List of usage examples for java.io FileReader FileReader
public FileReader(FileDescriptor fd)
From source file:DIA_Umpire_Quant.DIA_Umpire_IntLibSearch.java
/** * @param args the command line arguments *//* w ww .ja v a 2 s.com*/ public static void main(String[] args) throws FileNotFoundException, IOException, Exception { System.out.println( "================================================================================================="); System.out.println("DIA-Umpire targeted re-extraction analysis using internal library (version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length != 1) { System.out.println( "command format error, the correct format should be : java -jar -Xmx10G DIA_Umpire_IntLibSearch.jar diaumpire_module.params"); return; } try { ConsoleLogger.SetConsoleLogger(Level.INFO); ConsoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "diaumpire_intlibsearch.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 InternalLibID = ""; float ProbThreshold = 0.99f; float RTWindow_Int = -1f; float Freq = 0f; int TopNFrag = 6; TandemParam tandemPara = new TandemParam(DBSearchParam.SearchInstrumentType.TOF5600); HashMap<String, File> AssignFiles = 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 "InternalLibID": { InternalLibID = value; break; } case "RTWindow_Int": { RTWindow_Int = Float.parseFloat(value); break; } case "ProbThreshold": { ProbThreshold = Float.parseFloat(value); break; } case "TopNFrag": { TopNFrag = Integer.parseInt(value); break; } case "Freq": { Freq = Float.parseFloat(value); break; } case "Fasta": { tandemPara.FastaPath = value; break; } } } } //</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); } //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.FastaPath = tandemPara.FastaPath; FileList.add(DiaFile); } } } //<editor-fold defaultstate="collapsed" desc="Targete re-extraction using internal library"> Logger.getRootLogger().info( "================================================================================================="); if (FileList.size() > 1) { Logger.getRootLogger().info("Targeted re-extraction using internal library"); FragmentLibManager libManager = FragmentLibManager.ReadFragmentLibSerialization(WorkFolder, InternalLibID); if (libManager == null) { Logger.getRootLogger().info("Building internal spectral library"); libManager = new FragmentLibManager(InternalLibID); ArrayList<LCMSID> LCMSIDList = new ArrayList<>(); for (DIAPack dia : FileList) { LCMSIDList.add(dia.IDsummary); } libManager.ImportFragLibTopFrag(LCMSIDList, Freq, TopNFrag); libManager.WriteFragmentLibSerialization(WorkFolder); } libManager.ReduceMemoryUsage(); Logger.getRootLogger() .info("Building retention time prediction model and generate candidate peptide list"); for (int i = 0; i < FileList.size(); i++) { FileList.get(i).IDsummary.ClearMappedPep(); } for (int i = 0; i < FileList.size(); i++) { for (int j = i + 1; j < FileList.size(); j++) { RTAlignedPepIonMapping alignment = new RTAlignedPepIonMapping(WorkFolder, FileList.get(i).GetParameter(), FileList.get(i).IDsummary, FileList.get(j).IDsummary); alignment.GenerateModel(); alignment.GenerateMappedPepIon(); } FileList.get(i).ExportID(); FileList.get(i).IDsummary = null; } Logger.getRootLogger().info("Targeted matching........"); for (DIAPack diafile : FileList) { if (diafile.IDsummary == null) { diafile.ReadSerializedLCMSID(); } if (!diafile.IDsummary.GetMappedPepIonList().isEmpty()) { diafile.UseMappedIon = true; diafile.FilterMappedIonByProb = false; diafile.BuildStructure(); diafile.MS1FeatureMap.ReadPeakCluster(); diafile.MS1FeatureMap.ClearMonoisotopicPeakOfCluster(); diafile.GenerateMassCalibrationRTMap(); diafile.TargetedExtractionQuant(false, libManager, ProbThreshold, RTWindow_Int); diafile.MS1FeatureMap.ClearAllPeaks(); diafile.IDsummary.ReduceMemoryUsage(); diafile.IDsummary.RemoveLowProbMappedIon(ProbThreshold); diafile.ExportID(); Logger.getRootLogger().info("Peptide ions: " + diafile.IDsummary.GetPepIonList().size() + " Mapped ions: " + diafile.IDsummary.GetMappedPepIonList().size()); diafile.ClearStructure(); } diafile.IDsummary = null; System.gc(); } Logger.getRootLogger().info( "================================================================================================="); } //</editor-fold> Logger.getRootLogger().info("Job done"); Logger.getRootLogger().info( "================================================================================================="); } catch (Exception e) { Logger.getRootLogger().error(ExceptionUtils.getStackTrace(e)); throw e; } }
From source file:com.era7.bioinfo.annotation.AutomaticQualityControl.java
public static void main(String[] args) { if (args.length != 4) { System.out.println("This program expects four parameters: \n" + "1. Gene annotation XML filename \n" + "2. Reference protein set (.fasta)\n" + "3. Output TXT filename\n" + "4. Initial Blast XML results filename (the one used at the very beginning of the semiautomatic annotation process)\n"); } else {//from w w w. j ava 2 s . c o m BufferedWriter outBuff = null; try { File inFile = new File(args[0]); File fastaFile = new File(args[1]); File outFile = new File(args[2]); File blastFile = new File(args[3]); //Primero cargo todos los datos del archivo xml del blast BufferedReader buffReader = new BufferedReader(new FileReader(blastFile)); StringBuilder stBuilder = new StringBuilder(); String line = null; while ((line = buffReader.readLine()) != null) { stBuilder.append(line); } buffReader.close(); System.out.println("Creating blastoutput..."); BlastOutput blastOutput = new BlastOutput(stBuilder.toString()); System.out.println("BlastOutput created! :)"); stBuilder.delete(0, stBuilder.length()); HashMap<String, String> blastProteinsMap = new HashMap<String, String>(); ArrayList<Iteration> iterations = blastOutput.getBlastOutputIterations(); for (Iteration iteration : iterations) { blastProteinsMap.put(iteration.getQueryDef().split("\\|")[1].trim(), iteration.toString()); } //freeing some memory blastOutput = null; //------------------------------------------------------------------------ //Initializing writer for output file outBuff = new BufferedWriter(new FileWriter(outFile)); //reading gene annotation xml file..... buffReader = new BufferedReader(new FileReader(inFile)); stBuilder = new StringBuilder(); line = null; while ((line = buffReader.readLine()) != null) { stBuilder.append(line); } buffReader.close(); XMLElement genesXML = new XMLElement(stBuilder.toString()); //freeing some memory I don't need anymore stBuilder.delete(0, stBuilder.length()); //reading file with the reference proteins set ArrayList<String> proteinsReferenceSet = new ArrayList<String>(); buffReader = new BufferedReader(new FileReader(fastaFile)); while ((line = buffReader.readLine()) != null) { if (line.charAt(0) == '>') { proteinsReferenceSet.add(line.split("\\|")[1]); } } buffReader.close(); Element pGenes = genesXML.asJDomElement().getChild(PredictedGenes.TAG_NAME); List<Element> contigs = pGenes.getChildren(ContigXML.TAG_NAME); System.out.println("There are " + contigs.size() + " contigs to be checked... "); outBuff.write("There are " + contigs.size() + " contigs to be checked... \n"); outBuff.write("Proteins reference set: \n"); for (String st : proteinsReferenceSet) { outBuff.write(st + ","); } outBuff.write("\n"); for (Element elem : contigs) { ContigXML contig = new ContigXML(elem); //escribo el id del contig en el que estoy outBuff.write("Checking contig: " + contig.getId() + "\n"); outBuff.flush(); List<XMLElement> geneList = contig.getChildrenWith(PredictedGene.TAG_NAME); System.out.println("geneList.size() = " + geneList.size()); int numeroDeGenesParaAnalizar = geneList.size() / FACTOR; if (numeroDeGenesParaAnalizar == 0) { numeroDeGenesParaAnalizar++; } ArrayList<Integer> indicesUtilizados = new ArrayList<Integer>(); outBuff.write("\nThe contig has " + geneList.size() + " predicted genes, let's analyze: " + numeroDeGenesParaAnalizar + "\n"); for (int j = 0; j < numeroDeGenesParaAnalizar; j++) { int geneIndex; boolean geneIsDismissed = false; do { geneIsDismissed = false; geneIndex = (int) Math.round(Math.floor(Math.random() * geneList.size())); PredictedGene tempGene = new PredictedGene(geneList.get(geneIndex).asJDomElement()); if (tempGene.getStatus().equals(PredictedGene.STATUS_DISMISSED)) { geneIsDismissed = true; } } while (indicesUtilizados.contains(new Integer(geneIndex)) && geneIsDismissed); indicesUtilizados.add(geneIndex); System.out.println("geneIndex = " + geneIndex); //Ahora hay que sacar el gen correspondiente al indice y hacer el control de calidad PredictedGene gene = new PredictedGene(geneList.get(geneIndex).asJDomElement()); outBuff.write("\nAnalyzing gene with id: " + gene.getId() + " , annotation uniprot id: " + gene.getAnnotationUniprotId() + "\n"); outBuff.write("eValue: " + gene.getEvalue() + "\n"); //--------------PETICION POST HTTP BLAST---------------------- PostMethod post = new PostMethod(BLAST_URL); post.addParameter("program", "blastx"); post.addParameter("sequence", gene.getSequence()); post.addParameter("database", "uniprotkb"); post.addParameter("email", "ppareja@era7.com"); post.addParameter("exp", "1e-10"); post.addParameter("stype", "dna"); // execute the POST HttpClient client = new HttpClient(); int status = client.executeMethod(post); System.out.println("status post = " + status); InputStream inStream = post.getResponseBodyAsStream(); String fileName = "jobid.txt"; FileOutputStream outStream = new FileOutputStream(new File(fileName)); byte[] buffer = new byte[1024]; int len; while ((len = inStream.read(buffer)) != -1) { outStream.write(buffer, 0, len); } outStream.close(); //Once the file is created I just have to read one line in order to extract the job id buffReader = new BufferedReader(new FileReader(new File(fileName))); String jobId = buffReader.readLine(); buffReader.close(); System.out.println("jobId = " + jobId); //--------------HTTP CHECK JOB STATUS REQUEST---------------------- GetMethod get = new GetMethod(CHECK_JOB_STATUS_URL + jobId); String jobStatus = ""; do { try { Thread.sleep(1000);//sleep for 1000 ms } catch (InterruptedException ie) { //If this thread was intrrupted by nother thread } status = client.executeMethod(get); //System.out.println("status get = " + status); inStream = get.getResponseBodyAsStream(); fileName = "jobStatus.txt"; outStream = new FileOutputStream(new File(fileName)); while ((len = inStream.read(buffer)) != -1) { outStream.write(buffer, 0, len); } outStream.close(); //Once the file is created I just have to read one line in order to extract the job id buffReader = new BufferedReader(new FileReader(new File(fileName))); jobStatus = buffReader.readLine(); //System.out.println("jobStatus = " + jobStatus); buffReader.close(); } while (!jobStatus.equals(FINISHED_JOB_STATUS)); //Once I'm here the blast should've already finished //--------------JOB RESULTS HTTP REQUEST---------------------- get = new GetMethod(JOB_RESULT_URL + jobId + "/out"); status = client.executeMethod(get); System.out.println("status get = " + status); inStream = get.getResponseBodyAsStream(); fileName = "jobResults.txt"; outStream = new FileOutputStream(new File(fileName)); while ((len = inStream.read(buffer)) != -1) { outStream.write(buffer, 0, len); } outStream.close(); //--------parsing the blast results file----- TreeSet<GeneEValuePair> featuresBlast = new TreeSet<GeneEValuePair>(); buffReader = new BufferedReader(new FileReader(new File(fileName))); while ((line = buffReader.readLine()) != null) { if (line.length() > 3) { String prefix = line.substring(0, 3); if (prefix.equals("TR:") || prefix.equals("SP:")) { String[] columns = line.split(" "); String id = columns[1]; //System.out.println("id = " + id); String e = ""; String[] arraySt = line.split("\\.\\.\\."); if (arraySt.length > 1) { arraySt = arraySt[1].trim().split(" "); int contador = 0; for (int k = 0; k < arraySt.length && contador <= 2; k++) { String string = arraySt[k]; if (!string.equals("")) { contador++; if (contador == 2) { e = string; } } } } else { //Number before e- String[] arr = arraySt[0].split("e-")[0].split(" "); String numeroAntesE = arr[arr.length - 1]; String numeroDespuesE = arraySt[0].split("e-")[1].split(" ")[0]; e = numeroAntesE + "e-" + numeroDespuesE; } double eValue = Double.parseDouble(e); //System.out.println("eValue = " + eValue); GeneEValuePair g = new GeneEValuePair(id, eValue); featuresBlast.add(g); } } } GeneEValuePair currentGeneEValuePair = new GeneEValuePair(gene.getAnnotationUniprotId(), gene.getEvalue()); System.out.println("currentGeneEValuePair.id = " + currentGeneEValuePair.id); System.out.println("currentGeneEValuePair.eValue = " + currentGeneEValuePair.eValue); boolean blastContainsGene = false; for (GeneEValuePair geneEValuePair : featuresBlast) { if (geneEValuePair.id.equals(currentGeneEValuePair.id)) { blastContainsGene = true; //le pongo la e que tiene en el wu-blast para poder comparar currentGeneEValuePair.eValue = geneEValuePair.eValue; break; } } if (blastContainsGene) { outBuff.write("The protein was found in the WU-BLAST result.. \n"); //Una vez que se que esta en el blast tengo que ver que sea la mejor GeneEValuePair first = featuresBlast.first(); outBuff.write("Protein with best eValue according to the WU-BLAST result: " + first.id + " , " + first.eValue + "\n"); if (first.id.equals(currentGeneEValuePair.id)) { outBuff.write("Proteins with best eValue match up \n"); } else { if (first.eValue == currentGeneEValuePair.eValue) { outBuff.write( "The one with best eValue is not the same protein but has the same eValue \n"); } else if (first.eValue > currentGeneEValuePair.eValue) { outBuff.write( "The one with best eValue is not the same protein but has a worse eValue :) \n"); } else { outBuff.write( "The best protein from BLAST has an eValue smaller than ours, checking if it's part of the reference set...\n"); //System.exit(-1); if (proteinsReferenceSet.contains(first.id)) { //The protein is in the reference set and that shouldn't happen outBuff.write( "The protein was found on the reference set, checking if it belongs to the same contig...\n"); String iterationSt = blastProteinsMap.get(gene.getAnnotationUniprotId()); if (iterationSt != null) { outBuff.write( "The protein was found in the BLAST used at the beginning of the annotation process.\n"); Iteration iteration = new Iteration(iterationSt); ArrayList<Hit> hits = iteration.getIterationHits(); boolean contigFound = false; Hit errorHit = null; for (Hit hit : hits) { if (hit.getHitDef().indexOf(contig.getId()) >= 0) { contigFound = true; errorHit = hit; break; } } if (contigFound) { outBuff.write( "ERROR: A hit from the same contig was find in the Blast file: \n" + errorHit.toString() + "\n"); } else { outBuff.write("There is no hit with the same contig! :)\n"); } } else { outBuff.write( "The protein is NOT in the BLAST used at the beginning of the annotation process.\n"); } } else { //The protein was not found on the reference set so everything's ok outBuff.write( "The protein was not found on the reference, everything's ok :)\n"); } } } } else { outBuff.write("The protein was NOT found on the WU-BLAST !! :( \n"); //System.exit(-1); } } } } catch (Exception ex) { ex.printStackTrace(); } finally { try { //closing outputfile outBuff.close(); } catch (IOException ex) { Logger.getLogger(AutomaticQualityControl.class.getName()).log(Level.SEVERE, null, ex); } } } }
From source file:edu.msu.cme.rdp.probematch.cli.PrimerMatch.java
public static void main(String[] args) throws Exception { PrintStream out = new PrintStream(System.out); int maxDist = Integer.MAX_VALUE; try {//from w w w . j a v a 2s . c o m CommandLine line = new PosixParser().parse(options, args); if (line.hasOption("outFile")) { out = new PrintStream(new File(line.getOptionValue("outFile"))); } if (line.hasOption("maxDist")) { maxDist = Integer.valueOf(line.getOptionValue("maxDist")); } args = line.getArgs(); if (args.length != 2) { throw new Exception("Unexpected number of command line arguments"); } } catch (Exception e) { System.err.println("Error: " + e.getMessage()); new HelpFormatter().printHelp("PrimerMatch <primer_list | primer_file> <seq_file>", options); return; } List<PatternBitMask64> primers = new ArrayList(); if (new File(args[0]).exists()) { File primerFile = new File(args[0]); SequenceFormat seqformat = SeqUtils.guessFileFormat(primerFile); if (seqformat.equals(SequenceFormat.FASTA)) { SequenceReader reader = new SequenceReader(primerFile); Sequence seq; while ((seq = reader.readNextSequence()) != null) { primers.add(new PatternBitMask64(seq.getSeqString(), true, seq.getSeqName())); } reader.close(); } else { BufferedReader reader = new BufferedReader(new FileReader(args[0])); String line; while ((line = reader.readLine()) != null) { line = line.trim(); if (!line.equals("")) { primers.add(new PatternBitMask64(line, true)); } } reader.close(); } } else { for (String primer : args[0].split(",")) { primers.add(new PatternBitMask64(primer, true)); } } SeqReader seqReader = new SequenceReader(new File(args[1])); Sequence seq; String primerRegion; out.println("#seqname\tdesc\tprimer_index\tprimer_name\tposition\tmismatches\tseq_primer_region"); while ((seq = seqReader.readNextSequence()) != null) { for (int index = 0; index < primers.size(); index++) { PatternBitMask64 primer = primers.get(index); BitVector64Result results = BitVector64.process(seq.getSeqString().toCharArray(), primer, maxDist); for (BitVector64Match result : results.getResults()) { primerRegion = seq.getSeqString().substring( Math.max(0, result.getPosition() - primer.getPatternLength()), result.getPosition()); if (result.getPosition() < primer.getPatternLength()) { for (int pad = result.getPosition(); pad < primer.getPatternLength(); pad++) { primerRegion = "x" + primerRegion; } } out.println(seq.getSeqName() + "\t" + seq.getDesc() + "\t" + (index + 1) + "\t" + primer.getPrimerName() + "\t" + result.getPosition() + "\t" + result.getScore() + "\t" + primerRegion); } } } out.close(); seqReader.close(); }
From source file:edu.scripps.fl.pubchem.app.CIDDownloader.java
public static void main(String[] args) throws Exception { CIDDownloader fetcher = new CIDDownloader(); CommandLineHandler clh = new CommandLineHandler() { public void configureOptions(Options options) { options.addOption(OptionBuilder.withLongOpt("input_file").withType("").withValueSeparator('=') .hasArg().create()); options.addOption(OptionBuilder.withLongOpt("output_file").withType("").withValueSeparator('=') .hasArg().isRequired().create()); }// ww w . j a v a 2s. c o m }; args = clh.handle(args); String inputFile = clh.getCommandLine().getOptionValue("input_file"); String outputFile = clh.getCommandLine().getOptionValue("output_file"); fetcher.setOutputFile(outputFile); Iterator<?> iterator; if (null == inputFile) { if (args.length == 0) { log.info("Running query to find CIDs in PCAssayResult but not in PCCompound"); SQLQuery query = PubChemDB.getSession().createSQLQuery( "select distinct r.cid from pcassay_result r left join pccompound c on r.cid = c.cid where (r.cid is not null and r.cid > 0 ) and c.cid is null order by r.cid"); ScrollableResults scroll = query.scroll(ScrollMode.FORWARD_ONLY); iterator = new ScrollableResultsIterator<Integer>(Integer.class, scroll); } else { iterator = Arrays.asList(args).iterator(); } } else if ("-".equals(inputFile)) { log.info("Reading CIDs (one per line) from STDIN"); iterator = new LineIterator(new InputStreamReader(System.in)); } else { log.info("Reading CIDs (one per line) from " + inputFile); iterator = new LineIterator(new FileReader(inputFile)); } fetcher.process(iterator); System.exit(0); }
From source file:clientpaxos.ClientPaxos.java
/** * @param args the command line arguments *///from w w w. j a v a 2s.c o m public static void main(String[] args) throws IOException, InterruptedException, Exception { // TODO code application logic here String host = ""; int port = 0; try (BufferedReader br = new BufferedReader(new FileReader("ipserver.txt"))) { StringBuilder sb = new StringBuilder(); String line = br.readLine(); if (line != null) { host = line; line = br.readLine(); if (line != null) { port = Integer.parseInt(line); } } } scanner = new Scanner(System.in); //System.out.print("Input server IP hostname : "); //host = scan.nextLine(); //System.out.print("Input server Port : "); //port = scan.nextInt(); //scan.nextLine(); tcpSocket = new Socket(host, port); System.out.println("Connected"); Thread t = new Thread(new StringGetter()); t.start(); while (true) { sleep(100); if (!voteInput) { System.out.print("COMMAND : "); } //send msg to server String msg = scanner.next(); //if ((day && isAlive == 1) || (!day && role.equals("werewolf") && isAlive == 1)) { ParseCommand(msg); //} } }
From source file:gr.demokritos.iit.demos.Demo.java
public static void main(String[] args) { try {// w w w . j a v a2 s .c o m Options options = new Options(); options.addOption("h", HELP, false, "show help."); options.addOption("i", INPUT, true, "The file containing JSON " + " representations of tweets or SAG posts - 1 per line" + " default file looked for is " + DEFAULT_INFILE); options.addOption("o", OUTPUT, true, "Where to write the output " + " default file looked for is " + DEFAULT_OUTFILE); options.addOption("p", PROCESS, true, "Type of processing to do " + " ner for Named Entity Recognition re for Relation Extraction" + " default is NER"); options.addOption("s", SAG, false, "Whether to process as SAG posts" + " default is off - if passed means process as SAG posts"); CommandLineParser parser = new BasicParser(); CommandLine cmd = parser.parse(options, args); // DEFAULTS String filename = DEFAULT_INFILE; String outfilename = DEFAULT_OUTFILE; String process = NER; boolean isSAG = false; if (cmd.hasOption(HELP)) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("NER + RE extraction module", options); System.exit(0); } if (cmd.hasOption(INPUT)) { filename = cmd.getOptionValue(INPUT); } if (cmd.hasOption(OUTPUT)) { outfilename = cmd.getOptionValue(OUTPUT); } if (cmd.hasOption(SAG)) { isSAG = true; } if (cmd.hasOption(PROCESS)) { process = cmd.getOptionValue(PROCESS); } System.out.println(); System.out.println("Reading from file: " + filename); System.out.println("Process type: " + process); System.out.println("Processing SAG: " + isSAG); System.out.println("Writing to file: " + outfilename); System.out.println(); List<String> jsoni = new ArrayList(); Scanner in = new Scanner(new FileReader(filename)); while (in.hasNextLine()) { String json = in.nextLine(); jsoni.add(json); } PrintWriter writer = new PrintWriter(outfilename, "UTF-8"); System.out.println("Read " + jsoni.size() + " lines from " + filename); if (process.equalsIgnoreCase(RE)) { System.out.println("Running Relation Extraction"); System.out.println(); String json = API.RE(jsoni, isSAG); System.out.println(json); writer.print(json); } else { System.out.println("Running Named Entity Recognition"); System.out.println(); jsoni = API.NER(jsoni, isSAG); /* for(String json: jsoni){ NamedEntityList nel = NamedEntityList.fromJSON(json); nel.prettyPrint(); } */ for (String json : jsoni) { System.out.println(json); writer.print(json); } } writer.close(); } catch (ParseException | UnsupportedEncodingException | FileNotFoundException ex) { Logger.getLogger(Demo.class.getName()).log(Level.SEVERE, null, ex); } }
From source file:de.citec.csra.elancsv.parser.SimpleParser.java
public static void main(String[] args) throws IOException, ParseException { Options opts = new Options(); opts.addOption("file", true, "Tab-separated ELAN export file to load."); opts.addOption("tier", true, "Tier to analyze. Optional: Append ::num to interpret annotations numerically."); opts.addOption("format", true, "How to read information from the file name. %V -> participant, %A -> annoatator, %C -> condition, e.g. \"%V - %A\""); opts.addOption("help", false, "Print this help and exit"); CommandLineParser parser = new BasicParser(); CommandLine cmd = parser.parse(opts, args); if (cmd.hasOption("help")) { helpExit(opts, "where OPTION includes:"); }// w ww. java2 s. c o m String infile = cmd.getOptionValue("file"); if (infile == null) { helpExit(opts, "Error: no file given."); } String format = cmd.getOptionValue("format"); if (format == null) { helpExit(opts, "Error: no format given."); } String tier = cmd.getOptionValue("tier"); if (tier == null) { helpExit(opts, "Error: no tier given."); } // TODO count values in annotations (e.g. search all robot occurrences) String[] tn = tier.split("::"); boolean numeric = false; if (tn.length == 2 && tn[1].equals("num")) { numeric = true; tier = tn[0]; } format = "^" + format + "$"; format = format.replaceFirst("%V", "(?<V>.*?)"); format = format.replaceFirst("%A", "(?<A>.*?)"); format = format.replaceFirst("%C", "(?<C>.*?)"); Pattern pa = Pattern.compile(format); Map<String, Participant> participants = new HashMap<>(); BufferedReader br = new BufferedReader(new FileReader(infile)); String line; int lineno = 0; while ((line = br.readLine()) != null) { String[] parts = line.split("\t"); lineno++; if (parts.length < 5) { System.err.println("WARNING: line '" + lineno + "' too short '" + line + "'"); continue; } Annotation a = new Annotation(Long.valueOf(parts[ElanFormat.START.field]), Long.valueOf(parts[ElanFormat.STOP.field]), Long.valueOf(parts[ElanFormat.DURATION.field]), parts[ElanFormat.VALUE.field]); String tname = parts[ElanFormat.TIER.field]; String file = parts[ElanFormat.FILE.field].replaceAll(".eaf", ""); Matcher m = pa.matcher(file); String vp = file; String condition = "?"; String annotator = "?"; String participantID = vp; if (m.find()) { vp = m.group("V"); if (format.indexOf("<A>") > 0) { annotator = m.group("A"); } if (format.indexOf("<C>") > 0) { condition = m.group("C"); } } participantID = vp + ";" + annotator; if (!participants.containsKey(participantID)) { participants.put(participantID, new Participant(vp, condition, annotator)); } Participant p = participants.get(participantID); if (!p.tiers.containsKey(tname)) { p.tiers.put(tname, new Tier(tname)); } p.tiers.get(tname).annotations.add(a); } Map<String, Map<String, Number>> values = new HashMap<>(); Set<String> rownames = new HashSet<>(); String allCountKey = "c: all values"; String allDurationKey = "d: all values"; String allMeanKey = "m: all values"; for (Map.Entry<String, Participant> e : participants.entrySet()) { // System.out.println(e); Tier t = e.getValue().tiers.get(tier); String participantID = e.getKey(); if (!values.containsKey(participantID)) { values.put(participantID, new HashMap<String, Number>()); } Map<String, Number> row = values.get(participantID); //participant id if (t != null) { row.put(allCountKey, 0l); row.put(allDurationKey, 0l); row.put(allMeanKey, 0l); for (Annotation a : t.annotations) { long countAll = (long) row.get(allCountKey) + 1; long durationAll = (long) row.get(allDurationKey) + a.duration; long meanAll = durationAll / countAll; row.put(allCountKey, countAll); row.put(allDurationKey, durationAll); row.put(allMeanKey, meanAll); if (!numeric) { String countKey = "c: " + a.value; String durationKey = "d: " + a.value; String meanKey = "m: " + a.value; if (!row.containsKey(countKey)) { row.put(countKey, 0l); } if (!row.containsKey(durationKey)) { row.put(durationKey, 0l); } if (!row.containsKey(meanKey)) { row.put(meanKey, 0d); } long count = (long) row.get(countKey) + 1; long duration = (long) row.get(durationKey) + a.duration; double mean = duration * 1.0 / count; row.put(countKey, count); row.put(durationKey, duration); row.put(meanKey, mean); rownames.add(countKey); rownames.add(durationKey); rownames.add(meanKey); } else { String countKey = "c: " + t.name; String sumKey = "s: " + t.name; String meanKey = "m: " + t.name; if (!row.containsKey(countKey)) { row.put(countKey, 0l); } if (!row.containsKey(sumKey)) { row.put(sumKey, 0d); } if (!row.containsKey(meanKey)) { row.put(meanKey, 0d); } double d = 0; try { d = Double.valueOf(a.value); } catch (NumberFormatException ex) { } long count = (long) row.get(countKey) + 1; double sum = (double) row.get(sumKey) + d; double mean = sum / count; row.put(countKey, count); row.put(sumKey, sum); row.put(meanKey, mean); rownames.add(countKey); rownames.add(sumKey); rownames.add(meanKey); } } } } ArrayList<String> list = new ArrayList(rownames); Collections.sort(list); StringBuilder header = new StringBuilder("ID;Annotator;"); header.append(allCountKey); header.append(";"); header.append(allDurationKey); header.append(";"); header.append(allMeanKey); header.append(";"); for (String l : list) { header.append(l); header.append(";"); } System.out.println(header); for (Map.Entry<String, Map<String, Number>> e : values.entrySet()) { StringBuilder row = new StringBuilder(e.getKey()); row.append(";"); if (e.getValue().containsKey(allCountKey)) { row.append(e.getValue().get(allCountKey)); } else { row.append("0"); } row.append(";"); if (e.getValue().containsKey(allDurationKey)) { row.append(e.getValue().get(allDurationKey)); } else { row.append("0"); } row.append(";"); if (e.getValue().containsKey(allMeanKey)) { row.append(e.getValue().get(allMeanKey)); } else { row.append("0"); } row.append(";"); for (String l : list) { if (e.getValue().containsKey(l)) { row.append(e.getValue().get(l)); } else { row.append("0"); } row.append(";"); } System.out.println(row); } }
From source file:edu.upenn.egricelab.AlignerBoost.FilterSAMAlignPE.java
public static void main(String[] args) { if (args.length == 0) { printUsage();/* w ww . ja va 2 s . c o m*/ return; } try { parseOptions(args); } catch (IllegalArgumentException e) { System.err.println("Error: " + e.getMessage()); printUsage(); return; } // Read in chrList, if specified if (chrFile != null) { chrFilter = new HashSet<String>(); try { BufferedReader chrFilterIn = new BufferedReader(new FileReader(chrFile)); String chr = null; while ((chr = chrFilterIn.readLine()) != null) chrFilter.add(chr); chrFilterIn.close(); if (verbose > 0) System.err.println( "Only looking at alignments on " + chrFilter.size() + " specified chromosomes"); } catch (IOException e) { System.err.println("Error: " + e.getMessage()); return; } } if (verbose > 0) { // Start the processMonitor processMonitor = new Timer(); // Start the ProcessStatusTask statusTask = new ProcessStatusTask(); // Schedule to show the status every 1 second processMonitor.scheduleAtFixedRate(statusTask, 0, statusFreq); } // Read in known SNP file, if specified if (knownSnpFile != null) { if (verbose > 0) System.err.println("Checking known SNPs from user specified VCF file"); knownVCF = new VCFFileReader(new File(knownSnpFile)); } SamReaderFactory readerFac = SamReaderFactory.makeDefault(); SAMFileWriterFactory writerFac = new SAMFileWriterFactory(); if (!isSilent) readerFac.validationStringency(ValidationStringency.LENIENT); // use LENIENT stringency else readerFac.validationStringency(ValidationStringency.SILENT); // use SILENT stringency SamReader in = readerFac.open(new File(inFile)); SAMFileHeader inHeader = in.getFileHeader(); if (inHeader.getGroupOrder() == GroupOrder.reference && inHeader.getSortOrder() == SortOrder.coordinate) System.err.println("Warning: Input file '" + inFile + "' might be sorted by coordinate and cannot be correctly processed!"); SAMFileHeader header = inHeader.clone(); // copy the inFile header as outFile header // Add new programHeader SAMProgramRecord progRec = new SAMProgramRecord(progName); progRec.setProgramName(progName); progRec.setProgramVersion(progVer); progRec.setCommandLine(StringUtils.join(" ", args)); header.addProgramRecord(progRec); //System.err.println(inFile + " groupOrder: " + in.getFileHeader().getGroupOrder() + " sortOrder: " + in.getFileHeader().getSortOrder()); // reset the orders header.setGroupOrder(groupOrder); header.setSortOrder(sortOrder); // write SAMHeader String prevID = null; SAMRecord prevRecord = null; List<SAMRecord> alnList = new ArrayList<SAMRecord>(); List<SAMRecordPair> alnPEList = null; // Estimate fragment length distribution by scan one-pass through the alignments SAMRecordIterator results = in.iterator(); if (!NO_ESTIMATE) { if (verbose > 0) { System.err.println("Estimating insert fragment size distribution ..."); statusTask.reset(); statusTask.setInfo("alignments scanned"); } long N = 0; double fragL_S = 0; // fragLen sum double fragL_SS = 0; // fragLen^2 sum while (results.hasNext()) { SAMRecord record = results.next(); if (verbose > 0) statusTask.updateStatus(); if (record.getFirstOfPairFlag() && !record.isSecondaryOrSupplementary()) { double fragLen = Math.abs(record.getInferredInsertSize()); if (fragLen != 0 && fragLen >= MIN_FRAG_LEN && fragLen <= MAX_FRAG_LEN) { // only consider certain alignments N++; fragL_S += fragLen; fragL_SS += fragLen * fragLen; } // stop estimate if already enough if (MAX_ESTIMATE_SCAN > 0 && N >= MAX_ESTIMATE_SCAN) break; } } if (verbose > 0) statusTask.finish(); // estimate fragment size if (N >= MIN_ESTIMATE_BASE) { // override command line values MEAN_FRAG_LEN = fragL_S / N; SD_FRAG_LEN = Math.sqrt((N * fragL_SS - fragL_S * fragL_S) / (N * (N - 1))); String estStr = String.format("Estimated fragment size distribution: N(%.1f, %.1f)", MEAN_FRAG_LEN, SD_FRAG_LEN); if (verbose > 0) System.err.println(estStr); // also add the estimation to comment header.addComment(estStr); } else { System.err.println( "Unable to estimate the fragment size distribution due to too few observed alignments"); System.err.println( "You have to specify the '--mean-frag-len' and '--sd-frag-len' on the command line and re-run this step"); statusTask.cancel(); processMonitor.cancel(); return; } // Initiate the normal model normModel = new NormalDistribution(MEAN_FRAG_LEN, SD_FRAG_LEN); // reset the iterator, if necessary if (in.type() == SamReader.Type.SAM_TYPE) { try { in.close(); } catch (IOException e) { System.err.println(e.getMessage()); } in = readerFac.open(new File(inFile)); } results.close(); results = in.iterator(); } // end of NO_ESTIMATE SAMFileWriter out = OUT_IS_SAM ? writerFac.makeSAMWriter(header, false, new File(outFile)) : writerFac.makeBAMWriter(header, false, new File(outFile)); // check each alignment again if (verbose > 0) { System.err.println("Filtering alignments ..."); statusTask.reset(); statusTask.setInfo("alignments processed"); } while (results.hasNext()) { SAMRecord record = results.next(); if (verbose > 0) statusTask.updateStatus(); String ID = record.getReadName(); // fix read and quality string for this read, if is a secondary hit from multiple hits, used for BWA alignment if (ID.equals(prevID) && record.getReadLength() == 0) SAMAlignFixer.fixSAMRecordRead(record, prevRecord); if (chrFilter != null && !chrFilter.contains(record.getReferenceName())) { prevID = ID; prevRecord = record; continue; } // fix MD:Z string for certain aligners with invalid format (i.e. seqAlto) if (fixMD) SAMAlignFixer.fixMisStr(record); // fix alignment, ignore if failed (unmapped or empty) if (!SAMAlignFixer.fixSAMRecord(record, knownVCF, DO_1DP)) { prevID = ID; prevRecord = record; continue; } if (!record.getReadPairedFlag()) { System.err.println("Error: alignment is not from a paired-end read at\n" + record.getSAMString()); out.close(); statusTask.cancel(); processMonitor.cancel(); return; } if (!ID.equals(prevID) && prevID != null || !results.hasNext()) { // a non-first new ID meet, or end of alignments // create alnPEList from filtered alnList alnPEList = createAlnPEListFromAlnList(alnList); //System.err.printf("%d alignments for %s transformed to %d alnPairs%n", alnList.size(), prevID, alnPEList.size()); int totalPair = alnPEList.size(); // filter highly unlikely PEhits filterPEHits(alnPEList, MIN_ALIGN_RATE, MIN_IDENTITY); // calculate posterior mapQ for each pair calcPEHitPostP(alnPEList, totalPair, MAX_HIT); // filter hits by mapQ if (MIN_MAPQ > 0) filterPEHits(alnPEList, MIN_MAPQ); // sort the list first with an anonymous class of comparator, with DESCREASING order Collections.sort(alnPEList, Collections.reverseOrder()); // control max-best if (MAX_BEST != 0 && alnPEList.size() > MAX_BEST) { // potential too much best hits int nBestStratum = 0; int bestMapQ = alnPEList.get(0).getPEMapQ(); // best mapQ from first PE for (SAMRecordPair pr : alnPEList) if (pr.getPEMapQ() == bestMapQ) nBestStratum++; else break; // stop searching for sorted list if (nBestStratum > MAX_BEST) alnPEList.clear(); } // filter alignments with auxiliary filters if (!MAX_SENSITIVITY) filterPEHits(alnPEList, MAX_SEED_MIS, MAX_SEED_INDEL, MAX_ALL_MIS, MAX_ALL_INDEL); // report remaining secondary alignments, up-to MAX_REPORT for (int i = 0; i < alnPEList.size() && (MAX_REPORT == 0 || i < MAX_REPORT); i++) { SAMRecordPair repPair = alnPEList.get(i); if (doUpdateBit) repPair.setNotPrimaryAlignmentFlags(i != 0); int nReport = MAX_REPORT == 0 ? Math.min(alnPEList.size(), MAX_REPORT) : alnPEList.size(); int nFiltered = alnPEList.size(); if (repPair.fwdRecord != null) { repPair.fwdRecord.setAttribute("NH", nReport); repPair.fwdRecord.setAttribute("XN", nFiltered); out.addAlignment(repPair.fwdRecord); } if (repPair.revRecord != null) { repPair.revRecord.setAttribute("NH", nReport); repPair.revRecord.setAttribute("XN", nFiltered); out.addAlignment(repPair.revRecord); } } // reset list alnList.clear(); alnPEList.clear(); } // update if (!ID.equals(prevID)) { prevID = ID; prevRecord = record; } alnList.add(record); } // end while try { in.close(); out.close(); } catch (IOException e) { System.err.println(e.getMessage()); } // Terminate the monitor task and monitor if (verbose > 0) { statusTask.cancel(); statusTask.finish(); processMonitor.cancel(); } }
From source file:com.cyberway.issue.net.PublicSuffixes.java
/** * Utility method for dumping a regex String, based on a published public * suffix list, which matches any SURT-form hostname up through the broadest * 'private' (assigned/sold) domain-segment. That is, for any of the * SURT-form hostnames.../*from w w w . j a v a 2 s . c o m*/ * * com,example, com,example,www, com,example,california,www * * ...the regex will match 'com,example,'. * * @param args * @throws IOException */ public static void main(String args[]) throws IOException { String regex; if (args.length == 0 || "=".equals(args[0])) { // use bundled list regex = getTopmostAssignedSurtPrefixRegex(); } else { // use specified filename BufferedReader reader = new BufferedReader(new FileReader(args[0])); regex = getTopmostAssignedSurtPrefixRegex(reader); IOUtils.closeQuietly(reader); } boolean needsClose = false; BufferedWriter writer; if (args.length >= 2) { // writer to specified file writer = new BufferedWriter(new FileWriter(args[1])); needsClose = true; } else { // write to stdout writer = new BufferedWriter(new OutputStreamWriter(System.out)); } writer.append(regex); writer.flush(); if (needsClose) { writer.close(); } }
From source file:examples.nntp.post.java
public final static void main(String[] args) { String from, subject, newsgroup, filename, server, organization; String references;/*www . j av a 2s.c o m*/ BufferedReader stdin; FileReader fileReader = null; SimpleNNTPHeader header; NNTPClient client; if (args.length < 1) { System.err.println("Usage: post newsserver"); System.exit(1); } server = args[0]; stdin = new BufferedReader(new InputStreamReader(System.in)); try { System.out.print("From: "); System.out.flush(); from = stdin.readLine(); System.out.print("Subject: "); System.out.flush(); subject = stdin.readLine(); header = new SimpleNNTPHeader(from, subject); System.out.print("Newsgroup: "); System.out.flush(); newsgroup = stdin.readLine(); header.addNewsgroup(newsgroup); while (true) { System.out.print("Additional Newsgroup <Hit enter to end>: "); System.out.flush(); // Of course you don't want to do this because readLine() may be null newsgroup = stdin.readLine().trim(); if (newsgroup.length() == 0) break; header.addNewsgroup(newsgroup); } System.out.print("Organization: "); System.out.flush(); organization = stdin.readLine(); System.out.print("References: "); System.out.flush(); references = stdin.readLine(); if (organization != null && organization.length() > 0) header.addHeaderField("Organization", organization); if (references != null && organization.length() > 0) header.addHeaderField("References", references); header.addHeaderField("X-Newsreader", "NetComponents"); System.out.print("Filename: "); System.out.flush(); filename = stdin.readLine(); try { fileReader = new FileReader(filename); } catch (FileNotFoundException e) { System.err.println("File not found. " + e.getMessage()); System.exit(1); } client = new NNTPClient(); client.addProtocolCommandListener(new PrintCommandListener(new PrintWriter(System.out))); client.connect(server); if (!NNTPReply.isPositiveCompletion(client.getReplyCode())) { client.disconnect(); System.err.println("NNTP server refused connection."); System.exit(1); } if (client.isAllowedToPost()) { Writer writer = client.postArticle(); if (writer != null) { writer.write(header.toString()); Util.copyReader(fileReader, writer); writer.close(); client.completePendingCommand(); } } fileReader.close(); client.logout(); client.disconnect(); } catch (IOException e) { e.printStackTrace(); System.exit(1); } }