List of usage examples for org.apache.commons.lang3 StringUtils split
public static String[] split(final String str, final String separatorChars)
Splits the provided text into an array, separators specified.
From source file:edu.gmu.csd.processor.DataProcessor.java
public static WinningResult calculateMeanStandardDeviation(String raffle) { String[] dataFieldsArr = null; if (StringUtils.isNotEmpty(raffle)) { dataFieldsArr = StringUtils.split(raffle, ","); }/*from www .j a va2s. co m*/ WinningResult winningResult = null; if (null != dataFieldsArr) { double mean; double sum = 0; double squareSum = 0; double stndrdDeviation; // First for loop to calculate the mean. for (String meanData : dataFieldsArr) { sum = sum + Integer.parseInt(meanData); } mean = sum / dataFieldsArr.length; // Second for loop to calculate the standard deviation. for (String sdData : dataFieldsArr) { double square = Math.pow((Integer.parseInt(sdData) - mean), 2); squareSum = squareSum + square; } stndrdDeviation = Math.sqrt(squareSum / (dataFieldsArr.length - 1)); winningResult = new WinningResult(); winningResult.setMean(mean); winningResult.setStandardDeviation(stndrdDeviation); } return winningResult; }
From source file:SampleLang.java
/** * Check if the key is valid//from w ww. ja v a 2s . com * @param key license key value * @return true if key is valid, false otherwise. */ public static boolean checkLicenseKey(String key) { //checks if empty or null if (StringUtils.isBlank(key)) { return false; } //delete all white space key = StringUtils.deleteWhitespace(key); //Split String using the - separator String[] keySplit = StringUtils.split(key, "-"); //check lengths of whole and parts if (keySplit.length != 2 || keySplit[0].length() != 4 || keySplit[1].length() != 4) { return false; } //Check if first part is numeric if (!StringUtils.isNumeric(keySplit[0])) { return false; } //Check if second part contains only //the four characters 'J', 'A', 'V' and 'A' if (!StringUtils.containsOnly(keySplit[1], new char[] { 'J', 'A', 'V', 'A' })) { return false; } //Check if the fourth character //in the first part is a '0' if (StringUtils.indexOf(keySplit[0], '0') != 3) { return false; } //If all conditions are fulfilled, key is valid. return true; }
From source file:com.sixwonders.courtkiosk.CitationAdapter.java
public static ArrayList<Citation> adaptCitationData(ArrayList<JSONObject> jsonObjects) { ArrayList<Citation> citations = new ArrayList<Citation>(); try {/*w w w . j av a 2s . com*/ for (JSONObject jsonObject : jsonObjects) { Citation citation = new Citation(); //id,,,,,date_of_birth,defendant_address,defendant_city,defendant_state,drivers_license_number,court_date,court_location,court_address if (jsonObject.getInt("citation_number") != 0) { citation.setCitation_number(jsonObject.getInt("citation_number")); } if (!StringUtils.isEmpty(jsonObject.get("citation_date").toString())) { citation.setCitation_date(StringUtils.split(jsonObject.getString("citation_date"), ' ')[0]); } if (!StringUtils.isEmpty(jsonObject.get("first_name").toString())) { citation.setFirst_name(jsonObject.getString("first_name")); } if (!StringUtils.isEmpty(jsonObject.get("last_name").toString())) { citation.setFirst_name(jsonObject.getString("last_name")); } if (!StringUtils.isEmpty(jsonObject.get("court_location").toString())) { citation.setCourt_location(jsonObject.getString("court_location")); } citations.add(citation); } } catch (JSONException e) { e.printStackTrace(); } return citations; }
From source file:com.google.mr4c.util.PathUtils.java
/** * Takes the elements of one path and prepends any elements that are missing in another path *//*from w w w . jav a 2s.c om*/ public static String prependMissingPathElements(String path, String otherPath, String separator) { List<String> pathElements = Arrays.asList(StringUtils.split(path, separator)); List<String> otherElements = Arrays.asList(StringUtils.split(otherPath, separator)); List<String> toAdd = new ArrayList<String>(); for (String element : otherElements) { if (!pathElements.contains(element)) { toAdd.add(element); } } List<String> newElements = new ArrayList<String>(); newElements.addAll(toAdd); newElements.addAll(pathElements); return StringUtils.join(newElements, separator); }
From source file:info.mikaelsvensson.devtools.common.PathUtils.java
public static String getRelativePath(File source, File target) { source = source.isDirectory() ? source : source.getParentFile(); String sourceFixed = fixPath(source); String targetFixed = fixPath(target); String[] sourceParts = StringUtils.split(sourceFixed, SEP); String[] targetParts = StringUtils.split(targetFixed, SEP); int sharedParts = 0; for (int i = 0; i < sourceParts.length; i++) { String sourcePart = sourceParts[i]; if (targetParts.length == i) { break; }/*from w ww . ja v a 2 s.c o m*/ String targetPart = targetParts[i]; if (sourcePart.equals(targetPart)) { sharedParts = i; } } String toSharedRoot = StringUtils.repeat(".." + SEP, sourceParts.length - sharedParts - 1); String fromSharedRoot = StringUtils.join(targetParts, SEP, sharedParts + 1, targetParts.length); if (StringUtils.isEmpty(toSharedRoot) && StringUtils.isEmpty(fromSharedRoot)) { return "." + SEP; } else { return toSharedRoot + fromSharedRoot; } }
From source file:com.mb.framework.util.StringUtil.java
/** * This method is used for splitting string by separator * @param str//from w ww . j av a 2s. co m * @param separator * @return */ public static String[] split(String str, String separator) { return StringUtils.split(str, separator); }
From source file:eqtlmappingpipeline.util.ModuleEqtWestraReplication.java
/** * @param args the command line arguments *//*from w w w. j a v a2 s. c o m*/ public static void main(String[] args) throws IOException, LdCalculatorException { System.out.println(HEADER); System.out.println(); System.out.flush(); //flush to make sure header is before errors try { Thread.sleep(25); //Allows flush to complete } catch (InterruptedException ex) { } CommandLineParser parser = new PosixParser(); final CommandLine commandLine; try { commandLine = parser.parse(OPTIONS, args, true); } catch (ParseException ex) { System.err.println("Invalid command line arguments: " + ex.getMessage()); System.err.println(); new HelpFormatter().printHelp(" ", OPTIONS); System.exit(1); return; } final String[] genotypesBasePaths = commandLine.getOptionValues("g"); final RandomAccessGenotypeDataReaderFormats genotypeDataType; final String replicationQtlFilePath = commandLine.getOptionValue("e"); final String interactionQtlFilePath = commandLine.getOptionValue("i"); final String outputFilePath = commandLine.getOptionValue("o"); final double ldCutoff = Double.parseDouble(commandLine.getOptionValue("ld")); final int window = Integer.parseInt(commandLine.getOptionValue("w")); System.out.println("Genotype: " + Arrays.toString(genotypesBasePaths)); System.out.println("Interaction file: " + interactionQtlFilePath); System.out.println("Replication file: " + replicationQtlFilePath); System.out.println("Output: " + outputFilePath); System.out.println("LD: " + ldCutoff); System.out.println("Window: " + window); try { if (commandLine.hasOption("G")) { genotypeDataType = RandomAccessGenotypeDataReaderFormats .valueOf(commandLine.getOptionValue("G").toUpperCase()); } else { if (genotypesBasePaths[0].endsWith(".vcf")) { System.err.println( "Only vcf.gz is supported. Please see manual on how to do create a vcf.gz file."); System.exit(1); return; } try { genotypeDataType = RandomAccessGenotypeDataReaderFormats .matchFormatToPath(genotypesBasePaths[0]); } catch (GenotypeDataException e) { System.err .println("Unable to determine input 1 type based on specified path. Please specify -G"); System.exit(1); return; } } } catch (IllegalArgumentException e) { System.err.println("Error parsing --genotypesFormat \"" + commandLine.getOptionValue("G") + "\" is not a valid input data format"); System.exit(1); return; } final RandomAccessGenotypeData genotypeData; try { genotypeData = genotypeDataType.createFilteredGenotypeData(genotypesBasePaths, 100, null, null, null, 0.8); } catch (TabixFileNotFoundException e) { LOGGER.fatal("Tabix file not found for input data at: " + e.getPath() + "\n" + "Please see README on how to create a tabix file"); System.exit(1); return; } catch (IOException e) { LOGGER.fatal("Error reading input data: " + e.getMessage(), e); System.exit(1); return; } catch (IncompatibleMultiPartGenotypeDataException e) { LOGGER.fatal("Error combining the impute genotype data files: " + e.getMessage(), e); System.exit(1); return; } catch (GenotypeDataException e) { LOGGER.fatal("Error reading input data: " + e.getMessage(), e); System.exit(1); return; } ChrPosTreeMap<ArrayList<ReplicationQtl>> replicationQtls = new ChrPosTreeMap<>(); CSVReader replicationQtlReader = new CSVReader(new FileReader(replicationQtlFilePath), '\t'); String[] replicationHeader = replicationQtlReader.readNext(); String[] replicationLine; while ((replicationLine = replicationQtlReader.readNext()) != null) { try { GeneticVariant variant = genotypeData.getSnpVariantByPos(replicationLine[REPLICATION_SNP_CHR_COL], Integer.parseInt(replicationLine[REPLICATION_SNP_POS_COL])); if (variant == null) { continue; } Alleles variantAlleles = variant.getVariantAlleles(); String[] replicationAllelesString = StringUtils.split(replicationLine[REPLICATION_ALLELES_COL], '/'); Alleles replicationAlleles = Alleles.createBasedOnString(replicationAllelesString[0], replicationAllelesString[1]); Allele assessedAlleleReplication = Allele.create(replicationLine[REPLICATION_ALLELE_ASSESSED_COL]); boolean isAmbigous = replicationAlleles.isAtOrGcSnp(); if (!variantAlleles.equals(replicationAlleles)) { if (variantAlleles.equals(replicationAlleles.getComplement())) { assessedAlleleReplication = assessedAlleleReplication.getComplement(); } else { continue; } } ReplicationQtl replicationQtl = new ReplicationQtl(replicationLine[REPLICATION_SNP_CHR_COL], Integer.parseInt(replicationLine[REPLICATION_SNP_POS_COL]), replicationLine[REPLICATION_GENE_COL], Double.parseDouble(replicationLine[REPLICATION_BETA_COL]), assessedAlleleReplication.getAlleleAsString(), replicationLine, isAmbigous); ArrayList<ReplicationQtl> posReplicationQtls = replicationQtls.get(replicationQtl.getChr(), replicationQtl.getPos()); if (posReplicationQtls == null) { posReplicationQtls = new ArrayList<>(); replicationQtls.put(replicationQtl.getChr(), replicationQtl.getPos(), posReplicationQtls); } posReplicationQtls.add(replicationQtl); } catch (Exception e) { System.out.println(Arrays.toString(replicationLine)); throw e; } } int interactionSnpNotInGenotypeData = 0; int noReplicationQtlsInWindow = 0; int noReplicationQtlsInLd = 0; int multipleReplicationQtlsInLd = 0; int replicationTopSnpNotInGenotypeData = 0; final CSVWriter outputWriter = new CSVWriter(new FileWriter(new File(outputFilePath)), '\t', '\0'); final String[] outputLine = new String[15 + EXTRA_COL_FROM_REPLICATION.length]; int c = 0; outputLine[c++] = "Chr"; outputLine[c++] = "Pos"; outputLine[c++] = "SNP"; outputLine[c++] = "Gene"; outputLine[c++] = "Module"; outputLine[c++] = "DiscoveryZ"; outputLine[c++] = "ReplicationZ"; outputLine[c++] = "DiscoveryZCorrected"; outputLine[c++] = "ReplicationZCorrected"; outputLine[c++] = "DiscoveryAlleleAssessed"; outputLine[c++] = "ReplicationAlleleAssessed"; outputLine[c++] = "bestLd"; outputLine[c++] = "bestLd_dist"; outputLine[c++] = "nextLd"; outputLine[c++] = "replicationAmbigous"; for (int i = 0; i < EXTRA_COL_FROM_REPLICATION.length; ++i) { outputLine[c++] = replicationHeader[EXTRA_COL_FROM_REPLICATION[i]]; } outputWriter.writeNext(outputLine); HashSet<String> notFound = new HashSet<>(); CSVReader interactionQtlReader = new CSVReader(new FileReader(interactionQtlFilePath), '\t'); interactionQtlReader.readNext();//skip header String[] interactionQtlLine; while ((interactionQtlLine = interactionQtlReader.readNext()) != null) { String snp = interactionQtlLine[1]; String chr = interactionQtlLine[2]; int pos = Integer.parseInt(interactionQtlLine[3]); String gene = interactionQtlLine[4]; String alleleAssessed = interactionQtlLine[9]; String module = interactionQtlLine[12]; double discoveryZ = Double.parseDouble(interactionQtlLine[10]); GeneticVariant interactionQtlVariant = genotypeData.getSnpVariantByPos(chr, pos); if (interactionQtlVariant == null) { System.err.println("Interaction QTL SNP not found in genotype data: " + chr + ":" + pos); ++interactionSnpNotInGenotypeData; continue; } ReplicationQtl bestMatch = null; double bestMatchR2 = Double.NaN; Ld bestMatchLd = null; double nextBestR2 = Double.NaN; ArrayList<ReplicationQtl> sameSnpQtls = replicationQtls.get(chr, pos); if (sameSnpQtls != null) { for (ReplicationQtl sameSnpQtl : sameSnpQtls) { if (sameSnpQtl.getGene().equals(gene)) { bestMatch = sameSnpQtl; bestMatchR2 = 1; } } } NavigableMap<Integer, ArrayList<ReplicationQtl>> potentionalReplicationQtls = replicationQtls .getChrRange(chr, pos - window, true, pos + window, true); for (ArrayList<ReplicationQtl> potentialReplicationQtls : potentionalReplicationQtls.values()) { for (ReplicationQtl potentialReplicationQtl : potentialReplicationQtls) { if (!potentialReplicationQtl.getGene().equals(gene)) { continue; } GeneticVariant potentialReplicationQtlVariant = genotypeData .getSnpVariantByPos(potentialReplicationQtl.getChr(), potentialReplicationQtl.getPos()); if (potentialReplicationQtlVariant == null) { notFound.add(potentialReplicationQtl.getChr() + ":" + potentialReplicationQtl.getPos()); ++replicationTopSnpNotInGenotypeData; continue; } Ld ld = interactionQtlVariant.calculateLd(potentialReplicationQtlVariant); double r2 = ld.getR2(); if (r2 > 1) { r2 = 1; } if (bestMatch == null) { bestMatch = potentialReplicationQtl; bestMatchR2 = r2; bestMatchLd = ld; } else if (r2 > bestMatchR2) { bestMatch = potentialReplicationQtl; nextBestR2 = bestMatchR2; bestMatchR2 = r2; bestMatchLd = ld; } } } double replicationZ = Double.NaN; double replicationZCorrected = Double.NaN; double discoveryZCorrected = Double.NaN; String replicationAlleleAssessed = null; if (bestMatch != null) { replicationZ = bestMatch.getBeta(); replicationAlleleAssessed = bestMatch.getAssessedAllele(); if (pos != bestMatch.getPos()) { String commonHap = null; double commonHapFreq = -1; for (Map.Entry<String, Double> hapFreq : bestMatchLd.getHaplotypesFreq().entrySet()) { double f = hapFreq.getValue(); if (f > commonHapFreq) { commonHapFreq = f; commonHap = hapFreq.getKey(); } } String[] commonHapAlleles = StringUtils.split(commonHap, '/'); discoveryZCorrected = commonHapAlleles[0].equals(alleleAssessed) ? discoveryZ : discoveryZ * -1; replicationZCorrected = commonHapAlleles[1].equals(replicationAlleleAssessed) ? replicationZ : replicationZ * -1; } else { discoveryZCorrected = discoveryZ; replicationZCorrected = alleleAssessed.equals(replicationAlleleAssessed) ? replicationZ : replicationZ * -1; //replicationZCorrected = alleleAssessed.equals(replicationAlleleAssessed) || alleleAssessed.equals(String.valueOf(Utils.getComplementNucleotide(replicationAlleleAssessed.charAt(0)))) ? replicationZ : replicationZ * -1; } } c = 0; outputLine[c++] = chr; outputLine[c++] = String.valueOf(pos); outputLine[c++] = snp; outputLine[c++] = gene; outputLine[c++] = module; outputLine[c++] = String.valueOf(discoveryZ); outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(replicationZ); outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(discoveryZCorrected); outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(replicationZCorrected); outputLine[c++] = alleleAssessed; outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(bestMatch.getAssessedAllele()); outputLine[c++] = String.valueOf(bestMatchR2); outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(Math.abs(pos - bestMatch.getPos())); outputLine[c++] = String.valueOf(nextBestR2); outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(bestMatch.isIsAmbigous()); if (bestMatch == null) { for (int i = 0; i < EXTRA_COL_FROM_REPLICATION.length; ++i) { outputLine[c++] = "NA"; } } else { for (int i = 0; i < EXTRA_COL_FROM_REPLICATION.length; ++i) { outputLine[c++] = bestMatch.getLine()[EXTRA_COL_FROM_REPLICATION[i]]; } } outputWriter.writeNext(outputLine); } outputWriter.close(); for (String e : notFound) { System.err.println("Not found: " + e); } System.out.println("interactionSnpNotInGenotypeData: " + interactionSnpNotInGenotypeData); System.out.println("noReplicationQtlsInWindow: " + noReplicationQtlsInWindow); System.out.println("noReplicationQtlsInLd: " + noReplicationQtlsInLd); System.out.println("multipleReplicationQtlsInLd: " + multipleReplicationQtlsInLd); System.out.println("replicationTopSnpNotInGenotypeData: " + replicationTopSnpNotInGenotypeData); }
From source file:com.deploymentio.cfnstacker.template.VelocityUtil.java
public static String joinLinesWithSingleQuote(String content) { String[] lines = StringUtils.split(content, "\r\n"); for (int i = 0; i < lines.length; i++) { lines[i] = "'" + lines[i].replace("\\\"", "\\\\\"") + "\\n'"; }/*from www. j a v a2 s .c o m*/ return StringUtils.join(lines, " +\n"); }
From source file:com.jdom.util.collections.CollectionsUtil.java
public static Set<String> asSetFromLine(String line, char separator) { List<String> list = (StringUtils.isEmpty(line)) ? Collections.<String>emptyList() : Arrays.asList(StringUtils.split(line, separator)); return new HashSet<String>(list); }
From source file:com.opensearchserver.extractor.ResourceLink.java
public static String join(String... path) { String join = StringUtils.join(path, '/'); path = StringUtils.split(join, '/'); return StringUtils.join(path, '/'); }