List of usage examples for java.util HashMap clear
public void clear()
From source file:Main.java
public static void main(String[] args) { HashMap<String, String> hMap = new HashMap<String, String>(); hMap.put("1", "One"); hMap.put("2", "Two"); hMap.put("3", "Three"); hMap.clear(); System.out.println(hMap.size()); }
From source file:Main.java
public static void main(String[] a) { HashMap<String, String> map = new HashMap<String, String>(); map.put("key1", "value1"); map.put("key2", "value2"); map.put("key3", "value3"); map.clear(); System.out.println(map);//from w w w . j a v a2 s .co m }
From source file:Main.java
public static void main(String args[]) { HashMap<Integer, String> newmap = new HashMap<Integer, String>(); // populate hash map newmap.put(1, "tutorials"); newmap.put(2, "from"); newmap.put(3, "java2s.com"); System.out.println("Initial map elements: " + newmap); // clear hash map newmap.clear(); System.out.println("Map elements after clear: " + newmap); }
From source file:ms1quant.MS1Quant.java
/** * @param args the command line arguments MS1Quant parameterfile *//*from www . ja va2 s . c om*/ public static void main(String[] args) throws Exception { BufferedReader reader = null; try { System.out.println( "================================================================================================="); System.out.println("Umpire MS1 quantification and feature detection analysis (version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length < 3 || !args[1].startsWith("-mode")) { System.out .println("command : java -jar -Xmx10G MS1Quant.jar ms1quant.params -mode[1 or 2] [Option]"); System.out.println("\n-mode"); System.out.println("\t1:Single file mode--> mzXML_file PepXML_file"); System.out.println("\t\tEx: -mode1 file1.mzXML file1.pep.xml"); System.out.println( "\t2:Folder mode--> mzXML_Folder PepXML_Folder, all generated csv tables will be merged into a single csv file"); System.out.println("\t\tEx: -mode2 /data/mzxml/ /data/pepxml/"); System.out.println("\nOptions"); System.out.println( "\t-C\tNo of concurrent files to be processed (only for folder mode), Ex. -C5, default:1"); System.out.println("\t-p\tMinimum probability, Ex. -p0.9, default:0.9"); System.out.println("\t-ID\tDetect identified feature only"); System.out.println("\t-O\toutput folder, Ex. -O/data/"); return; } ConsoleLogger consoleLogger = new ConsoleLogger(); consoleLogger.SetConsoleLogger(Level.DEBUG); consoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "ms1quant_debug.log"); Logger logger = Logger.getRootLogger(); logger.debug("Command: " + Arrays.toString(args)); logger.info("MS1Quant version: " + UmpireInfo.GetInstance().Version); String parameterfile = args[0]; logger.info("Parameter file: " + parameterfile); File paramfile = new File(parameterfile); if (!paramfile.exists()) { logger.error("Parameter file " + paramfile.getAbsolutePath() + " cannot be found. The program will exit."); } reader = new BufferedReader(new FileReader(paramfile.getAbsolutePath())); String line = ""; InstrumentParameter param = new InstrumentParameter(InstrumentParameter.InstrumentType.TOF5600); int NoCPUs = 2; int NoFile = 1; param.DetermineBGByID = false; param.EstimateBG = true; //<editor-fold defaultstate="collapsed" desc="Read parameter file"> while ((line = reader.readLine()) != null) { if (!"".equals(line) && !line.startsWith("#")) { logger.info(line); //System.out.println(line); if (line.split("=").length < 2) { continue; } if (line.split("=").length < 2) { continue; } String type = line.split("=")[0].trim(); if (type.startsWith("para.")) { type = type.replace("para.", "SE."); } String value = line.split("=")[1].trim(); switch (type) { case "Thread": { NoCPUs = Integer.parseInt(value); break; } //<editor-fold defaultstate="collapsed" desc="instrument parameters"> case "SE.MS1PPM": { param.MS1PPM = Float.parseFloat(value); break; } case "SE.MS2PPM": { param.MS2PPM = Float.parseFloat(value); break; } case "SE.SN": { param.SNThreshold = Float.parseFloat(value); break; } case "SE.MS2SN": { param.MS2SNThreshold = Float.parseFloat(value); break; } case "SE.MinMSIntensity": { param.MinMSIntensity = Float.parseFloat(value); break; } case "SE.MinMSMSIntensity": { param.MinMSMSIntensity = Float.parseFloat(value); break; } case "SE.MinRTRange": { param.MinRTRange = Float.parseFloat(value); break; } case "SE.MaxNoPeakCluster": { param.MaxNoPeakCluster = Integer.parseInt(value); param.MaxMS2NoPeakCluster = Integer.parseInt(value); break; } case "SE.MinNoPeakCluster": { param.MinNoPeakCluster = Integer.parseInt(value); param.MinMS2NoPeakCluster = Integer.parseInt(value); break; } case "SE.MinMS2NoPeakCluster": { param.MinMS2NoPeakCluster = Integer.parseInt(value); break; } case "SE.MaxCurveRTRange": { param.MaxCurveRTRange = Float.parseFloat(value); break; } case "SE.Resolution": { param.Resolution = Integer.parseInt(value); break; } case "SE.RTtol": { param.RTtol = Float.parseFloat(value); break; } case "SE.NoPeakPerMin": { param.NoPeakPerMin = Integer.parseInt(value); break; } case "SE.StartCharge": { param.StartCharge = Integer.parseInt(value); break; } case "SE.EndCharge": { param.EndCharge = Integer.parseInt(value); break; } case "SE.MS2StartCharge": { param.MS2StartCharge = Integer.parseInt(value); break; } case "SE.MS2EndCharge": { param.MS2EndCharge = Integer.parseInt(value); break; } case "SE.NoMissedScan": { param.NoMissedScan = Integer.parseInt(value); break; } case "SE.Denoise": { param.Denoise = Boolean.valueOf(value); break; } case "SE.EstimateBG": { param.EstimateBG = Boolean.valueOf(value); break; } case "SE.RemoveGroupedPeaks": { param.RemoveGroupedPeaks = Boolean.valueOf(value); break; } case "SE.MinFrag": { param.MinFrag = Integer.parseInt(value); break; } case "SE.IsoPattern": { param.IsoPattern = Float.valueOf(value); break; } case "SE.StartRT": { param.startRT = Float.valueOf(value); } case "SE.EndRT": { param.endRT = Float.valueOf(value); } //</editor-fold> } } } //</editor-fold> int mode = 1; if (args[1].equals("-mode2")) { mode = 2; } else if (args[1].equals("-mode1")) { mode = 1; } else { logger.error("-mode number not recongized. The program will exit."); } String mzXML = ""; String pepXML = ""; String mzXMLPath = ""; String pepXMLPath = ""; File mzXMLfile = null; File pepXMLfile = null; File mzXMLfolder = null; File pepXMLfolder = null; int idx = 0; if (mode == 1) { mzXML = args[2]; logger.info("Mode1 mzXML file: " + mzXML); mzXMLfile = new File(mzXML); if (!mzXMLfile.exists()) { logger.error("Mode1 mzXML file " + mzXMLfile.getAbsolutePath() + " cannot be found. The program will exit."); return; } pepXML = args[3]; logger.info("Mode1 pepXML file: " + pepXML); pepXMLfile = new File(pepXML); if (!pepXMLfile.exists()) { logger.error("Mode1 pepXML file " + pepXMLfile.getAbsolutePath() + " cannot be found. The program will exit."); return; } idx = 4; } else if (mode == 2) { mzXMLPath = args[2]; logger.info("Mode2 mzXML folder: " + mzXMLPath); mzXMLfolder = new File(mzXMLPath); if (!mzXMLfolder.exists()) { logger.error("Mode2 mzXML folder " + mzXMLfolder.getAbsolutePath() + " does not exist. The program will exit."); return; } pepXMLPath = args[3]; logger.info("Mode2 pepXML folder: " + pepXMLPath); pepXMLfolder = new File(pepXMLPath); if (!pepXMLfolder.exists()) { logger.error("Mode2 pepXML folder " + pepXMLfolder.getAbsolutePath() + " does not exist. The program will exit."); return; } idx = 4; } String outputfolder = ""; float MinProb = 0f; for (int i = idx; i < args.length; i++) { if (args[i].startsWith("-")) { if (args[i].equals("-ID")) { param.TargetIDOnly = true; logger.info("Detect ID feature only: true"); } if (args[i].startsWith("-O")) { outputfolder = args[i].substring(2); logger.info("Output folder: " + outputfolder); File outputfile = new File(outputfolder); if (!outputfolder.endsWith("\\") | outputfolder.endsWith("/")) { outputfolder += "/"; } if (!outputfile.exists()) { outputfile.mkdir(); } } if (args[i].startsWith("-C")) { try { NoFile = Integer.parseInt(args[i].substring(2)); logger.info("No of concurrent files: " + NoFile); } catch (Exception ex) { logger.error(args[i] + " is not a correct integer format, will process only one file at a time."); } } if (args[i].startsWith("-p")) { try { MinProb = Float.parseFloat(args[i].substring(2)); logger.info("probability threshold: " + MinProb); } catch (Exception ex) { logger.error(args[i] + " is not a correct format, will use 0 as threshold instead."); } } } } reader.close(); TandemParam tandemparam = new TandemParam(DBSearchParam.SearchInstrumentType.TOF5600); PTMManager.GetInstance(); if (param.TargetIDOnly) { param.EstimateBG = false; param.ApexDelta = 1.5f; param.NoMissedScan = 10; param.MiniOverlapP = 0.2f; param.RemoveGroupedPeaks = false; param.CheckMonoIsotopicApex = false; param.DetectByCWT = false; param.FillGapByBK = false; param.IsoCorrThreshold = -1f; param.SmoothFactor = 3; } if (mode == 1) { logger.info("Processing " + mzXMLfile.getAbsolutePath() + "...."); long time = System.currentTimeMillis(); LCMSPeakMS1 LCMS1 = new LCMSPeakMS1(mzXMLfile.getAbsolutePath(), NoCPUs); LCMS1.SetParameter(param); LCMS1.Resume = false; if (!param.TargetIDOnly) { LCMS1.CreatePeakFolder(); } LCMS1.ExportPeakClusterTable = true; if (pepXMLfile.exists()) { tandemparam.InteractPepXMLPath = pepXMLfile.getAbsolutePath(); LCMS1.ParsePepXML(tandemparam, MinProb); logger.info("No. of PSMs included: " + LCMS1.IDsummary.PSMList.size()); logger.info("No. of Peptide ions included: " + LCMS1.IDsummary.GetPepIonList().size()); } if (param.TargetIDOnly) { LCMS1.SaveSerializationFile = false; } if (param.TargetIDOnly || !LCMS1.ReadPeakCluster()) { LCMS1.PeakClusterDetection(); } if (pepXMLfile.exists()) { LCMS1.AssignQuant(false); LCMS1.IDsummary.ExportPepID(outputfolder); } time = System.currentTimeMillis() - time; logger.info(LCMS1.ParentmzXMLName + " processed time:" + String.format("%d hour, %d min, %d sec", TimeUnit.MILLISECONDS.toHours(time), TimeUnit.MILLISECONDS.toMinutes(time) - TimeUnit.HOURS.toMinutes(TimeUnit.MILLISECONDS.toHours(time)), TimeUnit.MILLISECONDS.toSeconds(time) - TimeUnit.MINUTES.toSeconds(TimeUnit.MILLISECONDS.toMinutes(time)))); LCMS1.BaseClearAllPeaks(); LCMS1.SetSpectrumParser(null); LCMS1.IDsummary = null; LCMS1 = null; System.gc(); } else if (mode == 2) { LCMSID IDsummary = new LCMSID("", "", ""); logger.info("Parsing all pepXML files in " + pepXMLPath + "...."); for (File file : pepXMLfolder.listFiles()) { if (file.getName().toLowerCase().endsWith("pep.xml") || file.getName().toLowerCase().endsWith("pepxml")) { PepXMLParser pepXMLParser = new PepXMLParser(IDsummary, file.getAbsolutePath(), MinProb); } } HashMap<String, LCMSID> LCMSIDMap = IDsummary.GetLCMSIDFileMap(); ExecutorService executorPool = null; executorPool = Executors.newFixedThreadPool(NoFile); logger.info("Processing all mzXML files in " + mzXMLPath + "...."); for (File file : mzXMLfolder.listFiles()) { if (file.getName().toLowerCase().endsWith("mzxml")) { LCMSID id = LCMSIDMap.get(FilenameUtils.getBaseName(file.getName())); if (id == null || id.PSMList == null) { logger.warn("No IDs found in :" + FilenameUtils.getBaseName(file.getName()) + ". Quantification for this file is skipped"); continue; } if (!id.PSMList.isEmpty()) { MS1TargetQuantThread thread = new MS1TargetQuantThread(file, id, NoCPUs, outputfolder, param); executorPool.execute(thread); } } } LCMSIDMap.clear(); LCMSIDMap = null; IDsummary = null; executorPool.shutdown(); try { executorPool.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS); } catch (InterruptedException e) { logger.info("interrupted.."); } if (outputfolder == null | outputfolder.equals("")) { outputfolder = mzXMLPath; } logger.info("Merging PSM files.."); File output = new File(outputfolder); FileWriter writer = new FileWriter(output.getAbsolutePath() + "/PSM_merge.csv"); boolean header = false; for (File csvfile : output.listFiles()) { if (csvfile.getName().toLowerCase().endsWith("_psms.csv")) { BufferedReader outreader = new BufferedReader(new FileReader(csvfile)); String outline = outreader.readLine(); if (!header) { writer.write(outline + "\n"); header = true; } while ((outline = outreader.readLine()) != null) { writer.write(outline + "\n"); } outreader.close(); csvfile.delete(); } } writer.close(); } logger.info("MS1 quant module is complete."); } catch (Exception e) { Logger.getRootLogger().error(ExceptionUtils.getStackTrace(e)); throw e; } }
From source file:Main.java
public static void clearMap(HashMap hash) { if (hash != null) { hash.clear(); } hash = null; }
From source file:com.github.sakserv.lslock.cli.LockListerCli.java
/** * Loads the procLocksConents HashMap with <inode,pid> * * @throws IOException if /proc/locks doesn't exist */// w ww . ja va2s . c o m public static HashMap<Integer, Integer> parseProcLocks() throws IOException { // The hashmap provides the contents of /proc/locks // as <inode, pid> HashMap<Integer, Integer> procLocksContents = new HashMap<>(); // Clear the HashMap procLocksContents.clear(); // Read /proc/locks, load the HashMap try (BufferedReader br = new BufferedReader(new FileReader(new File("/proc/locks")))) { for (String line; (line = br.readLine()) != null;) { String[] lineSplit = line.split("\\s+"); String[] fileIdSplit = lineSplit[5].split(":"); Integer inode = Integer.parseInt(fileIdSplit[2]); Integer pid = Integer.parseInt(lineSplit[4]); procLocksContents.put(inode, pid); } } return procLocksContents; }
From source file:org.chililog.server.workbench.ApiUtils.java
/** * Gets the headers// w w w. ja va2s . c o m * * @param conn * @param headers * @return 1st response line */ public static String getResponseHeaders(URLConnection conn, HashMap<String, String> headers) { headers.clear(); String responseCode = ""; for (int i = 0;; i++) { String name = conn.getHeaderFieldKey(i); String value = conn.getHeaderField(i); if (name == null && value == null) { break; } if (name == null) { responseCode = value; } else { headers.put(name, value); } } return responseCode; }
From source file:controllers.SnLocationsController.java
public static void discoverHereNow() { String appid = params._contains(PARAM_APPID) ? params.get(PARAM_APPID) : ""; String limit = params._contains(PARAM_LIMIT) ? params.get(PARAM_LIMIT) : ""; limit = verifyRecordLimit(limit);/*w w w . j a v a 2s . c o m*/ String ids = params._contains(PARAM_IDS) ? params.get(PARAM_IDS) : ""; //Logger.info("appid, limit, ids : %s, %s, %s \n", appid, limit, ids); Logger.info("PARAMS -> appid:%s ; limit:%s ; ids:%s", appid, limit, ids); // using Async jobs ResponseModel responseModel = new ResponseModel(); ResponseMeta responseMeta = new ResponseMeta(); LinkedList<Object> dataList = new LinkedList<Object>(); HashMap params = new HashMap(); try { params.clear(); //-if (!StringUtils.isEmpty(limit)) params.put(PARAM_LIMIT, limit); FoursquareDiscoverPoiJob mFoursquarePoiJob = new FoursquareDiscoverPoiJob(); mFoursquarePoiJob.setIds(ids); mFoursquarePoiJob.setReqParams(params); dataList.addAll((LinkedList<Object>) mFoursquarePoiJob.doJobWithResult()); // HereNow part params.clear(); if (!StringUtils.isEmpty(limit)) params.put(PARAM_LIMIT, limit); FoursquareDiscoverHereNowJob mFoursquareDiscoverHereNowJob = new FoursquareDiscoverHereNowJob(); mFoursquareDiscoverHereNowJob.setReqParams(params); mFoursquareDiscoverHereNowJob.setPoiList(dataList); dataList = new LinkedList<Object>();//dataList.clear(); dataList.addAll((LinkedList<Object>) mFoursquareDiscoverHereNowJob.doJobWithResult()); response.status = Http.StatusCode.OK; responseMeta.code = response.status; responseModel.meta = responseMeta; responseModel.data = dataList; renderJSON(LocoUtils.getGson().toJson(responseModel)); } catch (Exception ex) { responseMeta.code = Http.StatusCode.INTERNAL_ERROR; gotError(responseMeta, ex); //renderJSON(responseModel); } }
From source file:org.mwc.debrief.sensorfusion.views.DataSupport.java
public static void sensorDataFor(final TrackWrapper primary, final TimeSeriesCollection newData, final HashMap<SensorWrapper, SensorSeries> index) { index.clear(); final Enumeration<Editable> sensors = primary.getSensors().elements(); while (sensors.hasMoreElements()) { final SensorWrapper sensor = (SensorWrapper) sensors.nextElement(); final SensorSeries series = new SensorSeries(sensor.getName(), sensor); final Enumeration<Editable> cuts = sensor.elements(); _previousVal = Double.NaN; index.put(sensor, series);/*from w ww. j av a 2 s.com*/ while (cuts.hasMoreElements()) { final SensorContactWrapper scw = (SensorContactWrapper) cuts.nextElement(); final double thisVal = scw.getBearing(); // wrap this in a try/catch - in case there are multiple entries try { series.add(create(scw.getTime(), thisVal, scw.getColor())); } catch (final Exception e) { // no probs, just ignore the new value } } if (!series.isEmpty()) newData.addSeries(series); } }
From source file:com.jajja.jorm.Database.java
/** * Closes and destroys all transactions for the current thread. */// w w w.j a va2 s .co m public static void close() { HashMap<String, Transaction> map = instance.getTransactions(); for (Transaction transaction : map.values()) { transaction.destroy(); } map.clear(); instance.transactions.remove(); }