List of usage examples for java.io LineNumberReader LineNumberReader
public LineNumberReader(Reader in)
From source file:io.fabric8.ConnectorMojo.java
private List<String> loadFile(File file) throws Exception { List<String> lines = new ArrayList<>(); LineNumberReader reader = new LineNumberReader(new FileReader(file)); String line;// w ww . ja v a 2s . c om do { line = reader.readLine(); if (line != null) { lines.add(line); } } while (line != null); reader.close(); return lines; }
From source file:org.fuin.esmp.AbstractEventStoreMojo.java
/** * Returns the string as list.//from www . j ava2 s . com * * @param str * String to split into lines. * * @return List of lines. * * @throws MojoExecutionException * Error splitting the string into lines. */ protected final List<String> asList(final String str) throws MojoExecutionException { try { final List<String> lines = new ArrayList<String>(); final LineNumberReader reader = new LineNumberReader(new StringReader(str)); String line; while ((line = reader.readLine()) != null) { lines.add(line); } return lines; } catch (final IOException ex) { throw new MojoExecutionException("Error creating string list", ex); } }
From source file:org.apache.zookeeper.server.quorum.QuorumPeerMainTest.java
/** * This test validates that if a quorum member determines that it is leader without the support of the rest of the * quorum (the other members do not believe it to be the leader) it will stop attempting to lead and become a follower. * * @throws IOException// w w w . j a va2 s . c o m * @throws InterruptedException */ @Test public void testElectionFraud() throws IOException, InterruptedException { // capture QuorumPeer logging ByteArrayOutputStream os = new ByteArrayOutputStream(); WriterAppender appender = getConsoleAppender(os, Level.INFO); Logger qlogger = Logger.getLogger(QuorumPeer.class); qlogger.addAppender(appender); numServers = 3; // used for assertions later boolean foundLeading = false; boolean foundLooking = false; boolean foundFollowing = false; try { // spin up a quorum, we use a small ticktime to make the test run faster servers = LaunchServers(numServers, 500); // find the leader int trueLeader = servers.findLeader(); Assert.assertTrue("There should be a leader", trueLeader >= 0); // find a follower int falseLeader = (trueLeader + 1) % numServers; Assert.assertTrue("All servers should join the quorum", servers.mt[falseLeader].main.quorumPeer.follower != null); // to keep the quorum peer running and force it to go into the looking state, we kill leader election // and close the connection to the leader servers.mt[falseLeader].main.quorumPeer.electionAlg.shutdown(); servers.mt[falseLeader].main.quorumPeer.follower.getSocket().close(); // wait for the falseLeader to disconnect waitForOne(servers.zk[falseLeader], States.CONNECTING); // convince falseLeader that it is the leader servers.mt[falseLeader].main.quorumPeer.setPeerState(QuorumPeer.ServerState.LEADING); // provide time for the falseleader to realize no followers have connected // (this is twice the timeout used in Leader#getEpochToPropose) Thread.sleep(2 * servers.mt[falseLeader].main.quorumPeer.initLimit * servers.mt[falseLeader].main.quorumPeer.tickTime); // Restart leader election servers.mt[falseLeader].main.quorumPeer.startLeaderElection(); // The previous client connection to falseLeader likely closed, create a new one servers.zk[falseLeader] = new ZooKeeper("127.0.0.1:" + servers.mt[falseLeader].getClientPort(), ClientBase.CONNECTION_TIMEOUT, this); // Wait for falseLeader to rejoin the quorum waitForOne(servers.zk[falseLeader], States.CONNECTED); // and ensure trueLeader is still the leader Assert.assertTrue(servers.mt[trueLeader].main.quorumPeer.leader != null); // Look through the logs for output that indicates the falseLeader is LEADING, then LOOKING, then FOLLOWING LineNumberReader r = new LineNumberReader(new StringReader(os.toString())); Pattern leading = Pattern.compile(".*myid=" + falseLeader + ".*LEADING.*"); Pattern looking = Pattern.compile(".*myid=" + falseLeader + ".*LOOKING.*"); Pattern following = Pattern.compile(".*myid=" + falseLeader + ".*FOLLOWING.*"); String line; while ((line = r.readLine()) != null) { if (!foundLeading) { foundLeading = leading.matcher(line).matches(); } else if (!foundLooking) { foundLooking = looking.matcher(line).matches(); } else if (following.matcher(line).matches()) { foundFollowing = true; break; } } } finally { qlogger.removeAppender(appender); } Assert.assertTrue("falseLeader never attempts to become leader", foundLeading); Assert.assertTrue("falseLeader never gives up on leadership", foundLooking); Assert.assertTrue("falseLeader never rejoins the quorum", foundFollowing); }
From source file:io.fabric8.ConnectorMojo.java
private List<String> loadFile(InputStream fis) throws Exception { List<String> lines = new ArrayList<>(); LineNumberReader reader = new LineNumberReader(new InputStreamReader(fis)); String line;//from www. j a v a2 s. co m do { line = reader.readLine(); if (line != null) { lines.add(line); } } while (line != null); reader.close(); return lines; }
From source file:org.fbk.cit.hlt.dirha.Evaluator.java
private Map<Integer, Sentence> read(File fin) throws IOException { LineNumberReader lr = new LineNumberReader(new InputStreamReader(new FileInputStream(fin), "UTF-8")); String line = null;/*from w w w. j a v a2 s . c o m*/ Map<Integer, Sentence> sentenceMap = new HashMap<>(); String sid = null; int count = 0; Sentence sentence = null; while ((line = lr.readLine()) != null) { String[] s = line.split("\t", -1); if (s.length > 5) { if (sid == null) { sid = s[0]; sentence = new Sentence(sid); } if (!s[0].equalsIgnoreCase(sid)) { sentenceMap.put(Integer.parseInt(sid), sentence); sid = s[0]; sentence = new Sentence(sid); } if (!s[6].trim().equalsIgnoreCase("O")) { ClassifierResults res = ClassifierResults.fromTSV(s, 2); sentence.add(s[0], res.getFrame(), res.getRole(), res.getToken().replace(" ", "")); } } } sentenceMap.put(Integer.parseInt(sid), sentence); return sentenceMap; }
From source file:org.gofleet.module.routing.RoutingMap.java
private int getNumberLines(File f) { LineNumberReader lineCounter; try {/* w w w . java 2 s .co m*/ lineCounter = new LineNumberReader(new InputStreamReader(new FileInputStream(f.getPath()))); while (lineCounter.readLine() != null) ; return lineCounter.getLineNumber(); } catch (Exception done) { log.error(done, done); return -1; } }
From source file:massbank.BatchSearchWorker.java
/** * T}t@C???iHTML`?j/*from w w w . j ava 2 s .c o m*/ * @param resultFile t@C * @param htmlFile YtpHTMLt@C */ private void createSummary(File resultFile, File htmlFile) { LineNumberReader in = null; PrintWriter out = null; try { //(1) t@C? String line; int cnt = 0; ArrayList<String> nameList = new ArrayList<String>(); ArrayList<String> top1LineList = new ArrayList<String>(); TreeSet<String> top1IdList = new TreeSet<String>(); in = new LineNumberReader(new FileReader(resultFile)); while ((line = in.readLine()) != null) { line = line.trim(); if (line.equals("")) { cnt = 0; } else { cnt++; if (cnt == 1) { nameList.add(line); } else if (cnt == 2) { if (line.equals("-1")) { top1LineList.add("Invalid"); } if (line.equals("0")) { top1LineList.add("0"); } } else if (cnt == 4) { String[] vals = line.split("\t"); String id = vals[0]; top1IdList.add(id); top1LineList.add(line); } } } //? http://www.massbank.jp/ T?[o??KEGG???s HashMap<String, ArrayList> massbank2mapList = new HashMap<String, ArrayList>(); //(2)p HashMap<String, String> massbank2keggList = new HashMap<String, String>(); //(2)p HashMap<String, ArrayList> map2keggList = new HashMap<String, ArrayList>(); //(3)p ArrayList<String> mapNameList = new ArrayList<String>(); //(4)p boolean isKeggReturn = false; // if (serverUrl.indexOf("www.massbank.jp") == -1) { // isKeggReturn = false; // } if (isKeggReturn) { //(2) KEGG ID, Map IDDB String where = "where MASSBANK in("; Iterator it = top1IdList.iterator(); while (it.hasNext()) { String id = (String) it.next(); where += "'" + id + "',"; } where = where.substring(0, where.length() - 1); where += ")"; String sql = "select MASSBANK, t1.KEGG, MAP from " + "(SELECT MASSBANK,KEGG FROM OTHER_DB_IDS " + where + ") t1, PATHWAY_CPDS t2" + " where t1.KEGG=t2.KEGG order by MAP,MASSBANK"; ArrayList<String> mapList = null; try { Class.forName("com.mysql.jdbc.Driver"); String connectUrl = "jdbc:mysql://localhost/MassBank_General"; Connection con = DriverManager.getConnection(connectUrl, "bird", "bird2006"); Statement stmt = con.createStatement(); ResultSet rs = stmt.executeQuery(sql); String prevId = ""; while (rs.next()) { String id = rs.getString(1); String kegg = rs.getString(2); String map = rs.getString(3); if (!id.equals(prevId)) { if (!prevId.equals("")) { massbank2mapList.put(prevId, mapList); } mapList = new ArrayList<String>(); massbank2keggList.put(id, kegg); } mapList.add(map); prevId = id; } massbank2mapList.put(prevId, mapList); rs.close(); stmt.close(); con.close(); } catch (Exception e) { e.printStackTrace(); } if (mapList != null) { //(3) Pathway Map?FtXg?? it = massbank2mapList.keySet().iterator(); while (it.hasNext()) { String id = (String) it.next(); String kegg = (String) massbank2keggList.get(id); ArrayList<String> list1 = massbank2mapList.get(id); for (int i = 0; i < list1.size(); i++) { String map = list1.get(i); ArrayList<String> list2 = null; if (map2keggList.containsKey(map)) { list2 = map2keggList.get(map); list2.add(kegg); } else { list2 = new ArrayList<String>(); list2.add(kegg); map2keggList.put(map, list2); } } } //(4) SOAPPathway Map?Ft?\bh?s it = map2keggList.keySet().iterator(); List<Callable<HashMap<String, String>>> tasks = new ArrayList(); while (it.hasNext()) { String map = (String) it.next(); mapNameList.add(map); ArrayList<String> list = map2keggList.get(map); String[] cpds = list.toArray(new String[] {}); Callable<HashMap<String, String>> task = new ColorPathway(map, cpds); tasks.add(task); } Collections.sort(mapNameList); // Xbhv?[10 ExecutorService exsv = Executors.newFixedThreadPool(10); List<Future<HashMap<String, String>>> results = exsv.invokeAll(tasks); // Pathway mapi[?? String saveRootPath = MassBankEnv.get(MassBankEnv.KEY_TOMCAT_APPTEMP_PATH) + "pathway"; File rootDir = new File(saveRootPath); if (!rootDir.exists()) { rootDir.mkdir(); } // String savePath = saveRootPath + File.separator + this.jobId; // File newDir = new File(savePath); // if ( !newDir.exists() ) { // newDir.mkdir(); // } //(6) Pathway mapURL for (Future<HashMap<String, String>> future : results) { HashMap<String, String> res = future.get(); it = res.keySet().iterator(); String map = (String) it.next(); String mapUrl = res.get(map); String filePath = saveRootPath + File.separator + this.jobId + "_" + map + ".png"; FileUtil.downloadFile(mapUrl, filePath); } } } //(7) ?o out = new PrintWriter(new BufferedWriter(new FileWriter(htmlFile))); // wb_?[?o String reqIonStr = "Both"; try { if (Integer.parseInt(this.ion) > 0) { reqIonStr = "Positive"; } else if (Integer.parseInt(this.ion) < 0) { reqIonStr = "Negative"; } } catch (NumberFormatException nfe) { nfe.printStackTrace(); } String title = "Summary of Batch Service Results"; out.println("<html>"); out.println("<head>"); out.println("<title>" + title + "</title>"); out.println("</head>"); out.println("<body>"); out.println("<h1>" + title + "</h1>"); out.println("<hr>"); out.println("<h3>Request Date : " + this.time + "</h3>"); out.println("Instrument Type : " + this.inst + "<br>"); out.println("MS Type : " + this.ms + "<br>"); out.println("Ion Mode : " + reqIonStr + "<br>"); out.println("<br>"); out.println("<hr>"); out.println("<table border=\"1\" cellspacing=\"0\" cellpadding=\"2\">"); String cols = String.valueOf(mapNameList.size()); out.println("<tr>"); out.println("<th bgcolor=\"LavenderBlush\" rowspan=\"1\">No.</th>"); out.println("<th bgcolor=\"LavenderBlush\" rowspan=\"1\">Query Name</th>"); out.println("<th bgcolor=\"LightCyan\" rowspan=\"1\">Score</th>"); out.println("<th bgcolor=\"LightCyan\" rowspan=\"1\">Hit</th>"); out.println("<th bgcolor=\"LightCyan\" rowspan=\"1\">MassBank ID</th>"); out.println("<th bgcolor=\"LightCyan\" rowspan=\"1\">Record Title</th>"); out.println("<th bgcolor=\"LightCyan\" rowspan=\"1\">Formula</th>"); out.println("<th bgcolor=\"LightCyan\" rowspan=\"1\">Exact Mass</th>"); if (isKeggReturn) { out.println("<th bgcolor=\"LightYellow\" rowspan=\"2\">KEGG ID</th>"); out.println( "<th bgcolor=\"LightYellow\" colspan=\"" + cols + "\">Colored Pathway Maps</th>"); } out.println("</tr>"); out.print("<tr bgcolor=\"moccasin\">"); for (int i = 0; i < mapNameList.size(); i++) { out.print("<th>MAP" + String.valueOf(i + 1) + "</th>"); } out.println("</tr>"); for (int i = 0; i < nameList.size(); i++) { out.println("<tr>"); String no = String.format("%5d", i + 1); no = no.replace(" ", " "); out.println("<td>" + no + "</td>"); // Query Name String queryName = nameList.get(i); out.println("<td nowrap>" + queryName + "</td>"); line = top1LineList.get(i); if (line.equals("0")) { if (isKeggReturn) { cols = String.valueOf(mapNameList.size() + 5); } else { cols = String.valueOf(6); } out.println("<td colspan=\"" + cols + "\">No Hit Record</td>"); } else if (line.equals("Invalid")) { if (isKeggReturn) { cols = String.valueOf(mapNameList.size() + 5); } else { cols = String.valueOf(4); } out.println("<td colspan=\"" + cols + "\">Invalid Query</td>"); } else { String[] data = formatLine(line); String id = data[0]; String recTitle = data[1]; String formula = data[2]; String emass = data[3]; String score = data[4]; String hit = data[5]; boolean isHiScore = false; if (Integer.parseInt(hit) >= 3 && Double.parseDouble(score) >= 0.8) { isHiScore = true; } // Score if (isHiScore) { out.println("<td><b>" + score + "</b></td>"); } else { out.println("<td>" + score + "</td>"); } // hit peak if (isHiScore) { out.println("<td align=\"right\"><b>" + hit + "</b></td>"); } else { out.println("<td align=\"right\">" + hit + "</td>"); } // MassBank ID & Link out.println("<td><a href=\"" + serverUrl + "jsp/FwdRecord.jsp?id=" + id + "\" target=\"_blank\">" + id + "</td>"); // Record Title out.println("<td>" + recTitle + "</td>"); // Formula out.println("<td nowrap>" + formula + "</td>"); // Exact Mass out.println("<td nowrap>" + emass + "</td>"); // KEGG ID & Link if (isKeggReturn) { String keggLink = " -"; if (massbank2keggList.containsKey(id)) { String keggUrl = "http://www.genome.jp/dbget-bin/www_bget?"; String kegg = massbank2keggList.get(id); switch (kegg.charAt(0)) { case 'C': keggUrl += "cpd:" + kegg; break; case 'D': keggUrl += "dr:" + kegg; break; case 'G': keggUrl += "gl:" + kegg; break; } keggLink = "<a href=\"" + keggUrl + "\" target=\"_blank\">" + kegg + "</a>"; } out.println("<td>" + keggLink + "</td>"); // Pathway Map Link if (massbank2mapList.containsKey(id)) { ArrayList<String> list = massbank2mapList.get(id); for (int l1 = mapNameList.size() - 1; l1 >= 0; l1--) { boolean isFound = false; String map = ""; for (int l2 = list.size() - 1; l2 >= 0; l2--) { map = list.get(l2); if (map.equals(mapNameList.get(l1))) { isFound = true; break; } } if (isFound) { ArrayList<String> list2 = map2keggList.get(map); String mapUrl = serverUrl + "temp/pathway/" + this.jobId + "_" + map + ".png"; out.println("<td nowrap><a href=\"" + mapUrl + "\" target=\"_blank\">map:" + map + "(" + list2.size() + ")</a></td>"); } else { out.println("<td> -</td>"); } } } else { for (int l1 = mapNameList.size() - 1; l1 >= 0; l1--) { out.println("<td> -</td>"); } } } } out.println("</tr>"); } out.println("</table>"); } catch (Exception e) { e.printStackTrace(); } finally { try { if (in != null) { in.close(); } } catch (IOException e) { } if (out != null) { out.flush(); out.close(); } } }
From source file:edu.stanford.muse.util.Util.java
/** * returns collection of lines from given file (UTF-8). * trims spaces from the lines,//w w w.j a v a 2 s. c o m * ignores lines starting with # if ignoreCommentLines is true */ public static List<String> getLinesFromReader(Reader reader, boolean ignoreCommentLines) throws IOException { LineNumberReader lnr = new LineNumberReader(reader); List<String> result = new ArrayList<String>(); while (true) { String line = lnr.readLine(); if (line == null) break; line = line.trim(); if (ignoreCommentLines && (line.length() == 0 || line.charAt(0) == '#')) continue; result.add(line); } return result; }
From source file:com.google.ratel.service.error.ErrorReport.java
/** * Return Java Source LineNumberReader for the given filename, or null if not found. * * @param filename the name of the Java source file, e.g. /examples/Page.java * @return LineNumberReader for the given source filename, or null if not found * @throws FileNotFoundException if file could not be found *///from w w w . ja va 2s . com protected LineNumberReader getJavaSourceReader(String filename) throws FileNotFoundException { if (serviceClass == null) { return null; } // Look for source file on classpath InputStream is = serviceClass.getResourceAsStream(filename); if (is != null) { return new LineNumberReader(new InputStreamReader(is)); } // Else search for source file under WEB-INF String rootPath = ratelConfig.getServletContext().getRealPath("/"); String webInfPath = rootPath + File.separator + "WEB-INF"; File sourceFile = null; File webInfDir = new File(webInfPath); if (webInfDir.isDirectory() && webInfDir.canRead()) { File[] dirList = webInfDir.listFiles(); if (dirList != null) { for (File file : dirList) { if (file.isDirectory() && file.canRead()) { String sourcePath = file.toString() + filename; sourceFile = new File(sourcePath); if (sourceFile.isFile() && sourceFile.canRead()) { FileInputStream fis = new FileInputStream(sourceFile); return new LineNumberReader(new InputStreamReader(fis)); } } } } } return null; }
From source file:net.sf.keystore_explorer.crypto.signing.JarSigner.java
private static String getManifestMainAttrs(JarFile jar) throws IOException { // Get full manifest content String manifestContent = getManifest(jar); LineNumberReader lnr = new LineNumberReader(new StringReader(manifestContent)); try {/* w ww .ja v a2 s .c om*/ StringBuilder sb = new StringBuilder(); String line = null; // Keep reading until a blank line is found - the end of the main // attributes while ((line = lnr.readLine()) != null) { if (line.trim().length() == 0) { break; } // Append attribute line sb.append(line); sb.append(CRLF); } return sb.toString(); } finally { IOUtils.closeQuietly(lnr); } }