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From source file:com.stgmastek.core.logic.ExecutionOrder.java
/** * Static method to setup the execution order. * This method essentially looks up in to the setup table BATCH_COLUMN_MAP to * get the details.Using the details it would setup the execution order for the batch * Once the execution order is set, it sets the order into the {@link BatchInfo#setOrderedMap(TreeMap)} * for all other objects to derive knowledge from. * Note: The batch could be run for - /* w w w . j ava 2 s .c o m*/ * <OL> * <LI> For a date i.e. all entities and all values for those entities. * <LI> For an entity i.e. batch for only policy records and all its values * i.e. P1, P2 ... Pn * <LI> For a single object identified as GENERAL type of job with a * sequence number i.e. JOB_SCHEDULE.job_seq * <LI> For only Meta events like ALL PRE and ALL POST * <LI> For any combination of above, a few given - * <UL> * <LI> Policy P1 and ALL PRE * <LI> ALL Agency records and Policy P1 * <LI> Policy P1 and Agency A1 * </UL> * </OL> * * Every step has inline comments associated with it. * * @param batchContext * The context for the batch * @return true * If the setup is done successfully * @throws BatchException * Any database I/O exception */ public synchronized static Boolean setExecutionOrder(BatchContext batchContext) throws BatchException { //Get request parameters HashMap<String, Object> params = batchContext.getRequestParams().getProcessRequestParams(); //Check whether it is a date batch run or specific batch run if (params.size() < 1) { batchContext.getBatchInfo().setDateRun(true); } Connection con = batchContext.getBATCHConnection(); IBatchDao bDao = DaoFactory.getBatchDao(); try { //Query the setup table to get the setup values LookupTable lookupTable = bDao.getLookupTable(con); Map<String, String> orderByLookupTable = bDao.getOrderByLookupTable(con); TreeMap<Integer, EntityParams> orderedMap = new TreeMap<Integer, EntityParams>(); //If it is date batch run, then for all entities, populate "ALL" if (batchContext.getBatchInfo().isDateRun()) { Iterator<String> lTableIter = lookupTable.keySet().iterator(); while (lTableIter.hasNext()) { String entity = lTableIter.next(); params.put(entity + "_1", "ALL"); } } //Iterate over each parameters set for (Entry<String, Object> entry : params.entrySet()) { String paramName = entry.getKey(); Object paramValue = entry.getValue(); if (logger.isDebugEnabled()) { logger.debug("In ExecutionOrder >>>> paramName ==>" + paramName); } String entity = null; //Strip the last occurrence of _ and get the entity name entity = paramName.substring(0, paramName.lastIndexOf("_")); if (logger.isDebugEnabled()) { logger.debug("In ExecutionOrder >>>> Entity ==>" + entity); } //Validate whether the entity is setup appropriately in //the BATCH_COLUMN_MAP table if (!lookupTable.containsKey(entity)) { //If the entity is not set, raise an exception and exit throw new BatchException("The entity " + entity + " is not set up in the COLUMN_MAP table."); } else { //Get the lookup record //Once found, get the details and set it against the entity List<ColumnLookup> lookupColumns = lookupTable.get(entity); Integer order = lookupColumns.get(0).getPrecedenceOrder(); if (!orderedMap.containsKey(order)) { EntityParams entityParams = new EntityParams(entity); orderedMap.put(order, entityParams); } EntityParams entityParams = orderedMap.get(order); entityParams.setLookupColumns(lookupColumns); entityParams.setOrderByMap(orderByLookupTable);//Added on 01-OCT-2013 - Mandar //Check 'ALL' or for specific entity values. //Note: Batch could be run for a date i.e. all entities (and all values) // or for any combination of entity and values if (!paramValue.equals("ALL")) { List<GroupInfo> list = entityParams.getValues(); //check if all exists. If exists do not write the new value if (list.size() == 0 || !list.get(0).getEntityValue().equals("ALL")) entityParams.getValues().add(new GroupInfo((String) paramValue)); } else { entityParams.setAll(new GroupInfo((String) paramValue)); } } } batchContext.getBatchInfo().setOrderedMap(orderedMap); } finally { bDao.releaseResources(null, null, con); } return true; }
From source file:com.likya.myra.jef.utils.JobQueueOperations.java
public static boolean persistDisabledJobQueue(ConfigurationManager configurationManager, HashMap<String, String> jobQueue) { FileOutputStream fos = null;/*from ww w . j ava 2s .c om*/ ObjectOutputStream out = null; if (jobQueue.size() == 0) { return true; } try { File fileTemp = new File(configurationManager.getFileToPersist() + "_disabled.temp"); //$NON-NLS-1$ fos = new FileOutputStream(fileTemp); out = new ObjectOutputStream(fos); out.writeObject(jobQueue); out.close(); File file = new File(configurationManager.getFileToPersist() + "_disabled"); if (file.exists()) { file.delete(); } fileTemp.renameTo(file); } catch (IOException ex) { ex.printStackTrace(); } return true; }
From source file:com.wso2telco.gsma.authenticators.util.OutboundMessage.java
/** * Prepare the USSD/SMS message from database config table for service provider, operator specific message or * default message stored in mobile-connect.xml. Message template can have ${variable} and relevant data to apply * to the template should be passed with map parameter. * * @param clientId sp client id/*w w w .j a v a2 s .c o m*/ * @param messageType ussd/sms message type * @param map additional variable data map for the message template * @param operator operator name * @return prepared ussd message */ public static String prepare(String clientId, MessageType messageType, HashMap<String, String> map, String operator) { MobileConnectConfig.OperatorSpecificMessage operatorSpecificMessage = null; String template = null; Map<String, String> data = new HashMap<String, String>(); // add default map values here // data.put("key", "value"); if (map != null && map.size() > 0) { for (Map.Entry<String, String> entry : map.entrySet()) { data.put(entry.getKey(), entry.getValue()); } } // Load operator specific message from hash map if (operator != null) { if (messageType == MessageType.USSD_LOGIN || messageType == MessageType.USSD_REGISTRATION) { operatorSpecificMessage = operatorSpecificMessageMap.get(operator); } else if (messageType == MessageType.USSD_PIN_LOGIN || messageType == MessageType.USSD_PIN_REGISTRATION) { operatorSpecificMessage = operatorSpecificPinMessageMap.get(operator); } else if (messageType == MessageType.SMS_LOGIN || messageType == MessageType.SMS_REGISTRATION) { operatorSpecificMessage = operatorSpecificSmsMessageMap.get(operator); } else if (messageType == MessageType.SMS_OTP) { operatorSpecificMessage = operatorSpecificSmsotpMessageMap.get(operator); } data.put("operator", operator); } // RULE 1 : first try to get login/registration messages from sp config table if (messageType == MessageType.USSD_LOGIN) { template = spConfigService.getUSSDLoginMessage(clientId); } else if (messageType == MessageType.USSD_REGISTRATION) { template = spConfigService.getUSSDRegistrationMessage(clientId); } else if (messageType == MessageType.USSD_PIN_LOGIN) { template = spConfigService.getUSSDPinLoginMessage(clientId); } else if (messageType == MessageType.USSD_PIN_REGISTRATION) { template = spConfigService.getUSSDPinRegistrationMessage(clientId); } else if (messageType == MessageType.SMS_LOGIN) { template = spConfigService.getSMSLoginMessage(clientId); } else if (messageType == MessageType.SMS_REGISTRATION) { template = spConfigService.getSMSRegistrationMessage(clientId); } else if (messageType == MessageType.SMS_OTP) { template = spConfigService.getSMSOTPMessage(clientId); } if (template == null) { // RULE 2 : if message template is not found, try loading them from operator specific config from xml if (operatorSpecificMessage != null) { if (messageType == MessageType.USSD_LOGIN) { template = operatorSpecificMessage.getLoginMessage(); } else if (messageType == MessageType.USSD_REGISTRATION) { template = operatorSpecificMessage.getRegistrationMessage(); } else if (messageType == MessageType.USSD_PIN_LOGIN) { template = operatorSpecificMessage.getLoginMessage(); } else if (messageType == MessageType.USSD_PIN_REGISTRATION) { template = operatorSpecificMessage.getRegistrationMessage(); } else if (messageType == MessageType.SMS_LOGIN) { template = operatorSpecificMessage.getLoginMessage(); } else if (messageType == MessageType.SMS_REGISTRATION) { template = operatorSpecificMessage.getRegistrationMessage(); } else if (messageType == MessageType.SMS_OTP) { template = operatorSpecificMessage.getSmsotpMessage(); } } else { // RULE 3 : if no operator specific message is found, try loading from common messages if (messageType == MessageType.USSD_LOGIN) { template = ussdConfig.getUssdLoginMessage(); } else if (messageType == MessageType.USSD_REGISTRATION) { template = ussdConfig.getUssdRegistrationMessage(); } else if (messageType == MessageType.USSD_PIN_LOGIN) { template = ussdConfig.getPinLoginMessage(); } else if (messageType == MessageType.USSD_PIN_REGISTRATION) { template = ussdConfig.getPinRegistrationMessage(); } else if (messageType == MessageType.SMS_LOGIN) { template = smsConfig.getLoginMessage(); } else if (messageType == MessageType.SMS_REGISTRATION) { template = smsConfig.getRegistrationMessage(); } else if (messageType == MessageType.SMS_OTP) { template = smsConfig.getSmsotpMessage(); } } } return template == null ? null : StrSubstitutor.replace(template, data); }
From source file:nl.wur.plantbreeding.www.marker2seq.GoDistribution.java
/** * Generate the Pie chart for a set of given Go terms. * @param distrib a HashMap of GO name and GO frequency * @param title the title of the GO graph * @param url the url used for the tooltips * @param session the HttpSession used to save the file * @param legend Print the legend or not * @param tooltips Add tooltip or not/* ww w. j a v a 2s .c om*/ * @param urls Add urls or not (link in the graph) * @param max Maximum number of item to display * @return a list containing the filename and the map for the figure * @throws IOException when something happens while writting the image */ public static String[] generateDistribution(final HashMap<String, Integer> distrib, final String title, final String url, final HttpSession session, final boolean legend, final boolean tooltips, final boolean urls, final int max) throws IOException { final PieChart piec = new PieChart(); final PieDataset piedata = piec.createDataset(distrib); final JFreeChart chart = piec.createChart(piedata, title, legend, tooltips, urls); final PiePlot plot = (PiePlot) chart.getPlot(); if (distrib.size() >= max) { plot.setLabelGenerator(null); } plot.setURLGenerator(new StandardPieURLGenerator(url, "section")); final ChartRenderingInfo info = new ChartRenderingInfo(new StandardEntityCollection()); final String filename = ServletUtilities.saveChartAsPNG(chart, 500, 400, info, session); final String map = ChartUtilities.getImageMap(filename, info); final String[] output = { filename, map }; return output; }
From source file:eu.sisob.uma.crawler.MatrixResultBuilder.java
public static void writeResultsList(File file, HashMap<String, Integer> universities_axis, HashMap<String, Integer> dept_axis, HashMap<String, HashMap<String, Map.Entry<Integer, Integer>>> resultsMatrix) { Map.Entry<Integer, Integer>[][] matrix = (Map.Entry<Integer, Integer>[][]) new Map.Entry[universities_axis .size()][dept_axis.size()];//from w w w .j ava 2 s . com String[] cols = new String[universities_axis.size()]; String[] rows = new String[dept_axis.size()]; int total_researchers = 0; int success_researchers = 0; for (String j : resultsMatrix.keySet()) { cols[universities_axis.get(j)] = j; for (String k : resultsMatrix.get(j).keySet()) { rows[dept_axis.get(k)] = k; } } for (String j : resultsMatrix.keySet()) { for (String k : resultsMatrix.get(j).keySet()) { Map.Entry<Integer, Integer> r = resultsMatrix.get(j).get(k); int x = universities_axis.get(j); int y = dept_axis.get(k); matrix[x][y] = r; success_researchers += r.getKey(); total_researchers += r.getValue(); } } String s = "\"UNIVERSITY\"\t\"SUBJECT\"\t\"RESEARCHERS FOUND\"\t\"TOTAL RESEARCHERS\""; s += "\r\n"; try { FileUtils.write(file, s, "UTF-8", false); } catch (IOException ex) { ProjectLogger.LOGGER.error("Error writing results list"); } s = ""; for (int i = 0; i < matrix.length; i++) { for (int j = 0; j < matrix[i].length; j++) { if (matrix[i][j] != null) { s += "\"" + cols[i] + "\"\t\"" + rows[j] + "\"\t" + matrix[i][j].getKey() + "\t" + matrix[i][j].getValue(); s += "\r\n"; } } if (s.length() > 1000) { try { FileUtils.write(file, s, "UTF-8", true); } catch (IOException ex) { ProjectLogger.LOGGER.error("Error writing matrix results"); } s = ""; } } s += "\r\nRESEARCHERS FOUND\t" + success_researchers; s += "\r\nNUMBER OF RESEARCHERS\t" + total_researchers; if (!s.equals("")) { try { FileUtils.write(file, s, "UTF-8", true); } catch (IOException ex) { ProjectLogger.LOGGER.error("Error writing matrix results"); } } }
From source file:eu.sisob.uma.crawler.MatrixResultBuilder.java
public static void writeResultsMatrix(File file, HashMap<String, Integer> universities_axis, HashMap<String, Integer> dept_axis, HashMap<String, HashMap<String, Map.Entry<Integer, Integer>>> resultsMatrix) { Map.Entry<Integer, Integer>[][] matrix = (Map.Entry<Integer, Integer>[][]) new Map.Entry[universities_axis .size()][dept_axis.size()];/* w w w . j av a2 s . c o m*/ String[] cols = new String[universities_axis.size()]; String[] rows = new String[dept_axis.size()]; int total_researchers = 0; int success_researchers = 0; for (String j : resultsMatrix.keySet()) { cols[universities_axis.get(j)] = j; for (String k : resultsMatrix.get(j).keySet()) { rows[dept_axis.get(k)] = k; } } for (String j : resultsMatrix.keySet()) { for (String k : resultsMatrix.get(j).keySet()) { Map.Entry<Integer, Integer> r = resultsMatrix.get(j).get(k); int x = universities_axis.get(j); int y = dept_axis.get(k); matrix[x][y] = r; success_researchers += r.getKey(); total_researchers += r.getValue(); } } try { FileUtils.write(file, "RESULTS TABLE\r\n", "UTF-8", false); } catch (IOException ex) { ProjectLogger.LOGGER.error("Error writing results matrix"); } String s = "#\t"; for (int i = 0; i < rows.length; i++) { s += rows[i] + "\t"; } s += "\r\n"; for (int i = 0; i < matrix.length; i++) { s += cols[i] + "\t"; for (int j = 0; j < matrix[i].length; j++) { if (matrix[i][j] != null) s += matrix[i][j].getKey() + "/" + matrix[i][j].getValue() + "\t"; else s += "\t"; } s += "\r\n"; if (s.length() > 1000) { try { FileUtils.write(file, s, "UTF-8", true); } catch (IOException ex) { ProjectLogger.LOGGER.error("Error writing matrix results"); } s = ""; } } if (!s.equals("")) { try { FileUtils.write(file, s, "UTF-8", true); } catch (IOException ex) { ProjectLogger.LOGGER.error("Error writing matrix results"); } } s = "\r\nTOTAL RESEARCHER = " + total_researchers + " - RESEARCHERS WITH RESULTS: " + success_researchers; try { FileUtils.write(file, s, "UTF-8", true); } catch (IOException ex) { ProjectLogger.LOGGER.error("Error writing matrix results"); } }
From source file:fr.paris.lutece.plugins.workflow.modules.ticketingfacilfamilles.web.task.AutomaticAssignmentTaskComponent.java
/** * build and return display Config Form Url * // w ww . ja v a2 s . c o m * @param task * task * @param mapParams * map of parameters to add to redirect url * @return display Config Form Url */ private static String getDisplayConfigFormUrl(ITask task, HashMap<String, String> mapParams) { UrlItem url = new UrlItem(URL_DISPLAY_CONFIG_FORM); url.addParameter(PARAMETER_TASK_ID, task.getId()); if ((mapParams != null) && (mapParams.size() > 0)) { for (Map.Entry<String, String> entry : mapParams.entrySet()) { url.addParameter(entry.getKey(), entry.getValue()); } } return url.toString(); }
From source file:info.mtgdb.api.Db.java
/** * //from www .j a v a 2s. c om * @param filters HashMap<String, String> containing a mapping of keys to values. For example colors and black. * @return ArrayList */ public static ArrayList<Card> filterCards(HashMap<String, String> filters) { StringBuilder sb = new StringBuilder(); sb.append(API_URL + "/cards/?"); for (String key : filters.keySet()) { String value = filters.get(key); sb.append(key + "=" + value + "&"); } if (filters.size() > 0) sb.deleteCharAt(sb.length() - 1); return getCardsFromUrl(sb.toString()); }
From source file:DIA_Umpire_Quant.DIA_Umpire_ProtQuant.java
/** * @param args the command line arguments *//*from w w w. j ava 2s . c o m*/ public static void main(String[] args) throws FileNotFoundException, IOException, Exception { System.out.println( "================================================================================================="); System.out.println( "DIA-Umpire protein quantitation module (version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length != 1) { System.out.println( "command format error, the correct format should be: java -jar -Xmx10G DIA_Umpire_PortQuant.jar diaumpire_module.params"); return; } try { ConsoleLogger.SetConsoleLogger(Level.INFO); ConsoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "diaumpire_orotquant.log"); } catch (Exception e) { } Logger.getRootLogger().info("Version: " + UmpireInfo.GetInstance().Version); Logger.getRootLogger().info("Parameter file:" + args[0]); BufferedReader reader = new BufferedReader(new FileReader(args[0])); String line = ""; String WorkFolder = ""; int NoCPUs = 2; String Combined_Prot = ""; boolean DefaultProtFiltering = true; float Freq = 0f; int TopNPep = 6; int TopNFrag = 6; String FilterWeight = "GW"; float MinWeight = 0.9f; TandemParam tandemPara = new TandemParam(DBSearchParam.SearchInstrumentType.TOF5600); HashMap<String, File> AssignFiles = new HashMap<>(); boolean ExportSaint = false; boolean SAINT_MS1 = false; boolean SAINT_MS2 = true; HashMap<String, String[]> BaitList = new HashMap<>(); HashMap<String, String> BaitName = new HashMap<>(); HashMap<String, String[]> ControlList = new HashMap<>(); HashMap<String, String> ControlName = new HashMap<>(); //<editor-fold defaultstate="collapsed" desc="Reading parameter file"> while ((line = reader.readLine()) != null) { line = line.trim(); Logger.getRootLogger().info(line); if (!"".equals(line) && !line.startsWith("#")) { //System.out.println(line); if (line.equals("==File list begin")) { do { line = reader.readLine(); line = line.trim(); if (line.equals("==File list end")) { continue; } else if (!"".equals(line)) { File newfile = new File(line); if (newfile.exists()) { AssignFiles.put(newfile.getAbsolutePath(), newfile); } else { Logger.getRootLogger().info("File: " + newfile + " does not exist."); } } } while (!line.equals("==File list end")); } if (line.split("=").length < 2) { continue; } String type = line.split("=")[0].trim(); String value = line.split("=")[1].trim(); switch (type) { case "Path": { WorkFolder = value; break; } case "path": { WorkFolder = value; break; } case "Thread": { NoCPUs = Integer.parseInt(value); break; } case "Fasta": { tandemPara.FastaPath = value; break; } case "Combined_Prot": { Combined_Prot = value; break; } case "DefaultProtFiltering": { DefaultProtFiltering = Boolean.parseBoolean(value); break; } case "DecoyPrefix": { if (!"".equals(value)) { tandemPara.DecoyPrefix = value; } break; } case "ProteinFDR": { tandemPara.ProtFDR = Float.parseFloat(value); break; } case "FilterWeight": { FilterWeight = value; break; } case "MinWeight": { MinWeight = Float.parseFloat(value); break; } case "TopNFrag": { TopNFrag = Integer.parseInt(value); break; } case "TopNPep": { TopNPep = Integer.parseInt(value); break; } case "Freq": { Freq = Float.parseFloat(value); break; } //<editor-fold defaultstate="collapsed" desc="SaintOutput"> case "ExportSaintInput": { ExportSaint = Boolean.parseBoolean(value); break; } case "QuantitationType": { switch (value) { case "MS1": { SAINT_MS1 = true; SAINT_MS2 = false; break; } case "MS2": { SAINT_MS1 = false; SAINT_MS2 = true; break; } case "BOTH": { SAINT_MS1 = true; SAINT_MS2 = true; break; } } break; } // case "BaitInputFile": { // SaintBaitFile = value; // break; // } // case "PreyInputFile": { // SaintPreyFile = value; // break; // } // case "InterationInputFile": { // SaintInteractionFile = value; // break; // } default: { if (type.startsWith("BaitName_")) { BaitName.put(type.substring(9), value); } if (type.startsWith("BaitFile_")) { BaitList.put(type.substring(9), value.split("\t")); } if (type.startsWith("ControlName_")) { ControlName.put(type.substring(12), value); } if (type.startsWith("ControlFile_")) { ControlList.put(type.substring(12), value.split("\t")); } break; } //</editor-fold> } } } //</editor-fold> //Initialize PTM manager using compomics library PTMManager.GetInstance(); //Check if the fasta file can be found if (!new File(tandemPara.FastaPath).exists()) { Logger.getRootLogger().info("Fasta file :" + tandemPara.FastaPath + " cannot be found, the process will be terminated, please check."); System.exit(1); } //Check if the prot.xml file can be found if (!new File(Combined_Prot).exists()) { Logger.getRootLogger().info("ProtXML file: " + Combined_Prot + " cannot be found, the export protein summary table will be empty."); } LCMSID protID = null; //Parse prot.xml and generate protein master list given an FDR if (Combined_Prot != null && !Combined_Prot.equals("")) { protID = LCMSID.ReadLCMSIDSerialization(Combined_Prot); if (!"".equals(Combined_Prot) && protID == null) { protID = new LCMSID(Combined_Prot, tandemPara.DecoyPrefix, tandemPara.FastaPath); ProtXMLParser protxmlparser = new ProtXMLParser(protID, Combined_Prot, 0f); //Use DIA-Umpire default protein FDR calculation if (DefaultProtFiltering) { protID.RemoveLowLocalPWProtein(0.8f); protID.RemoveLowMaxIniProbProtein(0.9f); protID.FilterByProteinDecoyFDRUsingMaxIniProb(tandemPara.DecoyPrefix, tandemPara.ProtFDR); } //Get protein FDR calculation without other filtering else { protID.FilterByProteinDecoyFDRUsingLocalPW(tandemPara.DecoyPrefix, tandemPara.ProtFDR); } protID.LoadSequence(); protID.WriteLCMSIDSerialization(Combined_Prot); } Logger.getRootLogger().info("Protein No.:" + protID.ProteinList.size()); } HashMap<String, HashMap<String, FragmentPeak>> IDSummaryFragments = new HashMap<>(); //Generate DIA file list ArrayList<DIAPack> FileList = new ArrayList<>(); try { File folder = new File(WorkFolder); if (!folder.exists()) { Logger.getRootLogger().info("The path : " + WorkFolder + " cannot be found."); System.exit(1); } for (final File fileEntry : folder.listFiles()) { if (fileEntry.isFile() && (fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzml")) && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q1.mzxml") && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q2.mzxml") && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) { AssignFiles.put(fileEntry.getAbsolutePath(), fileEntry); } if (fileEntry.isDirectory()) { for (final File fileEntry2 : fileEntry.listFiles()) { if (fileEntry2.isFile() && (fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzml")) && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q1.mzxml") && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q2.mzxml") && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) { AssignFiles.put(fileEntry2.getAbsolutePath(), fileEntry2); } } } } Logger.getRootLogger().info("No. of files assigned :" + AssignFiles.size()); for (File fileEntry : AssignFiles.values()) { Logger.getRootLogger().info(fileEntry.getAbsolutePath()); } for (File fileEntry : AssignFiles.values()) { String mzXMLFile = fileEntry.getAbsolutePath(); if (mzXMLFile.toLowerCase().endsWith(".mzxml") | mzXMLFile.toLowerCase().endsWith(".mzml")) { DIAPack DiaFile = new DIAPack(mzXMLFile, NoCPUs); Logger.getRootLogger().info( "================================================================================================="); Logger.getRootLogger().info("Processing " + mzXMLFile); if (!DiaFile.LoadDIASetting()) { Logger.getRootLogger().info("Loading DIA setting failed, job is incomplete"); System.exit(1); } if (!DiaFile.LoadParams()) { Logger.getRootLogger().info("Loading parameters failed, job is incomplete"); System.exit(1); } Logger.getRootLogger().info("Loading identification results " + mzXMLFile + "...."); //If the serialization file for ID file existed if (DiaFile.ReadSerializedLCMSID()) { DiaFile.IDsummary.ReduceMemoryUsage(); DiaFile.IDsummary.ClearAssignPeakCluster(); FileList.add(DiaFile); HashMap<String, FragmentPeak> FragMap = new HashMap<>(); IDSummaryFragments.put(FilenameUtils.getBaseName(mzXMLFile), FragMap); } } } //<editor-fold defaultstate="collapsed" desc="Peptide and fragment selection"> Logger.getRootLogger().info("Peptide and fragment selection across the whole dataset"); ArrayList<LCMSID> SummaryList = new ArrayList<>(); for (DIAPack diafile : FileList) { if (protID != null) { //Generate protein list according to mapping of peptide ions for each DIA file to the master protein list diafile.IDsummary.GenerateProteinByRefIDByPepSeq(protID, true); diafile.IDsummary.ReMapProPep(); } if ("GW".equals(FilterWeight)) { diafile.IDsummary.SetFilterByGroupWeight(); } else if ("PepW".equals(FilterWeight)) { diafile.IDsummary.SetFilterByWeight(); } SummaryList.add(diafile.IDsummary); } FragmentSelection fragselection = new FragmentSelection(SummaryList); fragselection.freqPercent = Freq; fragselection.GeneratePepFragScoreMap(); fragselection.GenerateTopFragMap(TopNFrag); fragselection.GenerateProtPepScoreMap(MinWeight); fragselection.GenerateTopPepMap(TopNPep); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Writing general reports"> ExportTable export = new ExportTable(WorkFolder, SummaryList, IDSummaryFragments, protID, fragselection); export.Export(TopNPep, TopNFrag, Freq); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="//<editor-fold defaultstate="collapsed" desc="Generate SAINT input files"> if (ExportSaint && protID != null) { HashMap<String, DIAPack> Filemap = new HashMap<>(); for (DIAPack DIAfile : FileList) { Filemap.put(DIAfile.GetBaseName(), DIAfile); } FileWriter baitfile = new FileWriter(WorkFolder + "SAINT_Bait_" + DateTimeTag.GetTag() + ".txt"); FileWriter preyfile = new FileWriter(WorkFolder + "SAINT_Prey_" + DateTimeTag.GetTag() + ".txt"); FileWriter interactionfileMS1 = null; FileWriter interactionfileMS2 = null; if (SAINT_MS1) { interactionfileMS1 = new FileWriter( WorkFolder + "SAINT_Interaction_MS1_" + DateTimeTag.GetTag() + ".txt"); } if (SAINT_MS2) { interactionfileMS2 = new FileWriter( WorkFolder + "SAINT_Interaction_MS2_" + DateTimeTag.GetTag() + ".txt"); } HashMap<String, String> PreyID = new HashMap<>(); for (String samplekey : ControlName.keySet()) { String name = ControlName.get(samplekey); for (String file : ControlList.get(samplekey)) { baitfile.write(FilenameUtils.getBaseName(file) + "\t" + name + "\t" + "C\n"); LCMSID IDsummary = Filemap.get(FilenameUtils.getBaseName(file)).IDsummary; if (SAINT_MS1) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS1, file, name, PreyID, 1); } if (SAINT_MS2) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS2, file, name, PreyID, 2); } } } for (String samplekey : BaitName.keySet()) { String name = BaitName.get(samplekey); for (String file : BaitList.get(samplekey)) { baitfile.write(FilenameUtils.getBaseName(file) + "\t" + name + "\t" + "T\n"); LCMSID IDsummary = Filemap.get(FilenameUtils.getBaseName(file)).IDsummary; if (SAINT_MS1) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS1, file, name, PreyID, 1); } if (SAINT_MS2) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS2, file, name, PreyID, 2); } } } baitfile.close(); if (SAINT_MS1) { interactionfileMS1.close(); } if (SAINT_MS2) { interactionfileMS2.close(); } for (String AccNo : PreyID.keySet()) { preyfile.write(AccNo + "\t" + PreyID.get(AccNo) + "\n"); } preyfile.close(); } //</editor-fold> Logger.getRootLogger().info("Job done"); Logger.getRootLogger().info( "================================================================================================="); } catch (Exception e) { Logger.getRootLogger().error(ExceptionUtils.getStackTrace(e)); throw e; } }
From source file:info.unyttig.helladroid.newzbin.NewzBinController.java
/** * Sends HTTP POST requests to Newzbin with given parameters. * /* w ww. j a v a 2 s . co m*/ * @param url Type:String - The url to connect to * @param kvPairs Type:Map - The map of parameters to post * @return Returns a HttpResponse with results * @throws ClientProtocolException * @throws IOException */ public static HttpResponse doPost(String url, HashMap<String, String> kvPairs) throws ClientProtocolException, IOException { HttpClient httpclient = new DefaultHttpClient(); HttpPost httppost = new HttpPost(url); httppost.addHeader("Content-type", "application/x-www-form-urlencoded"); if (kvPairs != null && kvPairs.isEmpty() == false) { ArrayList<NameValuePair> nameValuePairs = new ArrayList<NameValuePair>(kvPairs.size() + 4); nameValuePairs .add(new BasicNameValuePair("limit", preferences.getString("newzbin_search_limit", "10"))); nameValuePairs .add(new BasicNameValuePair("retention", preferences.getString("newzbin_retention", "7"))); nameValuePairs.add(new BasicNameValuePair("username", preferences.getString("newzbin_username", ""))); nameValuePairs.add(new BasicNameValuePair("password", preferences.getString("newzbin_password", ""))); String k, v; Iterator<String> itKeys = kvPairs.keySet().iterator(); while (itKeys.hasNext()) { k = itKeys.next(); v = kvPairs.get(k); nameValuePairs.add(new BasicNameValuePair(k, v)); } httppost.setEntity(new UrlEncodedFormEntity(nameValuePairs)); } return httpclient.execute(httppost); }