imageId); String baseName = FilenameUtils.getBaseName(imageRecord.getFile().getName()); String saveName = String.format(SERIE_SAVE_FORMAT, baseName, imageId + 1); set.putGeneric(MetaData.FILE_NAME, String.format(SERIE_NAME_FORMAT, imageRecord.getFile().getName(), imageId + 1)); set.putGeneric(MetaData.SAVE_NAME, saveName); }
From source file:com.frostwire.android.gui.transfers.YouTubeDownload.java
YouTubeDownload(TransferManager manager, YouTubeCrawledSearchResult sr) { this.manager = manager; this.sr = sr; this.downloadType = buildDownloadType(sr); this.size = sr.getSize(); String filename = sr.getFilename(); File savePath = SystemPaths.getTorrentData(); ensureDirectoryExits(savePath);//from w w w . jav a2s . c o m ensureDirectoryExits(SystemPaths.getTemp()); completeFile = buildFile(savePath, filename); tempVideo = buildTempFile(FilenameUtils.getBaseName(filename), "video"); tempAudio = buildTempFile(FilenameUtils.getBaseName(filename), "audio"); bytesReceived = 0; dateCreated = new Date(); httpClientListener = new HttpDownloadListenerImpl(); httpClient = HttpClientFactory.newInstance(); httpClient.setListener(httpClientListener); if (SystemUtils.isCurrentMountAlmostFull()) { this.status = STATUS_ERROR_DISK_FULL; } }
From source file:com.textocat.textokit.io.brat.BratCollectionReader.java
@Override public void initialize(UimaContext ctx) throws ResourceInitializationException { super.initialize(ctx); // initialize mappingFactory mappingFactory = InitializableFactory.create(ctx, mappingFactoryClassName, BratUimaMappingFactory.class); // make bratDocIter File[] annFiles = bratCollectionDir .listFiles((FileFilter) FileFilterUtils.suffixFileFilter(BratDocument.ANN_FILE_SUFFIX)); List<BratDocument> bratDocs = Lists.newArrayListWithExpectedSize(annFiles.length); for (File annFile : annFiles) { String docBaseName = FilenameUtils.getBaseName(annFile.getPath()); BratDocument bratDoc = new BratDocument(bratCollectionDir, docBaseName); if (bratDoc.exists()) { bratDocs.add(bratDoc);/* w w w. ja v a 2s .c o m*/ } else { throw new IllegalStateException(String.format("Missing txt file for %s", annFile)); } } totalDocsNum = bratDocs.size(); bratDocIter = bratDocs.iterator(); }
From source file:MSUmpire.Utility.ExportTable.java
private void ProteinLevelExport(int TopNPep, int TopNFrag, float Freq) throws IOException { FileWriter proWriter = new FileWriter(WorkFolder + "ProtSummary_" + DateTimeTag.GetTag() + ".xls"); FileWriter pepWriter = new FileWriter(WorkFolder + "PeptideSummary_" + DateTimeTag.GetTag() + ".xls"); FileWriter NOWriter = new FileWriter(WorkFolder + "IDNoSummary_" + DateTimeTag.GetTag() + ".xls"); FileWriter fragWriter = new FileWriter(WorkFolder + "FragSummary_" + DateTimeTag.GetTag() + ".xls"); //Fragment Summary////////////////////////////////////////// for (LCMSID IDsummary : FileList) { HashMap<String, FragmentPeak> FragMap = IDSummaryFragments .get(FilenameUtils.getBaseName(IDsummary.mzXMLFileName)); if (FragMap == null) { Logger.getRootLogger().error( "Cannot find fragment map for " + FilenameUtils.getBaseName(IDsummary.mzXMLFileName)); Logger.getRootLogger().debug("Printing all fragment maps"); for (String key : FragMap.keySet()) { Logger.getRootLogger().debug(key); }//from ww w. j av a2s. co m } for (String key : CombineProtID.ProteinList.keySet()) { if (IDsummary.ProteinList.containsKey(key)) { ProtID protein = IDsummary.ProteinList.get(key); for (PepIonID pep : protein.PeptideID.values()) { for (FragmentPeak frag : pep.FragmentPeaks) { final String mapkey = // key + ";" + pep.GetKey() + ";" + frag.IonType; key + ";" + pep.GetKey() + ";" + frag.IonType + ";+" + frag.Charge; // ProteinFragMap.putIfAbsent(mapkey, frag.FragMZ);// needs Java 8 if (!ProteinFragMap.containsKey(mapkey)) ProteinFragMap.put(mapkey, frag.FragMZ); frag.Prob1 = pep.MaxProbability; frag.Prob2 = pep.TargetedProbability(); frag.RT = pep.PeakRT; FragMap.put(mapkey, frag); } } } } } NOWriter.write( "File\tNo. Proteins\tNo. peptide ions (Spec-centric)\tNo. peptide ions (Pep-centric)\tNo. proein assoc. ions\n"); //ProteinSummary///////////// proWriter.write("Protein Key\t"); proWriter.write("Selected_peptides\t"); for (LCMSID IDSummary : FileList) { NOWriter.write(FilenameUtils.getBaseName(IDSummary.mzXMLFileName) + "\t" + IDSummary.ProteinList.size() + "\t" + IDSummary.GetPepIonList().size() + "\t" + IDSummary.GetMappedPepIonList().size() + "\t" + IDSummary.AssignedPepIonList.size() + "\n"); String file = FilenameUtils.getBaseName(IDSummary.mzXMLFileName); proWriter.write(file + "_Prob\t" + file + "_Peptides\t" + file + "_PSMs\t" + file + "_MS1_iBAQ\t" + file + "_Top" + TopNPep + "pep/Top" + TopNFrag + "fra ,Freq>" + Freq + "\t"); } proWriter.write("\n"); NOWriter.close(); if (CombineProtID != null) { for (String key : CombineProtID.ProteinList.keySet()) { proWriter.write(key + "\t"); for (final LCMSID IDsummary : FileList) { if (IDsummary.ProteinList.containsKey(key)) { final ProtID protein = IDsummary.ProteinList.get(key); proWriter.write(String.join("|", fragselection.TopPeps.get(protein.getAccNo()))); break; } } proWriter.write("\t"); for (LCMSID IDsummary : FileList) { if (IDsummary.ProteinList.containsKey(key)) { ProtID protein = IDsummary.ProteinList.get(key); proWriter.write(protein.Probability + "\t" + protein.PeptideID.size() + "\t" + protein.GetSpectralCount() + "\t" + protein.GetAbundanceByMS1_IBAQ() + "\t" + protein.GetAbundanceByTopCorrFragAcrossSample( fragselection.TopPeps.get(protein.getAccNo()), fragselection.TopFrags) + "\t"); } else { proWriter.write("\t\t\t\t\t"); } } proWriter.write("\n"); } proWriter.close(); } fragWriter.write("Fragment Key\tProtein\tPeptide\tFragment\tFragMz\t"); for (LCMSID IDSummary : FileList) { String file = FilenameUtils.getBaseName(IDSummary.mzXMLFileName); fragWriter.write(file + "_RT\t" + file + "_Spec_Centric_Prob\t" + file + "_Pep_Centric_Prob\t" + file + "_Intensity\t" + file + "_Corr\t" + file + "_PPM\t"); } fragWriter.write("\n"); for (final Map.Entry<String, Float> ent : new java.util.TreeMap<>(ProteinFragMap).entrySet()) { final String key = ent.getKey(); fragWriter.write(key + "\t" + key.split(";")[0] + "\t" + key.split(";")[1] + "\t" + key.split(";")[2] + key.split(";")[3] + "\t" + ent.getValue() + "\t"); for (LCMSID IDSummary : FileList) { if (IDSummaryFragments.get(FilenameUtils.getBaseName(IDSummary.mzXMLFileName)).containsKey(key)) { FragmentPeak fragmentPeak = IDSummaryFragments .get(FilenameUtils.getBaseName(IDSummary.mzXMLFileName)).get(key); fragWriter.write(fragmentPeak.RT + "\t" + fragmentPeak.Prob1 + "\t" + fragmentPeak.Prob2 + "\t" + fragmentPeak.intensity + "\t" + fragmentPeak.corr + "\t" + fragmentPeak.ppm + "\t"); } else { fragWriter.write("\t\t\t\t\t\t"); } } fragWriter.write("\n"); } fragWriter.close(); ////PepSummary/////////////////////////////////// for (LCMSID IDsummary : FileList) { HashMap<String, FragmentPeak> FragMap = new HashMap<>(); IDSummaryFragments.put(FilenameUtils.getBaseName(IDsummary.mzXMLFileName), FragMap); for (String key : IDsummary.GetPepIonList().keySet()) { if (!IdentifiedPepMap.contains(key)) { IdentifiedPepMap.add(key); } } for (String key : IDsummary.GetMappedPepIonList().keySet()) { if (!IdentifiedPepMap.contains(key)) { IdentifiedPepMap.add(key); } } } pepWriter.write("Peptide Key\tSequence\tModSeq\tProteins\tmz\tCharge\tMaxProb\t"); pepWriter.write("Selected_fragments\t"); for (LCMSID IDSummary : FileList) { String file = FilenameUtils.getBaseName(IDSummary.mzXMLFileName); pepWriter.write(file + "_Spec_Centric_Prob\t" + file + "_Pep_Centric_Prob\t" + file + "_PSMs\t" + file + "_RT\t" + file + "_MS1\t" + file + "_Top" + TopNFrag + "fra\t"); } pepWriter.write("\n"); for (String key : IdentifiedPepMap) { pepWriter.write(key + "\t"); float maxprob = 0f; boolean output = false; for (LCMSID IDSummary : FileList) { if (IDSummary.GetPepIonList().containsKey(key)) { PepIonID peptide = IDSummary.GetPepIonList().get(key); if (!output) { pepWriter.write( peptide.Sequence + "\t" + peptide.ModSequence + "\t" + peptide.ParentProteins() + "\t" + peptide.ObservedMz + "\t" + peptide.Charge + "\t"); output = true; } if (peptide.MaxProbability > maxprob) { maxprob = peptide.MaxProbability; } } if (IDSummary.GetMappedPepIonList().containsKey(key)) { PepIonID peptide = IDSummary.GetMappedPepIonList().get(key); if (!output) { pepWriter.write( peptide.Sequence + "\t" + peptide.ModSequence + "\t" + peptide.ParentProteins() + "\t" + peptide.ObservedMz + "\t" + peptide.Charge + "\t"); output = true; } if (peptide.TargetedProbability() > maxprob) { maxprob = peptide.TargetedProbability(); } } } pepWriter.write(maxprob + "\t"); for (final LCMSID IDSummary : FileList) { if (IDSummary.GetPepIonList().containsKey(key)) { final PepIonID peptide = IDSummary.GetPepIonList().get(key); pepWriter.write(String.join("|", fragselection.TopFrags.get(peptide.GetKey()))); break; } else if (IDSummary.GetMappedPepIonList().containsKey(key)) { final PepIonID peptide = IDSummary.GetMappedPepIonList().get(key); pepWriter.write(String.join("|", fragselection.TopFrags.get(peptide.GetKey()))); break; } else { } } pepWriter.write("\t"); for (LCMSID IDSummary : FileList) { if (IDSummary.GetPepIonList().containsKey(key)) { PepIonID peptide = IDSummary.GetPepIonList().get(key); pepWriter.write(peptide.MaxProbability + "\t-1\t" + peptide.GetSpectralCount() + "\t" + peptide.PeakRT + "\t" + peptide.PeakHeight[0] + "\t" + peptide.GetPepAbundanceByTopCorrFragAcrossSample( fragselection.TopFrags.get(peptide.GetKey())) + "\t"); } else if (IDSummary.GetMappedPepIonList().containsKey(key)) { PepIonID peptide = IDSummary.GetMappedPepIonList().get(key); pepWriter.write("-1\t" + peptide.TargetedProbability() + "\t" + peptide.GetSpectralCount() + "\t" + peptide.PeakRT + "\t" + peptide.PeakHeight[0] + "\t" + peptide.GetPepAbundanceByTopCorrFragAcrossSample( fragselection.TopFrags.get(peptide.GetKey())) + "\t"); } else { pepWriter.write("\t\t\t\t\t\t"); } } pepWriter.write("\n"); } pepWriter.close(); }
From source file:MSUmpire.BaseDataStructure.InstrumentParameter.java
public static InstrumentParameter ReadParametersSerialization(String filepath) { if (!new File(FilenameUtils.getFullPath(filepath) + FilenameUtils.getBaseName(filepath) + "_params.ser") .exists()) {//from w ww . j a v a 2 s . c o m return null; } try { Logger.getRootLogger().info("Reading parameters from file:" + FilenameUtils.getFullPath(filepath) + FilenameUtils.getBaseName(filepath) + "_params.ser..."); FileInputStream fileIn = new FileInputStream( FilenameUtils.getFullPath(filepath) + FilenameUtils.getBaseName(filepath) + "_params.ser"); ObjectInputStream in = new ObjectInputStream(fileIn); InstrumentParameter params = (InstrumentParameter) in.readObject(); in.close(); fileIn.close(); return params; } catch (Exception ex) { Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex)); return null; } }
From source file:com.mycompany.mytubeaws.UploadServlet.java
/** * Handles the HTTP <code>POST</code> method. * * @param request servlet request//from w w w . java 2s.c om * @param response servlet response * @throws ServletException if a servlet-specific error occurs * @throws IOException if an I/O error occurs */ @Override protected void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { String result = ""; String fileName = null; boolean uploaded = false; // configures upload settings DiskFileItemFactory factory = new DiskFileItemFactory(); // sets memory threshold - beyond which files are stored in disk factory.setSizeThreshold(1024 * 1024 * 3); // 3mb factory.setRepository(new File(System.getProperty("java.io.tmpdir"))); // sets temporary location to store files ServletFileUpload upload = new ServletFileUpload(factory); upload.setFileSizeMax(1024 * 1024 * 40); // sets maximum size of upload file upload.setSizeMax(1024 * 1024 * 50); // sets maximum size of request (include file + form data) try { List<FileItem> formItems = upload.parseRequest(request); // parses the request's content to extract file data if (formItems != null && formItems.size() > 0) // iterates over form's fields { for (FileItem item : formItems) // processes only fields that are not form fields { if (!item.isFormField()) { fileName = item.getName(); UUID id = UUID.randomUUID(); fileName = FilenameUtils.getBaseName(fileName) + "_ID-" + id.toString() + "." + FilenameUtils.getExtension(fileName); File file = File.createTempFile("aws-java-sdk-upload", ""); item.write(file); // write form item to file (?) if (file.length() == 0) throw new RuntimeException("No file selected or empty file uploaded."); try { s3.putObject(new PutObjectRequest(bucketName, fileName, file)); result += "File uploaded successfully; "; uploaded = true; } catch (AmazonServiceException ase) { System.out.println("Caught an AmazonServiceException, which means your request made it " + "to Amazon S3, but was rejected with an error response for some reason."); System.out.println("Error Message: " + ase.getMessage()); System.out.println("HTTP Status Code: " + ase.getStatusCode()); System.out.println("AWS Error Code: " + ase.getErrorCode()); System.out.println("Error Type: " + ase.getErrorType()); System.out.println("Request ID: " + ase.getRequestId()); result += "AmazonServiceException thrown; "; } catch (AmazonClientException ace) { System.out .println("Caught an AmazonClientException, which means the client encountered " + "a serious internal problem while trying to communicate with S3, " + "such as not being able to access the network."); System.out.println("Error Message: " + ace.getMessage()); result += "AmazonClientException thrown; "; } file.delete(); } } } } catch (Exception ex) { result += "Generic exception: '" + ex.getMessage() + "'; "; ex.printStackTrace(); } if (fileName != null && uploaded) result += "Generated file ID: " + fileName; System.out.println(result); request.setAttribute("resultText", result); request.getRequestDispatcher("/UploadResult.jsp").forward(request, response); }