List of usage examples for org.apache.commons.lang ArrayUtils toPrimitive
public static boolean[] toPrimitive(Boolean[] array)
Converts an array of object Booleans to primitives.
From source file:gda.device.scannable.ScannableUtils.java
private static double[] positionToArray(String name, Object currentPositionObj, int numberOfParts) throws DeviceException { if (currentPositionObj == null || numberOfParts == 0) { return null; }/*from w w w . j a v a2 s. c om*/ Double[] objectToArray = objectToArray(currentPositionObj); if (objectToArray.length == numberOfParts) { return ArrayUtils.toPrimitive(objectToArray); } throw new DeviceException("positionToArray error (" + currentPositionObj.toString() + ") of " + name + " as array sizes inconsistent. objectToArray.length = " + Integer.toString(objectToArray.length) + ", numberOfParts = " + Integer.toString(numberOfParts)); }
From source file:be.ugent.maf.cellmissy.gui.controller.analysis.singlecell.PlateHeatMapController.java
/** * * @return/* ww w .j a v a 2s. c om*/ */ private Map<Well, Double> computeValuesMap() { Map<Well, Double> valuesMap = new LinkedHashMap<>(); TrackCoordinatesPanel trackCoordinatesPanel = trackCoordinatesController.getTrackCoordinatesPanel(); int measurement = trackCoordinatesPanel.getMeasurementComboBox().getSelectedIndex(); int aggregation = trackCoordinatesPanel.getAggregationComboBox().getSelectedIndex(); Double value = 0.0; double min = 0.0000000000000000; double max = 0.0000000000000000; List<PlateCondition> plateConditionList = trackCoordinatesController.getPlateConditionList(); for (PlateCondition condition : plateConditionList) { SingleCellConditionDataHolder conditionDataHolder = trackCoordinatesController .getConditionDataHolder(condition); List<SingleCellWellDataHolder> singleCellWellDataHolders = conditionDataHolder .getSingleCellWellDataHolders(); for (SingleCellWellDataHolder wellDataHolder : singleCellWellDataHolders) { if (!wellDataHolder.getTrackDataHolders().isEmpty()) { Well well = wellDataHolder.getWell(); switch (measurement) { case 0: // number of trajectories int nrTrack = wellDataHolder.getTrackDataHolders().size(); value = (double) nrTrack; if (value > max) { max = value; } if (value < min) { min = value; } break; case 1: // speed Double[] trackSpeedsVector = wellDataHolder.getTrackSpeedsVector(); switch (aggregation) { case 0: // mean value = AnalysisUtils.computeMean( ArrayUtils.toPrimitive(AnalysisUtils.excludeNullValues(trackSpeedsVector))); if (value > max) { max = value; } if (value < min) { min = value; } break; case 1: // median value = AnalysisUtils.computeMedian( ArrayUtils.toPrimitive(AnalysisUtils.excludeNullValues(trackSpeedsVector))); if (value > max) { max = value; } if (value < min) { min = value; } break; } break; case 3: // directionality Double[] endPointDirectionalityRatios = wellDataHolder.getEndPointDirectionalityRatios(); switch (aggregation) { case 0: // mean value = AnalysisUtils.computeMean(ArrayUtils .toPrimitive(AnalysisUtils.excludeNullValues(endPointDirectionalityRatios))); if (value > max) { max = value; } if (value < min) { min = value; } break; case 1: // median value = AnalysisUtils.computeMedian(ArrayUtils .toPrimitive(AnalysisUtils.excludeNullValues(endPointDirectionalityRatios))); if (value > max) { max = value; } if (value < min) { min = value; } break; } break; } valuesMap.put(well, value); } } } heatMapPlatePanel.setMin(min); heatMapPlatePanel.setMax(max); return valuesMap; }
From source file:com.opengamma.analytics.financial.interestrate.swap.method.SwapCalculatorTest.java
@Test public void parSpreadCurveSensitivityFixedIborBeforeFirstFixing() { final ZonedDateTime referenceDate = DateUtils.getUTCDate(2012, 5, 14); final SwapFixedCoupon<Coupon> swap = SWAP_FIXED_IBOR_DEFINITION.toDerivative(referenceDate, CURVE_NAMES); final String fwdCurveName = ((CouponIbor) swap.getSecondLeg().getNthPayment(0)).getForwardCurveName(); InterestRateCurveSensitivity pscsComputed = swap.accept(PSCSC, CURVES); pscsComputed = pscsComputed.cleaned(); final double[] timesDsc = new double[swap.getSecondLeg().getNumberOfPayments()]; for (int loopcpn = 0; loopcpn < swap.getSecondLeg().getNumberOfPayments(); loopcpn++) { timesDsc[loopcpn] = swap.getSecondLeg().getNthPayment(loopcpn).getPaymentTime(); }/*from ww w. j ava 2 s . c o m*/ final List<DoublesPair> sensiDscFD = FDCurveSensitivityCalculator.curveSensitvityFDCalculator(swap, PSC, CURVES, swap.getFirstLeg().getDiscountCurve(), timesDsc, 1.0E-10); final List<DoublesPair> sensiDscComputed = pscsComputed.getSensitivities() .get(swap.getFirstLeg().getDiscountCurve()); assertTrue("parSpread: curve sensitivity - dsc", InterestRateCurveSensitivityUtils.compare(sensiDscFD, sensiDscComputed, TOLERANCE_SPREAD_DELTA)); final Set<Double> timesFwdSet = new TreeSet<>(); for (int loopcpn = 0; loopcpn < swap.getSecondLeg().getNumberOfPayments(); loopcpn++) { timesFwdSet.add(((CouponIbor) swap.getSecondLeg().getNthPayment(loopcpn)).getFixingPeriodStartTime()); timesFwdSet.add(((CouponIbor) swap.getSecondLeg().getNthPayment(loopcpn)).getFixingPeriodEndTime()); } final Double[] timesFwd = timesFwdSet.toArray(new Double[timesFwdSet.size()]); final List<DoublesPair> sensiFwdFD = FDCurveSensitivityCalculator.curveSensitvityFDCalculator(swap, PSC, CURVES, fwdCurveName, ArrayUtils.toPrimitive(timesFwd), 1.0E-10); final List<DoublesPair> sensiFwdComputed = pscsComputed.getSensitivities().get(fwdCurveName); assertTrue("parSpread: curve sensitivity - fwd", InterestRateCurveSensitivityUtils.compare(sensiFwdFD, sensiFwdComputed, TOLERANCE_SPREAD_DELTA)); }
From source file:aldenjava.opticalmapping.data.data.OptMapDataReader.java
private DataNode parseBNX() throws IOException { // Currently unused information, Only support one (single-color) channel // int labelChannel; // double avgIntensity; // double snr; // int noOfLables; // String originalMoleculeID; // int scanNumber; // int scanDirection; // String chipID; // int flowCell; // int runID; // int globalScanNumber; // BNX File Version 1.0 // #0h LabelChannel MoleculeId Length AvgIntensity SNR NumberofLabels OriginalMoleculeId ScanNumber ScanDirection ChipId Flowcell // #0f int int float float float int int int int string int // #1h LabelChannel LabelPositions[N] // #1f int float // #2h LabelChannel LabelPositions[N] // #2h int float // #Qh QualityScoreID QualityScores[N] // #Qf str float // BNX File Version 1.2 // #0h LabelChannel MoleculeId Length AvgIntensity SNR NumberofLabels OriginalMoleculeId ScanNumber ScanDirection ChipId Flowcell RunId GlobalScanNumber // #0f int int float float float int int int int string int int int // #1h LabelChannel LabelPositions[N] // #1f int float // #2h LabelChannel LabelPositions[N] // #2h int float // #Qh QualityScoreID QualityScores[N] // #Qf str float String name = ""; long size = -1; double[] snr = null; double[] intensity = null; long[] refp = null; boolean gotNameSizeInfo = false; boolean gotDetailInfo = false; boolean gotSNRInfo = false; boolean gotIntensityInfo = false; do {/* w w w .j av a2s . c o m*/ String s = this.nextline.trim(); String[] l = s.split("\t"); switch (l[0]) { case "0": name = l[1]; size = (long) Double.parseDouble(l[2]); gotNameSizeInfo = true; break; case "1": refp = new long[l.length - 2]; // last element should be the size of molecule for (int i = 1; i < l.length - 1; i++) refp[i - 1] = (long) Double.parseDouble(l[i]); gotDetailInfo = true; break; case "QX01": case "QX11": snr = new double[l.length - 1]; for (int i = 1; i < l.length; i++) snr[i - 1] = Double.parseDouble(l[i]); gotSNRInfo = true; break; case "QX02": case "QX12": intensity = new double[l.length - 1]; for (int i = 1; i < l.length; i++) intensity[i - 1] = Double.parseDouble(l[i]); gotIntensityInfo = true; break; default: } proceedNextLine(); } while ((this.nextline != null) && (this.nextline.startsWith("1") || this.nextline.startsWith("QX01") || this.nextline.startsWith("QX02") || this.nextline.startsWith("QX11") || this.nextline.startsWith("QX12"))); if (gotNameSizeInfo && gotDetailInfo && gotSNRInfo && gotIntensityInfo) { List<Long> refpList = new ArrayList<Long>(); for (int i = 0; i < refp.length; i++) if (snr[i] >= bnxSNR) refpList.add(refp[i]); refp = ArrayUtils.toPrimitive(refpList.toArray(new Long[refpList.size()])); BnxDataNode data = new BnxDataNode(name, size, refp, intensity, snr); return data; } else { System.err.println("Warning: incomplete record is found."); return null; } }
From source file:com.ironiacorp.statistics.r.AbstractRClient.java
@Override
@SuppressWarnings({ "unchecked", "cast" })
public LinearModelSummary linearModel(double[] data, Map<String, List<?>> factors) {
String datName = RandomStringUtils.randomAlphabetic(10);
assign(datName, data);//ww w .ja v a 2 s .c o m
for (String factorName : factors.keySet()) {
List<?> list = factors.get(factorName);
if (list.iterator().next() instanceof String) {
assignFactor(factorName, (List<String>) list);
} else {
// treat is as a numeric covariate
List<Double> d = new ArrayList<Double>();
for (Object object : list) {
d.add((Double) object);
}
assign(factorName, ArrayUtils.toPrimitive(d.toArray(new Double[] {})));
}
}
String modelDeclaration = datName + " ~ " + StringUtils.join(factors.keySet(), "+");
String lmName = RandomStringUtils.randomAlphabetic(10);
String command = lmName + "<-lm(" + modelDeclaration + ", na.action=na.exclude)";
voidEval(command);
REXP lmsum = eval("summary(" + lmName + ")");
REXP anova = eval("anova(" + lmName + ")");
return new LinearModelSummary(lmsum, anova, factors.keySet().toArray(new String[] {}));
}
From source file:it.iit.genomics.cru.structures.business.StructureMapper.java
private int[] getPdbPositions(String structureId, Chain chain, AAPosition search, MoleculeEntry protein) { ArrayList<Integer> positions = new ArrayList<>(); // Align the region to the chain SmithWaterman nw;// w ww . ja v a2 s. co m nw = new SmithWaterman(search.getGene().getUniprotSequence().getSequence(), chain.getAtomSequence()); String regionAlignedSequence = nw.getAlignmentSeqA(); String chainAlignedSequence = nw.getAlignmentSeqB(); int groupPosition = 0; // go to the first AA of the group, skiping non AA for (int chainAAindex = 0; chainAAindex < nw.getStartAlignmentB(); chainAAindex++) { Group group = chain.getAtomGroup(groupPosition); if (false == GroupType.AMINOACID.equals(group.getType())) { chainAAindex++; } groupPosition++; } int uniprotCursor = nw.getStartAlignmentA(); for (int aaPosition = 0; aaPosition < regionAlignedSequence.length(); aaPosition++) { char uniprotAA = regionAlignedSequence.charAt(aaPosition); char pdbAA = chainAlignedSequence.charAt(aaPosition); if ('-' == pdbAA) { uniprotCursor++; continue; } Group group = chain.getAtomGroup(groupPosition); groupPosition++; if (GroupType.AMINOACID.equals(group.getType())) { Integer pos = group.getResidueNumber().getSeqNum(); if ('-' == uniprotAA) { logger.warn("Position not aligned to uniprot: {0} {1} {2}", new Object[] { structureId, chain.getChainID(), pos }); } else if (uniprotCursor >= search.getStart() - 1 && uniprotCursor <= search.getEnd() - 1) { // Add residue positions.add(pos); int uniprotPos = uniprotCursor + 1; search.addPdbToProtein(structureId, pos, chain.getChainID(), new UniprotPosition(uniprotPos)); } } if ('-' != uniprotAA) { uniprotCursor++; } } return ArrayUtils.toPrimitive(positions.toArray(new Integer[positions.size()])); }
From source file:com.opengamma.analytics.financial.provider.curve.InflationBuildingCurveWithDiscountTestEUR.java
@Test(enabled = false) public void comparison1Unit2Units() { final InflationProviderDiscount[] units = new InflationProviderDiscount[2]; final CurveBuildingBlockBundle[] bb = new CurveBuildingBlockBundle[2]; final YieldAndDiscountCurve[] curveDsc = new YieldAndDiscountCurve[2]; final PriceIndexCurve[] curveInflation = new PriceIndexCurve[2]; for (int loopblock = 0; loopblock < 2; loopblock++) { units[loopblock] = CURVES_PAR_SPREAD_MQ_WITHOUT_TODAY_BLOCK.get(loopblock).getFirst(); bb[loopblock] = CURVES_PAR_SPREAD_MQ_WITHOUT_TODAY_BLOCK.get(loopblock).getSecond(); curveDsc[loopblock] = units[loopblock].getCurve(USD); curveInflation[loopblock] = units[loopblock].getCurve(US_CPI); }/*ww w. ja v a2 s .c o m*/ assertEquals("Curve construction: 1 unit / 3 units ", curveDsc[0].getNumberOfParameters(), curveDsc[1].getNumberOfParameters()); assertEquals("Curve construction: 1 unit / 3 units ", curveInflation[0].getNumberOfParameters(), curveInflation[1].getNumberOfParameters()); assertArrayEquals("Curve construction: 1 unit / 3 units ", ArrayUtils.toPrimitive(((YieldCurve) curveDsc[0]).getCurve().getXData()), ArrayUtils.toPrimitive(((YieldCurve) curveDsc[1]).getCurve().getXData()), TOLERANCE_CAL); assertArrayEquals("Curve construction: 1 unit / 3 units ", ArrayUtils.toPrimitive(((YieldCurve) curveDsc[0]).getCurve().getYData()), ArrayUtils.toPrimitive(((YieldCurve) curveDsc[1]).getCurve().getYData()), TOLERANCE_CAL); assertArrayEquals("Curve construction: 1 unit / 3 units ", ArrayUtils.toPrimitive(curveInflation[0].getCurve().getXData()), ArrayUtils.toPrimitive(curveInflation[1].getCurve().getXData()), TOLERANCE_CAL); assertArrayEquals("Curve construction: 1 unit / 3 units ", ArrayUtils.toPrimitive(curveInflation[0].getCurve().getYData()), ArrayUtils.toPrimitive(curveInflation[1].getCurve().getYData()), TOLERANCE_CAL); }
From source file:com.opengamma.analytics.financial.provider.curve.MulticurveBuildingDiscountingDiscountUSD2Test.java
@Test public void comparison1Unit2Units() { final MulticurveProviderDiscount[] units = new MulticurveProviderDiscount[2]; final CurveBuildingBlockBundle[] bb = new CurveBuildingBlockBundle[2]; final YieldAndDiscountCurve[] curveDsc = new YieldAndDiscountCurve[2]; final YieldAndDiscountCurve[] curveFwd = new YieldAndDiscountCurve[2]; for (int loopblock = 0; loopblock < 2; loopblock++) { units[loopblock] = CURVES_PAR_SPREAD_MQ_WITHOUT_TODAY_BLOCK.get(loopblock).getFirst(); bb[loopblock] = CURVES_PAR_SPREAD_MQ_WITHOUT_TODAY_BLOCK.get(loopblock).getSecond(); curveDsc[loopblock] = units[loopblock].getCurve(USD); curveFwd[loopblock] = units[loopblock].getCurve(USDLIBOR3M); }/* w ww .j a va 2s . c o m*/ assertEquals("Curve construction: 1 unit / 2 units ", curveDsc[0].getNumberOfParameters(), curveDsc[1].getNumberOfParameters()); assertEquals("Curve construction: 1 unit / 2 units ", curveFwd[0].getNumberOfParameters(), curveFwd[1].getNumberOfParameters()); assertArrayEquals("Curve construction: 1 unit / 2 units ", ArrayUtils.toPrimitive(((YieldCurve) curveDsc[0]).getCurve().getXData()), ArrayUtils.toPrimitive(((YieldCurve) curveDsc[1]).getCurve().getXData()), TOLERANCE_CAL); assertArrayEquals("Curve construction: 1 unit / 2 units ", ArrayUtils.toPrimitive(((YieldCurve) curveDsc[0]).getCurve().getYData()), ArrayUtils.toPrimitive(((YieldCurve) curveDsc[1]).getCurve().getYData()), TOLERANCE_CAL); assertArrayEquals("Curve construction: 1 unit / 2 units ", ArrayUtils.toPrimitive(((YieldCurve) curveFwd[0]).getCurve().getXData()), ArrayUtils.toPrimitive(((YieldCurve) curveFwd[1]).getCurve().getXData()), TOLERANCE_CAL); assertArrayEquals("Curve construction: 1 unit / 2 units ", ArrayUtils.toPrimitive(((YieldCurve) curveFwd[0]).getCurve().getYData()), ArrayUtils.toPrimitive(((YieldCurve) curveFwd[1]).getCurve().getYData()), TOLERANCE_CAL); assertEquals("Curve construction: 1 unit / 2 units ", bb[0].getBlock(CURVE_NAME_FWD3_USD).getFirst(), bb[1].getBlock(CURVE_NAME_FWD3_USD).getFirst()); // Test note: the discounting curve building blocks are not the same; in one case both curves are build together in the other one after the other. final int nbLineDsc = bb[0].getBlock(CURVE_NAME_DSC_USD).getSecond().getNumberOfRows(); final int nbLineFwd = bb[0].getBlock(CURVE_NAME_FWD3_USD).getSecond().getNumberOfRows(); assertEquals("Curve construction: 1 unit / 2 units ", bb[1].getBlock(CURVE_NAME_DSC_USD).getSecond().getNumberOfRows(), nbLineDsc); assertEquals("Curve construction: 1 unit / 2 units ", bb[1].getBlock(CURVE_NAME_FWD3_USD).getSecond().getNumberOfRows(), nbLineFwd); for (int loopline = 0; loopline < nbLineFwd; loopline++) { assertArrayEquals("Curve construction: 1 unit / 2 units ", bb[0].getBlock(CURVE_NAME_FWD3_USD).getSecond().getRowVector(loopline).getData(), bb[1].getBlock(CURVE_NAME_FWD3_USD).getSecond().getRowVector(loopline).getData(), TOLERANCE_CAL); for (int loopcol = 0; loopcol < nbLineDsc; loopcol++) { // Test rely on dsc being first assertEquals("Curve construction: 1 unit / 2 units ", bb[0].getBlock(CURVE_NAME_FWD3_USD).getSecond().getRowVector(loopline).getData()[loopcol], bb[1].getBlock(CURVE_NAME_FWD3_USD).getSecond().getRowVector(loopline).getData()[loopcol], TOLERANCE_CAL); } for (int loopcol = 0; loopcol < nbLineFwd - nbLineDsc; loopcol++) { // Test rely on dsc being first assertEquals("Curve construction: 1 unit / 2 units ", 0, bb[1].getBlock(CURVE_NAME_FWD3_USD) .getSecond().getRowVector(loopline).getData()[loopcol + nbLineDsc], TOLERANCE_CAL); } } }
From source file:com.stoxx.service.business.registration.RegistrationServiceImpl.java
public User saveUserToLiferayDB(UserProfileDetails userProfileDetails, ThemeDisplay themeDisplay, ServiceContext serviceContext) throws STOXXException { try {/*from w w w. j ava2 s . c o m*/ Group stoxxNetgroup = GroupLocalServiceUtil.getGroup(themeDisplay.getCompanyId(), STOXXConstants.STOXXNET_SITE_NAME); Group stoxxgroup = GroupLocalServiceUtil.getGroup(themeDisplay.getCompanyId(), STOXXConstants.STOXX_SITE_NAME); User adminDefaultUser = UserLocalServiceUtil.getDefaultUser(themeDisplay.getCompanyId()); logger.info("the ****************************>default user id is " + adminDefaultUser.getUserId() + EMAIL_ADDRESS_IS + adminDefaultUser.getEmailAddresses()); long[] groupIds = null; if (userProfileDetails.getUserType().equalsIgnoreCase(STOXXConstants.STOXX_VENDOR_USER)) { groupIds = new long[] { stoxxNetgroup.getGroupId() }; } else if (userProfileDetails.getUserType().equalsIgnoreCase(STOXXConstants.STOXX_GENERAL_USER) || userProfileDetails.getUserType().equalsIgnoreCase(STOXXConstants.STOXX_REGISTERED_USER)) { groupIds = new long[] { stoxxgroup.getGroupId() }; } else if (userProfileDetails.getUserType().equalsIgnoreCase(STOXXConstants.STOXX_STAFF_USER)) { groupIds = new long[] { stoxxNetgroup.getGroupId(), stoxxgroup.getGroupId() }; } User user = null; if (!(userProfileDetails.getUserType().equalsIgnoreCase(STOXXConstants.STOXX_VENDOR_USER))) { if (userProfileDetails.getUserType().equalsIgnoreCase(STOXXConstants.STOXX_REGISTERED_USER)) { if (null != userProfileDetails.getSalesEntryId()) { List<Long> roleList = new ArrayList<Long>(); Long salesEntryID = userProfileDetails.getSalesEntryId(); SalesEntry salesEntry = SalesEntryLocalServiceUtil.getSalesEntry(salesEntryID); if (!(salesEntry.getPackageNames().contains(StringPool.COMMA))) { Role packageRole = RoleLocalServiceUtil.getRole(themeDisplay.getCompanyId(), salesEntry.getPackageNames().trim()); long packageRoleId = packageRole.getRoleId(); roleList.add(packageRoleId); } else { for (String packageName : salesEntry.getPackageNames().split(StringPool.COMMA)) { Role packageRole = RoleLocalServiceUtil.getRole(themeDisplay.getCompanyId(), packageName.trim()); long packageRoleId = packageRole.getRoleId(); roleList.add(packageRoleId); } } if (StringUtils.isNotBlank(salesEntry.getKeyEmailAddress()) && salesEntry.getKeyEmailAddress().trim() .equalsIgnoreCase(userProfileDetails.getEmailAddress())) { if (isLicensedUser(userProfileDetails.getEmailAddress())) { Role keyAccntHolderUserRole = RoleLocalServiceUtil.getRole( themeDisplay.getCompanyId(), STOXXConstants.STOXX_KEY_ACCOUNT_HOLDER_ROLE); long roleKeyAccntHolder = keyAccntHolderUserRole.getRoleId(); roleList.add(roleKeyAccntHolder); } } long roleLicensed[] = ArrayUtils.toPrimitive(roleList.toArray(new Long[roleList.size()])); user = UserLocalServiceUtil.addUser(adminDefaultUser.getUserId(), themeDisplay.getCompanyId(), false, userProfileDetails.getPassword(), userProfileDetails.getPassword(), true, StringPool.BLANK, userProfileDetails.getEmailAddress(), 0, StringPool.BLANK, themeDisplay.getLocale(), userProfileDetails.getFirstName(), StringPool.BLANK, userProfileDetails.getLastName(), userProfileDetails.getPrefixId(), 0, userProfileDetails.isGender(), userProfileDetails.getBirthMonth(), userProfileDetails.getBirthDay(), userProfileDetails.getBirthYear(), userProfileDetails.getJobTitle(), groupIds, null, roleLicensed, null, false, serviceContext); } } else { user = UserLocalServiceUtil.addUser(adminDefaultUser.getUserId(), themeDisplay.getCompanyId(), false, userProfileDetails.getPassword(), userProfileDetails.getPassword(), true, StringPool.BLANK, userProfileDetails.getEmailAddress(), 0, StringPool.BLANK, themeDisplay.getLocale(), userProfileDetails.getFirstName(), StringPool.BLANK, userProfileDetails.getLastName(), userProfileDetails.getPrefixId(), 0, userProfileDetails.isGender(), userProfileDetails.getBirthMonth(), userProfileDetails.getBirthDay(), userProfileDetails.getBirthYear(), userProfileDetails.getJobTitle(), groupIds, null, null, null, false, serviceContext); } } Role powerUserRole = RoleLocalServiceUtil.getRole(themeDisplay.getCompanyId(), RoleConstants.POWER_USER); if (Validator.isNotNull(powerUserRole)) { long rolePower[] = { powerUserRole.getRoleId() }; if (Validator.isNotNull(user) && rolePower.length > 0) { RoleLocalServiceUtil.unsetUserRoles(user.getUserId(), rolePower); } } return user; } catch (PortalException e) { logger.error(e.getMessage(), e); throw new STOXXException(e.getMessage(), e); } catch (SystemException e) { logger.error(e.getMessage(), e); throw new STOXXException(e.getMessage(), e); } }
From source file:aldenjava.opticalmapping.data.data.OptMapDataReader.java
private DataNode parseXML() throws IOException { List<Long> reflList = null; long[] refl = null; String id = null;/* w w w. ja v a2 s . c o m*/ try { while (xmlReader.hasNext()) { int event = xmlReader.next(); switch (event) { case XMLEvent.START_ELEMENT: switch (xmlReader.getLocalName()) { case "RESTRICTION_MAP": ; id = xmlReader.getAttributeValue("", "ID"); break; case "FRAGMENTS": reflList = new ArrayList<Long>(); break; case "F": reflList.add(Long.parseLong(xmlReader.getAttributeValue("", "S"))); break; } break; case XMLEvent.END_ELEMENT: switch (xmlReader.getLocalName()) { case "RESTRICTION_MAP": ; return new DataNode(id, refl); case "FRAGMENTS": refl = ArrayUtils.toPrimitive(reflList.toArray(new Long[reflList.size()])); break; case "F": // Nothing to do break; } break; case XMLEvent.START_DOCUMENT: break; case XMLEvent.END_DOCUMENT: return null; } } } catch (XMLStreamException e) { throw new IOException("XML parse exception"); } return null; }