List of usage examples for java.io BufferedWriter append
public Writer append(CharSequence csq) throws IOException
From source file:br.bireme.ngrams.NGrams.java
public static void export(NGIndex index, final NGSchema schema, final String outFile, final String outFileEncoding) throws IOException { if (index == null) { throw new NullPointerException("index"); }/* w ww . ja va 2s . co m*/ if (schema == null) { throw new NullPointerException("schema"); } if (outFile == null) { throw new NullPointerException("outFile"); } if (outFileEncoding == null) { throw new NullPointerException("outFileEncoding"); } final Parameters parameters = schema.getParameters(); final TreeMap<Integer, String> fields = new TreeMap<>(); final IndexReader reader = index.getIndexSearcher().getIndexReader(); final int maxdoc = reader.maxDoc(); //final Bits liveDocs = MultiFields.getLiveDocs(reader); final Bits liveDocs = MultiBits.getLiveDocs(reader); final BufferedWriter writer = Files.newBufferedWriter(Paths.get(outFile), Charset.forName(outFileEncoding), StandardOpenOption.CREATE, StandardOpenOption.WRITE); boolean first = true; for (Map.Entry<Integer, br.bireme.ngrams.Field> entry : parameters.sfields.entrySet()) { fields.put(entry.getKey(), entry.getValue().name + NOT_NORMALIZED_FLD); } for (int docID = 0; docID < maxdoc; docID++) { if ((liveDocs != null) && (!liveDocs.get(docID))) continue; final Document doc = reader.document(docID); if (first) { first = false; } else { writer.newLine(); } writer.append(doc2pipe(doc, fields)); } writer.close(); reader.close(); }
From source file:de.dfki.km.perspecting.obie.experiments.RelevanceRatingExperiment.java
@Test public void avgCorrelations() throws Exception { String[] corpora = new String[] { "wikinews", "wikipedia", "gutenberg", "bbc_music", "bbc_nature" }; for (String corpus : corpora) { final String path = "/home/adrian/Dokumente/diss/scoobie/results/dbpedia_en2/correlation/" + corpus + "/"; // final String type = "pearson.csv"; final String[] types = new String[] { "pearson.csv", "spearman.csv" }; for (final String type : types) { File folder = new File(path); final File[] files = folder.listFiles(new FileFilter() { @Override/*from ww w .j ava 2 s.com*/ public boolean accept(File pathname) { return pathname.getName().endsWith(type); } }); DoubleMatrix2D m = new DenseDoubleMatrix2D(9, 9); m.assign(new DoubleFunction() { @Override public double apply(double arg0) { return 0; } }); for (File file : files) { BufferedReader br = new BufferedReader(new FileReader(file)); br.readLine(); int row = 0; try { for (String line = br.readLine(); line != null; line = br.readLine()) { String[] items = line.split("\t"); for (int col = 0; col < 9; col++) { double d = Double.parseDouble(items[col]); if (Double.isNaN(d)) d = 0.0; if (d < 0.001) d = 0.0; if (d > 1) d = 1; m.set(row, col, m.get(row, col) + d); } row++; if (row == 9) break; } } catch (Exception e) { throw new Exception(file.getName(), e); } br.close(); // System.out.println(m); } final double count = m.get(0, 0); m.assign(new DoubleFunction() { @Override public double apply(double arg0) { return arg0 / count; } }); BufferedWriter w = new BufferedWriter(new FileWriter( "/home/adrian/Dokumente/diss/scoobie/results/heatmap." + corpus + "." + type + ".gnup")); w.append("set terminal svg size 600,600 dynamic enhanced fname 'times' fsize 12 butt solid\n"); w.append("set output 'heatmaps." + corpus + "." + type + ".svg'\n"); w.append("unset key\n"); w.append("set view map\n"); w.append("set style data linespoints\n"); w.append("set xtics border in scale 0,0 mirror norotate offset character 0, 0, 0\n"); w.append("set ytics border in scale 0,0 mirror norotate offset character 0, 0, 0\n"); w.append("set xrange [ -0.500000 : 8.50000 ] noreverse nowriteback\n"); w.append("set yrange [ -0.500000 : 8.50000 ] reverse nowriteback\n"); w.append("set palette rgbformulae 2, -7, -7\n"); w.append("splot '-' matrix with image\n"); Formatter f = new Formatter(); f.setFormat("%1.1f"); f.setColumnSeparator(" "); w.append("#"); w.append(f.toString(m)); w.close(); // FileUtils.writeStringToFile(new // File("/home/adrian/Dokumente/diss/scoobie/results/bbc_wildlife/correlation/" // + doc[doc.length - 1] + ".pearson.csv"), // f.toString(matrix.pearsonCorrelationDoubleMatrix()), // "utf-8"); } } }
From source file:org.forgerock.openidm.audit.impl.CSVAuditLogger.java
private void writeEntry(BufferedWriter fileWriter, String type, File auditFile, Map<String, Object> obj, Collection<String> fieldOrder) throws IOException { String key = null;//from ww w. j a v a 2 s . c om Iterator<String> iter = fieldOrder.iterator(); while (iter.hasNext()) { key = iter.next(); Object value = obj.get(key); fileWriter.append("\""); if (value != null) { if (value instanceof Map) { value = new JsonValue((Map) value).toString(); } String rawStr = value.toString(); // Escape quotes with double quotes String escapedStr = rawStr.replaceAll("\"", "\"\""); fileWriter.append(escapedStr); } fileWriter.append("\""); if (iter.hasNext()) { fileWriter.append(","); } } fileWriter.append(recordDelim); }
From source file:org.talend.dataprofiler.core.migration.impl.MergeMetadataTask.java
/** * DOC Use replace method to migrate from 400 to 410. * // w w w .ja va2s.co m * @param result * @param migFolder * @param acceptFileExtentionNames * @param replaceStringMap * @return */ private boolean migrateFolder(File migFolder, final String[] acceptFileExtentionNames, Map<String, String> replaceStringMap) { ArrayList<File> fileList = new ArrayList<File>(); getAllFilesFromFolder(migFolder, fileList, new FilenameFilter() { public boolean accept(File dir, String name) { for (String extName : acceptFileExtentionNames) { if (name.endsWith(extName)) { return true; } } return false; } }); log.info("-------------- Migrating " + fileList.size() + " files"); //$NON-NLS-1$ //$NON-NLS-2$ int counter = 0; int errorCounter = 0; Throwable error = null; for (File sample : fileList) { log.info("-------------- Migrating (" + counter++ + ") : " + sample.getAbsolutePath()); //$NON-NLS-1$ //$NON-NLS-2$ try { BufferedReader fileReader = new BufferedReader(new FileReader(sample)); BufferedWriter fileWriter = new BufferedWriter( new FileWriter(new File(sample.getAbsolutePath() + MIGRATION_FILE_EXT))); while (fileReader.ready()) { String line = fileReader.readLine(); for (String key : replaceStringMap.keySet()) { line = line.replaceAll(key, replaceStringMap.get(key)); } fileWriter.append(line); fileWriter.newLine(); } fileWriter.flush(); fileWriter.close(); fileWriter = null; fileReader.close(); fileReader = null; // We must show called garbage collection,if set fileReader and fileWriter,then don't clear memory,will // warn a // message is file is in using. System.gc(); } catch (Exception e) { error = e; errorCounter++; log.error("!!!!!!!!!!! Error transforming (" + sample.getAbsolutePath() + ")\n" + e.getMessage(), //$NON-NLS-1$//$NON-NLS-2$ e); } log.info("-------------- Migration done of " + counter + " files" //$NON-NLS-1$ //$NON-NLS-2$ + (errorCounter != 0 ? (", there are " + errorCounter + " files in error.") : ".")); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ } if (error != null) { return false; } else { // remove original files and rename new ones to old ones for (File sample : fileList) { boolean isDeleted = sample.delete(); log.info(sample.getAbsolutePath() + (isDeleted ? " is deleted." : " failed to delete.")); //$NON-NLS-1$ //$NON-NLS-2$ boolean isrenamed = new File(sample.getAbsolutePath() + MIGRATION_FILE_EXT).renameTo(sample); log.info(sample.getAbsolutePath() + MIGRATION_FILE_EXT + (isrenamed ? " is renamed." : " failed to rename.")); //$NON-NLS-1$ //$NON-NLS-2$ } } return true; }
From source file:org.caboclo.util.Credentials.java
/** * Save cloud service credentials as an encrypted string of characters * * @param currentServer The cloud storage provider for which we want to save * the credentials/* ww w. java2 s. co m*/ * @param cred The plain-text credentials that will be saved on file */ public void saveCredentials(String currentServer, String cred) { StringBuilder strPath = new StringBuilder(); strPath.append(System.getProperty("user.home")).append(java.io.File.separator).append("backupcredentials"); BufferedWriter strout = null; try { //Create file if it does not exist File credentialsFile = new File(strPath.toString()); if (!credentialsFile.exists()) { credentialsFile.createNewFile(); } byte[] cypherCred = encryptCredentials(cred); strout = new BufferedWriter(new FileWriter(credentialsFile, true)); String encodedCred = new String(new Base64().encode(cypherCred)); String line = currentServer + ":" + encodedCred; strout.append(line); strout.newLine(); } catch (IOException ex) { Logger.getLogger(this.getClass().getName()).log(Level.SEVERE, null, ex); } catch (IllegalBlockSizeException ex) { Logger.getLogger(this.getClass().getName()).log(Level.SEVERE, null, ex); } catch (BadPaddingException ex) { Logger.getLogger(this.getClass().getName()).log(Level.SEVERE, null, ex); } catch (InvalidKeyException ex) { Logger.getLogger(this.getClass().getName()).log(Level.SEVERE, null, ex); } catch (NoSuchPaddingException ex) { Logger.getLogger(this.getClass().getName()).log(Level.SEVERE, null, ex); } catch (NoSuchAlgorithmException ex) { Logger.getLogger(this.getClass().getName()).log(Level.SEVERE, null, ex); } finally { try { if (strout != null) { strout.flush(); strout.close(); } } catch (IOException ex) { Logger.getLogger(this.getClass().getName()).log(Level.SEVERE, null, ex); } } }
From source file:MSUmpire.LCMSPeakStructure.LCMSPeakDIAMS2.java
private void PrepareMGF_MS1Cluster(LCMSPeakMS1 ms1lcms) throws IOException { ArrayList<PseudoMSMSProcessing> ScanList = new ArrayList<>(); ExecutorService executorPool = Executors.newFixedThreadPool(NoCPUs); for (PeakCluster ms1cluster : ms1lcms.PeakClusters) { final ArrayList<PrecursorFragmentPairEdge> frags = FragmentsClu2Cur.get(ms1cluster.Index); if (frags != null && DIA_MZ_Range.getX() <= ms1cluster.GetMaxMz() && DIA_MZ_Range.getY() >= ms1cluster.TargetMz()) { // if (DIA_MZ_Range.getX() <= ms1cluster.GetMaxMz() && DIA_MZ_Range.getY() >= ms1cluster.TargetMz() && FragmentsClu2Cur.containsKey(ms1cluster.Index)) { // ArrayList<PrecursorFragmentPairEdge> frags = FragmentsClu2Cur.get(ms1cluster.Index); ms1cluster.GroupedFragmentPeaks.addAll(frags); if (Last_MZ_Range == null || Last_MZ_Range.getY() < ms1cluster.TargetMz()) { PseudoMSMSProcessing mSMSProcessing = new PseudoMSMSProcessing(ms1cluster, parameter); ScanList.add(mSMSProcessing); }//from w ww .ja v a 2 s .c om } } for (PseudoMSMSProcessing proc : ScanList) { executorPool.execute(proc); } executorPool.shutdown(); try { executorPool.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS); } catch (InterruptedException e) { Logger.getRootLogger().info("interrupted.."); } String mgffile = FilenameUtils.getFullPath(ParentmzXMLName) + GetQ1Name() + ".mgf.temp"; String mgffile2 = FilenameUtils.getFullPath(ParentmzXMLName) + GetQ2Name() + ".mgf.temp"; // FileWriter mapwriter = new FileWriter(FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName) + ".ScanClusterMapping_Q1", true); // FileWriter mapwriter2 = new FileWriter(FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName) + ".ScanClusterMapping_Q2", true); // FileWriter mgfWriter = new FileWriter(mgffile, true); // FileWriter mgfWriter2 = new FileWriter(mgffile2, true); final BufferedWriter mapwriter = DIAPack.get_file(DIAPack.OutputFile.ScanClusterMapping_Q1, FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName) + ".ScanClusterMapping_Q1"), mapwriter2 = DIAPack.get_file(DIAPack.OutputFile.ScanClusterMapping_Q2, FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName) + ".ScanClusterMapping_Q2"), mgfWriter = DIAPack.get_file(DIAPack.OutputFile.Mgf_Q1, mgffile), mgfWriter2 = DIAPack.get_file(DIAPack.OutputFile.Mgf_Q2, mgffile2); for (PseudoMSMSProcessing mSMSProcessing : ScanList) { if (MatchedFragmentMap.size() > 0) { mSMSProcessing.RemoveMatchedFrag(MatchedFragmentMap); } XYPointCollection Scan = mSMSProcessing.GetScan(); if (Scan != null && Scan.PointCount() > parameter.MinFrag) { // StringBuilder mgfString = new StringBuilder(); if (mSMSProcessing.Precursorcluster.IsotopeComplete(3)) { final BufferedWriter mgfString = mgfWriter; parentDIA.Q1Scan++; mgfString.append("BEGIN IONS\n"); mgfString.append("PEPMASS=").append(String.valueOf(mSMSProcessing.Precursorcluster.TargetMz())) .append("\n"); mgfString.append("CHARGE=").append(String.valueOf(mSMSProcessing.Precursorcluster.Charge)) .append("+\n"); mgfString.append("RTINSECONDS=") .append(String.valueOf(mSMSProcessing.Precursorcluster.PeakHeightRT[0] * 60f)) .append("\n"); mgfString.append("TITLE=").append(GetQ1Name()).append(".") .append(String.valueOf(parentDIA.Q1Scan)).append(".") .append(String.valueOf(parentDIA.Q1Scan)).append(".") .append(String.valueOf(mSMSProcessing.Precursorcluster.Charge)).append("\n"); for (int i = 0; i < Scan.PointCount(); i++) { mgfString.append(String.valueOf(Scan.Data.get(i).getX())).append(" ") .append(String.valueOf(Scan.Data.get(i).getY())).append("\n"); } mgfString.append("END IONS\n\n"); mapwriter.write(parentDIA.Q1Scan + "_" + mSMSProcessing.Precursorcluster.Index + "\n"); // mgfWriter.write(mgfString.toString()); //} else if (mSMSProcessing.Precursorcluster.IsotopeComplete(2)) { } else { final BufferedWriter mgfString = mgfWriter2; parentDIA.Q2Scan++; mgfString.append("BEGIN IONS\n"); mgfString.append("PEPMASS=").append(String.valueOf(mSMSProcessing.Precursorcluster.TargetMz())) .append("\n"); mgfString.append("CHARGE=").append(String.valueOf(mSMSProcessing.Precursorcluster.Charge)) .append("+\n"); mgfString.append("RTINSECONDS=") .append(String.valueOf(mSMSProcessing.Precursorcluster.PeakHeightRT[0] * 60f)) .append("\n"); mgfString.append("TITLE=").append(GetQ2Name()).append(".") .append(String.valueOf(parentDIA.Q2Scan)).append(".") .append(String.valueOf(parentDIA.Q2Scan)).append(".") .append(String.valueOf(mSMSProcessing.Precursorcluster.Charge)).append("\n"); for (int i = 0; i < Scan.PointCount(); i++) { mgfString.append(String.valueOf(Scan.Data.get(i).getX())).append(" ") .append(String.valueOf(Scan.Data.get(i).getY())).append("\n"); } mgfString.append("END IONS\n\n"); mapwriter2.write(parentDIA.Q2Scan + "_" + mSMSProcessing.Precursorcluster.Index + "\n"); // mgfWriter2.write(mgfString.toString()); } } mSMSProcessing.Precursorcluster.GroupedFragmentPeaks.clear(); } // mgfWriter2.close(); // mgfWriter.close(); // mapwriter.close(); // mapwriter2.close(); }
From source file:com.oneops.boo.BooConfigInterpolator.java
private String readFileToString(File inputFile) throws IOException { BufferedReader bufrdr = new BufferedReader(new FileReader(inputFile)); StringWriter strWr = new StringWriter(); BufferedWriter wr = new BufferedWriter(strWr); try {/*from w ww . jav a 2s . c o m*/ char[] copyBuffer = new char[1024]; int readChars; do { readChars = bufrdr.read(copyBuffer, 0, 1024); if (readChars != -1) { boolean addNewLine = false; for (int charIndex = 0; charIndex < readChars; charIndex++) { char thisChar = copyBuffer[charIndex]; if (thisChar == '\n') { // Append the newline to the output. Add // another newline before the next character. wr.append('\n'); addNewLine = true; } else { if (addNewLine) { wr.append('\n'); addNewLine = false; } wr.append(thisChar); } } } } while (readChars != -1); } finally { bufrdr.close(); wr.close(); } return strWr.toString(); }
From source file:org.ihtsdo.statistics.Processor.java
/** * Prints the report.//from www .j ava 2 s .c o m * * @param bw the bw * @param tableMap the table map * @throws Exception the exception */ private void printReport(BufferedWriter bw, OutputFileTableMap tableMap) throws Exception { SQLStatementExecutor executor = new SQLStatementExecutor(connection); for (SelectTableMap select : tableMap.getSelect()) { String query = "Select * from " + select.getTableName(); if (executor.executeQuery(query, null)) { ResultSet rs = executor.getResultSet(); if (rs != null) { ResultSetMetaData meta = rs.getMetaData(); while (rs.next()) { for (int i = 0; i < meta.getColumnCount(); i++) { bw.append(rs.getObject(i + 1).toString()); if (i + 1 < meta.getColumnCount()) { bw.append(","); } else { bw.append("\r\n"); } } } meta = null; rs.close(); } } } executor = null; }
From source file:tds.websim.presentation.services.WebSimXHR.java
private static void writeCsvReportToResponse(SimReport report, HttpServletResponse response, String fileName) throws IOException { response.setContentType("text/csv"); response.addHeader("Content-Disposition", "attachment;filename=" + fileName); // TODO: Shiva, what's the encoding for the CSV report output? BufferedWriter responseWriter = new BufferedWriter( new OutputStreamWriter(response.getOutputStream(), "UTF-8")); for (Table reportTable : report.getTables()) { StringBuilder sb = new StringBuilder(); for (String tableHeader : reportTable.getTableHeaders()) { sb.append(tableHeader);//from ww w. ja v a 2 s . c o m sb.append(","); } responseWriter.append(sb.toString()); responseWriter.newLine(); for (TableRow tableRow : reportTable.getTableRows()) { sb = new StringBuilder(); for (String colVal : tableRow.getColVals()) { sb.append(colVal); sb.append(","); } responseWriter.append(sb.toString()); responseWriter.newLine(); } responseWriter.newLine(); } responseWriter.flush(); responseWriter.close(); }