diff --git a/api-src/org/labkey/api/targetedms/SkylineAnnotation.java b/api-src/org/labkey/api/targetedms/SkylineAnnotation.java index 16192137f..a0471c3c4 100644 --- a/api-src/org/labkey/api/targetedms/SkylineAnnotation.java +++ b/api-src/org/labkey/api/targetedms/SkylineAnnotation.java @@ -15,10 +15,6 @@ */ package org.labkey.api.targetedms; -import org.labkey.api.data.Container; - -import java.util.Date; - /** * User: vsharma * Date: 8/26/2015 @@ -26,6 +22,6 @@ */ public interface SkylineAnnotation { - public String getName(); - public String getValue(); + String getName(); + String getValue(); } diff --git a/api-src/org/labkey/api/targetedms/TargetedMSService.java b/api-src/org/labkey/api/targetedms/TargetedMSService.java index 50319d210..cc9cc995e 100644 --- a/api-src/org/labkey/api/targetedms/TargetedMSService.java +++ b/api-src/org/labkey/api/targetedms/TargetedMSService.java @@ -143,9 +143,6 @@ enum FolderType /** * Returns the name of a chromatogram library file according to the naming pattern used for creating * .clib files for a specific revision number in a given container. - * @param container - * @param revision - * @return */ String getChromLibFileName(@NotNull Container container, int revision); @@ -153,16 +150,12 @@ enum FolderType * Returns the revision number from the file name if the given file name matches the chromatogram library * naming pattern. Example: chromlib_314_rev5.clib; revision number is 5. * Returns null if the given file name does not match the expected pattern. - * @param chromLibFileName - * @return */ @Nullable Integer parseChromLibRevision(@NotNull String chromLibFileName); /** * - * @param sampleFileId - * @param container container that has the Skyline document that the sample file belongs to. * @return the replicate name associated with the given sampleFileId. Returns null if a database row with the given * sampleFileId does not exist, or if the Skyline document with the sample file is not in the given container. */ diff --git a/src/org/labkey/panoramapremium/PanoramaPremiumController.java b/src/org/labkey/panoramapremium/PanoramaPremiumController.java index 2b04b4191..019beac1a 100644 --- a/src/org/labkey/panoramapremium/PanoramaPremiumController.java +++ b/src/org/labkey/panoramapremium/PanoramaPremiumController.java @@ -118,7 +118,7 @@ else if(isMolecule) //skip selected precursors that are already excluded selectedRowsKeys.forEach(id -> { - List prec = precursorsList.stream().filter(p -> p.getId() == id).collect(Collectors.toList()); + List prec = precursorsList.stream().filter(p -> p.getId() == id).toList(); ExcludedPrecursor precursor = prec.get(0); precursor.setIsPeptide(isPeptide); diff --git a/src/org/labkey/panoramapremium/View/QCSummaryMenuCustomizer.java b/src/org/labkey/panoramapremium/View/QCSummaryMenuCustomizer.java index 7ce276a3a..9c135e1ff 100644 --- a/src/org/labkey/panoramapremium/View/QCSummaryMenuCustomizer.java +++ b/src/org/labkey/panoramapremium/View/QCSummaryMenuCustomizer.java @@ -13,8 +13,8 @@ public class QCSummaryMenuCustomizer implements NavTreeCustomizer { - private @NotNull String actionName; - private @NotNull String menuLabel; + private final @NotNull String actionName; + private final @NotNull String menuLabel; public QCSummaryMenuCustomizer(@NotNull String actionName, @NotNull String menuLabel) { diff --git a/src/org/labkey/targetedms/IrtPeptide.java b/src/org/labkey/targetedms/IrtPeptide.java index 5d8569224..f53aae040 100644 --- a/src/org/labkey/targetedms/IrtPeptide.java +++ b/src/org/labkey/targetedms/IrtPeptide.java @@ -113,7 +113,6 @@ public void setGeneralMoleculeId(Long generalMoleculeId) /** * Include a new import value in the weighted average iRT value for the peptide sequence. - * @param newObservation */ public void reweighValue(double newObservation) { diff --git a/src/org/labkey/targetedms/SkylineAuditLogManager.java b/src/org/labkey/targetedms/SkylineAuditLogManager.java index 6afc17043..a3d9077f7 100644 --- a/src/org/labkey/targetedms/SkylineAuditLogManager.java +++ b/src/org/labkey/targetedms/SkylineAuditLogManager.java @@ -392,7 +392,7 @@ public void deleteDocumentVersionLog(long pRunId) throws AuditLogException { SimpleFilter runAuditLogFilter = new SimpleFilter(FieldKey.fromParts("VersionId"), pRunId); - if (deleteEntryIds.size() > 0) + if (!deleteEntryIds.isEmpty()) { SimpleFilter entryFilter = new SimpleFilter( new SimpleFilter.InClause(FieldKey.fromParts("entryId"), deleteEntryIds, false) diff --git a/src/org/labkey/targetedms/SkylinePort/Irt/IRetentionScoreCalculator.java b/src/org/labkey/targetedms/SkylinePort/Irt/IRetentionScoreCalculator.java index ae788acb8..1a40721ce 100644 --- a/src/org/labkey/targetedms/SkylinePort/Irt/IRetentionScoreCalculator.java +++ b/src/org/labkey/targetedms/SkylinePort/Irt/IRetentionScoreCalculator.java @@ -28,7 +28,7 @@ public interface IRetentionScoreCalculator { - public String getName(); + String getName(); Double ScoreSequence(String modifiedSequence); diff --git a/src/org/labkey/targetedms/SkylinePort/Irt/IrtRegressionCalculator.java b/src/org/labkey/targetedms/SkylinePort/Irt/IrtRegressionCalculator.java index a40dcab9f..f5cd223ba 100644 --- a/src/org/labkey/targetedms/SkylinePort/Irt/IrtRegressionCalculator.java +++ b/src/org/labkey/targetedms/SkylinePort/Irt/IrtRegressionCalculator.java @@ -98,14 +98,14 @@ public static RegressionLine calcRegressionLine(IRetentionTimeProvider retention } } - if (existingPeptideList.size() > 0) + if (!existingPeptideList.isEmpty()) { pipelineLog.info("Attempting to calculate iRT regression line from shared peptides."); // Attempt to get a regression based on shared peptides CurrentCalculator calculator = new CurrentCalculator(standardPeptideList, existingPeptideList); ArrayList peptidesTimes = retentionTimes.getPeptideRetentionTimes(); //var peptidesTimes = retentionTimes.getPeptideRetentionTimes().toArray(); - RetentionTimeRegression regression = RetentionTimeRegression.FindThreshold(MIN_IRT_TO_TIME_CORRELATION, RetentionTimeRegression.getThresholdPrecision(), peptidesTimes, new ArrayList(), peptidesTimes, calculator, false); + RetentionTimeRegression regression = RetentionTimeRegression.FindThreshold(MIN_IRT_TO_TIME_CORRELATION, RetentionTimeRegression.getThresholdPrecision(), peptidesTimes, new ArrayList<>(), peptidesTimes, calculator, false); if (regression != null && regression.getPeptideTimes().size() >= MIN_IRT_TO_TIME_POINT_COUNT) { @@ -142,10 +142,10 @@ private static Statistics GetTrial(ArrayList listValues, int i, RefObjec private final static class CurrentCalculator extends RetentionScoreCalculatorSpec { - private LinkedHashMap _dictStandards = new LinkedHashMap<>(); - private LinkedHashMap _dictLibrary = new LinkedHashMap<>(); + private final LinkedHashMap _dictStandards = new LinkedHashMap<>(); + private final LinkedHashMap _dictLibrary = new LinkedHashMap<>(); - private double _unknownScore; + private final double _unknownScore; public CurrentCalculator(Iterable standardPeptides, Iterable libraryPeptides) { diff --git a/src/org/labkey/targetedms/SkylinePort/Irt/RegressionLine.java b/src/org/labkey/targetedms/SkylinePort/Irt/RegressionLine.java index 55fa701d3..9fb176fec 100644 --- a/src/org/labkey/targetedms/SkylinePort/Irt/RegressionLine.java +++ b/src/org/labkey/targetedms/SkylinePort/Irt/RegressionLine.java @@ -80,8 +80,7 @@ private void setIntercept(double value) for a given x. @param x Value in x dimension - @return - */ + */ @Override public double GetY(double x) { @@ -93,8 +92,7 @@ public double GetY(double x) for a given y. @param y Value in y dimension - @return - */ + */ public double GetX(double y) { return (y - getIntercept()) / getSlope(); diff --git a/src/org/labkey/targetedms/SkylinePort/Irt/RegressionLineElement.java b/src/org/labkey/targetedms/SkylinePort/Irt/RegressionLineElement.java index 85e156629..e685b97d2 100644 --- a/src/org/labkey/targetedms/SkylinePort/Irt/RegressionLineElement.java +++ b/src/org/labkey/targetedms/SkylinePort/Irt/RegressionLineElement.java @@ -32,7 +32,7 @@ */ public final class RegressionLineElement implements IRegressionFunction { - private RegressionLine _regressionLine; + private final RegressionLine _regressionLine; public RegressionLine getRegressionLine() { diff --git a/src/org/labkey/targetedms/SkylinePort/Irt/RetentionTimeRegression.java b/src/org/labkey/targetedms/SkylinePort/Irt/RetentionTimeRegression.java index 65e64da56..01d410bf8 100644 --- a/src/org/labkey/targetedms/SkylinePort/Irt/RetentionTimeRegression.java +++ b/src/org/labkey/targetedms/SkylinePort/Irt/RetentionTimeRegression.java @@ -306,10 +306,10 @@ private static Double GetRetentionTime(double score, IRegressionFunction convers */ public RetentionTimeStatistics CalcStatistics(ArrayList peptidesTimes, java.util.Map scoreCache) { - java.util.ArrayList listPeptides = new java.util.ArrayList(); - java.util.ArrayList listHydroScores = new java.util.ArrayList(); - java.util.ArrayList listPredictions = new java.util.ArrayList(); - java.util.ArrayList listRetentionTimes = new java.util.ArrayList(); + java.util.ArrayList listPeptides = new java.util.ArrayList<>(); + java.util.ArrayList listHydroScores = new java.util.ArrayList<>(); + java.util.ArrayList listPredictions = new java.util.ArrayList<>(); + java.util.ArrayList listRetentionTimes = new java.util.ArrayList<>(); boolean usableCalc = getCalculator().IsUsable(); @@ -500,7 +500,7 @@ public static RetentionTimeRegression CalcRegression(String name, ArrayList tempRef_s = new RefObject<>(s); RetentionTimeRegression tempVar = CalcRegression(name, calculators, measuredPeptides, null, false, statistics, tempRef_s); - s = tempRef_s.get(); + tempRef_s.get(); return tempVar; } @@ -514,8 +514,7 @@ This function chooses the best calculator (by r value) and returns a regression @param allPeptides If true, do not let the calculator pick which peptides to use in the regression @param statistics Statistics from the regression of the best calculator @param calculatorSpec The best calculator - @return - */ + */ public static RetentionTimeRegression CalcRegression(String name, ArrayList calculators, ArrayList measuredPeptides, RetentionTimeScoreCache scoreCache, boolean allPeptides, RefObject statistics, RefObject calculatorSpec) { // Get a list of peptide names for use by the calculators to choose their regression peptides @@ -545,7 +544,7 @@ public static RetentionTimeRegression CalcRegression(String name, ArrayList> listRTs = new ArrayList<>(calcs); - LinkedHashMap dictMeasuredPeptides = new LinkedHashMap(); + LinkedHashMap dictMeasuredPeptides = new LinkedHashMap<>(); for (MeasuredRetentionTime measured : measuredPeptides) { @@ -575,7 +574,7 @@ public static RetentionTimeRegression CalcRegression(String name, ArrayList()); + listRTs.set(i, new ArrayList<>()); calcPeptides.set(i, allPeptides ? listPeptides : calc.ChooseRegressionPeptides(listPeptides)); peptideScoresByCalc.set(i, RetentionTimeScoreCache.CalcScores(calc, calcPeptides.get(i), scoreCache)); } @@ -714,8 +713,8 @@ public static RetentionTimeRegression FindThreshold(double threshold, Integer pr RefObject tempRef_statisticsRefined = new RefObject<>(statisticsRefined); RefObject> tempRef_outIndexes = new RefObject<>(outIndexes); RetentionTimeRegression tempVar = regressionInitial.FindThreshold(threshold, precision, 0, measuredPeptides.size(), standardPeptides, variablePeptides, statisticsAll, calculator, scoreCache, isCanceled, tempRef_statisticsRefined, tempRef_outIndexes); - statisticsRefined = tempRef_statisticsRefined.get(); // TPG: TODO Proper handling of the ref conversion - outIndexes = tempRef_outIndexes.get(); + tempRef_statisticsRefined.get(); + tempRef_outIndexes.get(); return tempVar; } @@ -840,7 +839,7 @@ else if (!outIndexes.get().contains(i) && iNextStat < listPredictions.size()) Collections.sort(listDeltas); // Remove points with the highest deltas above mid - outIndexes.set(new LinkedHashSet()); + outIndexes.set(new LinkedHashSet<>()); int countOut = variablePeptides.size() - mid - 1; for (int i = 0; i < countOut; i++) { @@ -859,9 +858,9 @@ else if (!outIndexes.get().contains(i) && iNextStat < listPredictions.size()) peptidesTimesTry.addAll(requiredPeptides); RetentionScoreCalculatorSpec s = null; - RefObject tempRef_s = new RefObject(s); + RefObject tempRef_s = new RefObject<>(s); RetentionTimeRegression tempVar = CalcRegression(getName(), Lists.newArrayList(calculator), peptidesTimesTry, scoreCache, true, statisticsResult, tempRef_s); - s = tempRef_s.get(); // TPG TODO: By ref handled correctly? + tempRef_s.get(); return tempVar; } diff --git a/src/org/labkey/targetedms/SkylinePort/Irt/RetentionTimeScoreCache.java b/src/org/labkey/targetedms/SkylinePort/Irt/RetentionTimeScoreCache.java index 0307fc326..eabfd53e5 100644 --- a/src/org/labkey/targetedms/SkylinePort/Irt/RetentionTimeScoreCache.java +++ b/src/org/labkey/targetedms/SkylinePort/Irt/RetentionTimeScoreCache.java @@ -63,7 +63,7 @@ public void RecalculateCalcCache(RetentionScoreCalculatorSpec calculator) Map calcCache = _cache.get(calculator.getName()); if(calcCache != null) { - LinkedHashMap newCalcCache = new LinkedHashMap(); + LinkedHashMap newCalcCache = new LinkedHashMap<>(); for (String key : calcCache.keySet()) { @@ -77,7 +77,7 @@ public void RecalculateCalcCache(RetentionScoreCalculatorSpec calculator) public double CalcScore(IRetentionScoreCalculator calculator, String peptide) { - LinkedHashMap cacheCalc = null; + LinkedHashMap cacheCalc; cacheCalc = _cache.get(calculator.getName()); return CalcScore(calculator, peptide, cacheCalc); } diff --git a/src/org/labkey/targetedms/SkylinePort/Irt/RetentionTimeStatistics.java b/src/org/labkey/targetedms/SkylinePort/Irt/RetentionTimeStatistics.java index c9825664b..5eca73d9a 100644 --- a/src/org/labkey/targetedms/SkylinePort/Irt/RetentionTimeStatistics.java +++ b/src/org/labkey/targetedms/SkylinePort/Irt/RetentionTimeStatistics.java @@ -87,7 +87,7 @@ private void setListRetentionTimes(java.util.ArrayList value) public java.util.Map getScoreCache() { - LinkedHashMap scoreCache = new LinkedHashMap(); + LinkedHashMap scoreCache = new LinkedHashMap<>(); for (int i = 0; i < getPeptides().size(); i++) { String sequence = getPeptides().get(i); diff --git a/src/org/labkey/targetedms/SkylinePort/Irt/Statistics.java b/src/org/labkey/targetedms/SkylinePort/Irt/Statistics.java index 362f45649..0eefa6b07 100644 --- a/src/org/labkey/targetedms/SkylinePort/Irt/Statistics.java +++ b/src/org/labkey/targetedms/SkylinePort/Irt/Statistics.java @@ -354,8 +354,7 @@ public final double Covariance(Statistics s) @param s1 First set of numbers @param s2 Second set of numbers - @return - */ + */ public static double Covariance(Statistics s1, Statistics s2) { try @@ -549,7 +548,7 @@ public static Statistics Residuals(Statistics y, Statistics x) double a = ATerm2(y, x); double b = BTerm2(y, x); - java.util.ArrayList residuals = new java.util.ArrayList(); + java.util.ArrayList residuals = new java.util.ArrayList<>(); for (int i = 0; i < x.getLength(); i++) { residuals.add(y._list[i] - (a*x._list[i] + b)); diff --git a/src/org/labkey/targetedms/TargetedMSController.java b/src/org/labkey/targetedms/TargetedMSController.java index 7d131f35b..58719e055 100644 --- a/src/org/labkey/targetedms/TargetedMSController.java +++ b/src/org/labkey/targetedms/TargetedMSController.java @@ -7866,7 +7866,7 @@ public void validateForm(ClustergrammerForm form, Errors errors) public ApiResponse execute(ClustergrammerForm form, BindException errors) throws Exception { Map> results = TargetedMSManager.getClustergrammerQuery(getUser(), getContainer(), form.getSelectedIds()); - if (results.size() == 0) + if (results.isEmpty()) { errors.reject(ERROR_MSG, "No results for the selected file(s)"); return null; diff --git a/src/org/labkey/targetedms/TargetedMSFolderType.java b/src/org/labkey/targetedms/TargetedMSFolderType.java index 9a4d4ffdb..0097f3827 100644 --- a/src/org/labkey/targetedms/TargetedMSFolderType.java +++ b/src/org/labkey/targetedms/TargetedMSFolderType.java @@ -120,7 +120,7 @@ public void addManageLinks(NavTree adminNavTree, Container container, User user) if (container.hasPermission(user, AdminPermission.class)) { - if (Portal.getParts(container, RAW_FILES_TAB).size() == 0) + if (Portal.getParts(container, RAW_FILES_TAB).isEmpty()) { ActionURL url = new ActionURL(TargetedMSController.AddRawDataTabAction.class, container); NavTree addRawData = new NavTree("Add Raw Data Tab", url); diff --git a/src/org/labkey/targetedms/TargetedMSManager.java b/src/org/labkey/targetedms/TargetedMSManager.java index 5d9c2d546..6f299c5d9 100644 --- a/src/org/labkey/targetedms/TargetedMSManager.java +++ b/src/org/labkey/targetedms/TargetedMSManager.java @@ -911,7 +911,7 @@ public static TargetedMSRun getRunByLsid(String lsid, Container c) public static boolean updateSkydDataId(ITargetedMSRun run, ExpData newSkydData, User user) { - if (!(run instanceof TargetedMSRun)) + if (!(run instanceof TargetedMSRun targetedRun)) { throw new IllegalArgumentException("Invalid run type. Expected TargetedMSRun but received " + (run != null ? run.getClass().getName() : "null")); @@ -921,8 +921,6 @@ public static boolean updateSkydDataId(ITargetedMSRun run, ExpData newSkydData, throw new IllegalArgumentException("Cannot update with null newSkydData. A valid ExpData object is required"); } - TargetedMSRun targetedRun = (TargetedMSRun) run; - ExpRun expRun = ExperimentService.get().getExpRun(targetedRun.getExperimentRunLSID()); if (expRun == null) return false; diff --git a/src/org/labkey/targetedms/TargetedMSModule.java b/src/org/labkey/targetedms/TargetedMSModule.java index 8b2a2d289..d0469a0a9 100644 --- a/src/org/labkey/targetedms/TargetedMSModule.java +++ b/src/org/labkey/targetedms/TargetedMSModule.java @@ -82,7 +82,6 @@ import org.labkey.targetedms.search.ProteinSearchWebPart; import org.labkey.targetedms.view.CalibrationCurveView; import org.labkey.targetedms.view.CrossLinkedPeptideInfo; -import org.labkey.targetedms.view.FiguresOfMeritView; import org.labkey.targetedms.view.LibraryQueryViewWebPart; import org.labkey.targetedms.view.ReplicateSummaryWebPart; import org.labkey.targetedms.view.TargetedMSRunsWebPartView; diff --git a/src/org/labkey/targetedms/TargetedMSRun.java b/src/org/labkey/targetedms/TargetedMSRun.java index 0a776a1ce..040f97431 100644 --- a/src/org/labkey/targetedms/TargetedMSRun.java +++ b/src/org/labkey/targetedms/TargetedMSRun.java @@ -313,6 +313,7 @@ public void setCalibrationCurveCount(int calibrationCurveCount) public void setAuditLogEntriesCount(int auditLogEntriesCount){this._auditLogEntriesCount = auditLogEntriesCount;} + @Override public RunRepresentativeDataState getRepresentativeDataState() { return _representativeDataState; @@ -416,7 +417,7 @@ public TransitionSettings.FullScanSettings fetchFullScanSettings() { if (_fullScanSettings == null) { - _fullScanSettings = TargetedMSManager.get().getTransitionFullScanSettings(getId()); + _fullScanSettings = TargetedMSManager.getTransitionFullScanSettings(getId()); } return _fullScanSettings; } diff --git a/src/org/labkey/targetedms/TargetedMSServiceImpl.java b/src/org/labkey/targetedms/TargetedMSServiceImpl.java index b0aa66b11..bd37e00b5 100644 --- a/src/org/labkey/targetedms/TargetedMSServiceImpl.java +++ b/src/org/labkey/targetedms/TargetedMSServiceImpl.java @@ -276,6 +276,7 @@ public ITargetedMSRun getRunByLsid(String lsid, Container container) return TargetedMSManager.getRunByLsid(lsid, container); } + @Override public boolean updateSkydDataId(ITargetedMSRun run, ExpData newSkydData, User user) { return TargetedMSManager.updateSkydDataId(run, newSkydData, user); diff --git a/src/org/labkey/targetedms/calculations/NormalizationMethodAreas.java b/src/org/labkey/targetedms/calculations/NormalizationMethodAreas.java index c2494d5ed..8e889f2f3 100644 --- a/src/org/labkey/targetedms/calculations/NormalizationMethodAreas.java +++ b/src/org/labkey/targetedms/calculations/NormalizationMethodAreas.java @@ -42,12 +42,12 @@ */ public class NormalizationMethodAreas { - private TargetedMSRun _run; - private User _user; - private Container _container; - private ReplicateDataSet _replicateDataSet; + private final TargetedMSRun _run; + private final User _user; + private final Container _container; + private final ReplicateDataSet _replicateDataSet; private Collection _standardEntries; - private Map> _moleculeDataSets = new HashMap<>(); + private final Map>> _moleculeDataSets = new HashMap<>(); public NormalizationMethodAreas(TargetedMSRun run, User user, Container container, ReplicateDataSet replicateDataSet) { @@ -59,14 +59,7 @@ public NormalizationMethodAreas(TargetedMSRun run, User user, Container containe public NormalizationFactors getNormalizationFactors(NormalizationMethod normalizationMethod) { - return new NormalizationFactors() - { - @Override - public double getNormalizationFactor(long sampleFileId) - { - return 1.0 / getAreaForNormalization(normalizationMethod, sampleFileId); - } - }; + return sampleFileId -> 1.0 / getAreaForNormalization(normalizationMethod, sampleFileId); } public boolean hasNormalizationFactors(NormalizationMethod normalizationMethod) @@ -93,7 +86,7 @@ public double getAreaForNormalization(NormalizationMethod normalizationMethod, l { Optional isotopeLabelOptional = _replicateDataSet.listIsotopeLabels().stream().filter(label -> isotopeLabelName.equals(label.getName())).findFirst(); - if (!isotopeLabelOptional.isPresent()) + if (isotopeLabelOptional.isEmpty()) { return 0; } @@ -101,21 +94,21 @@ public double getAreaForNormalization(NormalizationMethod normalizationMethod, l } } double total = 0; - for (GeneralMoleculeResultDataSet generalMoleculeResultDataSet : getMoleculeDataSets(normalizationMethod)) + for (GeneralMoleculeResultDataSet generalMoleculeResultDataSet : getMoleculeDataSets(normalizationMethod)) { total += generalMoleculeResultDataSet.getTotalArea(sampleFileId, isotopeLabel); } return total; } - private List getMoleculeDataSets(NormalizationMethod normalizationMethod) + private List> getMoleculeDataSets(NormalizationMethod normalizationMethod) { NormalizationMethod.RatioToSurrogate ratioToSurrogate = null; if (normalizationMethod instanceof NormalizationMethod.RatioToSurrogate) { ratioToSurrogate = (NormalizationMethod.RatioToSurrogate) normalizationMethod; } - List dataSets = _moleculeDataSets.get(normalizationMethod); + List> dataSets = _moleculeDataSets.get(normalizationMethod); if (dataSets != null) { return dataSets; @@ -146,7 +139,7 @@ else if (normalizationMethod.equals(NormalizationMethod.GLOBAL_STANDARDS)) continue; } } - GeneralMolecule generalMolecule; + GeneralMolecule generalMolecule; if (standardEntry.getPeptideId() != null) { generalMolecule = PeptideManager.getPeptide(_container, standardEntry.getPeptideId()); @@ -155,7 +148,7 @@ else if (normalizationMethod.equals(NormalizationMethod.GLOBAL_STANDARDS)) { generalMolecule = MoleculeManager.getMolecule(_container, standardEntry.getMoleculeId()); } - dataSets.add(new GeneralMoleculeResultDataSet(_user, _container, _replicateDataSet, generalMolecule)); + dataSets.add(new GeneralMoleculeResultDataSet<>(_user, _container, _replicateDataSet, generalMolecule)); } _moleculeDataSets.put(normalizationMethod, dataSets); return dataSets; diff --git a/src/org/labkey/targetedms/calculations/ReplicateDataSet.java b/src/org/labkey/targetedms/calculations/ReplicateDataSet.java index 3efda49c3..f873d9612 100644 --- a/src/org/labkey/targetedms/calculations/ReplicateDataSet.java +++ b/src/org/labkey/targetedms/calculations/ReplicateDataSet.java @@ -29,9 +29,9 @@ import java.util.Collection; import java.util.Collections; -import java.util.HashMap; import java.util.HashSet; import java.util.Map; +import java.util.Objects; import java.util.Set; import java.util.function.Function; import java.util.stream.Collectors; @@ -41,11 +41,11 @@ */ public class ReplicateDataSet { - Map _replicates = new HashMap<>(); - Map _fileIdToReplicateId = new HashMap<>(); + Map _replicates; + Map _fileIdToReplicateId; Map> _replicateAnnotations; Map _isotopeLabels; - private boolean _useTransitionChromInfos; + private final boolean _useTransitionChromInfos; public ReplicateDataSet(TargetedMSRun run) { @@ -92,11 +92,7 @@ public String getIsotopeLabelName(long isotopeLabelId) public Map getReplicateAnnotations(Replicate replicate) { Map annotations = _replicateAnnotations.get(replicate.getId()); - if (annotations != null) - { - return annotations; - } - return Collections.emptyMap(); + return Objects.requireNonNullElse(annotations, Collections.emptyMap()); } @Nullable diff --git a/src/org/labkey/targetedms/calculations/quantification/CalibrationCurveDataSet.java b/src/org/labkey/targetedms/calculations/quantification/CalibrationCurveDataSet.java index 845edb537..215b611ca 100644 --- a/src/org/labkey/targetedms/calculations/quantification/CalibrationCurveDataSet.java +++ b/src/org/labkey/targetedms/calculations/quantification/CalibrationCurveDataSet.java @@ -23,7 +23,7 @@ public class CalibrationCurveDataSet { private NormalizationMethod normalizationMethod = NormalizationMethod.NONE; private RegressionFit regressionFit = RegressionFit.NONE; private RegressionWeighting regressionWeighting = RegressionWeighting.NONE; - private List replicates = new ArrayList<>(); + private final List replicates = new ArrayList<>(); public Replicate addReplicate(SampleType sampleType, Double analyteConcentration, double sampleDilutionFactor, boolean excludeFromCalibration) { Replicate replicate = new Replicate(sampleType, analyteConcentration, sampleDilutionFactor, excludeFromCalibration); @@ -115,10 +115,10 @@ public Double getCalculatedConcentration(String label, CalibrationCurve calibrat * Created by nicksh on 4/15/2016. */ public static class Replicate extends ReplicateData { - private SampleType sampleType; - private Double analyteConcentration; - private double sampleDilutionFactor; - private boolean excludeFromCalibration; + private final SampleType sampleType; + private final Double analyteConcentration; + private final double sampleDilutionFactor; + private final boolean excludeFromCalibration; public Replicate(SampleType sampleType, Double analyteConcentration, double sampleDilutionFactor, boolean excludeFromCalibration) { this.sampleType = sampleType; this.analyteConcentration = analyteConcentration; diff --git a/src/org/labkey/targetedms/calculations/quantification/DesignMatrix.java b/src/org/labkey/targetedms/calculations/quantification/DesignMatrix.java index 9dab6b520..2d800e3d8 100644 --- a/src/org/labkey/targetedms/calculations/quantification/DesignMatrix.java +++ b/src/org/labkey/targetedms/calculations/quantification/DesignMatrix.java @@ -97,7 +97,7 @@ public static DesignMatrix getDesignMatrix(FoldChangeDataSet dataSet, boolean in } return new DesignMatrix(dataSet, matrixColumns.toArray(new double[matrixColumns.size()][]), - contrastValueMatrix, columnNames.toArray(new String[columnNames.size()])); + contrastValueMatrix, columnNames.toArray(new String[0])); } private static RealMatrix matrixFromColumnVectors(double[][] columnVectors) { diff --git a/src/org/labkey/targetedms/calculations/quantification/FoldChangeDataSet.java b/src/org/labkey/targetedms/calculations/quantification/FoldChangeDataSet.java index cd488c2ee..047c7d516 100644 --- a/src/org/labkey/targetedms/calculations/quantification/FoldChangeDataSet.java +++ b/src/org/labkey/targetedms/calculations/quantification/FoldChangeDataSet.java @@ -60,7 +60,7 @@ public FoldChangeDataSet(Collection abundances, this.features = features.stream().mapToInt(Integer::intValue).toArray(); this.runs = runs.stream().mapToInt(Integer::intValue).toArray(); this.subjects = subjects.stream().mapToInt(Integer::intValue).toArray(); - this.subjectControls = ArrayUtils.toPrimitive(subjectControls.toArray(new Boolean[subjectControls.size()])); + this.subjectControls = ArrayUtils.toPrimitive(subjectControls.toArray(new Boolean[0])); if (this.abundances.length == 0) { featureCount = 0; subjectCount = 0; diff --git a/src/org/labkey/targetedms/calculations/quantification/GroupComparisonDataSet.java b/src/org/labkey/targetedms/calculations/quantification/GroupComparisonDataSet.java index 22c82191d..a262d04a2 100644 --- a/src/org/labkey/targetedms/calculations/quantification/GroupComparisonDataSet.java +++ b/src/org/labkey/targetedms/calculations/quantification/GroupComparisonDataSet.java @@ -25,7 +25,7 @@ public class GroupComparisonDataSet { private NormalizationMethod normalizationMethod = NormalizationMethod.NONE; - private List replicates = new ArrayList<>(); + private final List replicates = new ArrayList<>(); public Replicate addReplicate(boolean control, Object bioReplicate) { Replicate replicate = new Replicate(control, bioReplicate); @@ -45,7 +45,7 @@ public void setNormalizationMethod(NormalizationMethod normalizationMethod) { public LinearFitResult calculateFoldChange(String label) { List replicates = removeIncompleteReplicates(label, this.replicates); - if (replicates.size() == 0) { + if (replicates.isEmpty()) { return null; } List summarizedRows; @@ -114,7 +114,7 @@ List removeIncompleteReplicates(String label, List replica List completeReplicates = new ArrayList<>(); for (Replicate replicateData : replicates) { TransitionAreas transitionAreas = replicateData.getTransitionAreas(label); - if (transitionAreas == null || transitionAreas.getKeys().size() == 0) { + if (transitionAreas == null || transitionAreas.getKeys().isEmpty()) { continue; } if (requiredTransitions != null && !transitionAreas.getKeys().containsAll(requiredTransitions)) { @@ -145,8 +145,8 @@ private Double calculateMean(Iterable values) { } public class Replicate extends ReplicateData { - private boolean control; - private Object bioReplicate; + private final boolean control; + private final Object bioReplicate; public Replicate(boolean control, Object bioReplicate) { this.control = control; diff --git a/src/org/labkey/targetedms/calculations/quantification/LinearModel.java b/src/org/labkey/targetedms/calculations/quantification/LinearModel.java index 944b4835b..6b102fc37 100644 --- a/src/org/labkey/targetedms/calculations/quantification/LinearModel.java +++ b/src/org/labkey/targetedms/calculations/quantification/LinearModel.java @@ -27,11 +27,11 @@ import java.util.stream.IntStream; class LinearModel { - private RealMatrix designMatrix; - private RealMatrix contrastValues; - private QRDecomposition qrDecomposition; - private RealMatrix matrixCrossproductInverse; - private int[] independentColumnIndices; + private final RealMatrix designMatrix; + private final RealMatrix contrastValues; + private final QRDecomposition qrDecomposition; + private final RealMatrix matrixCrossproductInverse; + private final int[] independentColumnIndices; public LinearModel(RealMatrix designMatrix, RealMatrix contrastValues) { this.designMatrix = designMatrix; this.contrastValues = contrastValues; diff --git a/src/org/labkey/targetedms/calculations/quantification/NormalizationMethod.java b/src/org/labkey/targetedms/calculations/quantification/NormalizationMethod.java index 664377e2d..29256aca5 100644 --- a/src/org/labkey/targetedms/calculations/quantification/NormalizationMethod.java +++ b/src/org/labkey/targetedms/calculations/quantification/NormalizationMethod.java @@ -28,7 +28,7 @@ public abstract class NormalizationMethod { public static NormalizationMethod fromName(String name) { - if (name == null || name.length() == 0) { + if (name == null || name.isEmpty()) { return null; } if (name.startsWith(ratio_prefix)) { @@ -86,7 +86,7 @@ public String getIsotopeLabelTypeName() { } public String getIsotopeLabelTitle() { - if (isotopeLabelName == null || isotopeLabelName.length() == 0) { + if (isotopeLabelName == null || isotopeLabelName.isEmpty()) { return isotopeLabelName; } return isotopeLabelName.substring(0, 1).toUpperCase(Locale.US) + isotopeLabelName.substring(1); diff --git a/src/org/labkey/targetedms/calculations/quantification/RegressionFit.java b/src/org/labkey/targetedms/calculations/quantification/RegressionFit.java index d3de70d03..5771e3eb7 100644 --- a/src/org/labkey/targetedms/calculations/quantification/RegressionFit.java +++ b/src/org/labkey/targetedms/calculations/quantification/RegressionFit.java @@ -112,7 +112,7 @@ public String getLabel() { } public CalibrationCurve fit(List points) { - if (points.size() == 0) { + if (points.isEmpty()) { CalibrationCurve curve = new CalibrationCurve(); curve.setErrorMessage("Unable to calculate curve, since there are no data points available"); return curve; diff --git a/src/org/labkey/targetedms/calculations/quantification/RegressionWeighting.java b/src/org/labkey/targetedms/calculations/quantification/RegressionWeighting.java index 6905f4849..44f35a8fa 100644 --- a/src/org/labkey/targetedms/calculations/quantification/RegressionWeighting.java +++ b/src/org/labkey/targetedms/calculations/quantification/RegressionWeighting.java @@ -44,8 +44,8 @@ public double getWeighting(double x, double y) { = Collections.unmodifiableList(Arrays.asList(NONE, ONE_OVER_X, ONE_OVER_X_SQUARED)); - private String name; - private String label; + private final String name; + private final String label; private RegressionWeighting(String name, String label) { this.name = name; this.label = label; diff --git a/src/org/labkey/targetedms/calculations/quantification/SampleType.java b/src/org/labkey/targetedms/calculations/quantification/SampleType.java index eab0bd958..41bb0922c 100644 --- a/src/org/labkey/targetedms/calculations/quantification/SampleType.java +++ b/src/org/labkey/targetedms/calculations/quantification/SampleType.java @@ -23,15 +23,15 @@ public enum SampleType { solvent(new Color(255,226,43)), blank(Color.blue), double_blank(new Color(255, 230, 216)); - private Color color; - private SampleType(Color color) { + private final Color color; + SampleType(Color color) { this.color = color; } public Color getColor() { return color; } public static SampleType fromName(String name) { - if (name == null || 0 == name.length()) { + if (name == null || name.isEmpty()) { return unknown; } try { diff --git a/src/org/labkey/targetedms/calculations/quantification/TransitionAreas.java b/src/org/labkey/targetedms/calculations/quantification/TransitionAreas.java index 6f8851e2a..5f9b6dbe4 100644 --- a/src/org/labkey/targetedms/calculations/quantification/TransitionAreas.java +++ b/src/org/labkey/targetedms/calculations/quantification/TransitionAreas.java @@ -65,7 +65,7 @@ private HashMap toMap() { } public boolean isEmpty() { - return keys.size() == 0; + return keys.isEmpty(); } public TransitionAreas merge(TransitionAreas that) { diff --git a/src/org/labkey/targetedms/chart/ComparisonAxis.java b/src/org/labkey/targetedms/chart/ComparisonAxis.java index 18ff4bbb6..13be14e84 100644 --- a/src/org/labkey/targetedms/chart/ComparisonAxis.java +++ b/src/org/labkey/targetedms/chart/ComparisonAxis.java @@ -66,15 +66,15 @@ private String getDisplayLabel(String category, Graphics2D g2, float width) private void calculateDisplayLabels(float availableWidth, Graphics2D g2) { CategoryPlot plot = (CategoryPlot) getPlot(); - java.util.List categories = plot.getCategoriesForAxis(this); + java.util.List categories = plot.getCategoriesForAxis(this); Map originalLabels = getFullLengthLabels(categories); FontMetrics fm = g2.getFontMetrics(getTickLabelFont()); final Font font = fm.getFont(); final int originalSize = font.getSize(); - final int smallestSize = originalSize; // 8; // Changing the font makes the legend overlap category labels. - for(int i = originalSize; i >= smallestSize; i--) + // 8; // Changing the font makes the legend overlap category labels. + for(int i = originalSize; i >= originalSize; i--) { Font newFont = font.deriveFont((float)i); if(tryFont(availableWidth, originalLabels.values(), newFont, g2)) @@ -90,7 +90,7 @@ private void calculateDisplayLabels(float availableWidth, Graphics2D g2) // Full size labels did not fit. Try minimized labels while(minimizeLabels(trimmedLabels)) { - for(int i = originalSize; i >= smallestSize; i--) + for(int i = originalSize; i >= originalSize; i--) { Font newFont = font.deriveFont((float)i); if(tryFont(availableWidth, trimmedLabels.values(), newFont, g2)) @@ -104,7 +104,7 @@ private void calculateDisplayLabels(float availableWidth, Graphics2D g2) // If we are here we did not find a combination of labels and font size that fits. // Select the smallest font-size and trimmed labels - setTickLabelFont(font.deriveFont((float)smallestSize)); + setTickLabelFont(font.deriveFont((float) originalSize)); _displayLabels = trimmedLabels; } @@ -157,7 +157,7 @@ private boolean tryFont(float availableWidth, Collection labels, Font fo static class GeneralMoleculeAxis extends ComparisonAxis { - private Map _categoryMap; + private final Map _categoryMap; public GeneralMoleculeAxis(String label, Map categoryMap) { super(label); @@ -167,10 +167,10 @@ public GeneralMoleculeAxis(String label, Map categor @Override protected Map getFullLengthLabels(Collection categories) { - Iterator iterator = categories.iterator(); + Iterator iterator = categories.iterator(); Map originalLabels = new HashMap<>(); while (iterator.hasNext()) { - String category = iterator.next().toString(); + String category = iterator.next(); ComparisonCategory pepCategory = _categoryMap.get(category); if(pepCategory != null) { @@ -207,10 +207,10 @@ public ReplicateAxis(String label) @Override protected Map getFullLengthLabels(Collection categories) { - Iterator iterator = categories.iterator(); + Iterator iterator = categories.iterator(); Map originalLabels = new HashMap<>(); while (iterator.hasNext()) { - String category = iterator.next().toString(); + String category = iterator.next(); originalLabels.put(category, category); } return originalLabels; diff --git a/src/org/labkey/targetedms/chart/ComparisonCategory.java b/src/org/labkey/targetedms/chart/ComparisonCategory.java index ae1ae5c5d..6c65b27e8 100644 --- a/src/org/labkey/targetedms/chart/ComparisonCategory.java +++ b/src/org/labkey/targetedms/chart/ComparisonCategory.java @@ -276,7 +276,7 @@ private static String getPeptideChargeMapKey(ComparisonCategory.PeptideCategory private static void makeUniquePrefixes(List peptideCategories, int prefixLen) { - if(peptideCategories == null || peptideCategories.size() == 0) + if(peptideCategories == null || peptideCategories.isEmpty()) return; if(peptideCategories.size() == 1) diff --git a/src/org/labkey/targetedms/chart/PrecursorColorIndexer.java b/src/org/labkey/targetedms/chart/PrecursorColorIndexer.java index 339c24d14..94dd56ea0 100644 --- a/src/org/labkey/targetedms/chart/PrecursorColorIndexer.java +++ b/src/org/labkey/targetedms/chart/PrecursorColorIndexer.java @@ -34,7 +34,7 @@ public class PrecursorColorIndexer { private long _lightLabelId = Integer.MAX_VALUE; private int _minCharge = Integer.MAX_VALUE; - private int _isotopeLabelCount; + private final int _isotopeLabelCount; public PrecursorColorIndexer(long runId, User user, Container container) { diff --git a/src/org/labkey/targetedms/chart/ReplicateLabelMinimizer.java b/src/org/labkey/targetedms/chart/ReplicateLabelMinimizer.java index 587abe82b..fa3bcc2a7 100644 --- a/src/org/labkey/targetedms/chart/ReplicateLabelMinimizer.java +++ b/src/org/labkey/targetedms/chart/ReplicateLabelMinimizer.java @@ -43,7 +43,7 @@ private ReplicateLabelMinimizer() {} public static Map minimize(List labels) { - if(labels == null || labels.size() == 0) + if(labels == null || labels.isEmpty()) return Collections.emptyMap(); List normalizedLabels = normalizeLabels(labels); @@ -101,9 +101,9 @@ private static Map originalLabels(List labels) private static List normalizeLabels(List labels) { List normalized = new ArrayList<>(labels.size()); - for(Object label: labels) + for(String label: labels) { - normalized.add(normalizeLabel((String) label)); + normalized.add(normalizeLabel(label)); } return normalized; } @@ -225,18 +225,18 @@ public void testReplicateNameMinimization() iteration++; if(iteration == 1) { - assertEquals(labels.get("Prefix_name_1_Suffix"), "name_1_Suffix"); - assertEquals(labels.get("Prefix_name_2_Suffix"), "name_2_Suffix"); + assertEquals("name_1_Suffix", labels.get("Prefix_name_1_Suffix")); + assertEquals("name_2_Suffix", labels.get("Prefix_name_2_Suffix")); } if(iteration == 2) { - assertEquals(labels.get("Prefix_name_1_Suffix"), "1_Suffix"); - assertEquals(labels.get("Prefix_name_2_Suffix"), "2_Suffix"); + assertEquals("1_Suffix", labels.get("Prefix_name_1_Suffix")); + assertEquals("2_Suffix", labels.get("Prefix_name_2_Suffix")); } if(iteration == 3) { - assertEquals(labels.get("Prefix_name_1_Suffix"), "1"); - assertEquals(labels.get("Prefix_name_2_Suffix"), "2"); + assertEquals("1", labels.get("Prefix_name_1_Suffix")); + assertEquals("2", labels.get("Prefix_name_2_Suffix")); } } assertEquals(3, iteration); @@ -250,13 +250,13 @@ public void testReplicateNameMinimization() iteration++; if(iteration == 1) { - assertEquals(labels.get("1,ABC-XYZ_File1"), "1...XYZ_File1"); - assertEquals(labels.get("2_ABC-XYZ_File2"), "2...XYZ_File2"); + assertEquals("1...XYZ_File1", labels.get("1,ABC-XYZ_File1")); + assertEquals("2...XYZ_File2", labels.get("2_ABC-XYZ_File2")); } if(iteration == 2) { - assertEquals(labels.get("1,ABC-XYZ_File1"), "1...File1"); - assertEquals(labels.get("2_ABC-XYZ_File2"), "2...File2"); + assertEquals("1...File1", labels.get("1,ABC-XYZ_File1")); + assertEquals("2...File2", labels.get("2_ABC-XYZ_File2")); } } assertEquals(2, iteration); diff --git a/src/org/labkey/targetedms/chart/RetentionTimeBoxAndWhiskerRenderer.java b/src/org/labkey/targetedms/chart/RetentionTimeBoxAndWhiskerRenderer.java index 4212a4b5e..c1b413b81 100644 --- a/src/org/labkey/targetedms/chart/RetentionTimeBoxAndWhiskerRenderer.java +++ b/src/org/labkey/targetedms/chart/RetentionTimeBoxAndWhiskerRenderer.java @@ -47,7 +47,7 @@ public RetentionTimeBoxAndWhiskerRenderer() setItemMargin(0.1); } - // Need to override drawVertical and drawHorizontal methods so that we can draw the FWHM line and whisters + // Need to override drawVertical and drawHorizontal methods so that we can draw the FWHM line and whiskers @Override public void drawHorizontalItem(Graphics2D g2, CategoryItemRendererState state, Rectangle2D dataArea, CategoryPlot plot, CategoryAxis domainAxis, ValueAxis rangeAxis, CategoryDataset dataset, int row, int column) { @@ -57,7 +57,7 @@ public void drawHorizontalItem(Graphics2D g2, CategoryItemRendererState state, R // TODO } - // Need to override drawVertical and drawHorizontal methods so that we can draw the FWHM line and whisters + // Need to override drawVertical and drawHorizontal methods so that we can draw the FWHM line and whiskers @Override public void drawVerticalItem(Graphics2D g2, CategoryItemRendererState state, Rectangle2D dataArea, CategoryPlot plot, CategoryAxis domainAxis, ValueAxis rangeAxis, CategoryDataset dataset, int row, int column) { @@ -66,9 +66,8 @@ public void drawVerticalItem(Graphics2D g2, CategoryItemRendererState state, Rec // Draw the FWHM lines DefaultBoxAndWhiskerCategoryDataset rtDataset = (DefaultBoxAndWhiskerCategoryDataset) dataset; - if(!(rtDataset.getItem(row, column) instanceof ComparisonDataset.RetentionTimeDatasetItem)) + if(!(rtDataset.getItem(row, column) instanceof ComparisonDataset.RetentionTimeDatasetItem item)) return; - ComparisonDataset.RetentionTimeDatasetItem item = (ComparisonDataset.RetentionTimeDatasetItem) rtDataset.getItem(row, column); RectangleEdge location = plot.getRangeAxisEdge(); diff --git a/src/org/labkey/targetedms/chromlib/ChromLibSqliteSchemaCreator.java b/src/org/labkey/targetedms/chromlib/ChromLibSqliteSchemaCreator.java index 02d183560..c6e3891cf 100644 --- a/src/org/labkey/targetedms/chromlib/ChromLibSqliteSchemaCreator.java +++ b/src/org/labkey/targetedms/chromlib/ChromLibSqliteSchemaCreator.java @@ -178,16 +178,15 @@ private void createTable(Connection conn, Table tableName, Constants.ColumnDef[] { try (Statement stmt = conn.createStatement()) { - StringBuilder indexSQL = new StringBuilder("CREATE INDEX IDX_"); - indexSQL.append(tableName); - indexSQL.append("_"); - indexSQL.append(column.baseColumn().name()); - indexSQL.append(" ON "); - indexSQL.append(tableName); - indexSQL.append("("); - indexSQL.append(column.baseColumn().name()); - indexSQL.append(")"); - stmt.execute(indexSQL.toString()); + String indexSQL = "CREATE INDEX IDX_" + tableName + + "_" + + column.baseColumn().name() + + " ON " + + tableName + + "(" + + column.baseColumn().name() + + ")"; + stmt.execute(indexSQL); } } } diff --git a/src/org/labkey/targetedms/chromlib/ChromatogramLibraryUtils.java b/src/org/labkey/targetedms/chromlib/ChromatogramLibraryUtils.java index eb5f6e410..b6ebe713e 100644 --- a/src/org/labkey/targetedms/chromlib/ChromatogramLibraryUtils.java +++ b/src/org/labkey/targetedms/chromlib/ChromatogramLibraryUtils.java @@ -254,7 +254,7 @@ public static TargetedMSController.ChromLibAnalyteCounts getLibraryAnalyteCounts SQLiteConfig config = new SQLiteConfig(); config.setReadOnly(true); - try (Connection conn = DriverManager.getConnection("jdbc:sqlite:/" + archiveFile.toAbsolutePath().toString(), config.toProperties())) + try (Connection conn = DriverManager.getConnection("jdbc:sqlite:/" + archiveFile.toAbsolutePath(), config.toProperties())) { TargetedMSController.ChromLibAnalyteCounts analyteCountsInLib = new TargetedMSController.ChromLibAnalyteCounts(); analyteCountsInLib.setPeptideGroupCount(getCountsIn(Constants.Table.Protein, conn, null)); diff --git a/src/org/labkey/targetedms/chromlib/ContainerChromatogramLibraryWriter.java b/src/org/labkey/targetedms/chromlib/ContainerChromatogramLibraryWriter.java index d4d3aa256..b8f99f6b1 100644 --- a/src/org/labkey/targetedms/chromlib/ContainerChromatogramLibraryWriter.java +++ b/src/org/labkey/targetedms/chromlib/ContainerChromatogramLibraryWriter.java @@ -397,7 +397,7 @@ private void saveProteomicsPrecursors(TargetedMSRun run) { if(precursor.getGeneralMoleculeId() != lastPeptideId) { - if(peptidePrecursors.size() > 0) + if(!peptidePrecursors.isEmpty()) { Peptide peptide = PeptideManager.getPeptide(_container, lastPeptideId); LibPeptide libPeptide = makeLibPeptide(peptide, peptidePrecursors, run); @@ -410,7 +410,7 @@ private void saveProteomicsPrecursors(TargetedMSRun run) } peptidePrecursors.add(precursor); } - if(peptidePrecursors.size() > 0) + if(!peptidePrecursors.isEmpty()) { Peptide peptide = PeptideManager.getPeptide(_container, lastPeptideId); LibPeptide libPeptide = makeLibPeptide(peptide, peptidePrecursors, run); @@ -430,7 +430,7 @@ private void saveMoleculePrecursors(TargetedMSRun run) { if(precursor.getGeneralMoleculeId() != lastMoleculeId) { - if(moleculePrecursors.size() > 0) + if(!moleculePrecursors.isEmpty()) { Molecule molecule = MoleculeManager.getMolecule(_container, lastMoleculeId); LibPeptide libMolecule = makeLibMolecule(molecule, moleculePrecursors, run); @@ -443,7 +443,7 @@ private void saveMoleculePrecursors(TargetedMSRun run) } moleculePrecursors.add(precursor); } - if(moleculePrecursors.size() > 0) + if(!moleculePrecursors.isEmpty()) { Molecule molecule = MoleculeManager.getMolecule(_container, lastMoleculeId); LibPeptide libMolecule = makeLibMolecule(molecule, moleculePrecursors, run); @@ -479,7 +479,7 @@ private void addPeptides(PeptideGroup pepGroup, LibProtein protein, TargetedMSRu for(Peptide peptide: peptides) { List precursors = PrecursorManager.getPrecursorsForPeptide(peptide.getId(), schema); - if(precursors.size() == 0) + if(precursors.isEmpty()) { throw new IllegalStateException(String.format("No precursors found for peptide '%s'. Empty peptides are not allowed in library folders." + " Empty peptides can be removed in Skyline by selecting Refine > Remove Empty Peptides.", peptide.getSequence())); @@ -538,12 +538,12 @@ private LibPeptide makeLibPeptide(Peptide peptide) libPeptide.setStartIndex(peptide.getStartIndex()); libPeptide.setEndIndex(peptide.getEndIndex()); String previousAa = peptide.getPreviousAa(); - if(previousAa != null && previousAa.length() > 0) + if(previousAa != null && !previousAa.isEmpty()) { libPeptide.setPreviousAa(previousAa.charAt(0)); } String nextAa = peptide.getNextAa(); - if(nextAa != null && nextAa.length() > 0) + if(nextAa != null && !nextAa.isEmpty()) { libPeptide.setNextAa(nextAa.charAt(0)); } diff --git a/src/org/labkey/targetedms/chromlib/LibInfoDao.java b/src/org/labkey/targetedms/chromlib/LibInfoDao.java index 3b8d93fdb..948ebd2b7 100644 --- a/src/org/labkey/targetedms/chromlib/LibInfoDao.java +++ b/src/org/labkey/targetedms/chromlib/LibInfoDao.java @@ -41,15 +41,14 @@ public void save(LibInfo libInfo, Connection connection) throws SQLException { if(libInfo != null) { - StringBuilder sql = new StringBuilder(); - sql.append("INSERT INTO "); - sql.append(Table.LibInfo); - sql.append(" ("); - sql.append(getInsertColumnSql()); - sql.append(")"); - sql.append(" VALUES (?,?,?,?,?,?,?,?,?)"); + String sql = "INSERT INTO " + + Table.LibInfo + + " (" + + getInsertColumnSql() + + ")" + + " VALUES (?,?,?,?,?,?,?,?,?)"; - try (PreparedStatement stmt = connection.prepareStatement(sql.toString())) + try (PreparedStatement stmt = connection.prepareStatement(sql)) { int colIndex = 1; stmt.setString(colIndex++, libInfo.getPanoramaServer()); diff --git a/src/org/labkey/targetedms/chromlib/LibIrtLibrary.java b/src/org/labkey/targetedms/chromlib/LibIrtLibrary.java index 21b557273..af394a006 100644 --- a/src/org/labkey/targetedms/chromlib/LibIrtLibrary.java +++ b/src/org/labkey/targetedms/chromlib/LibIrtLibrary.java @@ -74,9 +74,7 @@ public void setTimeSource(Integer timeSource) public boolean equals(Object o) { if (this == o) return true; - if (!(o instanceof LibIrtLibrary)) return false; - - LibIrtLibrary that = (LibIrtLibrary) o; + if (!(o instanceof LibIrtLibrary that)) return false; if (!_modifiedSequence.equals(that._modifiedSequence)) return false; if (!_irtValue.equals(that._irtValue)) return false; diff --git a/src/org/labkey/targetedms/chromlib/LibIsotopeModification.java b/src/org/labkey/targetedms/chromlib/LibIsotopeModification.java index 228da2156..0e4ace2e7 100644 --- a/src/org/labkey/targetedms/chromlib/LibIsotopeModification.java +++ b/src/org/labkey/targetedms/chromlib/LibIsotopeModification.java @@ -159,9 +159,7 @@ public void setLabel2H(Boolean label2H) public boolean equals(Object o) { if (this == o) return true; - if (!(o instanceof LibIsotopeModification)) return false; - - LibIsotopeModification that = (LibIsotopeModification) o; + if (!(o instanceof LibIsotopeModification that)) return false; if (_aminoAcid != null ? !_aminoAcid.equals(that._aminoAcid) : that._aminoAcid != null) return false; if (_formula != null ? !_formula.equals(that._formula) : that._formula != null) return false; diff --git a/src/org/labkey/targetedms/chromlib/LibPeptide.java b/src/org/labkey/targetedms/chromlib/LibPeptide.java index fd233a3ed..8ed2be4ab 100644 --- a/src/org/labkey/targetedms/chromlib/LibPeptide.java +++ b/src/org/labkey/targetedms/chromlib/LibPeptide.java @@ -223,9 +223,7 @@ public int getCacheSize() public boolean equals(Object o) { if (this == o) return true; - if (!(o instanceof LibPeptide)) return false; - - LibPeptide peptide = (LibPeptide) o; + if (!(o instanceof LibPeptide peptide)) return false; if (!_calcNeutralMass.equals(peptide._calcNeutralMass)) return false; if (_endIndex != null ? !_endIndex.equals(peptide._endIndex) : peptide._endIndex != null) return false; diff --git a/src/org/labkey/targetedms/chromlib/LibPeptideDao.java b/src/org/labkey/targetedms/chromlib/LibPeptideDao.java index e283d7e2d..0693b6f0d 100644 --- a/src/org/labkey/targetedms/chromlib/LibPeptideDao.java +++ b/src/org/labkey/targetedms/chromlib/LibPeptideDao.java @@ -105,7 +105,7 @@ protected Constants.ColumnDef[] getColumns() @Override public void saveAll(Collection peptides, Connection connection) throws SQLException { - if(peptides.size() > 0) + if(!peptides.isEmpty()) { super.saveAll(peptides, connection); diff --git a/src/org/labkey/targetedms/chromlib/LibPeptideStructuralModification.java b/src/org/labkey/targetedms/chromlib/LibPeptideStructuralModification.java index 84d203187..50737d3a3 100644 --- a/src/org/labkey/targetedms/chromlib/LibPeptideStructuralModification.java +++ b/src/org/labkey/targetedms/chromlib/LibPeptideStructuralModification.java @@ -71,9 +71,7 @@ public void setMassDiff(Double massDiff) public boolean equals(Object o) { if (this == o) return true; - if (!(o instanceof LibPeptideStructuralModification)) return false; - - LibPeptideStructuralModification that = (LibPeptideStructuralModification) o; + if (!(o instanceof LibPeptideStructuralModification that)) return false; if (_peptideId != that._peptideId) return false; if (_structuralModificationId != that._structuralModificationId) return false; diff --git a/src/org/labkey/targetedms/chromlib/LibPrecursorDao.java b/src/org/labkey/targetedms/chromlib/LibPrecursorDao.java index 5eb67d9cd..5b62fcd4a 100644 --- a/src/org/labkey/targetedms/chromlib/LibPrecursorDao.java +++ b/src/org/labkey/targetedms/chromlib/LibPrecursorDao.java @@ -131,7 +131,7 @@ protected Constants.ColumnDef[] getColumns() @Override public void saveAll(Collection precursors, Connection connection) throws SQLException { - if(precursors.size() > 0) + if(!precursors.isEmpty()) { super.saveAll(precursors, connection); diff --git a/src/org/labkey/targetedms/chromlib/LibPrecursorIsotopeModification.java b/src/org/labkey/targetedms/chromlib/LibPrecursorIsotopeModification.java index 7cf961706..75c42c3b1 100644 --- a/src/org/labkey/targetedms/chromlib/LibPrecursorIsotopeModification.java +++ b/src/org/labkey/targetedms/chromlib/LibPrecursorIsotopeModification.java @@ -70,9 +70,7 @@ public void setMassDiff(Double massDiff) public boolean equals(Object o) { if (this == o) return true; - if (!(o instanceof LibPrecursorIsotopeModification)) return false; - - LibPrecursorIsotopeModification that = (LibPrecursorIsotopeModification) o; + if (!(o instanceof LibPrecursorIsotopeModification that)) return false; if (_isotopeModificationId != that._isotopeModificationId) return false; if (_precursorId != that._precursorId) return false; diff --git a/src/org/labkey/targetedms/chromlib/LibPrecursorRetentionTime.java b/src/org/labkey/targetedms/chromlib/LibPrecursorRetentionTime.java index 62eb57917..1069d4181 100644 --- a/src/org/labkey/targetedms/chromlib/LibPrecursorRetentionTime.java +++ b/src/org/labkey/targetedms/chromlib/LibPrecursorRetentionTime.java @@ -94,9 +94,7 @@ public void setOptimizationStep(Integer optimizationStep) public boolean equals(Object o) { if (this == o) return true; - if (!(o instanceof LibPrecursorRetentionTime)) return false; - - LibPrecursorRetentionTime that = (LibPrecursorRetentionTime) o; + if (!(o instanceof LibPrecursorRetentionTime that)) return false; if (_precursorId != that._precursorId) return false; if (_sampleFileId != that._sampleFileId) return false; diff --git a/src/org/labkey/targetedms/chromlib/LibProteinDao.java b/src/org/labkey/targetedms/chromlib/LibProteinDao.java index 6ad8adfbc..ed0a4031b 100644 --- a/src/org/labkey/targetedms/chromlib/LibProteinDao.java +++ b/src/org/labkey/targetedms/chromlib/LibProteinDao.java @@ -81,7 +81,7 @@ protected Constants.ColumnDef[] getColumns() @Override public void saveAll(Collection proteins, Connection connection) throws SQLException { - if(proteins != null && proteins.size() > 0) + if(proteins != null && !proteins.isEmpty()) { super.saveAll(proteins, connection); diff --git a/src/org/labkey/targetedms/chromlib/LibStructuralModLoss.java b/src/org/labkey/targetedms/chromlib/LibStructuralModLoss.java index 42d1c1d1f..533dc9eba 100644 --- a/src/org/labkey/targetedms/chromlib/LibStructuralModLoss.java +++ b/src/org/labkey/targetedms/chromlib/LibStructuralModLoss.java @@ -71,9 +71,7 @@ public void setMassDiffAvg(Double massDiffAvg) public boolean equals(Object o) { if (this == o) return true; - if (!(o instanceof LibStructuralModLoss)) return false; - - LibStructuralModLoss that = (LibStructuralModLoss) o; + if (!(o instanceof LibStructuralModLoss that)) return false; if (_formula != null ? !_formula.equals(that._formula) : that._formula != null) return false; if (_massDiffAvg != null ? !_massDiffAvg.equals(that._massDiffAvg) : that._massDiffAvg != null) return false; diff --git a/src/org/labkey/targetedms/chromlib/LibStructuralModification.java b/src/org/labkey/targetedms/chromlib/LibStructuralModification.java index 0ac3030cb..8f04fc513 100644 --- a/src/org/labkey/targetedms/chromlib/LibStructuralModification.java +++ b/src/org/labkey/targetedms/chromlib/LibStructuralModification.java @@ -149,9 +149,7 @@ List getModLosses() public boolean equals(Object o) { if (this == o) return true; - if (!(o instanceof LibStructuralModification)) return false; - - LibStructuralModification that = (LibStructuralModification) o; + if (!(o instanceof LibStructuralModification that)) return false; if (_aminoAcid != null ? !_aminoAcid.equals(that._aminoAcid) : that._aminoAcid != null) return false; if (_explicitMod != null ? !_explicitMod.equals(that._explicitMod) : that._explicitMod != null) return false; diff --git a/src/org/labkey/targetedms/chromlib/LibTransition.java b/src/org/labkey/targetedms/chromlib/LibTransition.java index 7409d73af..bd932df43 100644 --- a/src/org/labkey/targetedms/chromlib/LibTransition.java +++ b/src/org/labkey/targetedms/chromlib/LibTransition.java @@ -26,7 +26,6 @@ import org.labkey.targetedms.parser.TransitionSettings; import java.util.ArrayList; -import java.util.Collection; import java.util.List; import java.util.Objects; @@ -65,7 +64,7 @@ public class LibTransition extends AbstractLibEntity private String _adduct; - private List _optimizations = new ArrayList<>(); + private final List _optimizations = new ArrayList<>(); public LibTransition() {} diff --git a/src/org/labkey/targetedms/chromlib/LibTransitionDao.java b/src/org/labkey/targetedms/chromlib/LibTransitionDao.java index 9d3e95471..2e747dbe6 100644 --- a/src/org/labkey/targetedms/chromlib/LibTransitionDao.java +++ b/src/org/labkey/targetedms/chromlib/LibTransitionDao.java @@ -128,7 +128,7 @@ protected List parseQueryResult(ResultSet rs) throws SQLException @Override public void saveAll(Collection transitions, Connection connection) throws SQLException { - if (transitions.size() > 0) + if (!transitions.isEmpty()) { super.saveAll(transitions, connection); diff --git a/src/org/labkey/targetedms/conflict/ConflictTransition.java b/src/org/labkey/targetedms/conflict/ConflictTransition.java index 3b2d21738..5588a1b03 100644 --- a/src/org/labkey/targetedms/conflict/ConflictTransition.java +++ b/src/org/labkey/targetedms/conflict/ConflictTransition.java @@ -17,8 +17,6 @@ import org.labkey.targetedms.parser.GeneralPrecursor; import org.labkey.targetedms.parser.GeneralTransition; -import org.labkey.targetedms.parser.Precursor; -import org.labkey.targetedms.parser.Transition; /** * User: vsharma diff --git a/src/org/labkey/targetedms/datasource/MsDataSourceUtil.java b/src/org/labkey/targetedms/datasource/MsDataSourceUtil.java index c228b84aa..0ab9a7b3c 100644 --- a/src/org/labkey/targetedms/datasource/MsDataSourceUtil.java +++ b/src/org/labkey/targetedms/datasource/MsDataSourceUtil.java @@ -127,7 +127,7 @@ private ExpData getDataForSampleFile(SampleFile sampleFile, Container container, { List expDatas = getExpData(sampleFile.getFileName(), container, rawFilesDir, expSvc); - if(expDatas.size() == 0) + if(expDatas.isEmpty()) { return null; } @@ -277,7 +277,7 @@ private Path getDataPath(String fileName, MsDataSource dataSource, Container con { List expDatas = getExpData(fileName, container, rawFilesDir, expSvc); - if (expDatas.size() > 0) + if (!expDatas.isEmpty()) { for (ExpData data : expDatas) { diff --git a/src/org/labkey/targetedms/datasource/MsMultiDataSource.java b/src/org/labkey/targetedms/datasource/MsMultiDataSource.java index 7cb099f2d..82cd81d5d 100644 --- a/src/org/labkey/targetedms/datasource/MsMultiDataSource.java +++ b/src/org/labkey/targetedms/datasource/MsMultiDataSource.java @@ -12,8 +12,8 @@ class MsMultiDataSource extends MsDataSource { - private List _dirSources; - private List _fileSources; + private final List _dirSources; + private final List _fileSources; MsMultiDataSource() { diff --git a/src/org/labkey/targetedms/datasource/PsiInstruments.java b/src/org/labkey/targetedms/datasource/PsiInstruments.java index 53f437c4e..9038ecf9c 100644 --- a/src/org/labkey/targetedms/datasource/PsiInstruments.java +++ b/src/org/labkey/targetedms/datasource/PsiInstruments.java @@ -41,7 +41,7 @@ public class PsiInstruments { - private static Map _instruments = new HashMap<>(); + private static final Map _instruments = new HashMap<>(); private static final Logger LOG = LogManager.getLogger(PsiInstruments.class); diff --git a/src/org/labkey/targetedms/parser/ComplexFragmentIonName.java b/src/org/labkey/targetedms/parser/ComplexFragmentIonName.java index 2be1ec446..bad195517 100644 --- a/src/org/labkey/targetedms/parser/ComplexFragmentIonName.java +++ b/src/org/labkey/targetedms/parser/ComplexFragmentIonName.java @@ -151,7 +151,7 @@ public static boolean looksLikeIntactPrecursor(String name) return false; } // Current format: Precursors always look like some number of "p" separated by hyphens - if ("".equals(name.substring(1).replace("-p", ""))) { + if (name.substring(1).replace("-p", "").isEmpty()) { return true; } if (name.indexOf('}') < 0) { diff --git a/src/org/labkey/targetedms/parser/DataSettings.java b/src/org/labkey/targetedms/parser/DataSettings.java index 6c5128656..5f2c9d1e9 100644 --- a/src/org/labkey/targetedms/parser/DataSettings.java +++ b/src/org/labkey/targetedms/parser/DataSettings.java @@ -40,9 +40,9 @@ public enum AnnotationType { true_false(JdbcType.BOOLEAN, false, true), value_list(JdbcType.VARCHAR, false, true); - private JdbcType _dataType; - private boolean _isMeasure; - private boolean _isDimension; + private final JdbcType _dataType; + private final boolean _isMeasure; + private final boolean _isDimension; AnnotationType(JdbcType dataType, boolean isMeasure, boolean isDimension) { @@ -88,11 +88,11 @@ public enum AnnotationTarget { transition_result } - private Map _annotationDefinitions = new HashMap<>(); - private Map> _targetAnnotationsMap = + private final Map _annotationDefinitions = new HashMap<>(); + private final Map> _targetAnnotationsMap = new HashMap<>(); - private List _groupComparisons = new ArrayList<>(); - private List _listDatas = new ArrayList<>(); + private final List _groupComparisons = new ArrayList<>(); + private final List _listDatas = new ArrayList<>(); public void addAnnotations(String name, String targetsString, String type, String lookup) { diff --git a/src/org/labkey/targetedms/parser/Instrument.java b/src/org/labkey/targetedms/parser/Instrument.java index eb8a07310..94b7067d5 100644 --- a/src/org/labkey/targetedms/parser/Instrument.java +++ b/src/org/labkey/targetedms/parser/Instrument.java @@ -94,9 +94,7 @@ public void setDetector(String detector) public boolean equals(Object o) { if (this == o) return true; - if (!(o instanceof Instrument)) return false; - - Instrument that = (Instrument) o; + if (!(o instanceof Instrument that)) return false; if (analyzer != null ? !analyzer.equals(that.analyzer) : that.analyzer != null) return false; if (detector != null ? !detector.equals(that.detector) : that.detector != null) return false; diff --git a/src/org/labkey/targetedms/parser/Peptide.java b/src/org/labkey/targetedms/parser/Peptide.java index 58e128106..fbc2d9f0e 100644 --- a/src/org/labkey/targetedms/parser/Peptide.java +++ b/src/org/labkey/targetedms/parser/Peptide.java @@ -385,7 +385,7 @@ public static String stripModifications(String modifiedSequence, List(unmodifiedSequence.length() - 1, strModification)); + modifications.add(new Pair<>(unmodifiedSequence.length() - 1, strModification)); } modificationStart = null; } diff --git a/src/org/labkey/targetedms/parser/PeptideSettings.java b/src/org/labkey/targetedms/parser/PeptideSettings.java index 6165663fc..24980211b 100644 --- a/src/org/labkey/targetedms/parser/PeptideSettings.java +++ b/src/org/labkey/targetedms/parser/PeptideSettings.java @@ -868,6 +868,7 @@ public static final class SpectrumLibrary extends SkylineEntity implements ISpec private Boolean _useExplicitPeakBounds; private String _panoramaServer; + @Override public long getRunId() { return _runId; diff --git a/src/org/labkey/targetedms/parser/PeptideSettingsParser.java b/src/org/labkey/targetedms/parser/PeptideSettingsParser.java index f994b769e..4e37d9522 100644 --- a/src/org/labkey/targetedms/parser/PeptideSettingsParser.java +++ b/src/org/labkey/targetedms/parser/PeptideSettingsParser.java @@ -230,7 +230,7 @@ else if(XmlUtil.isStartElement(reader, evtType, HEAVY_MODIFICATIONS)) // If we did not find either the "internal_standard" attribute or elements, check if we have // a "heavy" isotope label. If we do, set "heavy" as the internal standard - if(internalStandards.size() == 0 && isotopeLabelNames.contains(PeptideSettings.HEAVY_LABEL)) + if(internalStandards.isEmpty() && isotopeLabelNames.contains(PeptideSettings.HEAVY_LABEL)) { internalStandards.add(PeptideSettings.HEAVY_LABEL); } diff --git a/src/org/labkey/targetedms/parser/SampleFile.java b/src/org/labkey/targetedms/parser/SampleFile.java index 79a2e4897..b3c24c25b 100644 --- a/src/org/labkey/targetedms/parser/SampleFile.java +++ b/src/org/labkey/targetedms/parser/SampleFile.java @@ -54,6 +54,7 @@ public class SampleFile extends SkylineEntity implements ISampleFile private List _instrumentInfoList; + @Override public long getReplicateId() { return _replicateId; diff --git a/src/org/labkey/targetedms/parser/SpectrumFilter.java b/src/org/labkey/targetedms/parser/SpectrumFilter.java index 0c329795e..6da0bbda6 100644 --- a/src/org/labkey/targetedms/parser/SpectrumFilter.java +++ b/src/org/labkey/targetedms/parser/SpectrumFilter.java @@ -26,7 +26,6 @@ import javax.xml.stream.XMLStreamReader; import java.io.StringReader; import java.util.ArrayList; -import java.util.Arrays; import java.util.List; import java.util.Map; import java.util.Objects; diff --git a/src/org/labkey/targetedms/parser/Target.java b/src/org/labkey/targetedms/parser/Target.java index 8b6634b11..bae200fd4 100644 --- a/src/org/labkey/targetedms/parser/Target.java +++ b/src/org/labkey/targetedms/parser/Target.java @@ -129,7 +129,7 @@ public static Target fromChromatogramTextId(String textId) return null; } - if (parts.size() > 0) + if (!parts.isEmpty()) { target.name = parts.get(0); } diff --git a/src/org/labkey/targetedms/parser/TransitionSettings.java b/src/org/labkey/targetedms/parser/TransitionSettings.java index 58a9b0872..e1d3e4902 100644 --- a/src/org/labkey/targetedms/parser/TransitionSettings.java +++ b/src/org/labkey/targetedms/parser/TransitionSettings.java @@ -419,7 +419,7 @@ public static final class PredictionSettings private Predictor _cePredictor; private Predictor _dpPredictor; - private Map _optimizedLibraries = new HashMap<>(); + private final Map _optimizedLibraries = new HashMap<>(); public long getRunId() { diff --git a/src/org/labkey/targetedms/parser/XmlUtil.java b/src/org/labkey/targetedms/parser/XmlUtil.java index 86e4aaea8..1ada096b7 100644 --- a/src/org/labkey/targetedms/parser/XmlUtil.java +++ b/src/org/labkey/targetedms/parser/XmlUtil.java @@ -66,7 +66,7 @@ public static Double readDouble(XMLStreamReader reader, String endElementName) t int evtType = reader.next(); if (evtType == XMLStreamReader.END_ELEMENT && endElementName.equalsIgnoreCase(reader.getLocalName())) { - if (sb.length() == 0) + if (sb.isEmpty()) { return null; } diff --git a/src/org/labkey/targetedms/parser/list/ListData.java b/src/org/labkey/targetedms/parser/list/ListData.java index b9f0f8845..600ed89dc 100644 --- a/src/org/labkey/targetedms/parser/list/ListData.java +++ b/src/org/labkey/targetedms/parser/list/ListData.java @@ -21,9 +21,9 @@ public class ListData { - private ListDefinition _listDefinition; - private List _columns; - private List> _columnDatas; + private final ListDefinition _listDefinition; + private final List _columns; + private final List> _columnDatas; public ListData() { diff --git a/src/org/labkey/targetedms/parser/proto/ChromatogramGroupDataOuterClass.java b/src/org/labkey/targetedms/parser/proto/ChromatogramGroupDataOuterClass.java index 726ebb171..e609ce1d2 100644 --- a/src/org/labkey/targetedms/parser/proto/ChromatogramGroupDataOuterClass.java +++ b/src/org/labkey/targetedms/parser/proto/ChromatogramGroupDataOuterClass.java @@ -248,6 +248,7 @@ protected java.lang.Object newInstance( * repeated float times = 1; * @return The count of times. */ + @Override public int getTimesCount() { return times_.size(); } @@ -256,6 +257,7 @@ public int getTimesCount() { * @param index The index of the element to return. * @return The times at the given index. */ + @Override public float getTimes(int index) { return times_.getFloat(index); } @@ -276,7 +278,7 @@ public final boolean isInitialized() { public void writeTo(com.google.protobuf.CodedOutputStream output) throws java.io.IOException { getSerializedSize(); - if (getTimesList().size() > 0) { + if (!getTimesList().isEmpty()) { output.writeUInt32NoTag(10); output.writeUInt32NoTag(timesMemoizedSerializedSize); } @@ -293,7 +295,7 @@ public int getSerializedSize() { size = 0; { - int dataSize = 0; + int dataSize; dataSize = 4 * getTimesList().size(); size += dataSize; if (!getTimesList().isEmpty()) { @@ -313,12 +315,11 @@ public boolean equals(final java.lang.Object obj) { if (obj == this) { return true; } - if (!(obj instanceof org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.TimeList)) { + if (!(obj instanceof TimeList other)) { return super.equals(obj); } - org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.TimeList other = (org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.TimeList) obj; - if (!getTimesList() + if (!getTimesList() .equals(other.getTimesList())) return false; if (!getUnknownFields().equals(other.getUnknownFields())) return false; return true; @@ -638,6 +639,7 @@ private void ensureTimesIsMutable(int capacity) { * repeated float times = 1; * @return A list containing the times. */ + @Override public java.util.List getTimesList() { times_.makeImmutable(); @@ -647,6 +649,7 @@ private void ensureTimesIsMutable(int capacity) { * repeated float times = 1; * @return The count of times. */ + @Override public int getTimesCount() { return times_.size(); } @@ -655,6 +658,7 @@ public int getTimesCount() { * @param index The index of the element to return. * @return The times at the given index. */ + @Override public float getTimes(int index) { return times_.getFloat(index); } @@ -737,25 +741,34 @@ public static org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass } private static final com.google.protobuf.Parser - PARSER = new com.google.protobuf.AbstractParser() { - @java.lang.Override - public TimeList parsePartialFrom( - com.google.protobuf.CodedInputStream input, - com.google.protobuf.ExtensionRegistryLite extensionRegistry) - throws com.google.protobuf.InvalidProtocolBufferException { - Builder builder = newBuilder(); - try { - builder.mergeFrom(input, extensionRegistry); - } catch (com.google.protobuf.InvalidProtocolBufferException e) { - throw e.setUnfinishedMessage(builder.buildPartial()); - } catch (com.google.protobuf.UninitializedMessageException e) { - throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); - } catch (java.io.IOException e) { - throw new com.google.protobuf.InvalidProtocolBufferException(e) - .setUnfinishedMessage(builder.buildPartial()); + PARSER = new com.google.protobuf.AbstractParser<>() + { + @java.lang.Override + public TimeList parsePartialFrom( + com.google.protobuf.CodedInputStream input, + com.google.protobuf.ExtensionRegistryLite extensionRegistry) + throws com.google.protobuf.InvalidProtocolBufferException + { + Builder builder = newBuilder(); + try + { + builder.mergeFrom(input, extensionRegistry); + } + catch (com.google.protobuf.InvalidProtocolBufferException e) + { + throw e.setUnfinishedMessage(builder.buildPartial()); + } + catch (com.google.protobuf.UninitializedMessageException e) + { + throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); + } + catch (java.io.IOException e) + { + throw new com.google.protobuf.InvalidProtocolBufferException(e) + .setUnfinishedMessage(builder.buildPartial()); + } + return builder.buildPartial(); } - return builder.buildPartial(); - } }; public static com.google.protobuf.Parser parser() { @@ -848,6 +861,7 @@ protected java.lang.Object newInstance( * repeated int32 scanIds = 2; * @return The count of scanIds. */ + @Override public int getScanIdsCount() { return scanIds_.size(); } @@ -856,6 +870,7 @@ public int getScanIdsCount() { * @param index The index of the element to return. * @return The scanIds at the given index. */ + @Override public int getScanIds(int index) { return scanIds_.getInt(index); } @@ -876,7 +891,7 @@ public final boolean isInitialized() { public void writeTo(com.google.protobuf.CodedOutputStream output) throws java.io.IOException { getSerializedSize(); - if (getScanIdsList().size() > 0) { + if (!getScanIdsList().isEmpty()) { output.writeUInt32NoTag(18); output.writeUInt32NoTag(scanIdsMemoizedSerializedSize); } @@ -916,12 +931,11 @@ public boolean equals(final java.lang.Object obj) { if (obj == this) { return true; } - if (!(obj instanceof org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.ScanIdList)) { + if (!(obj instanceof ScanIdList other)) { return super.equals(obj); } - org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.ScanIdList other = (org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.ScanIdList) obj; - if (!getScanIdsList() + if (!getScanIdsList() .equals(other.getScanIdsList())) return false; if (!getUnknownFields().equals(other.getUnknownFields())) return false; return true; @@ -1234,6 +1248,7 @@ private void ensureScanIdsIsMutable() { * repeated int32 scanIds = 2; * @return A list containing the scanIds. */ + @Override public java.util.List getScanIdsList() { scanIds_.makeImmutable(); @@ -1243,6 +1258,7 @@ private void ensureScanIdsIsMutable() { * repeated int32 scanIds = 2; * @return The count of scanIds. */ + @Override public int getScanIdsCount() { return scanIds_.size(); } @@ -1251,6 +1267,7 @@ public int getScanIdsCount() { * @param index The index of the element to return. * @return The scanIds at the given index. */ + @Override public int getScanIds(int index) { return scanIds_.getInt(index); } @@ -1333,25 +1350,34 @@ public static org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass } private static final com.google.protobuf.Parser - PARSER = new com.google.protobuf.AbstractParser() { - @java.lang.Override - public ScanIdList parsePartialFrom( - com.google.protobuf.CodedInputStream input, - com.google.protobuf.ExtensionRegistryLite extensionRegistry) - throws com.google.protobuf.InvalidProtocolBufferException { - Builder builder = newBuilder(); - try { - builder.mergeFrom(input, extensionRegistry); - } catch (com.google.protobuf.InvalidProtocolBufferException e) { - throw e.setUnfinishedMessage(builder.buildPartial()); - } catch (com.google.protobuf.UninitializedMessageException e) { - throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); - } catch (java.io.IOException e) { - throw new com.google.protobuf.InvalidProtocolBufferException(e) - .setUnfinishedMessage(builder.buildPartial()); + PARSER = new com.google.protobuf.AbstractParser<>() + { + @java.lang.Override + public ScanIdList parsePartialFrom( + com.google.protobuf.CodedInputStream input, + com.google.protobuf.ExtensionRegistryLite extensionRegistry) + throws com.google.protobuf.InvalidProtocolBufferException + { + Builder builder = newBuilder(); + try + { + builder.mergeFrom(input, extensionRegistry); + } + catch (com.google.protobuf.InvalidProtocolBufferException e) + { + throw e.setUnfinishedMessage(builder.buildPartial()); + } + catch (com.google.protobuf.UninitializedMessageException e) + { + throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); + } + catch (java.io.IOException e) + { + throw new com.google.protobuf.InvalidProtocolBufferException(e) + .setUnfinishedMessage(builder.buildPartial()); + } + return builder.buildPartial(); } - return builder.buildPartial(); - } }; public static com.google.protobuf.Parser parser() { @@ -1515,6 +1541,7 @@ public int getTimeListIndex() { * repeated float intensities = 2; * @return The count of intensities. */ + @Override public int getIntensitiesCount() { return intensities_.size(); } @@ -1523,6 +1550,7 @@ public int getIntensitiesCount() { * @param index The index of the element to return. * @return The intensities at the given index. */ + @Override public float getIntensities(int index) { return intensities_.getFloat(index); } @@ -1545,6 +1573,7 @@ public float getIntensities(int index) { * repeated float massErrorsDeprecated = 3; * @return The count of massErrorsDeprecated. */ + @Override public int getMassErrorsDeprecatedCount() { return massErrorsDeprecated_.size(); } @@ -1553,6 +1582,7 @@ public int getMassErrorsDeprecatedCount() { * @param index The index of the element to return. * @return The massErrorsDeprecated at the given index. */ + @Override public float getMassErrorsDeprecated(int index) { return massErrorsDeprecated_.getFloat(index); } @@ -1575,6 +1605,7 @@ public float getMassErrorsDeprecated(int index) { * repeated sint32 massErrors100X = 5; * @return The count of massErrors100X. */ + @Override public int getMassErrors100XCount() { return massErrors100X_.size(); } @@ -1583,6 +1614,7 @@ public int getMassErrors100XCount() { * @param index The index of the element to return. * @return The massErrors100X at the given index. */ + @Override public int getMassErrors100X(int index) { return massErrors100X_.getInt(index); } @@ -1621,14 +1653,14 @@ public void writeTo(com.google.protobuf.CodedOutputStream output) if (timeListIndex_ != 0) { output.writeInt32(1, timeListIndex_); } - if (getIntensitiesList().size() > 0) { + if (!getIntensitiesList().isEmpty()) { output.writeUInt32NoTag(18); output.writeUInt32NoTag(intensitiesMemoizedSerializedSize); } for (int i = 0; i < intensities_.size(); i++) { output.writeFloatNoTag(intensities_.getFloat(i)); } - if (getMassErrorsDeprecatedList().size() > 0) { + if (!getMassErrorsDeprecatedList().isEmpty()) { output.writeUInt32NoTag(26); output.writeUInt32NoTag(massErrorsDeprecatedMemoizedSerializedSize); } @@ -1638,7 +1670,7 @@ public void writeTo(com.google.protobuf.CodedOutputStream output) if (scanIdListIndex_ != 0) { output.writeInt32(4, scanIdListIndex_); } - if (getMassErrors100XList().size() > 0) { + if (!getMassErrors100XList().isEmpty()) { output.writeUInt32NoTag(42); output.writeUInt32NoTag(massErrors100XMemoizedSerializedSize); } @@ -1659,7 +1691,7 @@ public int getSerializedSize() { .computeInt32Size(1, timeListIndex_); } { - int dataSize = 0; + int dataSize; dataSize = 4 * getIntensitiesList().size(); size += dataSize; if (!getIntensitiesList().isEmpty()) { @@ -1670,7 +1702,7 @@ public int getSerializedSize() { intensitiesMemoizedSerializedSize = dataSize; } { - int dataSize = 0; + int dataSize; dataSize = 4 * getMassErrorsDeprecatedList().size(); size += dataSize; if (!getMassErrorsDeprecatedList().isEmpty()) { @@ -1708,12 +1740,11 @@ public boolean equals(final java.lang.Object obj) { if (obj == this) { return true; } - if (!(obj instanceof org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.Chromatogram)) { + if (!(obj instanceof Chromatogram other)) { return super.equals(obj); } - org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.Chromatogram other = (org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.Chromatogram) obj; - if (getTimeListIndex() + if (getTimeListIndex() != other.getTimeListIndex()) return false; if (!getIntensitiesList() .equals(other.getIntensitiesList())) return false; @@ -2186,6 +2217,7 @@ private void ensureIntensitiesIsMutable(int capacity) { * repeated float intensities = 2; * @return A list containing the intensities. */ + @Override public java.util.List getIntensitiesList() { intensities_.makeImmutable(); @@ -2195,6 +2227,7 @@ private void ensureIntensitiesIsMutable(int capacity) { * repeated float intensities = 2; * @return The count of intensities. */ + @Override public int getIntensitiesCount() { return intensities_.size(); } @@ -2203,6 +2236,7 @@ public int getIntensitiesCount() { * @param index The index of the element to return. * @return The intensities at the given index. */ + @Override public float getIntensities(int index) { return intensities_.getFloat(index); } @@ -2276,6 +2310,7 @@ private void ensureMassErrorsDeprecatedIsMutable(int capacity) { * repeated float massErrorsDeprecated = 3; * @return A list containing the massErrorsDeprecated. */ + @Override public java.util.List getMassErrorsDeprecatedList() { massErrorsDeprecated_.makeImmutable(); @@ -2285,6 +2320,7 @@ private void ensureMassErrorsDeprecatedIsMutable(int capacity) { * repeated float massErrorsDeprecated = 3; * @return The count of massErrorsDeprecated. */ + @Override public int getMassErrorsDeprecatedCount() { return massErrorsDeprecated_.size(); } @@ -2293,6 +2329,7 @@ public int getMassErrorsDeprecatedCount() { * @param index The index of the element to return. * @return The massErrorsDeprecated at the given index. */ + @Override public float getMassErrorsDeprecated(int index) { return massErrorsDeprecated_.getFloat(index); } @@ -2360,6 +2397,7 @@ private void ensureMassErrors100XIsMutable() { * repeated sint32 massErrors100X = 5; * @return A list containing the massErrors100X. */ + @Override public java.util.List getMassErrors100XList() { massErrors100X_.makeImmutable(); @@ -2369,6 +2407,7 @@ private void ensureMassErrors100XIsMutable() { * repeated sint32 massErrors100X = 5; * @return The count of massErrors100X. */ + @Override public int getMassErrors100XCount() { return massErrors100X_.size(); } @@ -2377,6 +2416,7 @@ public int getMassErrors100XCount() { * @param index The index of the element to return. * @return The massErrors100X at the given index. */ + @Override public int getMassErrors100X(int index) { return massErrors100X_.getInt(index); } @@ -2503,25 +2543,34 @@ public static org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass } private static final com.google.protobuf.Parser - PARSER = new com.google.protobuf.AbstractParser() { - @java.lang.Override - public Chromatogram parsePartialFrom( - com.google.protobuf.CodedInputStream input, - com.google.protobuf.ExtensionRegistryLite extensionRegistry) - throws com.google.protobuf.InvalidProtocolBufferException { - Builder builder = newBuilder(); - try { - builder.mergeFrom(input, extensionRegistry); - } catch (com.google.protobuf.InvalidProtocolBufferException e) { - throw e.setUnfinishedMessage(builder.buildPartial()); - } catch (com.google.protobuf.UninitializedMessageException e) { - throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); - } catch (java.io.IOException e) { - throw new com.google.protobuf.InvalidProtocolBufferException(e) - .setUnfinishedMessage(builder.buildPartial()); + PARSER = new com.google.protobuf.AbstractParser<>() + { + @java.lang.Override + public Chromatogram parsePartialFrom( + com.google.protobuf.CodedInputStream input, + com.google.protobuf.ExtensionRegistryLite extensionRegistry) + throws com.google.protobuf.InvalidProtocolBufferException + { + Builder builder = newBuilder(); + try + { + builder.mergeFrom(input, extensionRegistry); + } + catch (com.google.protobuf.InvalidProtocolBufferException e) + { + throw e.setUnfinishedMessage(builder.buildPartial()); + } + catch (com.google.protobuf.UninitializedMessageException e) + { + throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); + } + catch (java.io.IOException e) + { + throw new com.google.protobuf.InvalidProtocolBufferException(e) + .setUnfinishedMessage(builder.buildPartial()); + } + return builder.buildPartial(); } - return builder.buildPartial(); - } }; public static com.google.protobuf.Parser parser() { @@ -2632,6 +2681,7 @@ protected java.lang.Object newInstance( * repeated float startTimes = 1; * @return The count of startTimes. */ + @Override public int getStartTimesCount() { return startTimes_.size(); } @@ -2640,6 +2690,7 @@ public int getStartTimesCount() { * @param index The index of the element to return. * @return The startTimes at the given index. */ + @Override public float getStartTimes(int index) { return startTimes_.getFloat(index); } @@ -2662,6 +2713,7 @@ public float getStartTimes(int index) { * repeated float endTimes = 2; * @return The count of endTimes. */ + @Override public int getEndTimesCount() { return endTimes_.size(); } @@ -2670,6 +2722,7 @@ public int getEndTimesCount() { * @param index The index of the element to return. * @return The endTimes at the given index. */ + @Override public float getEndTimes(int index) { return endTimes_.getFloat(index); } @@ -2690,14 +2743,14 @@ public final boolean isInitialized() { public void writeTo(com.google.protobuf.CodedOutputStream output) throws java.io.IOException { getSerializedSize(); - if (getStartTimesList().size() > 0) { + if (!getStartTimesList().isEmpty()) { output.writeUInt32NoTag(10); output.writeUInt32NoTag(startTimesMemoizedSerializedSize); } for (int i = 0; i < startTimes_.size(); i++) { output.writeFloatNoTag(startTimes_.getFloat(i)); } - if (getEndTimesList().size() > 0) { + if (!getEndTimesList().isEmpty()) { output.writeUInt32NoTag(18); output.writeUInt32NoTag(endTimesMemoizedSerializedSize); } @@ -2714,7 +2767,7 @@ public int getSerializedSize() { size = 0; { - int dataSize = 0; + int dataSize; dataSize = 4 * getStartTimesList().size(); size += dataSize; if (!getStartTimesList().isEmpty()) { @@ -2725,7 +2778,7 @@ public int getSerializedSize() { startTimesMemoizedSerializedSize = dataSize; } { - int dataSize = 0; + int dataSize; dataSize = 4 * getEndTimesList().size(); size += dataSize; if (!getEndTimesList().isEmpty()) { @@ -2745,12 +2798,11 @@ public boolean equals(final java.lang.Object obj) { if (obj == this) { return true; } - if (!(obj instanceof org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.TimeIntervals)) { + if (!(obj instanceof TimeIntervals other)) { return super.equals(obj); } - org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.TimeIntervals other = (org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.TimeIntervals) obj; - if (!getStartTimesList() + if (!getStartTimesList() .equals(other.getStartTimesList())) return false; if (!getEndTimesList() .equals(other.getEndTimesList())) return false; @@ -3109,6 +3161,7 @@ private void ensureStartTimesIsMutable(int capacity) { * repeated float startTimes = 1; * @return A list containing the startTimes. */ + @Override public java.util.List getStartTimesList() { startTimes_.makeImmutable(); @@ -3118,6 +3171,7 @@ private void ensureStartTimesIsMutable(int capacity) { * repeated float startTimes = 1; * @return The count of startTimes. */ + @Override public int getStartTimesCount() { return startTimes_.size(); } @@ -3126,6 +3180,7 @@ public int getStartTimesCount() { * @param index The index of the element to return. * @return The startTimes at the given index. */ + @Override public float getStartTimes(int index) { return startTimes_.getFloat(index); } @@ -3199,6 +3254,7 @@ private void ensureEndTimesIsMutable(int capacity) { * repeated float endTimes = 2; * @return A list containing the endTimes. */ + @Override public java.util.List getEndTimesList() { endTimes_.makeImmutable(); @@ -3208,6 +3264,7 @@ private void ensureEndTimesIsMutable(int capacity) { * repeated float endTimes = 2; * @return The count of endTimes. */ + @Override public int getEndTimesCount() { return endTimes_.size(); } @@ -3216,6 +3273,7 @@ public int getEndTimesCount() { * @param index The index of the element to return. * @return The endTimes at the given index. */ + @Override public float getEndTimes(int index) { return endTimes_.getFloat(index); } @@ -3298,25 +3356,34 @@ public static org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass } private static final com.google.protobuf.Parser - PARSER = new com.google.protobuf.AbstractParser() { - @java.lang.Override - public TimeIntervals parsePartialFrom( - com.google.protobuf.CodedInputStream input, - com.google.protobuf.ExtensionRegistryLite extensionRegistry) - throws com.google.protobuf.InvalidProtocolBufferException { - Builder builder = newBuilder(); - try { - builder.mergeFrom(input, extensionRegistry); - } catch (com.google.protobuf.InvalidProtocolBufferException e) { - throw e.setUnfinishedMessage(builder.buildPartial()); - } catch (com.google.protobuf.UninitializedMessageException e) { - throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); - } catch (java.io.IOException e) { - throw new com.google.protobuf.InvalidProtocolBufferException(e) - .setUnfinishedMessage(builder.buildPartial()); + PARSER = new com.google.protobuf.AbstractParser<>() + { + @java.lang.Override + public TimeIntervals parsePartialFrom( + com.google.protobuf.CodedInputStream input, + com.google.protobuf.ExtensionRegistryLite extensionRegistry) + throws com.google.protobuf.InvalidProtocolBufferException + { + Builder builder = newBuilder(); + try + { + builder.mergeFrom(input, extensionRegistry); + } + catch (com.google.protobuf.InvalidProtocolBufferException e) + { + throw e.setUnfinishedMessage(builder.buildPartial()); + } + catch (com.google.protobuf.UninitializedMessageException e) + { + throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); + } + catch (java.io.IOException e) + { + throw new com.google.protobuf.InvalidProtocolBufferException(e) + .setUnfinishedMessage(builder.buildPartial()); + } + return builder.buildPartial(); } - return builder.buildPartial(); - } }; public static com.google.protobuf.Parser parser() { @@ -3636,12 +3703,11 @@ public boolean equals(final java.lang.Object obj) { if (obj == this) { return true; } - if (!(obj instanceof org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData)) { + if (!(obj instanceof ChromatogramGroupData other)) { return super.equals(obj); } - org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData other = (org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData) obj; - if (!getTimeListsList() + if (!getTimeListsList() .equals(other.getTimeListsList())) return false; if (!getScanIdListsList() .equals(other.getScanIdListsList())) return false; @@ -4224,7 +4290,7 @@ public Builder mergeFrom( java.util.Collections.emptyList(); private void ensureTimeListsIsMutable() { if (!((bitField0_ & 0x00000001) != 0)) { - timeLists_ = new java.util.ArrayList(timeLists_); + timeLists_ = new java.util.ArrayList<>(timeLists_); bitField0_ |= 0x00000001; } } @@ -4235,6 +4301,7 @@ private void ensureTimeListsIsMutable() { /** * repeated .ChromatogramGroupData.TimeList timeLists = 1; */ + @Override public java.util.List getTimeListsList() { if (timeListsBuilder_ == null) { return java.util.Collections.unmodifiableList(timeLists_); @@ -4245,6 +4312,7 @@ public java.util.Listrepeated .ChromatogramGroupData.TimeList timeLists = 1; */ + @Override public int getTimeListsCount() { if (timeListsBuilder_ == null) { return timeLists_.size(); @@ -4255,6 +4323,7 @@ public int getTimeListsCount() { /** * repeated .ChromatogramGroupData.TimeList timeLists = 1; */ + @Override public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.TimeList getTimeLists(int index) { if (timeListsBuilder_ == null) { return timeLists_.get(index); @@ -4405,6 +4474,7 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Chroma /** * repeated .ChromatogramGroupData.TimeList timeLists = 1; */ + @Override public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.TimeListOrBuilder getTimeListsOrBuilder( int index) { if (timeListsBuilder_ == null) { @@ -4415,7 +4485,8 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Chroma /** * repeated .ChromatogramGroupData.TimeList timeLists = 1; */ - public java.util.List + @Override + public java.util.List getTimeListsOrBuilderList() { if (timeListsBuilder_ != null) { return timeListsBuilder_.getMessageOrBuilderList(); @@ -4449,8 +4520,7 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Chroma org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.TimeList, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.TimeList.Builder, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.TimeListOrBuilder> getTimeListsFieldBuilder() { if (timeListsBuilder_ == null) { - timeListsBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3< - org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.TimeList, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.TimeList.Builder, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.TimeListOrBuilder>( + timeListsBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<>( timeLists_, ((bitField0_ & 0x00000001) != 0), getParentForChildren(), @@ -4464,7 +4534,7 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Chroma java.util.Collections.emptyList(); private void ensureScanIdListsIsMutable() { if (!((bitField0_ & 0x00000002) != 0)) { - scanIdLists_ = new java.util.ArrayList(scanIdLists_); + scanIdLists_ = new java.util.ArrayList<>(scanIdLists_); bitField0_ |= 0x00000002; } } @@ -4475,6 +4545,7 @@ private void ensureScanIdListsIsMutable() { /** * repeated .ChromatogramGroupData.ScanIdList scanIdLists = 2; */ + @Override public java.util.List getScanIdListsList() { if (scanIdListsBuilder_ == null) { return java.util.Collections.unmodifiableList(scanIdLists_); @@ -4485,6 +4556,7 @@ public java.util.Listrepeated .ChromatogramGroupData.ScanIdList scanIdLists = 2; */ + @Override public int getScanIdListsCount() { if (scanIdListsBuilder_ == null) { return scanIdLists_.size(); @@ -4495,6 +4567,7 @@ public int getScanIdListsCount() { /** * repeated .ChromatogramGroupData.ScanIdList scanIdLists = 2; */ + @Override public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.ScanIdList getScanIdLists(int index) { if (scanIdListsBuilder_ == null) { return scanIdLists_.get(index); @@ -4645,6 +4718,7 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Chroma /** * repeated .ChromatogramGroupData.ScanIdList scanIdLists = 2; */ + @Override public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.ScanIdListOrBuilder getScanIdListsOrBuilder( int index) { if (scanIdListsBuilder_ == null) { @@ -4655,7 +4729,8 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Chroma /** * repeated .ChromatogramGroupData.ScanIdList scanIdLists = 2; */ - public java.util.List + @Override + public java.util.List getScanIdListsOrBuilderList() { if (scanIdListsBuilder_ != null) { return scanIdListsBuilder_.getMessageOrBuilderList(); @@ -4689,8 +4764,7 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Chroma org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.ScanIdList, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.ScanIdList.Builder, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.ScanIdListOrBuilder> getScanIdListsFieldBuilder() { if (scanIdListsBuilder_ == null) { - scanIdListsBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3< - org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.ScanIdList, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.ScanIdList.Builder, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.ScanIdListOrBuilder>( + scanIdListsBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<>( scanIdLists_, ((bitField0_ & 0x00000002) != 0), getParentForChildren(), @@ -4704,7 +4778,7 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Chroma java.util.Collections.emptyList(); private void ensureChromatogramsIsMutable() { if (!((bitField0_ & 0x00000004) != 0)) { - chromatograms_ = new java.util.ArrayList(chromatograms_); + chromatograms_ = new java.util.ArrayList<>(chromatograms_); bitField0_ |= 0x00000004; } } @@ -4715,6 +4789,7 @@ private void ensureChromatogramsIsMutable() { /** * repeated .ChromatogramGroupData.Chromatogram chromatograms = 3; */ + @Override public java.util.List getChromatogramsList() { if (chromatogramsBuilder_ == null) { return java.util.Collections.unmodifiableList(chromatograms_); @@ -4725,6 +4800,7 @@ public java.util.Listrepeated .ChromatogramGroupData.Chromatogram chromatograms = 3; */ + @Override public int getChromatogramsCount() { if (chromatogramsBuilder_ == null) { return chromatograms_.size(); @@ -4735,6 +4811,7 @@ public int getChromatogramsCount() { /** * repeated .ChromatogramGroupData.Chromatogram chromatograms = 3; */ + @Override public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.Chromatogram getChromatograms(int index) { if (chromatogramsBuilder_ == null) { return chromatograms_.get(index); @@ -4885,6 +4962,7 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Chroma /** * repeated .ChromatogramGroupData.Chromatogram chromatograms = 3; */ + @Override public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.ChromatogramOrBuilder getChromatogramsOrBuilder( int index) { if (chromatogramsBuilder_ == null) { @@ -4895,7 +4973,8 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Chroma /** * repeated .ChromatogramGroupData.Chromatogram chromatograms = 3; */ - public java.util.List + @Override + public java.util.List getChromatogramsOrBuilderList() { if (chromatogramsBuilder_ != null) { return chromatogramsBuilder_.getMessageOrBuilderList(); @@ -4929,8 +5008,7 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Chroma org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.Chromatogram, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.Chromatogram.Builder, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.ChromatogramOrBuilder> getChromatogramsFieldBuilder() { if (chromatogramsBuilder_ == null) { - chromatogramsBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3< - org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.Chromatogram, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.Chromatogram.Builder, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.ChromatogramOrBuilder>( + chromatogramsBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<>( chromatograms_, ((bitField0_ & 0x00000004) != 0), getParentForChildren(), @@ -5107,6 +5185,7 @@ public Builder clearInferZeroes() { * .ChromatogramGroupData.TimeIntervals timeIntervals = 10; * @return Whether the timeIntervals field is set. */ + @Override public boolean hasTimeIntervals() { return ((bitField0_ & 0x00000100) != 0); } @@ -5114,6 +5193,7 @@ public boolean hasTimeIntervals() { * .ChromatogramGroupData.TimeIntervals timeIntervals = 10; * @return The timeIntervals. */ + @Override public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.TimeIntervals getTimeIntervals() { if (timeIntervalsBuilder_ == null) { return timeIntervals_ == null ? org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.TimeIntervals.getDefaultInstance() : timeIntervals_; @@ -5196,6 +5276,7 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Chroma /** * .ChromatogramGroupData.TimeIntervals timeIntervals = 10; */ + @Override public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.TimeIntervalsOrBuilder getTimeIntervalsOrBuilder() { if (timeIntervalsBuilder_ != null) { return timeIntervalsBuilder_.getMessageOrBuilder(); @@ -5211,8 +5292,7 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Chroma org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.TimeIntervals, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.TimeIntervals.Builder, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.TimeIntervalsOrBuilder> getTimeIntervalsFieldBuilder() { if (timeIntervalsBuilder_ == null) { - timeIntervalsBuilder_ = new com.google.protobuf.SingleFieldBuilderV3< - org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.TimeIntervals, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.TimeIntervals.Builder, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupData.TimeIntervalsOrBuilder>( + timeIntervalsBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<>( getTimeIntervals(), getParentForChildren(), isClean()); @@ -5247,25 +5327,34 @@ public static org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass } private static final com.google.protobuf.Parser - PARSER = new com.google.protobuf.AbstractParser() { - @java.lang.Override - public ChromatogramGroupData parsePartialFrom( - com.google.protobuf.CodedInputStream input, - com.google.protobuf.ExtensionRegistryLite extensionRegistry) - throws com.google.protobuf.InvalidProtocolBufferException { - Builder builder = newBuilder(); - try { - builder.mergeFrom(input, extensionRegistry); - } catch (com.google.protobuf.InvalidProtocolBufferException e) { - throw e.setUnfinishedMessage(builder.buildPartial()); - } catch (com.google.protobuf.UninitializedMessageException e) { - throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); - } catch (java.io.IOException e) { - throw new com.google.protobuf.InvalidProtocolBufferException(e) - .setUnfinishedMessage(builder.buildPartial()); + PARSER = new com.google.protobuf.AbstractParser<>() + { + @java.lang.Override + public ChromatogramGroupData parsePartialFrom( + com.google.protobuf.CodedInputStream input, + com.google.protobuf.ExtensionRegistryLite extensionRegistry) + throws com.google.protobuf.InvalidProtocolBufferException + { + Builder builder = newBuilder(); + try + { + builder.mergeFrom(input, extensionRegistry); + } + catch (com.google.protobuf.InvalidProtocolBufferException e) + { + throw e.setUnfinishedMessage(builder.buildPartial()); + } + catch (com.google.protobuf.UninitializedMessageException e) + { + throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); + } + catch (java.io.IOException e) + { + throw new com.google.protobuf.InvalidProtocolBufferException(e) + .setUnfinishedMessage(builder.buildPartial()); + } + return builder.buildPartial(); } - return builder.buildPartial(); - } }; public static com.google.protobuf.Parser parser() { @@ -5567,6 +5656,7 @@ public double getRetentionTime() { * repeated int32 scanIdParts = 2; * @return The count of scanIdParts. */ + @Override public int getScanIdPartsCount() { return scanIdParts_.size(); } @@ -5575,6 +5665,7 @@ public int getScanIdPartsCount() { * @param index The index of the element to return. * @return The scanIdParts at the given index. */ + @Override public int getScanIdParts(int index) { return scanIdParts_.getInt(index); } @@ -5636,6 +5727,7 @@ public java.lang.String getScanIdText() { * repeated int32 precursorIndex = 4; * @return The count of precursorIndex. */ + @Override public int getPrecursorIndexCount() { return precursorIndex_.size(); } @@ -5644,6 +5736,7 @@ public int getPrecursorIndexCount() { * @param index The index of the element to return. * @return The precursorIndex at the given index. */ + @Override public int getPrecursorIndex(int index) { return precursorIndex_.getInt(index); } @@ -5700,7 +5793,7 @@ public void writeTo(com.google.protobuf.CodedOutputStream output) if (java.lang.Double.doubleToRawLongBits(retentionTime_) != 0) { output.writeDouble(1, retentionTime_); } - if (getScanIdPartsList().size() > 0) { + if (!getScanIdPartsList().isEmpty()) { output.writeUInt32NoTag(18); output.writeUInt32NoTag(scanIdPartsMemoizedSerializedSize); } @@ -5710,7 +5803,7 @@ public void writeTo(com.google.protobuf.CodedOutputStream output) if (!com.google.protobuf.GeneratedMessageV3.isStringEmpty(scanIdText_)) { com.google.protobuf.GeneratedMessageV3.writeString(output, 3, scanIdText_); } - if (getPrecursorIndexList().size() > 0) { + if (!getPrecursorIndexList().isEmpty()) { output.writeUInt32NoTag(34); output.writeUInt32NoTag(precursorIndexMemoizedSerializedSize); } @@ -5792,12 +5885,11 @@ public boolean equals(final java.lang.Object obj) { if (obj == this) { return true; } - if (!(obj instanceof org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ResultFileMetaDataProto.SpectrumMetadata)) { + if (!(obj instanceof SpectrumMetadata other)) { return super.equals(obj); } - org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ResultFileMetaDataProto.SpectrumMetadata other = (org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ResultFileMetaDataProto.SpectrumMetadata) obj; - if (java.lang.Double.doubleToLongBits(getRetentionTime()) + if (java.lang.Double.doubleToLongBits(getRetentionTime()) != java.lang.Double.doubleToLongBits( other.getRetentionTime())) return false; if (!getScanIdPartsList() @@ -6264,6 +6356,7 @@ private void ensureScanIdPartsIsMutable() { * repeated int32 scanIdParts = 2; * @return A list containing the scanIdParts. */ + @Override public java.util.List getScanIdPartsList() { scanIdParts_.makeImmutable(); @@ -6273,6 +6366,7 @@ private void ensureScanIdPartsIsMutable() { * repeated int32 scanIdParts = 2; * @return The count of scanIdParts. */ + @Override public int getScanIdPartsCount() { return scanIdParts_.size(); } @@ -6281,6 +6375,7 @@ public int getScanIdPartsCount() { * @param index The index of the element to return. * @return The scanIdParts at the given index. */ + @Override public int getScanIdParts(int index) { return scanIdParts_.getInt(index); } @@ -6342,6 +6437,7 @@ public Builder clearScanIdParts() { * string scanIdText = 3; * @return The scanIdText. */ + @Override public java.lang.String getScanIdText() { java.lang.Object ref = scanIdText_; if (!(ref instanceof java.lang.String)) { @@ -6358,6 +6454,7 @@ public java.lang.String getScanIdText() { * string scanIdText = 3; * @return The bytes for scanIdText. */ + @Override public com.google.protobuf.ByteString getScanIdTextBytes() { java.lang.Object ref = scanIdText_; @@ -6420,6 +6517,7 @@ private void ensurePrecursorIndexIsMutable() { * repeated int32 precursorIndex = 4; * @return A list containing the precursorIndex. */ + @Override public java.util.List getPrecursorIndexList() { precursorIndex_.makeImmutable(); @@ -6429,6 +6527,7 @@ private void ensurePrecursorIndexIsMutable() { * repeated int32 precursorIndex = 4; * @return The count of precursorIndex. */ + @Override public int getPrecursorIndexCount() { return precursorIndex_.size(); } @@ -6437,6 +6536,7 @@ public int getPrecursorIndexCount() { * @param index The index of the element to return. * @return The precursorIndex at the given index. */ + @Override public int getPrecursorIndex(int index) { return precursorIndex_.getInt(index); } @@ -6615,25 +6715,34 @@ public static org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass } private static final com.google.protobuf.Parser - PARSER = new com.google.protobuf.AbstractParser() { - @java.lang.Override - public SpectrumMetadata parsePartialFrom( - com.google.protobuf.CodedInputStream input, - com.google.protobuf.ExtensionRegistryLite extensionRegistry) - throws com.google.protobuf.InvalidProtocolBufferException { - Builder builder = newBuilder(); - try { - builder.mergeFrom(input, extensionRegistry); - } catch (com.google.protobuf.InvalidProtocolBufferException e) { - throw e.setUnfinishedMessage(builder.buildPartial()); - } catch (com.google.protobuf.UninitializedMessageException e) { - throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); - } catch (java.io.IOException e) { - throw new com.google.protobuf.InvalidProtocolBufferException(e) - .setUnfinishedMessage(builder.buildPartial()); + PARSER = new com.google.protobuf.AbstractParser<>() + { + @java.lang.Override + public SpectrumMetadata parsePartialFrom( + com.google.protobuf.CodedInputStream input, + com.google.protobuf.ExtensionRegistryLite extensionRegistry) + throws com.google.protobuf.InvalidProtocolBufferException + { + Builder builder = newBuilder(); + try + { + builder.mergeFrom(input, extensionRegistry); + } + catch (com.google.protobuf.InvalidProtocolBufferException e) + { + throw e.setUnfinishedMessage(builder.buildPartial()); + } + catch (com.google.protobuf.UninitializedMessageException e) + { + throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); + } + catch (java.io.IOException e) + { + throw new com.google.protobuf.InvalidProtocolBufferException(e) + .setUnfinishedMessage(builder.buildPartial()); + } + return builder.buildPartial(); } - return builder.buildPartial(); - } }; public static com.google.protobuf.Parser parser() { @@ -6844,12 +6953,11 @@ public boolean equals(final java.lang.Object obj) { if (obj == this) { return true; } - if (!(obj instanceof org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ResultFileMetaDataProto.Precursor)) { + if (!(obj instanceof Precursor other)) { return super.equals(obj); } - org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ResultFileMetaDataProto.Precursor other = (org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ResultFileMetaDataProto.Precursor) obj; - if (java.lang.Double.doubleToLongBits(getTargetMz()) + if (java.lang.Double.doubleToLongBits(getTargetMz()) != java.lang.Double.doubleToLongBits( other.getTargetMz())) return false; if (java.lang.Double.doubleToLongBits(getIsolationWindowLower()) @@ -7387,25 +7495,34 @@ public static org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass } private static final com.google.protobuf.Parser - PARSER = new com.google.protobuf.AbstractParser() { - @java.lang.Override - public Precursor parsePartialFrom( - com.google.protobuf.CodedInputStream input, - com.google.protobuf.ExtensionRegistryLite extensionRegistry) - throws com.google.protobuf.InvalidProtocolBufferException { - Builder builder = newBuilder(); - try { - builder.mergeFrom(input, extensionRegistry); - } catch (com.google.protobuf.InvalidProtocolBufferException e) { - throw e.setUnfinishedMessage(builder.buildPartial()); - } catch (com.google.protobuf.UninitializedMessageException e) { - throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); - } catch (java.io.IOException e) { - throw new com.google.protobuf.InvalidProtocolBufferException(e) - .setUnfinishedMessage(builder.buildPartial()); + PARSER = new com.google.protobuf.AbstractParser<>() + { + @java.lang.Override + public Precursor parsePartialFrom( + com.google.protobuf.CodedInputStream input, + com.google.protobuf.ExtensionRegistryLite extensionRegistry) + throws com.google.protobuf.InvalidProtocolBufferException + { + Builder builder = newBuilder(); + try + { + builder.mergeFrom(input, extensionRegistry); + } + catch (com.google.protobuf.InvalidProtocolBufferException e) + { + throw e.setUnfinishedMessage(builder.buildPartial()); + } + catch (com.google.protobuf.UninitializedMessageException e) + { + throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); + } + catch (java.io.IOException e) + { + throw new com.google.protobuf.InvalidProtocolBufferException(e) + .setUnfinishedMessage(builder.buildPartial()); + } + return builder.buildPartial(); } - return builder.buildPartial(); - } }; public static com.google.protobuf.Parser parser() { @@ -7514,6 +7631,7 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Result * repeated string scanDescriptions = 3; * @return A list containing the scanDescriptions. */ + @Override public com.google.protobuf.ProtocolStringList getScanDescriptionsList() { return scanDescriptions_; @@ -7522,6 +7640,7 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Result * repeated string scanDescriptions = 3; * @return The count of scanDescriptions. */ + @Override public int getScanDescriptionsCount() { return scanDescriptions_.size(); } @@ -7530,6 +7649,7 @@ public int getScanDescriptionsCount() { * @param index The index of the element to return. * @return The scanDescriptions at the given index. */ + @Override public java.lang.String getScanDescriptions(int index) { return scanDescriptions_.get(index); } @@ -7538,6 +7658,7 @@ public java.lang.String getScanDescriptions(int index) { * @param index The index of the value to return. * @return The bytes of the scanDescriptions at the given index. */ + @Override public com.google.protobuf.ByteString getScanDescriptionsBytes(int index) { return scanDescriptions_.getByteString(index); @@ -7551,6 +7672,7 @@ public java.lang.String getScanDescriptions(int index) { * repeated string analyzers = 4; * @return A list containing the analyzers. */ + @Override public com.google.protobuf.ProtocolStringList getAnalyzersList() { return analyzers_; @@ -7559,6 +7681,7 @@ public java.lang.String getScanDescriptions(int index) { * repeated string analyzers = 4; * @return The count of analyzers. */ + @Override public int getAnalyzersCount() { return analyzers_.size(); } @@ -7567,6 +7690,7 @@ public int getAnalyzersCount() { * @param index The index of the element to return. * @return The analyzers at the given index. */ + @Override public java.lang.String getAnalyzers(int index) { return analyzers_.get(index); } @@ -7575,6 +7699,7 @@ public java.lang.String getAnalyzers(int index) { * @param index The index of the value to return. * @return The bytes of the analyzers at the given index. */ + @Override public com.google.protobuf.ByteString getAnalyzersBytes(int index) { return analyzers_.getByteString(index); @@ -7649,12 +7774,11 @@ public boolean equals(final java.lang.Object obj) { if (obj == this) { return true; } - if (!(obj instanceof org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ResultFileMetaDataProto)) { + if (!(obj instanceof ResultFileMetaDataProto other)) { return super.equals(obj); } - org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ResultFileMetaDataProto other = (org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ResultFileMetaDataProto) obj; - if (!getSpectraList() + if (!getSpectraList() .equals(other.getSpectraList())) return false; if (!getPrecursorsList() .equals(other.getPrecursorsList())) return false; @@ -8104,7 +8228,7 @@ public Builder mergeFrom( java.util.Collections.emptyList(); private void ensureSpectraIsMutable() { if (!((bitField0_ & 0x00000001) != 0)) { - spectra_ = new java.util.ArrayList(spectra_); + spectra_ = new java.util.ArrayList<>(spectra_); bitField0_ |= 0x00000001; } } @@ -8115,6 +8239,7 @@ private void ensureSpectraIsMutable() { /** * repeated .ResultFileMetaDataProto.SpectrumMetadata spectra = 1; */ + @Override public java.util.List getSpectraList() { if (spectraBuilder_ == null) { return java.util.Collections.unmodifiableList(spectra_); @@ -8125,6 +8250,7 @@ public java.util.Listrepeated .ResultFileMetaDataProto.SpectrumMetadata spectra = 1; */ + @Override public int getSpectraCount() { if (spectraBuilder_ == null) { return spectra_.size(); @@ -8135,6 +8261,7 @@ public int getSpectraCount() { /** * repeated .ResultFileMetaDataProto.SpectrumMetadata spectra = 1; */ + @Override public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ResultFileMetaDataProto.SpectrumMetadata getSpectra(int index) { if (spectraBuilder_ == null) { return spectra_.get(index); @@ -8285,6 +8412,7 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Result /** * repeated .ResultFileMetaDataProto.SpectrumMetadata spectra = 1; */ + @Override public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ResultFileMetaDataProto.SpectrumMetadataOrBuilder getSpectraOrBuilder( int index) { if (spectraBuilder_ == null) { @@ -8295,7 +8423,8 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Result /** * repeated .ResultFileMetaDataProto.SpectrumMetadata spectra = 1; */ - public java.util.List + @Override + public java.util.List getSpectraOrBuilderList() { if (spectraBuilder_ != null) { return spectraBuilder_.getMessageOrBuilderList(); @@ -8329,8 +8458,7 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Result org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ResultFileMetaDataProto.SpectrumMetadata, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ResultFileMetaDataProto.SpectrumMetadata.Builder, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ResultFileMetaDataProto.SpectrumMetadataOrBuilder> getSpectraFieldBuilder() { if (spectraBuilder_ == null) { - spectraBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3< - org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ResultFileMetaDataProto.SpectrumMetadata, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ResultFileMetaDataProto.SpectrumMetadata.Builder, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ResultFileMetaDataProto.SpectrumMetadataOrBuilder>( + spectraBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<>( spectra_, ((bitField0_ & 0x00000001) != 0), getParentForChildren(), @@ -8344,7 +8472,7 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Result java.util.Collections.emptyList(); private void ensurePrecursorsIsMutable() { if (!((bitField0_ & 0x00000002) != 0)) { - precursors_ = new java.util.ArrayList(precursors_); + precursors_ = new java.util.ArrayList<>(precursors_); bitField0_ |= 0x00000002; } } @@ -8355,6 +8483,7 @@ private void ensurePrecursorsIsMutable() { /** * repeated .ResultFileMetaDataProto.Precursor precursors = 2; */ + @Override public java.util.List getPrecursorsList() { if (precursorsBuilder_ == null) { return java.util.Collections.unmodifiableList(precursors_); @@ -8365,6 +8494,7 @@ public java.util.Listrepeated .ResultFileMetaDataProto.Precursor precursors = 2; */ + @Override public int getPrecursorsCount() { if (precursorsBuilder_ == null) { return precursors_.size(); @@ -8375,6 +8505,7 @@ public int getPrecursorsCount() { /** * repeated .ResultFileMetaDataProto.Precursor precursors = 2; */ + @Override public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ResultFileMetaDataProto.Precursor getPrecursors(int index) { if (precursorsBuilder_ == null) { return precursors_.get(index); @@ -8525,6 +8656,7 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Result /** * repeated .ResultFileMetaDataProto.Precursor precursors = 2; */ + @Override public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ResultFileMetaDataProto.PrecursorOrBuilder getPrecursorsOrBuilder( int index) { if (precursorsBuilder_ == null) { @@ -8535,7 +8667,8 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Result /** * repeated .ResultFileMetaDataProto.Precursor precursors = 2; */ - public java.util.List + @Override + public java.util.List getPrecursorsOrBuilderList() { if (precursorsBuilder_ != null) { return precursorsBuilder_.getMessageOrBuilderList(); @@ -8569,8 +8702,7 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Result org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ResultFileMetaDataProto.Precursor, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ResultFileMetaDataProto.Precursor.Builder, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ResultFileMetaDataProto.PrecursorOrBuilder> getPrecursorsFieldBuilder() { if (precursorsBuilder_ == null) { - precursorsBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3< - org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ResultFileMetaDataProto.Precursor, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ResultFileMetaDataProto.Precursor.Builder, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ResultFileMetaDataProto.PrecursorOrBuilder>( + precursorsBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<>( precursors_, ((bitField0_ & 0x00000002) != 0), getParentForChildren(), @@ -8592,6 +8724,7 @@ private void ensureScanDescriptionsIsMutable() { * repeated string scanDescriptions = 3; * @return A list containing the scanDescriptions. */ + @Override public com.google.protobuf.ProtocolStringList getScanDescriptionsList() { scanDescriptions_.makeImmutable(); @@ -8601,6 +8734,7 @@ private void ensureScanDescriptionsIsMutable() { * repeated string scanDescriptions = 3; * @return The count of scanDescriptions. */ + @Override public int getScanDescriptionsCount() { return scanDescriptions_.size(); } @@ -8609,6 +8743,7 @@ public int getScanDescriptionsCount() { * @param index The index of the element to return. * @return The scanDescriptions at the given index. */ + @Override public java.lang.String getScanDescriptions(int index) { return scanDescriptions_.get(index); } @@ -8617,6 +8752,7 @@ public java.lang.String getScanDescriptions(int index) { * @param index The index of the value to return. * @return The bytes of the scanDescriptions at the given index. */ + @Override public com.google.protobuf.ByteString getScanDescriptionsBytes(int index) { return scanDescriptions_.getByteString(index); @@ -8671,8 +8807,8 @@ public Builder addAllScanDescriptions( public Builder clearScanDescriptions() { scanDescriptions_ = com.google.protobuf.LazyStringArrayList.emptyList(); - bitField0_ = (bitField0_ & ~0x00000004);; - onChanged(); + bitField0_ = (bitField0_ & ~0x00000004); + onChanged(); return this; } /** @@ -8703,6 +8839,7 @@ private void ensureAnalyzersIsMutable() { * repeated string analyzers = 4; * @return A list containing the analyzers. */ + @Override public com.google.protobuf.ProtocolStringList getAnalyzersList() { analyzers_.makeImmutable(); @@ -8712,6 +8849,7 @@ private void ensureAnalyzersIsMutable() { * repeated string analyzers = 4; * @return The count of analyzers. */ + @Override public int getAnalyzersCount() { return analyzers_.size(); } @@ -8720,6 +8858,7 @@ public int getAnalyzersCount() { * @param index The index of the element to return. * @return The analyzers at the given index. */ + @Override public java.lang.String getAnalyzers(int index) { return analyzers_.get(index); } @@ -8728,6 +8867,7 @@ public java.lang.String getAnalyzers(int index) { * @param index The index of the value to return. * @return The bytes of the analyzers at the given index. */ + @Override public com.google.protobuf.ByteString getAnalyzersBytes(int index) { return analyzers_.getByteString(index); @@ -8782,8 +8922,8 @@ public Builder addAllAnalyzers( public Builder clearAnalyzers() { analyzers_ = com.google.protobuf.LazyStringArrayList.emptyList(); - bitField0_ = (bitField0_ & ~0x00000008);; - onChanged(); + bitField0_ = (bitField0_ & ~0x00000008); + onChanged(); return this; } /** @@ -8828,25 +8968,34 @@ public static org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass } private static final com.google.protobuf.Parser - PARSER = new com.google.protobuf.AbstractParser() { - @java.lang.Override - public ResultFileMetaDataProto parsePartialFrom( - com.google.protobuf.CodedInputStream input, - com.google.protobuf.ExtensionRegistryLite extensionRegistry) - throws com.google.protobuf.InvalidProtocolBufferException { - Builder builder = newBuilder(); - try { - builder.mergeFrom(input, extensionRegistry); - } catch (com.google.protobuf.InvalidProtocolBufferException e) { - throw e.setUnfinishedMessage(builder.buildPartial()); - } catch (com.google.protobuf.UninitializedMessageException e) { - throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); - } catch (java.io.IOException e) { - throw new com.google.protobuf.InvalidProtocolBufferException(e) - .setUnfinishedMessage(builder.buildPartial()); + PARSER = new com.google.protobuf.AbstractParser<>() + { + @java.lang.Override + public ResultFileMetaDataProto parsePartialFrom( + com.google.protobuf.CodedInputStream input, + com.google.protobuf.ExtensionRegistryLite extensionRegistry) + throws com.google.protobuf.InvalidProtocolBufferException + { + Builder builder = newBuilder(); + try + { + builder.mergeFrom(input, extensionRegistry); + } + catch (com.google.protobuf.InvalidProtocolBufferException e) + { + throw e.setUnfinishedMessage(builder.buildPartial()); + } + catch (com.google.protobuf.UninitializedMessageException e) + { + throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); + } + catch (java.io.IOException e) + { + throw new com.google.protobuf.InvalidProtocolBufferException(e) + .setUnfinishedMessage(builder.buildPartial()); + } + return builder.buildPartial(); } - return builder.buildPartial(); - } }; public static com.google.protobuf.Parser parser() { @@ -9093,6 +9242,7 @@ public enum FilterOperation public static final int FILTER_OP_NOT_STARTS_WITH_VALUE = 12; + @Override public final int getNumber() { if (this == UNRECOGNIZED) { throw new java.lang.IllegalArgumentException( @@ -9140,12 +9290,16 @@ public static FilterOperation forNumber(int value) { } private static final com.google.protobuf.Internal.EnumLiteMap< FilterOperation> internalValueMap = - new com.google.protobuf.Internal.EnumLiteMap() { - public FilterOperation findValueByNumber(int number) { - return FilterOperation.forNumber(number); - } - }; + new com.google.protobuf.Internal.EnumLiteMap<>() + { + @Override + public FilterOperation findValueByNumber(int number) + { + return FilterOperation.forNumber(number); + } + }; + @Override public final com.google.protobuf.Descriptors.EnumValueDescriptor getValueDescriptor() { if (this == UNRECOGNIZED) { @@ -9154,6 +9308,7 @@ public FilterOperation findValueByNumber(int number) { } return getDescriptor().getValues().get(ordinal()); } + @Override public final com.google.protobuf.Descriptors.EnumDescriptor getDescriptorForType() { return getDescriptor(); @@ -9179,7 +9334,7 @@ public static FilterOperation valueOf( private final int value; - private FilterOperation(int value) { + FilterOperation(int value) { this.value = value; } @@ -9340,12 +9495,11 @@ public boolean equals(final java.lang.Object obj) { if (obj == this) { return true; } - if (!(obj instanceof org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.AccessionNumber)) { + if (!(obj instanceof AccessionNumber other)) { return super.equals(obj); } - org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.AccessionNumber other = (org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.AccessionNumber) obj; - if (getTypeName() + if (getTypeName() != other.getTypeName()) return false; if (!getValue() .equals(other.getValue())) return false; @@ -9680,6 +9834,7 @@ public Builder clearTypeName() { * string value = 2; * @return The value. */ + @Override public java.lang.String getValue() { java.lang.Object ref = value_; if (!(ref instanceof java.lang.String)) { @@ -9696,6 +9851,7 @@ public java.lang.String getValue() { * string value = 2; * @return The bytes for value. */ + @Override public com.google.protobuf.ByteString getValueBytes() { java.lang.Object ref = value_; @@ -9773,25 +9929,34 @@ public static org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass } private static final com.google.protobuf.Parser - PARSER = new com.google.protobuf.AbstractParser() { - @java.lang.Override - public AccessionNumber parsePartialFrom( - com.google.protobuf.CodedInputStream input, - com.google.protobuf.ExtensionRegistryLite extensionRegistry) - throws com.google.protobuf.InvalidProtocolBufferException { - Builder builder = newBuilder(); - try { - builder.mergeFrom(input, extensionRegistry); - } catch (com.google.protobuf.InvalidProtocolBufferException e) { - throw e.setUnfinishedMessage(builder.buildPartial()); - } catch (com.google.protobuf.UninitializedMessageException e) { - throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); - } catch (java.io.IOException e) { - throw new com.google.protobuf.InvalidProtocolBufferException(e) - .setUnfinishedMessage(builder.buildPartial()); + PARSER = new com.google.protobuf.AbstractParser<>() + { + @java.lang.Override + public AccessionNumber parsePartialFrom( + com.google.protobuf.CodedInputStream input, + com.google.protobuf.ExtensionRegistryLite extensionRegistry) + throws com.google.protobuf.InvalidProtocolBufferException + { + Builder builder = newBuilder(); + try + { + builder.mergeFrom(input, extensionRegistry); + } + catch (com.google.protobuf.InvalidProtocolBufferException e) + { + throw e.setUnfinishedMessage(builder.buildPartial()); + } + catch (com.google.protobuf.UninitializedMessageException e) + { + throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); + } + catch (java.io.IOException e) + { + throw new com.google.protobuf.InvalidProtocolBufferException(e) + .setUnfinishedMessage(builder.buildPartial()); + } + return builder.buildPartial(); } - return builder.buildPartial(); - } }; public static com.google.protobuf.Parser parser() { @@ -10452,12 +10617,11 @@ public boolean equals(final java.lang.Object obj) { if (obj == this) { return true; } - if (!(obj instanceof org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.Target)) { + if (!(obj instanceof Target other)) { return super.equals(obj); } - org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.Target other = (org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.Target) obj; - if (!getModifiedPeptideSequence() + if (!getModifiedPeptideSequence() .equals(other.getModifiedPeptideSequence())) return false; if (!getFormula() .equals(other.getFormula())) return false; @@ -10924,6 +11088,7 @@ public Builder mergeFrom( * string modifiedPeptideSequence = 1; * @return The modifiedPeptideSequence. */ + @Override public java.lang.String getModifiedPeptideSequence() { java.lang.Object ref = modifiedPeptideSequence_; if (!(ref instanceof java.lang.String)) { @@ -10940,6 +11105,7 @@ public java.lang.String getModifiedPeptideSequence() { * string modifiedPeptideSequence = 1; * @return The bytes for modifiedPeptideSequence. */ + @Override public com.google.protobuf.ByteString getModifiedPeptideSequenceBytes() { java.lang.Object ref = modifiedPeptideSequence_; @@ -10996,6 +11162,7 @@ public Builder setModifiedPeptideSequenceBytes( * string formula = 2; * @return The formula. */ + @Override public java.lang.String getFormula() { java.lang.Object ref = formula_; if (!(ref instanceof java.lang.String)) { @@ -11012,6 +11179,7 @@ public java.lang.String getFormula() { * string formula = 2; * @return The bytes for formula. */ + @Override public com.google.protobuf.ByteString getFormulaBytes() { java.lang.Object ref = formula_; @@ -11068,6 +11236,7 @@ public Builder setFormulaBytes( * string name = 3; * @return The name. */ + @Override public java.lang.String getName() { java.lang.Object ref = name_; if (!(ref instanceof java.lang.String)) { @@ -11084,6 +11253,7 @@ public java.lang.String getName() { * string name = 3; * @return The bytes for name. */ + @Override public com.google.protobuf.ByteString getNameBytes() { java.lang.Object ref = name_; @@ -11204,6 +11374,7 @@ public Builder clearAverageMass() { * string inChiKey = 6; * @return The inChiKey. */ + @Override public java.lang.String getInChiKey() { java.lang.Object ref = inChiKey_; if (!(ref instanceof java.lang.String)) { @@ -11220,6 +11391,7 @@ public java.lang.String getInChiKey() { * string inChiKey = 6; * @return The bytes for inChiKey. */ + @Override public com.google.protobuf.ByteString getInChiKeyBytes() { java.lang.Object ref = inChiKey_; @@ -11276,6 +11448,7 @@ public Builder setInChiKeyBytes( * string cas = 7; * @return The cas. */ + @Override public java.lang.String getCas() { java.lang.Object ref = cas_; if (!(ref instanceof java.lang.String)) { @@ -11292,6 +11465,7 @@ public java.lang.String getCas() { * string cas = 7; * @return The bytes for cas. */ + @Override public com.google.protobuf.ByteString getCasBytes() { java.lang.Object ref = cas_; @@ -11348,6 +11522,7 @@ public Builder setCasBytes( * string hmdb = 8; * @return The hmdb. */ + @Override public java.lang.String getHmdb() { java.lang.Object ref = hmdb_; if (!(ref instanceof java.lang.String)) { @@ -11364,6 +11539,7 @@ public java.lang.String getHmdb() { * string hmdb = 8; * @return The bytes for hmdb. */ + @Override public com.google.protobuf.ByteString getHmdbBytes() { java.lang.Object ref = hmdb_; @@ -11420,6 +11596,7 @@ public Builder setHmdbBytes( * string inChi = 9; * @return The inChi. */ + @Override public java.lang.String getInChi() { java.lang.Object ref = inChi_; if (!(ref instanceof java.lang.String)) { @@ -11436,6 +11613,7 @@ public java.lang.String getInChi() { * string inChi = 9; * @return The bytes for inChi. */ + @Override public com.google.protobuf.ByteString getInChiBytes() { java.lang.Object ref = inChi_; @@ -11492,6 +11670,7 @@ public Builder setInChiBytes( * string smiles = 10; * @return The smiles. */ + @Override public java.lang.String getSmiles() { java.lang.Object ref = smiles_; if (!(ref instanceof java.lang.String)) { @@ -11508,6 +11687,7 @@ public java.lang.String getSmiles() { * string smiles = 10; * @return The bytes for smiles. */ + @Override public com.google.protobuf.ByteString getSmilesBytes() { java.lang.Object ref = smiles_; @@ -11564,6 +11744,7 @@ public Builder setSmilesBytes( * string kegg = 11; * @return The kegg. */ + @Override public java.lang.String getKegg() { java.lang.Object ref = kegg_; if (!(ref instanceof java.lang.String)) { @@ -11580,6 +11761,7 @@ public java.lang.String getKegg() { * string kegg = 11; * @return The bytes for kegg. */ + @Override public com.google.protobuf.ByteString getKeggBytes() { java.lang.Object ref = kegg_; @@ -11657,25 +11839,34 @@ public static org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass } private static final com.google.protobuf.Parser - PARSER = new com.google.protobuf.AbstractParser() { - @java.lang.Override - public Target parsePartialFrom( - com.google.protobuf.CodedInputStream input, - com.google.protobuf.ExtensionRegistryLite extensionRegistry) - throws com.google.protobuf.InvalidProtocolBufferException { - Builder builder = newBuilder(); - try { - builder.mergeFrom(input, extensionRegistry); - } catch (com.google.protobuf.InvalidProtocolBufferException e) { - throw e.setUnfinishedMessage(builder.buildPartial()); - } catch (com.google.protobuf.UninitializedMessageException e) { - throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); - } catch (java.io.IOException e) { - throw new com.google.protobuf.InvalidProtocolBufferException(e) - .setUnfinishedMessage(builder.buildPartial()); + PARSER = new com.google.protobuf.AbstractParser<>() + { + @java.lang.Override + public Target parsePartialFrom( + com.google.protobuf.CodedInputStream input, + com.google.protobuf.ExtensionRegistryLite extensionRegistry) + throws com.google.protobuf.InvalidProtocolBufferException + { + Builder builder = newBuilder(); + try + { + builder.mergeFrom(input, extensionRegistry); + } + catch (com.google.protobuf.InvalidProtocolBufferException e) + { + throw e.setUnfinishedMessage(builder.buildPartial()); + } + catch (com.google.protobuf.UninitializedMessageException e) + { + throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); + } + catch (java.io.IOException e) + { + throw new com.google.protobuf.InvalidProtocolBufferException(e) + .setUnfinishedMessage(builder.buildPartial()); + } + return builder.buildPartial(); } - return builder.buildPartial(); - } }; public static com.google.protobuf.Parser parser() { @@ -11826,6 +12017,7 @@ public int getTargetIndex() { * repeated int32 filterIndexes = 2; * @return The count of filterIndexes. */ + @Override public int getFilterIndexesCount() { return filterIndexes_.size(); } @@ -11838,6 +12030,7 @@ public int getFilterIndexesCount() { * @param index The index of the element to return. * @return The filterIndexes at the given index. */ + @Override public int getFilterIndexes(int index) { return filterIndexes_.getInt(index); } @@ -11900,7 +12093,7 @@ public void writeTo(com.google.protobuf.CodedOutputStream output) if (targetIndex_ != 0) { output.writeInt32(1, targetIndex_); } - if (getFilterIndexesList().size() > 0) { + if (!getFilterIndexesList().isEmpty()) { output.writeUInt32NoTag(18); output.writeUInt32NoTag(filterIndexesMemoizedSerializedSize); } @@ -11950,12 +12143,11 @@ public boolean equals(final java.lang.Object obj) { if (obj == this) { return true; } - if (!(obj instanceof org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.ChromatogramGroupId)) { + if (!(obj instanceof ChromatogramGroupId other)) { return super.equals(obj); } - org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.ChromatogramGroupId other = (org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.ChromatogramGroupId) obj; - if (getTargetIndex() + if (getTargetIndex() != other.getTargetIndex()) return false; if (!getFilterIndexesList() .equals(other.getFilterIndexesList())) return false; @@ -12350,6 +12542,7 @@ private void ensureFilterIndexesIsMutable() { * repeated int32 filterIndexes = 2; * @return A list containing the filterIndexes. */ + @Override public java.util.List getFilterIndexesList() { filterIndexes_.makeImmutable(); @@ -12363,6 +12556,7 @@ private void ensureFilterIndexesIsMutable() { * repeated int32 filterIndexes = 2; * @return The count of filterIndexes. */ + @Override public int getFilterIndexesCount() { return filterIndexes_.size(); } @@ -12375,6 +12569,7 @@ public int getFilterIndexesCount() { * @param index The index of the element to return. * @return The filterIndexes at the given index. */ + @Override public int getFilterIndexes(int index) { return filterIndexes_.getInt(index); } @@ -12452,6 +12647,7 @@ public Builder clearFilterIndexes() { * string qcTraceName = 3; * @return The qcTraceName. */ + @Override public java.lang.String getQcTraceName() { java.lang.Object ref = qcTraceName_; if (!(ref instanceof java.lang.String)) { @@ -12468,6 +12664,7 @@ public java.lang.String getQcTraceName() { * string qcTraceName = 3; * @return The bytes for qcTraceName. */ + @Override public com.google.protobuf.ByteString getQcTraceNameBytes() { java.lang.Object ref = qcTraceName_; @@ -12545,25 +12742,34 @@ public static org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass } private static final com.google.protobuf.Parser - PARSER = new com.google.protobuf.AbstractParser() { - @java.lang.Override - public ChromatogramGroupId parsePartialFrom( - com.google.protobuf.CodedInputStream input, - com.google.protobuf.ExtensionRegistryLite extensionRegistry) - throws com.google.protobuf.InvalidProtocolBufferException { - Builder builder = newBuilder(); - try { - builder.mergeFrom(input, extensionRegistry); - } catch (com.google.protobuf.InvalidProtocolBufferException e) { - throw e.setUnfinishedMessage(builder.buildPartial()); - } catch (com.google.protobuf.UninitializedMessageException e) { - throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); - } catch (java.io.IOException e) { - throw new com.google.protobuf.InvalidProtocolBufferException(e) - .setUnfinishedMessage(builder.buildPartial()); + PARSER = new com.google.protobuf.AbstractParser<>() + { + @java.lang.Override + public ChromatogramGroupId parsePartialFrom( + com.google.protobuf.CodedInputStream input, + com.google.protobuf.ExtensionRegistryLite extensionRegistry) + throws com.google.protobuf.InvalidProtocolBufferException + { + Builder builder = newBuilder(); + try + { + builder.mergeFrom(input, extensionRegistry); + } + catch (com.google.protobuf.InvalidProtocolBufferException e) + { + throw e.setUnfinishedMessage(builder.buildPartial()); + } + catch (com.google.protobuf.UninitializedMessageException e) + { + throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); + } + catch (java.io.IOException e) + { + throw new com.google.protobuf.InvalidProtocolBufferException(e) + .setUnfinishedMessage(builder.buildPartial()); + } + return builder.buildPartial(); } - return builder.buildPartial(); - } }; public static com.google.protobuf.Parser parser() { @@ -12871,12 +13077,11 @@ public boolean equals(final java.lang.Object obj) { if (obj == this) { return true; } - if (!(obj instanceof org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.SpectrumFilter.Predicate)) { + if (!(obj instanceof Predicate other)) { return super.equals(obj); } - org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.SpectrumFilter.Predicate other = (org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.SpectrumFilter.Predicate) obj; - if (!getPropertyPath() + if (!getPropertyPath() .equals(other.getPropertyPath())) return false; if (operation_ != other.operation_) return false; if (!getOperand() @@ -13196,6 +13401,7 @@ public Builder mergeFrom( * string propertyPath = 1; * @return The propertyPath. */ + @Override public java.lang.String getPropertyPath() { java.lang.Object ref = propertyPath_; if (!(ref instanceof java.lang.String)) { @@ -13212,6 +13418,7 @@ public java.lang.String getPropertyPath() { * string propertyPath = 1; * @return The bytes for propertyPath. */ + @Override public com.google.protobuf.ByteString getPropertyPathBytes() { java.lang.Object ref = propertyPath_; @@ -13321,6 +13528,7 @@ public Builder clearOperation() { * string operand = 3; * @return The operand. */ + @Override public java.lang.String getOperand() { java.lang.Object ref = operand_; if (!(ref instanceof java.lang.String)) { @@ -13337,6 +13545,7 @@ public java.lang.String getOperand() { * string operand = 3; * @return The bytes for operand. */ + @Override public com.google.protobuf.ByteString getOperandBytes() { java.lang.Object ref = operand_; @@ -13414,25 +13623,34 @@ public static org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass } private static final com.google.protobuf.Parser - PARSER = new com.google.protobuf.AbstractParser() { - @java.lang.Override - public Predicate parsePartialFrom( - com.google.protobuf.CodedInputStream input, - com.google.protobuf.ExtensionRegistryLite extensionRegistry) - throws com.google.protobuf.InvalidProtocolBufferException { - Builder builder = newBuilder(); - try { - builder.mergeFrom(input, extensionRegistry); - } catch (com.google.protobuf.InvalidProtocolBufferException e) { - throw e.setUnfinishedMessage(builder.buildPartial()); - } catch (com.google.protobuf.UninitializedMessageException e) { - throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); - } catch (java.io.IOException e) { - throw new com.google.protobuf.InvalidProtocolBufferException(e) - .setUnfinishedMessage(builder.buildPartial()); + PARSER = new com.google.protobuf.AbstractParser<>() + { + @java.lang.Override + public Predicate parsePartialFrom( + com.google.protobuf.CodedInputStream input, + com.google.protobuf.ExtensionRegistryLite extensionRegistry) + throws com.google.protobuf.InvalidProtocolBufferException + { + Builder builder = newBuilder(); + try + { + builder.mergeFrom(input, extensionRegistry); + } + catch (com.google.protobuf.InvalidProtocolBufferException e) + { + throw e.setUnfinishedMessage(builder.buildPartial()); + } + catch (com.google.protobuf.UninitializedMessageException e) + { + throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); + } + catch (java.io.IOException e) + { + throw new com.google.protobuf.InvalidProtocolBufferException(e) + .setUnfinishedMessage(builder.buildPartial()); + } + return builder.buildPartial(); } - return builder.buildPartial(); - } }; public static com.google.protobuf.Parser parser() { @@ -13532,12 +13750,11 @@ public boolean equals(final java.lang.Object obj) { if (obj == this) { return true; } - if (!(obj instanceof org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.SpectrumFilter)) { + if (!(obj instanceof SpectrumFilter other)) { return super.equals(obj); } - org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.SpectrumFilter other = (org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.SpectrumFilter) obj; - if (!getPredicatesList() + if (!getPredicatesList() .equals(other.getPredicatesList())) return false; if (!getUnknownFields().equals(other.getUnknownFields())) return false; return true; @@ -13870,7 +14087,7 @@ public Builder mergeFrom( java.util.Collections.emptyList(); private void ensurePredicatesIsMutable() { if (!((bitField0_ & 0x00000001) != 0)) { - predicates_ = new java.util.ArrayList(predicates_); + predicates_ = new java.util.ArrayList<>(predicates_); bitField0_ |= 0x00000001; } } @@ -13881,6 +14098,7 @@ private void ensurePredicatesIsMutable() { /** * repeated .ChromatogramGroupIdsProto.SpectrumFilter.Predicate predicates = 1; */ + @Override public java.util.List getPredicatesList() { if (predicatesBuilder_ == null) { return java.util.Collections.unmodifiableList(predicates_); @@ -13891,6 +14109,7 @@ public java.util.Listrepeated .ChromatogramGroupIdsProto.SpectrumFilter.Predicate predicates = 1; */ + @Override public int getPredicatesCount() { if (predicatesBuilder_ == null) { return predicates_.size(); @@ -13901,6 +14120,7 @@ public int getPredicatesCount() { /** * repeated .ChromatogramGroupIdsProto.SpectrumFilter.Predicate predicates = 1; */ + @Override public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.SpectrumFilter.Predicate getPredicates(int index) { if (predicatesBuilder_ == null) { return predicates_.get(index); @@ -14051,6 +14271,7 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Chroma /** * repeated .ChromatogramGroupIdsProto.SpectrumFilter.Predicate predicates = 1; */ + @Override public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.SpectrumFilter.PredicateOrBuilder getPredicatesOrBuilder( int index) { if (predicatesBuilder_ == null) { @@ -14061,7 +14282,8 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Chroma /** * repeated .ChromatogramGroupIdsProto.SpectrumFilter.Predicate predicates = 1; */ - public java.util.List + @Override + public java.util.List getPredicatesOrBuilderList() { if (predicatesBuilder_ != null) { return predicatesBuilder_.getMessageOrBuilderList(); @@ -14095,8 +14317,7 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Chroma org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.SpectrumFilter.Predicate, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.SpectrumFilter.Predicate.Builder, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.SpectrumFilter.PredicateOrBuilder> getPredicatesFieldBuilder() { if (predicatesBuilder_ == null) { - predicatesBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3< - org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.SpectrumFilter.Predicate, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.SpectrumFilter.Predicate.Builder, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.SpectrumFilter.PredicateOrBuilder>( + predicatesBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<>( predicates_, ((bitField0_ & 0x00000001) != 0), getParentForChildren(), @@ -14132,25 +14353,34 @@ public static org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass } private static final com.google.protobuf.Parser - PARSER = new com.google.protobuf.AbstractParser() { - @java.lang.Override - public SpectrumFilter parsePartialFrom( - com.google.protobuf.CodedInputStream input, - com.google.protobuf.ExtensionRegistryLite extensionRegistry) - throws com.google.protobuf.InvalidProtocolBufferException { - Builder builder = newBuilder(); - try { - builder.mergeFrom(input, extensionRegistry); - } catch (com.google.protobuf.InvalidProtocolBufferException e) { - throw e.setUnfinishedMessage(builder.buildPartial()); - } catch (com.google.protobuf.UninitializedMessageException e) { - throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); - } catch (java.io.IOException e) { - throw new com.google.protobuf.InvalidProtocolBufferException(e) - .setUnfinishedMessage(builder.buildPartial()); + PARSER = new com.google.protobuf.AbstractParser<>() + { + @java.lang.Override + public SpectrumFilter parsePartialFrom( + com.google.protobuf.CodedInputStream input, + com.google.protobuf.ExtensionRegistryLite extensionRegistry) + throws com.google.protobuf.InvalidProtocolBufferException + { + Builder builder = newBuilder(); + try + { + builder.mergeFrom(input, extensionRegistry); + } + catch (com.google.protobuf.InvalidProtocolBufferException e) + { + throw e.setUnfinishedMessage(builder.buildPartial()); + } + catch (com.google.protobuf.UninitializedMessageException e) + { + throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); + } + catch (java.io.IOException e) + { + throw new com.google.protobuf.InvalidProtocolBufferException(e) + .setUnfinishedMessage(builder.buildPartial()); + } + return builder.buildPartial(); } - return builder.buildPartial(); - } }; public static com.google.protobuf.Parser parser() { @@ -14346,12 +14576,11 @@ public boolean equals(final java.lang.Object obj) { if (obj == this) { return true; } - if (!(obj instanceof org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto)) { + if (!(obj instanceof ChromatogramGroupIdsProto other)) { return super.equals(obj); } - org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto other = (org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto) obj; - if (!getTargetsList() + if (!getTargetsList() .equals(other.getTargetsList())) return false; if (!getFiltersList() .equals(other.getFiltersList())) return false; @@ -14806,7 +15035,7 @@ public Builder mergeFrom( java.util.Collections.emptyList(); private void ensureTargetsIsMutable() { if (!((bitField0_ & 0x00000001) != 0)) { - targets_ = new java.util.ArrayList(targets_); + targets_ = new java.util.ArrayList<>(targets_); bitField0_ |= 0x00000001; } } @@ -14817,6 +15046,7 @@ private void ensureTargetsIsMutable() { /** * repeated .ChromatogramGroupIdsProto.Target targets = 1; */ + @Override public java.util.List getTargetsList() { if (targetsBuilder_ == null) { return java.util.Collections.unmodifiableList(targets_); @@ -14827,6 +15057,7 @@ public java.util.Listrepeated .ChromatogramGroupIdsProto.Target targets = 1; */ + @Override public int getTargetsCount() { if (targetsBuilder_ == null) { return targets_.size(); @@ -14837,6 +15068,7 @@ public int getTargetsCount() { /** * repeated .ChromatogramGroupIdsProto.Target targets = 1; */ + @Override public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.Target getTargets(int index) { if (targetsBuilder_ == null) { return targets_.get(index); @@ -14987,6 +15219,7 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Chroma /** * repeated .ChromatogramGroupIdsProto.Target targets = 1; */ + @Override public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.TargetOrBuilder getTargetsOrBuilder( int index) { if (targetsBuilder_ == null) { @@ -14997,7 +15230,8 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Chroma /** * repeated .ChromatogramGroupIdsProto.Target targets = 1; */ - public java.util.List + @Override + public java.util.List getTargetsOrBuilderList() { if (targetsBuilder_ != null) { return targetsBuilder_.getMessageOrBuilderList(); @@ -15031,8 +15265,7 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Chroma org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.Target, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.Target.Builder, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.TargetOrBuilder> getTargetsFieldBuilder() { if (targetsBuilder_ == null) { - targetsBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3< - org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.Target, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.Target.Builder, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.TargetOrBuilder>( + targetsBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<>( targets_, ((bitField0_ & 0x00000001) != 0), getParentForChildren(), @@ -15046,7 +15279,7 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Chroma java.util.Collections.emptyList(); private void ensureFiltersIsMutable() { if (!((bitField0_ & 0x00000002) != 0)) { - filters_ = new java.util.ArrayList(filters_); + filters_ = new java.util.ArrayList<>(filters_); bitField0_ |= 0x00000002; } } @@ -15057,6 +15290,7 @@ private void ensureFiltersIsMutable() { /** * repeated .ChromatogramGroupIdsProto.SpectrumFilter filters = 2; */ + @Override public java.util.List getFiltersList() { if (filtersBuilder_ == null) { return java.util.Collections.unmodifiableList(filters_); @@ -15067,6 +15301,7 @@ public java.util.Listrepeated .ChromatogramGroupIdsProto.SpectrumFilter filters = 2; */ + @Override public int getFiltersCount() { if (filtersBuilder_ == null) { return filters_.size(); @@ -15077,6 +15312,7 @@ public int getFiltersCount() { /** * repeated .ChromatogramGroupIdsProto.SpectrumFilter filters = 2; */ + @Override public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.SpectrumFilter getFilters(int index) { if (filtersBuilder_ == null) { return filters_.get(index); @@ -15227,6 +15463,7 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Chroma /** * repeated .ChromatogramGroupIdsProto.SpectrumFilter filters = 2; */ + @Override public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.SpectrumFilterOrBuilder getFiltersOrBuilder( int index) { if (filtersBuilder_ == null) { @@ -15237,7 +15474,8 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Chroma /** * repeated .ChromatogramGroupIdsProto.SpectrumFilter filters = 2; */ - public java.util.List + @Override + public java.util.List getFiltersOrBuilderList() { if (filtersBuilder_ != null) { return filtersBuilder_.getMessageOrBuilderList(); @@ -15271,8 +15509,7 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Chroma org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.SpectrumFilter, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.SpectrumFilter.Builder, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.SpectrumFilterOrBuilder> getFiltersFieldBuilder() { if (filtersBuilder_ == null) { - filtersBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3< - org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.SpectrumFilter, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.SpectrumFilter.Builder, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.SpectrumFilterOrBuilder>( + filtersBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<>( filters_, ((bitField0_ & 0x00000002) != 0), getParentForChildren(), @@ -15286,7 +15523,7 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Chroma java.util.Collections.emptyList(); private void ensureChromatogramGroupIdsIsMutable() { if (!((bitField0_ & 0x00000004) != 0)) { - chromatogramGroupIds_ = new java.util.ArrayList(chromatogramGroupIds_); + chromatogramGroupIds_ = new java.util.ArrayList<>(chromatogramGroupIds_); bitField0_ |= 0x00000004; } } @@ -15297,6 +15534,7 @@ private void ensureChromatogramGroupIdsIsMutable() { /** * repeated .ChromatogramGroupIdsProto.ChromatogramGroupId chromatogramGroupIds = 3; */ + @Override public java.util.List getChromatogramGroupIdsList() { if (chromatogramGroupIdsBuilder_ == null) { return java.util.Collections.unmodifiableList(chromatogramGroupIds_); @@ -15307,6 +15545,7 @@ public java.util.Listrepeated .ChromatogramGroupIdsProto.ChromatogramGroupId chromatogramGroupIds = 3; */ + @Override public int getChromatogramGroupIdsCount() { if (chromatogramGroupIdsBuilder_ == null) { return chromatogramGroupIds_.size(); @@ -15317,6 +15556,7 @@ public int getChromatogramGroupIdsCount() { /** * repeated .ChromatogramGroupIdsProto.ChromatogramGroupId chromatogramGroupIds = 3; */ + @Override public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.ChromatogramGroupId getChromatogramGroupIds(int index) { if (chromatogramGroupIdsBuilder_ == null) { return chromatogramGroupIds_.get(index); @@ -15467,6 +15707,7 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Chroma /** * repeated .ChromatogramGroupIdsProto.ChromatogramGroupId chromatogramGroupIds = 3; */ + @Override public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.ChromatogramGroupIdOrBuilder getChromatogramGroupIdsOrBuilder( int index) { if (chromatogramGroupIdsBuilder_ == null) { @@ -15477,7 +15718,8 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Chroma /** * repeated .ChromatogramGroupIdsProto.ChromatogramGroupId chromatogramGroupIds = 3; */ - public java.util.List + @Override + public java.util.List getChromatogramGroupIdsOrBuilderList() { if (chromatogramGroupIdsBuilder_ != null) { return chromatogramGroupIdsBuilder_.getMessageOrBuilderList(); @@ -15511,8 +15753,7 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Chroma org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.ChromatogramGroupId, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.ChromatogramGroupId.Builder, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.ChromatogramGroupIdOrBuilder> getChromatogramGroupIdsFieldBuilder() { if (chromatogramGroupIdsBuilder_ == null) { - chromatogramGroupIdsBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3< - org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.ChromatogramGroupId, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.ChromatogramGroupId.Builder, org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.ChromatogramGroupIdOrBuilder>( + chromatogramGroupIdsBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<>( chromatogramGroupIds_, ((bitField0_ & 0x00000004) != 0), getParentForChildren(), @@ -15548,25 +15789,34 @@ public static org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass } private static final com.google.protobuf.Parser - PARSER = new com.google.protobuf.AbstractParser() { - @java.lang.Override - public ChromatogramGroupIdsProto parsePartialFrom( - com.google.protobuf.CodedInputStream input, - com.google.protobuf.ExtensionRegistryLite extensionRegistry) - throws com.google.protobuf.InvalidProtocolBufferException { - Builder builder = newBuilder(); - try { - builder.mergeFrom(input, extensionRegistry); - } catch (com.google.protobuf.InvalidProtocolBufferException e) { - throw e.setUnfinishedMessage(builder.buildPartial()); - } catch (com.google.protobuf.UninitializedMessageException e) { - throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); - } catch (java.io.IOException e) { - throw new com.google.protobuf.InvalidProtocolBufferException(e) - .setUnfinishedMessage(builder.buildPartial()); + PARSER = new com.google.protobuf.AbstractParser<>() + { + @java.lang.Override + public ChromatogramGroupIdsProto parsePartialFrom( + com.google.protobuf.CodedInputStream input, + com.google.protobuf.ExtensionRegistryLite extensionRegistry) + throws com.google.protobuf.InvalidProtocolBufferException + { + Builder builder = newBuilder(); + try + { + builder.mergeFrom(input, extensionRegistry); + } + catch (com.google.protobuf.InvalidProtocolBufferException e) + { + throw e.setUnfinishedMessage(builder.buildPartial()); + } + catch (com.google.protobuf.UninitializedMessageException e) + { + throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); + } + catch (java.io.IOException e) + { + throw new com.google.protobuf.InvalidProtocolBufferException(e) + .setUnfinishedMessage(builder.buildPartial()); + } + return builder.buildPartial(); } - return builder.buildPartial(); - } }; public static com.google.protobuf.Parser parser() { @@ -15660,7 +15910,7 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Chroma getDescriptor() { return descriptor; } - private static com.google.protobuf.Descriptors.FileDescriptor + private static final com.google.protobuf.Descriptors.FileDescriptor descriptor; static { java.lang.String[] descriptorData = { diff --git a/src/org/labkey/targetedms/parser/proto/SkylineDocument.java b/src/org/labkey/targetedms/parser/proto/SkylineDocument.java index 1bfb70ad4..92a6f382b 100644 --- a/src/org/labkey/targetedms/parser/proto/SkylineDocument.java +++ b/src/org/labkey/targetedms/parser/proto/SkylineDocument.java @@ -104,6 +104,7 @@ public enum UserSet public static final int USER_SET_MATCHED_VALUE = 4; + @Override public final int getNumber() { if (this == UNRECOGNIZED) { throw new java.lang.IllegalArgumentException( @@ -143,12 +144,16 @@ public static UserSet forNumber(int value) { } private static final com.google.protobuf.Internal.EnumLiteMap< UserSet> internalValueMap = - new com.google.protobuf.Internal.EnumLiteMap() { - public UserSet findValueByNumber(int number) { - return UserSet.forNumber(number); - } - }; + new com.google.protobuf.Internal.EnumLiteMap<>() + { + @Override + public UserSet findValueByNumber(int number) + { + return UserSet.forNumber(number); + } + }; + @Override public final com.google.protobuf.Descriptors.EnumValueDescriptor getValueDescriptor() { if (this == UNRECOGNIZED) { @@ -157,6 +162,7 @@ public UserSet findValueByNumber(int number) { } return getDescriptor().getValues().get(ordinal()); } + @Override public final com.google.protobuf.Descriptors.EnumDescriptor getDescriptorForType() { return getDescriptor(); @@ -182,7 +188,7 @@ public static UserSet valueOf( private final int value; - private UserSet(int value) { + UserSet(int value) { this.value = value; } @@ -223,6 +229,7 @@ public enum OptionalBool public static final int OPTIONAL_BOOL_FALSE_VALUE = 2; + @Override public final int getNumber() { if (this == UNRECOGNIZED) { throw new java.lang.IllegalArgumentException( @@ -260,12 +267,16 @@ public static OptionalBool forNumber(int value) { } private static final com.google.protobuf.Internal.EnumLiteMap< OptionalBool> internalValueMap = - new com.google.protobuf.Internal.EnumLiteMap() { - public OptionalBool findValueByNumber(int number) { - return OptionalBool.forNumber(number); - } - }; + new com.google.protobuf.Internal.EnumLiteMap<>() + { + @Override + public OptionalBool findValueByNumber(int number) + { + return OptionalBool.forNumber(number); + } + }; + @Override public final com.google.protobuf.Descriptors.EnumValueDescriptor getValueDescriptor() { if (this == UNRECOGNIZED) { @@ -274,6 +285,7 @@ public OptionalBool findValueByNumber(int number) { } return getDescriptor().getValues().get(ordinal()); } + @Override public final com.google.protobuf.Descriptors.EnumDescriptor getDescriptorForType() { return getDescriptor(); @@ -299,7 +311,7 @@ public static OptionalBool valueOf( private final int value; - private OptionalBool(int value) { + OptionalBool(int value) { this.value = value; } @@ -340,6 +352,7 @@ public enum PeakIdentification public static final int PEAK_IDENTIFICATION_ALIGNED_VALUE = 2; + @Override public final int getNumber() { if (this == UNRECOGNIZED) { throw new java.lang.IllegalArgumentException( @@ -377,12 +390,16 @@ public static PeakIdentification forNumber(int value) { } private static final com.google.protobuf.Internal.EnumLiteMap< PeakIdentification> internalValueMap = - new com.google.protobuf.Internal.EnumLiteMap() { - public PeakIdentification findValueByNumber(int number) { - return PeakIdentification.forNumber(number); - } - }; + new com.google.protobuf.Internal.EnumLiteMap<>() + { + @Override + public PeakIdentification findValueByNumber(int number) + { + return PeakIdentification.forNumber(number); + } + }; + @Override public final com.google.protobuf.Descriptors.EnumValueDescriptor getValueDescriptor() { if (this == UNRECOGNIZED) { @@ -391,6 +408,7 @@ public PeakIdentification findValueByNumber(int number) { } return getDescriptor().getValues().get(ordinal()); } + @Override public final com.google.protobuf.Descriptors.EnumDescriptor getDescriptorForType() { return getDescriptor(); @@ -416,7 +434,7 @@ public static PeakIdentification valueOf( private final int value; - private PeakIdentification(int value) { + PeakIdentification(int value) { this.value = value; } @@ -521,6 +539,7 @@ public enum IonType public static final int ION_TYPE_zHH_VALUE = 10; + @Override public final int getNumber() { if (this == UNRECOGNIZED) { throw new java.lang.IllegalArgumentException( @@ -566,12 +585,16 @@ public static IonType forNumber(int value) { } private static final com.google.protobuf.Internal.EnumLiteMap< IonType> internalValueMap = - new com.google.protobuf.Internal.EnumLiteMap() { - public IonType findValueByNumber(int number) { - return IonType.forNumber(number); - } - }; + new com.google.protobuf.Internal.EnumLiteMap<>() + { + @Override + public IonType findValueByNumber(int number) + { + return IonType.forNumber(number); + } + }; + @Override public final com.google.protobuf.Descriptors.EnumValueDescriptor getValueDescriptor() { if (this == UNRECOGNIZED) { @@ -580,6 +603,7 @@ public IonType findValueByNumber(int number) { } return getDescriptor().getValues().get(ordinal()); } + @Override public final com.google.protobuf.Descriptors.EnumDescriptor getDescriptorForType() { return getDescriptor(); @@ -605,7 +629,7 @@ public static IonType valueOf( private final int value; - private IonType(int value) { + IonType(int value) { this.value = value; } @@ -646,6 +670,7 @@ public enum LossInclusion public static final int Always_VALUE = 2; + @Override public final int getNumber() { if (this == UNRECOGNIZED) { throw new java.lang.IllegalArgumentException( @@ -683,12 +708,16 @@ public static LossInclusion forNumber(int value) { } private static final com.google.protobuf.Internal.EnumLiteMap< LossInclusion> internalValueMap = - new com.google.protobuf.Internal.EnumLiteMap() { - public LossInclusion findValueByNumber(int number) { - return LossInclusion.forNumber(number); - } - }; + new com.google.protobuf.Internal.EnumLiteMap<>() + { + @Override + public LossInclusion findValueByNumber(int number) + { + return LossInclusion.forNumber(number); + } + }; + @Override public final com.google.protobuf.Descriptors.EnumValueDescriptor getValueDescriptor() { if (this == UNRECOGNIZED) { @@ -697,6 +726,7 @@ public LossInclusion findValueByNumber(int number) { } return getDescriptor().getValues().get(ordinal()); } + @Override public final com.google.protobuf.Descriptors.EnumDescriptor getDescriptorForType() { return getDescriptor(); @@ -722,7 +752,7 @@ public static LossInclusion valueOf( private final int value; - private LossInclusion(int value) { + LossInclusion(int value) { this.value = value; } @@ -956,12 +986,11 @@ public boolean equals(final java.lang.Object obj) { if (obj == this) { return true; } - if (!(obj instanceof org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.Annotations)) { + if (!(obj instanceof Annotations other)) { return super.equals(obj); } - org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.Annotations other = (org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.Annotations) obj; - if (!getNote() + if (!getNote() .equals(other.getNote())) return false; if (getColor() != other.getColor()) return false; @@ -1329,6 +1358,7 @@ public Builder mergeFrom( * string note = 1; * @return The note. */ + @Override public java.lang.String getNote() { java.lang.Object ref = note_; if (!(ref instanceof java.lang.String)) { @@ -1345,6 +1375,7 @@ public java.lang.String getNote() { * string note = 1; * @return The bytes for note. */ + @Override public com.google.protobuf.ByteString getNoteBytes() { java.lang.Object ref = note_; @@ -1432,7 +1463,7 @@ public Builder clearColor() { java.util.Collections.emptyList(); private void ensureValuesIsMutable() { if (!((bitField0_ & 0x00000004) != 0)) { - values_ = new java.util.ArrayList(values_); + values_ = new java.util.ArrayList<>(values_); bitField0_ |= 0x00000004; } } @@ -1443,6 +1474,7 @@ private void ensureValuesIsMutable() { /** * repeated .SkylineDocumentProto.AnnotationValue values = 3; */ + @Override public java.util.List getValuesList() { if (valuesBuilder_ == null) { return java.util.Collections.unmodifiableList(values_); @@ -1453,6 +1485,7 @@ public java.util.Listrepeated .SkylineDocumentProto.AnnotationValue values = 3; */ + @Override public int getValuesCount() { if (valuesBuilder_ == null) { return values_.size(); @@ -1463,6 +1496,7 @@ public int getValuesCount() { /** * repeated .SkylineDocumentProto.AnnotationValue values = 3; */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.AnnotationValue getValues(int index) { if (valuesBuilder_ == null) { return values_.get(index); @@ -1613,6 +1647,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.A /** * repeated .SkylineDocumentProto.AnnotationValue values = 3; */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.AnnotationValueOrBuilder getValuesOrBuilder( int index) { if (valuesBuilder_ == null) { @@ -1623,7 +1658,8 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.A /** * repeated .SkylineDocumentProto.AnnotationValue values = 3; */ - public java.util.List + @Override + public java.util.List getValuesOrBuilderList() { if (valuesBuilder_ != null) { return valuesBuilder_.getMessageOrBuilderList(); @@ -1657,8 +1693,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.A org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.AnnotationValue, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.AnnotationValue.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.AnnotationValueOrBuilder> getValuesFieldBuilder() { if (valuesBuilder_ == null) { - valuesBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3< - org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.AnnotationValue, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.AnnotationValue.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.AnnotationValueOrBuilder>( + valuesBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<>( values_, ((bitField0_ & 0x00000004) != 0), getParentForChildren(), @@ -1694,25 +1729,34 @@ public static org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocument } private static final com.google.protobuf.Parser - PARSER = new com.google.protobuf.AbstractParser() { - @java.lang.Override - public Annotations parsePartialFrom( - com.google.protobuf.CodedInputStream input, - com.google.protobuf.ExtensionRegistryLite extensionRegistry) - throws com.google.protobuf.InvalidProtocolBufferException { - Builder builder = newBuilder(); - try { - builder.mergeFrom(input, extensionRegistry); - } catch (com.google.protobuf.InvalidProtocolBufferException e) { - throw e.setUnfinishedMessage(builder.buildPartial()); - } catch (com.google.protobuf.UninitializedMessageException e) { - throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); - } catch (java.io.IOException e) { - throw new com.google.protobuf.InvalidProtocolBufferException(e) - .setUnfinishedMessage(builder.buildPartial()); + PARSER = new com.google.protobuf.AbstractParser<>() + { + @java.lang.Override + public Annotations parsePartialFrom( + com.google.protobuf.CodedInputStream input, + com.google.protobuf.ExtensionRegistryLite extensionRegistry) + throws com.google.protobuf.InvalidProtocolBufferException + { + Builder builder = newBuilder(); + try + { + builder.mergeFrom(input, extensionRegistry); + } + catch (com.google.protobuf.InvalidProtocolBufferException e) + { + throw e.setUnfinishedMessage(builder.buildPartial()); + } + catch (com.google.protobuf.UninitializedMessageException e) + { + throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); + } + catch (java.io.IOException e) + { + throw new com.google.protobuf.InvalidProtocolBufferException(e) + .setUnfinishedMessage(builder.buildPartial()); + } + return builder.buildPartial(); } - return builder.buildPartial(); - } }; public static com.google.protobuf.Parser parser() { @@ -1919,12 +1963,11 @@ public boolean equals(final java.lang.Object obj) { if (obj == this) { return true; } - if (!(obj instanceof org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.AnnotationValue)) { + if (!(obj instanceof AnnotationValue other)) { return super.equals(obj); } - org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.AnnotationValue other = (org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.AnnotationValue) obj; - if (!getName() + if (!getName() .equals(other.getName())) return false; if (!getTextValue() .equals(other.getTextValue())) return false; @@ -2229,6 +2272,7 @@ public Builder mergeFrom( * string name = 1; * @return The name. */ + @Override public java.lang.String getName() { java.lang.Object ref = name_; if (!(ref instanceof java.lang.String)) { @@ -2245,6 +2289,7 @@ public java.lang.String getName() { * string name = 1; * @return The bytes for name. */ + @Override public com.google.protobuf.ByteString getNameBytes() { java.lang.Object ref = name_; @@ -2301,6 +2346,7 @@ public Builder setNameBytes( * string textValue = 2; * @return The textValue. */ + @Override public java.lang.String getTextValue() { java.lang.Object ref = textValue_; if (!(ref instanceof java.lang.String)) { @@ -2317,6 +2363,7 @@ public java.lang.String getTextValue() { * string textValue = 2; * @return The bytes for textValue. */ + @Override public com.google.protobuf.ByteString getTextValueBytes() { java.lang.Object ref = textValue_; @@ -2394,25 +2441,34 @@ public static org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocument } private static final com.google.protobuf.Parser - PARSER = new com.google.protobuf.AbstractParser() { - @java.lang.Override - public AnnotationValue parsePartialFrom( - com.google.protobuf.CodedInputStream input, - com.google.protobuf.ExtensionRegistryLite extensionRegistry) - throws com.google.protobuf.InvalidProtocolBufferException { - Builder builder = newBuilder(); - try { - builder.mergeFrom(input, extensionRegistry); - } catch (com.google.protobuf.InvalidProtocolBufferException e) { - throw e.setUnfinishedMessage(builder.buildPartial()); - } catch (com.google.protobuf.UninitializedMessageException e) { - throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); - } catch (java.io.IOException e) { - throw new com.google.protobuf.InvalidProtocolBufferException(e) - .setUnfinishedMessage(builder.buildPartial()); + PARSER = new com.google.protobuf.AbstractParser<>() + { + @java.lang.Override + public AnnotationValue parsePartialFrom( + com.google.protobuf.CodedInputStream input, + com.google.protobuf.ExtensionRegistryLite extensionRegistry) + throws com.google.protobuf.InvalidProtocolBufferException + { + Builder builder = newBuilder(); + try + { + builder.mergeFrom(input, extensionRegistry); + } + catch (com.google.protobuf.InvalidProtocolBufferException e) + { + throw e.setUnfinishedMessage(builder.buildPartial()); + } + catch (com.google.protobuf.UninitializedMessageException e) + { + throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); + } + catch (java.io.IOException e) + { + throw new com.google.protobuf.InvalidProtocolBufferException(e) + .setUnfinishedMessage(builder.buildPartial()); + } + return builder.buildPartial(); } - return builder.buildPartial(); - } }; public static com.google.protobuf.Parser parser() { @@ -2863,12 +2919,11 @@ public boolean equals(final java.lang.Object obj) { if (obj == this) { return true; } - if (!(obj instanceof org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionPeak.PeakShapeValues)) { + if (!(obj instanceof PeakShapeValues other)) { return super.equals(obj); } - org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionPeak.PeakShapeValues other = (org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionPeak.PeakShapeValues) obj; - if (java.lang.Float.floatToIntBits(getStdDev()) + if (java.lang.Float.floatToIntBits(getStdDev()) != java.lang.Float.floatToIntBits( other.getStdDev())) return false; if (java.lang.Float.floatToIntBits(getSkewness()) @@ -3358,25 +3413,34 @@ public static org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocument } private static final com.google.protobuf.Parser - PARSER = new com.google.protobuf.AbstractParser() { - @java.lang.Override - public PeakShapeValues parsePartialFrom( - com.google.protobuf.CodedInputStream input, - com.google.protobuf.ExtensionRegistryLite extensionRegistry) - throws com.google.protobuf.InvalidProtocolBufferException { - Builder builder = newBuilder(); - try { - builder.mergeFrom(input, extensionRegistry); - } catch (com.google.protobuf.InvalidProtocolBufferException e) { - throw e.setUnfinishedMessage(builder.buildPartial()); - } catch (com.google.protobuf.UninitializedMessageException e) { - throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); - } catch (java.io.IOException e) { - throw new com.google.protobuf.InvalidProtocolBufferException(e) - .setUnfinishedMessage(builder.buildPartial()); + PARSER = new com.google.protobuf.AbstractParser<>() + { + @java.lang.Override + public PeakShapeValues parsePartialFrom( + com.google.protobuf.CodedInputStream input, + com.google.protobuf.ExtensionRegistryLite extensionRegistry) + throws com.google.protobuf.InvalidProtocolBufferException + { + Builder builder = newBuilder(); + try + { + builder.mergeFrom(input, extensionRegistry); + } + catch (com.google.protobuf.InvalidProtocolBufferException e) + { + throw e.setUnfinishedMessage(builder.buildPartial()); + } + catch (com.google.protobuf.UninitializedMessageException e) + { + throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); + } + catch (java.io.IOException e) + { + throw new com.google.protobuf.InvalidProtocolBufferException(e) + .setUnfinishedMessage(builder.buildPartial()); + } + return builder.buildPartial(); } - return builder.buildPartial(); - } }; public static com.google.protobuf.Parser parser() { @@ -3987,12 +4051,11 @@ public boolean equals(final java.lang.Object obj) { if (obj == this) { return true; } - if (!(obj instanceof org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionPeak)) { + if (!(obj instanceof TransitionPeak other)) { return super.equals(obj); } - org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionPeak other = (org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionPeak) obj; - if (getReplicateIndex() + if (getReplicateIndex() != other.getReplicateIndex()) return false; if (getFileIndexInReplicate() != other.getFileIndexInReplicate()) return false; @@ -4836,6 +4899,7 @@ public Builder clearFileIndexInReplicate() { * .google.protobuf.FloatValue massError = 3; * @return Whether the massError field is set. */ + @Override public boolean hasMassError() { return ((bitField0_ & 0x00000004) != 0); } @@ -4843,6 +4907,7 @@ public boolean hasMassError() { * .google.protobuf.FloatValue massError = 3; * @return The massError. */ + @Override public com.google.protobuf.FloatValue getMassError() { if (massErrorBuilder_ == null) { return massError_ == null ? com.google.protobuf.FloatValue.getDefaultInstance() : massError_; @@ -4925,6 +4990,7 @@ public com.google.protobuf.FloatValue.Builder getMassErrorBuilder() { /** * .google.protobuf.FloatValue massError = 3; */ + @Override public com.google.protobuf.FloatValueOrBuilder getMassErrorOrBuilder() { if (massErrorBuilder_ != null) { return massErrorBuilder_.getMessageOrBuilder(); @@ -4940,8 +5006,7 @@ public com.google.protobuf.FloatValueOrBuilder getMassErrorOrBuilder() { com.google.protobuf.FloatValue, com.google.protobuf.FloatValue.Builder, com.google.protobuf.FloatValueOrBuilder> getMassErrorFieldBuilder() { if (massErrorBuilder_ == null) { - massErrorBuilder_ = new com.google.protobuf.SingleFieldBuilderV3< - com.google.protobuf.FloatValue, com.google.protobuf.FloatValue.Builder, com.google.protobuf.FloatValueOrBuilder>( + massErrorBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<>( getMassError(), getParentForChildren(), isClean()); @@ -5053,6 +5118,7 @@ public Builder clearEndRetentionTime() { * .google.protobuf.DoubleValue ionMobility = 7; * @return Whether the ionMobility field is set. */ + @Override public boolean hasIonMobility() { return ((bitField0_ & 0x00000040) != 0); } @@ -5060,6 +5126,7 @@ public boolean hasIonMobility() { * .google.protobuf.DoubleValue ionMobility = 7; * @return The ionMobility. */ + @Override public com.google.protobuf.DoubleValue getIonMobility() { if (ionMobilityBuilder_ == null) { return ionMobility_ == null ? com.google.protobuf.DoubleValue.getDefaultInstance() : ionMobility_; @@ -5142,6 +5209,7 @@ public com.google.protobuf.DoubleValue.Builder getIonMobilityBuilder() { /** * .google.protobuf.DoubleValue ionMobility = 7; */ + @Override public com.google.protobuf.DoubleValueOrBuilder getIonMobilityOrBuilder() { if (ionMobilityBuilder_ != null) { return ionMobilityBuilder_.getMessageOrBuilder(); @@ -5157,8 +5225,7 @@ public com.google.protobuf.DoubleValueOrBuilder getIonMobilityOrBuilder() { com.google.protobuf.DoubleValue, com.google.protobuf.DoubleValue.Builder, com.google.protobuf.DoubleValueOrBuilder> getIonMobilityFieldBuilder() { if (ionMobilityBuilder_ == null) { - ionMobilityBuilder_ = new com.google.protobuf.SingleFieldBuilderV3< - com.google.protobuf.DoubleValue, com.google.protobuf.DoubleValue.Builder, com.google.protobuf.DoubleValueOrBuilder>( + ionMobilityBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<>( getIonMobility(), getParentForChildren(), isClean()); @@ -5174,6 +5241,7 @@ public com.google.protobuf.DoubleValueOrBuilder getIonMobilityOrBuilder() { * .google.protobuf.DoubleValue ionMobilityWindow = 8; * @return Whether the ionMobilityWindow field is set. */ + @Override public boolean hasIonMobilityWindow() { return ((bitField0_ & 0x00000080) != 0); } @@ -5181,6 +5249,7 @@ public boolean hasIonMobilityWindow() { * .google.protobuf.DoubleValue ionMobilityWindow = 8; * @return The ionMobilityWindow. */ + @Override public com.google.protobuf.DoubleValue getIonMobilityWindow() { if (ionMobilityWindowBuilder_ == null) { return ionMobilityWindow_ == null ? com.google.protobuf.DoubleValue.getDefaultInstance() : ionMobilityWindow_; @@ -5263,6 +5332,7 @@ public com.google.protobuf.DoubleValue.Builder getIonMobilityWindowBuilder() { /** * .google.protobuf.DoubleValue ionMobilityWindow = 8; */ + @Override public com.google.protobuf.DoubleValueOrBuilder getIonMobilityWindowOrBuilder() { if (ionMobilityWindowBuilder_ != null) { return ionMobilityWindowBuilder_.getMessageOrBuilder(); @@ -5278,8 +5348,7 @@ public com.google.protobuf.DoubleValueOrBuilder getIonMobilityWindowOrBuilder() com.google.protobuf.DoubleValue, com.google.protobuf.DoubleValue.Builder, com.google.protobuf.DoubleValueOrBuilder> getIonMobilityWindowFieldBuilder() { if (ionMobilityWindowBuilder_ == null) { - ionMobilityWindowBuilder_ = new com.google.protobuf.SingleFieldBuilderV3< - com.google.protobuf.DoubleValue, com.google.protobuf.DoubleValue.Builder, com.google.protobuf.DoubleValueOrBuilder>( + ionMobilityWindowBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<>( getIonMobilityWindow(), getParentForChildren(), isClean()); @@ -5625,6 +5694,7 @@ public Builder clearRankByLevel() { * .SkylineDocumentProto.OptionalInt pointsAcrossPeak = 18; * @return Whether the pointsAcrossPeak field is set. */ + @Override public boolean hasPointsAcrossPeak() { return ((bitField0_ & 0x00020000) != 0); } @@ -5632,6 +5702,7 @@ public boolean hasPointsAcrossPeak() { * .SkylineDocumentProto.OptionalInt pointsAcrossPeak = 18; * @return The pointsAcrossPeak. */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.OptionalInt getPointsAcrossPeak() { if (pointsAcrossPeakBuilder_ == null) { return pointsAcrossPeak_ == null ? org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.OptionalInt.getDefaultInstance() : pointsAcrossPeak_; @@ -5714,6 +5785,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.O /** * .SkylineDocumentProto.OptionalInt pointsAcrossPeak = 18; */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.OptionalIntOrBuilder getPointsAcrossPeakOrBuilder() { if (pointsAcrossPeakBuilder_ != null) { return pointsAcrossPeakBuilder_.getMessageOrBuilder(); @@ -5729,8 +5801,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.O org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.OptionalInt, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.OptionalInt.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.OptionalIntOrBuilder> getPointsAcrossPeakFieldBuilder() { if (pointsAcrossPeakBuilder_ == null) { - pointsAcrossPeakBuilder_ = new com.google.protobuf.SingleFieldBuilderV3< - org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.OptionalInt, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.OptionalInt.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.OptionalIntOrBuilder>( + pointsAcrossPeakBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<>( getPointsAcrossPeak(), getParentForChildren(), isClean()); @@ -5831,6 +5902,7 @@ public Builder clearOptimizationStep() { * .SkylineDocumentProto.Annotations annotations = 24; * @return Whether the annotations field is set. */ + @Override public boolean hasAnnotations() { return ((bitField0_ & 0x00100000) != 0); } @@ -5838,6 +5910,7 @@ public boolean hasAnnotations() { * .SkylineDocumentProto.Annotations annotations = 24; * @return The annotations. */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.Annotations getAnnotations() { if (annotationsBuilder_ == null) { return annotations_ == null ? org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.Annotations.getDefaultInstance() : annotations_; @@ -5920,6 +5993,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.A /** * .SkylineDocumentProto.Annotations annotations = 24; */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.AnnotationsOrBuilder getAnnotationsOrBuilder() { if (annotationsBuilder_ != null) { return annotationsBuilder_.getMessageOrBuilder(); @@ -5935,8 +6009,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.A org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.Annotations, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.Annotations.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.AnnotationsOrBuilder> getAnnotationsFieldBuilder() { if (annotationsBuilder_ == null) { - annotationsBuilder_ = new com.google.protobuf.SingleFieldBuilderV3< - org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.Annotations, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.Annotations.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.AnnotationsOrBuilder>( + annotationsBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<>( getAnnotations(), getParentForChildren(), isClean()); @@ -5984,6 +6057,7 @@ public Builder clearForcedIntegration() { * .SkylineDocumentProto.TransitionPeak.PeakShapeValues peakShapeValues = 26; * @return Whether the peakShapeValues field is set. */ + @Override public boolean hasPeakShapeValues() { return ((bitField0_ & 0x00400000) != 0); } @@ -5991,6 +6065,7 @@ public boolean hasPeakShapeValues() { * .SkylineDocumentProto.TransitionPeak.PeakShapeValues peakShapeValues = 26; * @return The peakShapeValues. */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionPeak.PeakShapeValues getPeakShapeValues() { if (peakShapeValuesBuilder_ == null) { return peakShapeValues_ == null ? org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionPeak.PeakShapeValues.getDefaultInstance() : peakShapeValues_; @@ -6073,6 +6148,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.T /** * .SkylineDocumentProto.TransitionPeak.PeakShapeValues peakShapeValues = 26; */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionPeak.PeakShapeValuesOrBuilder getPeakShapeValuesOrBuilder() { if (peakShapeValuesBuilder_ != null) { return peakShapeValuesBuilder_.getMessageOrBuilder(); @@ -6088,8 +6164,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.T org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionPeak.PeakShapeValues, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionPeak.PeakShapeValues.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionPeak.PeakShapeValuesOrBuilder> getPeakShapeValuesFieldBuilder() { if (peakShapeValuesBuilder_ == null) { - peakShapeValuesBuilder_ = new com.google.protobuf.SingleFieldBuilderV3< - org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionPeak.PeakShapeValues, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionPeak.PeakShapeValues.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionPeak.PeakShapeValuesOrBuilder>( + peakShapeValuesBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<>( getPeakShapeValues(), getParentForChildren(), isClean()); @@ -6105,6 +6180,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.T * .google.protobuf.DoubleValue ionMobilityCollisionCrossSection = 27; * @return Whether the ionMobilityCollisionCrossSection field is set. */ + @Override public boolean hasIonMobilityCollisionCrossSection() { return ((bitField0_ & 0x00800000) != 0); } @@ -6112,6 +6188,7 @@ public boolean hasIonMobilityCollisionCrossSection() { * .google.protobuf.DoubleValue ionMobilityCollisionCrossSection = 27; * @return The ionMobilityCollisionCrossSection. */ + @Override public com.google.protobuf.DoubleValue getIonMobilityCollisionCrossSection() { if (ionMobilityCollisionCrossSectionBuilder_ == null) { return ionMobilityCollisionCrossSection_ == null ? com.google.protobuf.DoubleValue.getDefaultInstance() : ionMobilityCollisionCrossSection_; @@ -6194,6 +6271,7 @@ public com.google.protobuf.DoubleValue.Builder getIonMobilityCollisionCrossSecti /** * .google.protobuf.DoubleValue ionMobilityCollisionCrossSection = 27; */ + @Override public com.google.protobuf.DoubleValueOrBuilder getIonMobilityCollisionCrossSectionOrBuilder() { if (ionMobilityCollisionCrossSectionBuilder_ != null) { return ionMobilityCollisionCrossSectionBuilder_.getMessageOrBuilder(); @@ -6209,8 +6287,7 @@ public com.google.protobuf.DoubleValueOrBuilder getIonMobilityCollisionCrossSect com.google.protobuf.DoubleValue, com.google.protobuf.DoubleValue.Builder, com.google.protobuf.DoubleValueOrBuilder> getIonMobilityCollisionCrossSectionFieldBuilder() { if (ionMobilityCollisionCrossSectionBuilder_ == null) { - ionMobilityCollisionCrossSectionBuilder_ = new com.google.protobuf.SingleFieldBuilderV3< - com.google.protobuf.DoubleValue, com.google.protobuf.DoubleValue.Builder, com.google.protobuf.DoubleValueOrBuilder>( + ionMobilityCollisionCrossSectionBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<>( getIonMobilityCollisionCrossSection(), getParentForChildren(), isClean()); @@ -6245,25 +6322,34 @@ public static org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocument } private static final com.google.protobuf.Parser - PARSER = new com.google.protobuf.AbstractParser() { - @java.lang.Override - public TransitionPeak parsePartialFrom( - com.google.protobuf.CodedInputStream input, - com.google.protobuf.ExtensionRegistryLite extensionRegistry) - throws com.google.protobuf.InvalidProtocolBufferException { - Builder builder = newBuilder(); - try { - builder.mergeFrom(input, extensionRegistry); - } catch (com.google.protobuf.InvalidProtocolBufferException e) { - throw e.setUnfinishedMessage(builder.buildPartial()); - } catch (com.google.protobuf.UninitializedMessageException e) { - throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); - } catch (java.io.IOException e) { - throw new com.google.protobuf.InvalidProtocolBufferException(e) - .setUnfinishedMessage(builder.buildPartial()); + PARSER = new com.google.protobuf.AbstractParser<>() + { + @java.lang.Override + public TransitionPeak parsePartialFrom( + com.google.protobuf.CodedInputStream input, + com.google.protobuf.ExtensionRegistryLite extensionRegistry) + throws com.google.protobuf.InvalidProtocolBufferException + { + Builder builder = newBuilder(); + try + { + builder.mergeFrom(input, extensionRegistry); + } + catch (com.google.protobuf.InvalidProtocolBufferException e) + { + throw e.setUnfinishedMessage(builder.buildPartial()); + } + catch (com.google.protobuf.UninitializedMessageException e) + { + throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); + } + catch (java.io.IOException e) + { + throw new com.google.protobuf.InvalidProtocolBufferException(e) + .setUnfinishedMessage(builder.buildPartial()); + } + return builder.buildPartial(); } - return builder.buildPartial(); - } }; public static com.google.protobuf.Parser parser() { @@ -6427,12 +6513,11 @@ public boolean equals(final java.lang.Object obj) { if (obj == this) { return true; } - if (!(obj instanceof org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionResults)) { + if (!(obj instanceof TransitionResults other)) { return super.equals(obj); } - org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionResults other = (org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionResults) obj; - if (!getPeaksList() + if (!getPeaksList() .equals(other.getPeaksList())) return false; if (!getUnknownFields().equals(other.getUnknownFields())) return false; return true; @@ -6765,7 +6850,7 @@ public Builder mergeFrom( java.util.Collections.emptyList(); private void ensurePeaksIsMutable() { if (!((bitField0_ & 0x00000001) != 0)) { - peaks_ = new java.util.ArrayList(peaks_); + peaks_ = new java.util.ArrayList<>(peaks_); bitField0_ |= 0x00000001; } } @@ -6776,6 +6861,7 @@ private void ensurePeaksIsMutable() { /** * repeated .SkylineDocumentProto.TransitionPeak peaks = 1; */ + @Override public java.util.List getPeaksList() { if (peaksBuilder_ == null) { return java.util.Collections.unmodifiableList(peaks_); @@ -6786,6 +6872,7 @@ public java.util.Listrepeated .SkylineDocumentProto.TransitionPeak peaks = 1; */ + @Override public int getPeaksCount() { if (peaksBuilder_ == null) { return peaks_.size(); @@ -6796,6 +6883,7 @@ public int getPeaksCount() { /** * repeated .SkylineDocumentProto.TransitionPeak peaks = 1; */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionPeak getPeaks(int index) { if (peaksBuilder_ == null) { return peaks_.get(index); @@ -6946,6 +7034,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.T /** * repeated .SkylineDocumentProto.TransitionPeak peaks = 1; */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionPeakOrBuilder getPeaksOrBuilder( int index) { if (peaksBuilder_ == null) { @@ -6956,7 +7045,8 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.T /** * repeated .SkylineDocumentProto.TransitionPeak peaks = 1; */ - public java.util.List + @Override + public java.util.List getPeaksOrBuilderList() { if (peaksBuilder_ != null) { return peaksBuilder_.getMessageOrBuilderList(); @@ -6990,8 +7080,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.T org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionPeak, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionPeak.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionPeakOrBuilder> getPeaksFieldBuilder() { if (peaksBuilder_ == null) { - peaksBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3< - org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionPeak, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionPeak.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionPeakOrBuilder>( + peaksBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<>( peaks_, ((bitField0_ & 0x00000001) != 0), getParentForChildren(), @@ -7027,25 +7116,34 @@ public static org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocument } private static final com.google.protobuf.Parser - PARSER = new com.google.protobuf.AbstractParser() { - @java.lang.Override - public TransitionResults parsePartialFrom( - com.google.protobuf.CodedInputStream input, - com.google.protobuf.ExtensionRegistryLite extensionRegistry) - throws com.google.protobuf.InvalidProtocolBufferException { - Builder builder = newBuilder(); - try { - builder.mergeFrom(input, extensionRegistry); - } catch (com.google.protobuf.InvalidProtocolBufferException e) { - throw e.setUnfinishedMessage(builder.buildPartial()); - } catch (com.google.protobuf.UninitializedMessageException e) { - throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); - } catch (java.io.IOException e) { - throw new com.google.protobuf.InvalidProtocolBufferException(e) - .setUnfinishedMessage(builder.buildPartial()); + PARSER = new com.google.protobuf.AbstractParser<>() + { + @java.lang.Override + public TransitionResults parsePartialFrom( + com.google.protobuf.CodedInputStream input, + com.google.protobuf.ExtensionRegistryLite extensionRegistry) + throws com.google.protobuf.InvalidProtocolBufferException + { + Builder builder = newBuilder(); + try + { + builder.mergeFrom(input, extensionRegistry); + } + catch (com.google.protobuf.InvalidProtocolBufferException e) + { + throw e.setUnfinishedMessage(builder.buildPartial()); + } + catch (com.google.protobuf.UninitializedMessageException e) + { + throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); + } + catch (java.io.IOException e) + { + throw new com.google.protobuf.InvalidProtocolBufferException(e) + .setUnfinishedMessage(builder.buildPartial()); + } + return builder.buildPartial(); } - return builder.buildPartial(); - } }; public static com.google.protobuf.Parser parser() { @@ -8696,12 +8794,11 @@ public boolean equals(final java.lang.Object obj) { if (obj == this) { return true; } - if (!(obj instanceof org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.Transition)) { + if (!(obj instanceof Transition other)) { return super.equals(obj); } - org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.Transition other = (org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.Transition) obj; - if (hasFormula() != other.hasFormula()) return false; + if (hasFormula() != other.hasFormula()) return false; if (hasFormula()) { if (!getFormula() .equals(other.getFormula())) return false; @@ -9983,6 +10080,7 @@ public Builder mergeFrom( * .google.protobuf.StringValue formula = 1; * @return Whether the formula field is set. */ + @Override public boolean hasFormula() { return ((bitField0_ & 0x00000001) != 0); } @@ -9990,6 +10088,7 @@ public boolean hasFormula() { * .google.protobuf.StringValue formula = 1; * @return The formula. */ + @Override public com.google.protobuf.StringValue getFormula() { if (formulaBuilder_ == null) { return formula_ == null ? com.google.protobuf.StringValue.getDefaultInstance() : formula_; @@ -10072,6 +10171,7 @@ public com.google.protobuf.StringValue.Builder getFormulaBuilder() { /** * .google.protobuf.StringValue formula = 1; */ + @Override public com.google.protobuf.StringValueOrBuilder getFormulaOrBuilder() { if (formulaBuilder_ != null) { return formulaBuilder_.getMessageOrBuilder(); @@ -10087,8 +10187,7 @@ public com.google.protobuf.StringValueOrBuilder getFormulaOrBuilder() { com.google.protobuf.StringValue, com.google.protobuf.StringValue.Builder, com.google.protobuf.StringValueOrBuilder> getFormulaFieldBuilder() { if (formulaBuilder_ == null) { - formulaBuilder_ = new com.google.protobuf.SingleFieldBuilderV3< - com.google.protobuf.StringValue, com.google.protobuf.StringValue.Builder, com.google.protobuf.StringValueOrBuilder>( + formulaBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<>( getFormula(), getParentForChildren(), isClean()); @@ -10108,6 +10207,7 @@ public com.google.protobuf.StringValueOrBuilder getFormulaOrBuilder() { * .google.protobuf.DoubleValue averageMassH = 2; * @return Whether the averageMassH field is set. */ + @Override public boolean hasAverageMassH() { return ((bitField0_ & 0x00000002) != 0); } @@ -10119,6 +10219,7 @@ public boolean hasAverageMassH() { * .google.protobuf.DoubleValue averageMassH = 2; * @return The averageMassH. */ + @Override public com.google.protobuf.DoubleValue getAverageMassH() { if (averageMassHBuilder_ == null) { return averageMassH_ == null ? com.google.protobuf.DoubleValue.getDefaultInstance() : averageMassH_; @@ -10225,6 +10326,7 @@ public com.google.protobuf.DoubleValue.Builder getAverageMassHBuilder() { * * .google.protobuf.DoubleValue averageMassH = 2; */ + @Override public com.google.protobuf.DoubleValueOrBuilder getAverageMassHOrBuilder() { if (averageMassHBuilder_ != null) { return averageMassHBuilder_.getMessageOrBuilder(); @@ -10244,8 +10346,7 @@ public com.google.protobuf.DoubleValueOrBuilder getAverageMassHOrBuilder() { com.google.protobuf.DoubleValue, com.google.protobuf.DoubleValue.Builder, com.google.protobuf.DoubleValueOrBuilder> getAverageMassHFieldBuilder() { if (averageMassHBuilder_ == null) { - averageMassHBuilder_ = new com.google.protobuf.SingleFieldBuilderV3< - com.google.protobuf.DoubleValue, com.google.protobuf.DoubleValue.Builder, com.google.protobuf.DoubleValueOrBuilder>( + averageMassHBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<>( getAverageMassH(), getParentForChildren(), isClean()); @@ -10265,6 +10366,7 @@ public com.google.protobuf.DoubleValueOrBuilder getAverageMassHOrBuilder() { * .google.protobuf.DoubleValue monoMassH = 3; * @return Whether the monoMassH field is set. */ + @Override public boolean hasMonoMassH() { return ((bitField0_ & 0x00000004) != 0); } @@ -10276,6 +10378,7 @@ public boolean hasMonoMassH() { * .google.protobuf.DoubleValue monoMassH = 3; * @return The monoMassH. */ + @Override public com.google.protobuf.DoubleValue getMonoMassH() { if (monoMassHBuilder_ == null) { return monoMassH_ == null ? com.google.protobuf.DoubleValue.getDefaultInstance() : monoMassH_; @@ -10382,6 +10485,7 @@ public com.google.protobuf.DoubleValue.Builder getMonoMassHBuilder() { * * .google.protobuf.DoubleValue monoMassH = 3; */ + @Override public com.google.protobuf.DoubleValueOrBuilder getMonoMassHOrBuilder() { if (monoMassHBuilder_ != null) { return monoMassHBuilder_.getMessageOrBuilder(); @@ -10401,8 +10505,7 @@ public com.google.protobuf.DoubleValueOrBuilder getMonoMassHOrBuilder() { com.google.protobuf.DoubleValue, com.google.protobuf.DoubleValue.Builder, com.google.protobuf.DoubleValueOrBuilder> getMonoMassHFieldBuilder() { if (monoMassHBuilder_ == null) { - monoMassHBuilder_ = new com.google.protobuf.SingleFieldBuilderV3< - com.google.protobuf.DoubleValue, com.google.protobuf.DoubleValue.Builder, com.google.protobuf.DoubleValueOrBuilder>( + monoMassHBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<>( getMonoMassH(), getParentForChildren(), isClean()); @@ -10422,6 +10525,7 @@ public com.google.protobuf.DoubleValueOrBuilder getMonoMassHOrBuilder() { * .google.protobuf.StringValue custom_ion_name = 6; * @return Whether the customIonName field is set. */ + @Override public boolean hasCustomIonName() { return ((bitField0_ & 0x00000008) != 0); } @@ -10433,6 +10537,7 @@ public boolean hasCustomIonName() { * .google.protobuf.StringValue custom_ion_name = 6; * @return The customIonName. */ + @Override public com.google.protobuf.StringValue getCustomIonName() { if (customIonNameBuilder_ == null) { return customIonName_ == null ? com.google.protobuf.StringValue.getDefaultInstance() : customIonName_; @@ -10539,6 +10644,7 @@ public com.google.protobuf.StringValue.Builder getCustomIonNameBuilder() { * * .google.protobuf.StringValue custom_ion_name = 6; */ + @Override public com.google.protobuf.StringValueOrBuilder getCustomIonNameOrBuilder() { if (customIonNameBuilder_ != null) { return customIonNameBuilder_.getMessageOrBuilder(); @@ -10558,8 +10664,7 @@ public com.google.protobuf.StringValueOrBuilder getCustomIonNameOrBuilder() { com.google.protobuf.StringValue, com.google.protobuf.StringValue.Builder, com.google.protobuf.StringValueOrBuilder> getCustomIonNameFieldBuilder() { if (customIonNameBuilder_ == null) { - customIonNameBuilder_ = new com.google.protobuf.SingleFieldBuilderV3< - com.google.protobuf.StringValue, com.google.protobuf.StringValue.Builder, com.google.protobuf.StringValueOrBuilder>( + customIonNameBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<>( getCustomIonName(), getParentForChildren(), isClean()); @@ -10575,6 +10680,7 @@ public com.google.protobuf.StringValueOrBuilder getCustomIonNameOrBuilder() { * .google.protobuf.StringValue measured_ion_name = 7; * @return Whether the measuredIonName field is set. */ + @Override public boolean hasMeasuredIonName() { return ((bitField0_ & 0x00000010) != 0); } @@ -10582,6 +10688,7 @@ public boolean hasMeasuredIonName() { * .google.protobuf.StringValue measured_ion_name = 7; * @return The measuredIonName. */ + @Override public com.google.protobuf.StringValue getMeasuredIonName() { if (measuredIonNameBuilder_ == null) { return measuredIonName_ == null ? com.google.protobuf.StringValue.getDefaultInstance() : measuredIonName_; @@ -10664,6 +10771,7 @@ public com.google.protobuf.StringValue.Builder getMeasuredIonNameBuilder() { /** * .google.protobuf.StringValue measured_ion_name = 7; */ + @Override public com.google.protobuf.StringValueOrBuilder getMeasuredIonNameOrBuilder() { if (measuredIonNameBuilder_ != null) { return measuredIonNameBuilder_.getMessageOrBuilder(); @@ -10679,8 +10787,7 @@ public com.google.protobuf.StringValueOrBuilder getMeasuredIonNameOrBuilder() { com.google.protobuf.StringValue, com.google.protobuf.StringValue.Builder, com.google.protobuf.StringValueOrBuilder> getMeasuredIonNameFieldBuilder() { if (measuredIonNameBuilder_ == null) { - measuredIonNameBuilder_ = new com.google.protobuf.SingleFieldBuilderV3< - com.google.protobuf.StringValue, com.google.protobuf.StringValue.Builder, com.google.protobuf.StringValueOrBuilder>( + measuredIonNameBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<>( getMeasuredIonName(), getParentForChildren(), isClean()); @@ -10696,6 +10803,7 @@ public com.google.protobuf.StringValueOrBuilder getMeasuredIonNameOrBuilder() { * .SkylineDocumentProto.OptionalInt decoyMassShift = 8; * @return Whether the decoyMassShift field is set. */ + @Override public boolean hasDecoyMassShift() { return ((bitField0_ & 0x00000020) != 0); } @@ -10703,6 +10811,7 @@ public boolean hasDecoyMassShift() { * .SkylineDocumentProto.OptionalInt decoyMassShift = 8; * @return The decoyMassShift. */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.OptionalInt getDecoyMassShift() { if (decoyMassShiftBuilder_ == null) { return decoyMassShift_ == null ? org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.OptionalInt.getDefaultInstance() : decoyMassShift_; @@ -10785,6 +10894,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.O /** * .SkylineDocumentProto.OptionalInt decoyMassShift = 8; */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.OptionalIntOrBuilder getDecoyMassShiftOrBuilder() { if (decoyMassShiftBuilder_ != null) { return decoyMassShiftBuilder_.getMessageOrBuilder(); @@ -10800,8 +10910,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.O org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.OptionalInt, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.OptionalInt.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.OptionalIntOrBuilder> getDecoyMassShiftFieldBuilder() { if (decoyMassShiftBuilder_ == null) { - decoyMassShiftBuilder_ = new com.google.protobuf.SingleFieldBuilderV3< - org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.OptionalInt, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.OptionalInt.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.OptionalIntOrBuilder>( + decoyMassShiftBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<>( getDecoyMassShift(), getParentForChildren(), isClean()); @@ -10849,6 +10958,7 @@ public Builder clearMassIndex() { * .SkylineDocumentProto.OptionalInt isotopeDistRank = 11; * @return Whether the isotopeDistRank field is set. */ + @Override public boolean hasIsotopeDistRank() { return ((bitField0_ & 0x00000080) != 0); } @@ -10856,6 +10966,7 @@ public boolean hasIsotopeDistRank() { * .SkylineDocumentProto.OptionalInt isotopeDistRank = 11; * @return The isotopeDistRank. */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.OptionalInt getIsotopeDistRank() { if (isotopeDistRankBuilder_ == null) { return isotopeDistRank_ == null ? org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.OptionalInt.getDefaultInstance() : isotopeDistRank_; @@ -10938,6 +11049,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.O /** * .SkylineDocumentProto.OptionalInt isotopeDistRank = 11; */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.OptionalIntOrBuilder getIsotopeDistRankOrBuilder() { if (isotopeDistRankBuilder_ != null) { return isotopeDistRankBuilder_.getMessageOrBuilder(); @@ -10953,8 +11065,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.O org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.OptionalInt, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.OptionalInt.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.OptionalIntOrBuilder> getIsotopeDistRankFieldBuilder() { if (isotopeDistRankBuilder_ == null) { - isotopeDistRankBuilder_ = new com.google.protobuf.SingleFieldBuilderV3< - org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.OptionalInt, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.OptionalInt.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.OptionalIntOrBuilder>( + isotopeDistRankBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<>( getIsotopeDistRank(), getParentForChildren(), isClean()); @@ -10970,6 +11081,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.O * .google.protobuf.FloatValue isotopeDistProportion = 12; * @return Whether the isotopeDistProportion field is set. */ + @Override public boolean hasIsotopeDistProportion() { return ((bitField0_ & 0x00000100) != 0); } @@ -10977,6 +11089,7 @@ public boolean hasIsotopeDistProportion() { * .google.protobuf.FloatValue isotopeDistProportion = 12; * @return The isotopeDistProportion. */ + @Override public com.google.protobuf.FloatValue getIsotopeDistProportion() { if (isotopeDistProportionBuilder_ == null) { return isotopeDistProportion_ == null ? com.google.protobuf.FloatValue.getDefaultInstance() : isotopeDistProportion_; @@ -11059,6 +11172,7 @@ public com.google.protobuf.FloatValue.Builder getIsotopeDistProportionBuilder() /** * .google.protobuf.FloatValue isotopeDistProportion = 12; */ + @Override public com.google.protobuf.FloatValueOrBuilder getIsotopeDistProportionOrBuilder() { if (isotopeDistProportionBuilder_ != null) { return isotopeDistProportionBuilder_.getMessageOrBuilder(); @@ -11074,8 +11188,7 @@ public com.google.protobuf.FloatValueOrBuilder getIsotopeDistProportionOrBuilder com.google.protobuf.FloatValue, com.google.protobuf.FloatValue.Builder, com.google.protobuf.FloatValueOrBuilder> getIsotopeDistProportionFieldBuilder() { if (isotopeDistProportionBuilder_ == null) { - isotopeDistProportionBuilder_ = new com.google.protobuf.SingleFieldBuilderV3< - com.google.protobuf.FloatValue, com.google.protobuf.FloatValue.Builder, com.google.protobuf.FloatValueOrBuilder>( + isotopeDistProportionBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<>( getIsotopeDistProportion(), getParentForChildren(), isClean()); @@ -11263,6 +11376,7 @@ public Builder clearLostMass() { * .SkylineDocumentProto.Annotations annotations = 18; * @return Whether the annotations field is set. */ + @Override public boolean hasAnnotations() { return ((bitField0_ & 0x00004000) != 0); } @@ -11270,6 +11384,7 @@ public boolean hasAnnotations() { * .SkylineDocumentProto.Annotations annotations = 18; * @return The annotations. */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.Annotations getAnnotations() { if (annotationsBuilder_ == null) { return annotations_ == null ? org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.Annotations.getDefaultInstance() : annotations_; @@ -11352,6 +11467,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.A /** * .SkylineDocumentProto.Annotations annotations = 18; */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.AnnotationsOrBuilder getAnnotationsOrBuilder() { if (annotationsBuilder_ != null) { return annotationsBuilder_.getMessageOrBuilder(); @@ -11367,8 +11483,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.A org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.Annotations, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.Annotations.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.AnnotationsOrBuilder> getAnnotationsFieldBuilder() { if (annotationsBuilder_ == null) { - annotationsBuilder_ = new com.google.protobuf.SingleFieldBuilderV3< - org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.Annotations, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.Annotations.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.AnnotationsOrBuilder>( + annotationsBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<>( getAnnotations(), getParentForChildren(), isClean()); @@ -11448,6 +11563,7 @@ public Builder clearProductMz() { * .google.protobuf.DoubleValue collisionEnergy = 21; * @return Whether the collisionEnergy field is set. */ + @Override public boolean hasCollisionEnergy() { return ((bitField0_ & 0x00020000) != 0); } @@ -11455,6 +11571,7 @@ public boolean hasCollisionEnergy() { * .google.protobuf.DoubleValue collisionEnergy = 21; * @return The collisionEnergy. */ + @Override public com.google.protobuf.DoubleValue getCollisionEnergy() { if (collisionEnergyBuilder_ == null) { return collisionEnergy_ == null ? com.google.protobuf.DoubleValue.getDefaultInstance() : collisionEnergy_; @@ -11537,6 +11654,7 @@ public com.google.protobuf.DoubleValue.Builder getCollisionEnergyBuilder() { /** * .google.protobuf.DoubleValue collisionEnergy = 21; */ + @Override public com.google.protobuf.DoubleValueOrBuilder getCollisionEnergyOrBuilder() { if (collisionEnergyBuilder_ != null) { return collisionEnergyBuilder_.getMessageOrBuilder(); @@ -11552,8 +11670,7 @@ public com.google.protobuf.DoubleValueOrBuilder getCollisionEnergyOrBuilder() { com.google.protobuf.DoubleValue, com.google.protobuf.DoubleValue.Builder, com.google.protobuf.DoubleValueOrBuilder> getCollisionEnergyFieldBuilder() { if (collisionEnergyBuilder_ == null) { - collisionEnergyBuilder_ = new com.google.protobuf.SingleFieldBuilderV3< - com.google.protobuf.DoubleValue, com.google.protobuf.DoubleValue.Builder, com.google.protobuf.DoubleValueOrBuilder>( + collisionEnergyBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<>( getCollisionEnergy(), getParentForChildren(), isClean()); @@ -11569,6 +11686,7 @@ public com.google.protobuf.DoubleValueOrBuilder getCollisionEnergyOrBuilder() { * .google.protobuf.DoubleValue declusteringPotential = 22; * @return Whether the declusteringPotential field is set. */ + @Override public boolean hasDeclusteringPotential() { return ((bitField0_ & 0x00040000) != 0); } @@ -11576,6 +11694,7 @@ public boolean hasDeclusteringPotential() { * .google.protobuf.DoubleValue declusteringPotential = 22; * @return The declusteringPotential. */ + @Override public com.google.protobuf.DoubleValue getDeclusteringPotential() { if (declusteringPotentialBuilder_ == null) { return declusteringPotential_ == null ? com.google.protobuf.DoubleValue.getDefaultInstance() : declusteringPotential_; @@ -11658,6 +11777,7 @@ public com.google.protobuf.DoubleValue.Builder getDeclusteringPotentialBuilder() /** * .google.protobuf.DoubleValue declusteringPotential = 22; */ + @Override public com.google.protobuf.DoubleValueOrBuilder getDeclusteringPotentialOrBuilder() { if (declusteringPotentialBuilder_ != null) { return declusteringPotentialBuilder_.getMessageOrBuilder(); @@ -11673,8 +11793,7 @@ public com.google.protobuf.DoubleValueOrBuilder getDeclusteringPotentialOrBuilde com.google.protobuf.DoubleValue, com.google.protobuf.DoubleValue.Builder, com.google.protobuf.DoubleValueOrBuilder> getDeclusteringPotentialFieldBuilder() { if (declusteringPotentialBuilder_ == null) { - declusteringPotentialBuilder_ = new com.google.protobuf.SingleFieldBuilderV3< - com.google.protobuf.DoubleValue, com.google.protobuf.DoubleValue.Builder, com.google.protobuf.DoubleValueOrBuilder>( + declusteringPotentialBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<>( getDeclusteringPotential(), getParentForChildren(), isClean()); @@ -11687,7 +11806,7 @@ public com.google.protobuf.DoubleValueOrBuilder getDeclusteringPotentialOrBuilde java.util.Collections.emptyList(); private void ensureLossesIsMutable() { if (!((bitField0_ & 0x00080000) != 0)) { - losses_ = new java.util.ArrayList(losses_); + losses_ = new java.util.ArrayList<>(losses_); bitField0_ |= 0x00080000; } } @@ -11698,6 +11817,7 @@ private void ensureLossesIsMutable() { /** * repeated .SkylineDocumentProto.TransitionLoss losses = 23; */ + @Override public java.util.List getLossesList() { if (lossesBuilder_ == null) { return java.util.Collections.unmodifiableList(losses_); @@ -11708,6 +11828,7 @@ public java.util.Listrepeated .SkylineDocumentProto.TransitionLoss losses = 23; */ + @Override public int getLossesCount() { if (lossesBuilder_ == null) { return losses_.size(); @@ -11718,6 +11839,7 @@ public int getLossesCount() { /** * repeated .SkylineDocumentProto.TransitionLoss losses = 23; */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionLoss getLosses(int index) { if (lossesBuilder_ == null) { return losses_.get(index); @@ -11868,6 +11990,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.T /** * repeated .SkylineDocumentProto.TransitionLoss losses = 23; */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionLossOrBuilder getLossesOrBuilder( int index) { if (lossesBuilder_ == null) { @@ -11878,7 +12001,8 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.T /** * repeated .SkylineDocumentProto.TransitionLoss losses = 23; */ - public java.util.List + @Override + public java.util.List getLossesOrBuilderList() { if (lossesBuilder_ != null) { return lossesBuilder_.getMessageOrBuilderList(); @@ -11912,8 +12036,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.T org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionLoss, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionLoss.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionLossOrBuilder> getLossesFieldBuilder() { if (lossesBuilder_ == null) { - lossesBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3< - org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionLoss, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionLoss.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionLossOrBuilder>( + lossesBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<>( losses_, ((bitField0_ & 0x00080000) != 0), getParentForChildren(), @@ -11983,6 +12106,7 @@ public Builder clearFragmentType() { * .SkylineDocumentProto.TransitionLibInfo libInfo = 25; * @return Whether the libInfo field is set. */ + @Override public boolean hasLibInfo() { return ((bitField0_ & 0x00200000) != 0); } @@ -11990,6 +12114,7 @@ public boolean hasLibInfo() { * .SkylineDocumentProto.TransitionLibInfo libInfo = 25; * @return The libInfo. */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionLibInfo getLibInfo() { if (libInfoBuilder_ == null) { return libInfo_ == null ? org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionLibInfo.getDefaultInstance() : libInfo_; @@ -12072,6 +12197,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.T /** * .SkylineDocumentProto.TransitionLibInfo libInfo = 25; */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionLibInfoOrBuilder getLibInfoOrBuilder() { if (libInfoBuilder_ != null) { return libInfoBuilder_.getMessageOrBuilder(); @@ -12087,8 +12213,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.T org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionLibInfo, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionLibInfo.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionLibInfoOrBuilder> getLibInfoFieldBuilder() { if (libInfoBuilder_ == null) { - libInfoBuilder_ = new com.google.protobuf.SingleFieldBuilderV3< - org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionLibInfo, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionLibInfo.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionLibInfoOrBuilder>( + libInfoBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<>( getLibInfo(), getParentForChildren(), isClean()); @@ -12104,6 +12229,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.T * .SkylineDocumentProto.TransitionResults results = 26; * @return Whether the results field is set. */ + @Override public boolean hasResults() { return ((bitField0_ & 0x00400000) != 0); } @@ -12111,6 +12237,7 @@ public boolean hasResults() { * .SkylineDocumentProto.TransitionResults results = 26; * @return The results. */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionResults getResults() { if (resultsBuilder_ == null) { return results_ == null ? org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionResults.getDefaultInstance() : results_; @@ -12193,6 +12320,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.T /** * .SkylineDocumentProto.TransitionResults results = 26; */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionResultsOrBuilder getResultsOrBuilder() { if (resultsBuilder_ != null) { return resultsBuilder_.getMessageOrBuilder(); @@ -12208,8 +12336,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.T org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionResults, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionResults.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionResultsOrBuilder> getResultsFieldBuilder() { if (resultsBuilder_ == null) { - resultsBuilder_ = new com.google.protobuf.SingleFieldBuilderV3< - org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionResults, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionResults.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionResultsOrBuilder>( + resultsBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<>( getResults(), getParentForChildren(), isClean()); @@ -12225,6 +12352,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.T * .google.protobuf.DoubleValue averageMass = 27; * @return Whether the averageMass field is set. */ + @Override public boolean hasAverageMass() { return ((bitField0_ & 0x00800000) != 0); } @@ -12232,6 +12360,7 @@ public boolean hasAverageMass() { * .google.protobuf.DoubleValue averageMass = 27; * @return The averageMass. */ + @Override public com.google.protobuf.DoubleValue getAverageMass() { if (averageMassBuilder_ == null) { return averageMass_ == null ? com.google.protobuf.DoubleValue.getDefaultInstance() : averageMass_; @@ -12314,6 +12443,7 @@ public com.google.protobuf.DoubleValue.Builder getAverageMassBuilder() { /** * .google.protobuf.DoubleValue averageMass = 27; */ + @Override public com.google.protobuf.DoubleValueOrBuilder getAverageMassOrBuilder() { if (averageMassBuilder_ != null) { return averageMassBuilder_.getMessageOrBuilder(); @@ -12329,8 +12459,7 @@ public com.google.protobuf.DoubleValueOrBuilder getAverageMassOrBuilder() { com.google.protobuf.DoubleValue, com.google.protobuf.DoubleValue.Builder, com.google.protobuf.DoubleValueOrBuilder> getAverageMassFieldBuilder() { if (averageMassBuilder_ == null) { - averageMassBuilder_ = new com.google.protobuf.SingleFieldBuilderV3< - com.google.protobuf.DoubleValue, com.google.protobuf.DoubleValue.Builder, com.google.protobuf.DoubleValueOrBuilder>( + averageMassBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<>( getAverageMass(), getParentForChildren(), isClean()); @@ -12346,6 +12475,7 @@ public com.google.protobuf.DoubleValueOrBuilder getAverageMassOrBuilder() { * .google.protobuf.DoubleValue monoMass = 28; * @return Whether the monoMass field is set. */ + @Override public boolean hasMonoMass() { return ((bitField0_ & 0x01000000) != 0); } @@ -12353,6 +12483,7 @@ public boolean hasMonoMass() { * .google.protobuf.DoubleValue monoMass = 28; * @return The monoMass. */ + @Override public com.google.protobuf.DoubleValue getMonoMass() { if (monoMassBuilder_ == null) { return monoMass_ == null ? com.google.protobuf.DoubleValue.getDefaultInstance() : monoMass_; @@ -12435,6 +12566,7 @@ public com.google.protobuf.DoubleValue.Builder getMonoMassBuilder() { /** * .google.protobuf.DoubleValue monoMass = 28; */ + @Override public com.google.protobuf.DoubleValueOrBuilder getMonoMassOrBuilder() { if (monoMassBuilder_ != null) { return monoMassBuilder_.getMessageOrBuilder(); @@ -12450,8 +12582,7 @@ public com.google.protobuf.DoubleValueOrBuilder getMonoMassOrBuilder() { com.google.protobuf.DoubleValue, com.google.protobuf.DoubleValue.Builder, com.google.protobuf.DoubleValueOrBuilder> getMonoMassFieldBuilder() { if (monoMassBuilder_ == null) { - monoMassBuilder_ = new com.google.protobuf.SingleFieldBuilderV3< - com.google.protobuf.DoubleValue, com.google.protobuf.DoubleValue.Builder, com.google.protobuf.DoubleValueOrBuilder>( + monoMassBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<>( getMonoMass(), getParentForChildren(), isClean()); @@ -12467,6 +12598,7 @@ public com.google.protobuf.DoubleValueOrBuilder getMonoMassOrBuilder() { * .google.protobuf.StringValue adduct = 29; * @return Whether the adduct field is set. */ + @Override public boolean hasAdduct() { return ((bitField0_ & 0x02000000) != 0); } @@ -12474,6 +12606,7 @@ public boolean hasAdduct() { * .google.protobuf.StringValue adduct = 29; * @return The adduct. */ + @Override public com.google.protobuf.StringValue getAdduct() { if (adductBuilder_ == null) { return adduct_ == null ? com.google.protobuf.StringValue.getDefaultInstance() : adduct_; @@ -12556,6 +12689,7 @@ public com.google.protobuf.StringValue.Builder getAdductBuilder() { /** * .google.protobuf.StringValue adduct = 29; */ + @Override public com.google.protobuf.StringValueOrBuilder getAdductOrBuilder() { if (adductBuilder_ != null) { return adductBuilder_.getMessageOrBuilder(); @@ -12571,8 +12705,7 @@ public com.google.protobuf.StringValueOrBuilder getAdductOrBuilder() { com.google.protobuf.StringValue, com.google.protobuf.StringValue.Builder, com.google.protobuf.StringValueOrBuilder> getAdductFieldBuilder() { if (adductBuilder_ == null) { - adductBuilder_ = new com.google.protobuf.SingleFieldBuilderV3< - com.google.protobuf.StringValue, com.google.protobuf.StringValue.Builder, com.google.protobuf.StringValueOrBuilder>( + adductBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<>( getAdduct(), getParentForChildren(), isClean()); @@ -12588,6 +12721,7 @@ public com.google.protobuf.StringValueOrBuilder getAdductOrBuilder() { * .google.protobuf.StringValue molecule_id = 30; * @return Whether the moleculeId field is set. */ + @Override public boolean hasMoleculeId() { return ((bitField0_ & 0x04000000) != 0); } @@ -12595,6 +12729,7 @@ public boolean hasMoleculeId() { * .google.protobuf.StringValue molecule_id = 30; * @return The moleculeId. */ + @Override public com.google.protobuf.StringValue getMoleculeId() { if (moleculeIdBuilder_ == null) { return moleculeId_ == null ? com.google.protobuf.StringValue.getDefaultInstance() : moleculeId_; @@ -12677,6 +12812,7 @@ public com.google.protobuf.StringValue.Builder getMoleculeIdBuilder() { /** * .google.protobuf.StringValue molecule_id = 30; */ + @Override public com.google.protobuf.StringValueOrBuilder getMoleculeIdOrBuilder() { if (moleculeIdBuilder_ != null) { return moleculeIdBuilder_.getMessageOrBuilder(); @@ -12692,8 +12828,7 @@ public com.google.protobuf.StringValueOrBuilder getMoleculeIdOrBuilder() { com.google.protobuf.StringValue, com.google.protobuf.StringValue.Builder, com.google.protobuf.StringValueOrBuilder> getMoleculeIdFieldBuilder() { if (moleculeIdBuilder_ == null) { - moleculeIdBuilder_ = new com.google.protobuf.SingleFieldBuilderV3< - com.google.protobuf.StringValue, com.google.protobuf.StringValue.Builder, com.google.protobuf.StringValueOrBuilder>( + moleculeIdBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<>( getMoleculeId(), getParentForChildren(), isClean()); @@ -12741,6 +12876,7 @@ public Builder clearNotQuantitative() { * .google.protobuf.DoubleValue explicitCollisionEnergy = 32; * @return Whether the explicitCollisionEnergy field is set. */ + @Override public boolean hasExplicitCollisionEnergy() { return ((bitField0_ & 0x10000000) != 0); } @@ -12748,6 +12884,7 @@ public boolean hasExplicitCollisionEnergy() { * .google.protobuf.DoubleValue explicitCollisionEnergy = 32; * @return The explicitCollisionEnergy. */ + @Override public com.google.protobuf.DoubleValue getExplicitCollisionEnergy() { if (explicitCollisionEnergyBuilder_ == null) { return explicitCollisionEnergy_ == null ? com.google.protobuf.DoubleValue.getDefaultInstance() : explicitCollisionEnergy_; @@ -12830,6 +12967,7 @@ public com.google.protobuf.DoubleValue.Builder getExplicitCollisionEnergyBuilder /** * .google.protobuf.DoubleValue explicitCollisionEnergy = 32; */ + @Override public com.google.protobuf.DoubleValueOrBuilder getExplicitCollisionEnergyOrBuilder() { if (explicitCollisionEnergyBuilder_ != null) { return explicitCollisionEnergyBuilder_.getMessageOrBuilder(); @@ -12845,8 +12983,7 @@ public com.google.protobuf.DoubleValueOrBuilder getExplicitCollisionEnergyOrBuil com.google.protobuf.DoubleValue, com.google.protobuf.DoubleValue.Builder, com.google.protobuf.DoubleValueOrBuilder> getExplicitCollisionEnergyFieldBuilder() { if (explicitCollisionEnergyBuilder_ == null) { - explicitCollisionEnergyBuilder_ = new com.google.protobuf.SingleFieldBuilderV3< - com.google.protobuf.DoubleValue, com.google.protobuf.DoubleValue.Builder, com.google.protobuf.DoubleValueOrBuilder>( + explicitCollisionEnergyBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<>( getExplicitCollisionEnergy(), getParentForChildren(), isClean()); @@ -12862,6 +12999,7 @@ public com.google.protobuf.DoubleValueOrBuilder getExplicitCollisionEnergyOrBuil * .google.protobuf.DoubleValue explicitIonMobilityHighEnergyOffset = 33; * @return Whether the explicitIonMobilityHighEnergyOffset field is set. */ + @Override public boolean hasExplicitIonMobilityHighEnergyOffset() { return ((bitField0_ & 0x20000000) != 0); } @@ -12869,6 +13007,7 @@ public boolean hasExplicitIonMobilityHighEnergyOffset() { * .google.protobuf.DoubleValue explicitIonMobilityHighEnergyOffset = 33; * @return The explicitIonMobilityHighEnergyOffset. */ + @Override public com.google.protobuf.DoubleValue getExplicitIonMobilityHighEnergyOffset() { if (explicitIonMobilityHighEnergyOffsetBuilder_ == null) { return explicitIonMobilityHighEnergyOffset_ == null ? com.google.protobuf.DoubleValue.getDefaultInstance() : explicitIonMobilityHighEnergyOffset_; @@ -12951,6 +13090,7 @@ public com.google.protobuf.DoubleValue.Builder getExplicitIonMobilityHighEnergyO /** * .google.protobuf.DoubleValue explicitIonMobilityHighEnergyOffset = 33; */ + @Override public com.google.protobuf.DoubleValueOrBuilder getExplicitIonMobilityHighEnergyOffsetOrBuilder() { if (explicitIonMobilityHighEnergyOffsetBuilder_ != null) { return explicitIonMobilityHighEnergyOffsetBuilder_.getMessageOrBuilder(); @@ -12966,8 +13106,7 @@ public com.google.protobuf.DoubleValueOrBuilder getExplicitIonMobilityHighEnergy com.google.protobuf.DoubleValue, com.google.protobuf.DoubleValue.Builder, com.google.protobuf.DoubleValueOrBuilder> getExplicitIonMobilityHighEnergyOffsetFieldBuilder() { if (explicitIonMobilityHighEnergyOffsetBuilder_ == null) { - explicitIonMobilityHighEnergyOffsetBuilder_ = new com.google.protobuf.SingleFieldBuilderV3< - com.google.protobuf.DoubleValue, com.google.protobuf.DoubleValue.Builder, com.google.protobuf.DoubleValueOrBuilder>( + explicitIonMobilityHighEnergyOffsetBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<>( getExplicitIonMobilityHighEnergyOffset(), getParentForChildren(), isClean()); @@ -12983,6 +13122,7 @@ public com.google.protobuf.DoubleValueOrBuilder getExplicitIonMobilityHighEnergy * .google.protobuf.DoubleValue explicitSLens = 34; * @return Whether the explicitSLens field is set. */ + @Override public boolean hasExplicitSLens() { return ((bitField0_ & 0x40000000) != 0); } @@ -12990,6 +13130,7 @@ public boolean hasExplicitSLens() { * .google.protobuf.DoubleValue explicitSLens = 34; * @return The explicitSLens. */ + @Override public com.google.protobuf.DoubleValue getExplicitSLens() { if (explicitSLensBuilder_ == null) { return explicitSLens_ == null ? com.google.protobuf.DoubleValue.getDefaultInstance() : explicitSLens_; @@ -13072,6 +13213,7 @@ public com.google.protobuf.DoubleValue.Builder getExplicitSLensBuilder() { /** * .google.protobuf.DoubleValue explicitSLens = 34; */ + @Override public com.google.protobuf.DoubleValueOrBuilder getExplicitSLensOrBuilder() { if (explicitSLensBuilder_ != null) { return explicitSLensBuilder_.getMessageOrBuilder(); @@ -13087,8 +13229,7 @@ public com.google.protobuf.DoubleValueOrBuilder getExplicitSLensOrBuilder() { com.google.protobuf.DoubleValue, com.google.protobuf.DoubleValue.Builder, com.google.protobuf.DoubleValueOrBuilder> getExplicitSLensFieldBuilder() { if (explicitSLensBuilder_ == null) { - explicitSLensBuilder_ = new com.google.protobuf.SingleFieldBuilderV3< - com.google.protobuf.DoubleValue, com.google.protobuf.DoubleValue.Builder, com.google.protobuf.DoubleValueOrBuilder>( + explicitSLensBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<>( getExplicitSLens(), getParentForChildren(), isClean()); @@ -13104,6 +13245,7 @@ public com.google.protobuf.DoubleValueOrBuilder getExplicitSLensOrBuilder() { * .google.protobuf.DoubleValue explicitConeVoltage = 35; * @return Whether the explicitConeVoltage field is set. */ + @Override public boolean hasExplicitConeVoltage() { return ((bitField0_ & 0x80000000) != 0); } @@ -13111,6 +13253,7 @@ public boolean hasExplicitConeVoltage() { * .google.protobuf.DoubleValue explicitConeVoltage = 35; * @return The explicitConeVoltage. */ + @Override public com.google.protobuf.DoubleValue getExplicitConeVoltage() { if (explicitConeVoltageBuilder_ == null) { return explicitConeVoltage_ == null ? com.google.protobuf.DoubleValue.getDefaultInstance() : explicitConeVoltage_; @@ -13193,6 +13336,7 @@ public com.google.protobuf.DoubleValue.Builder getExplicitConeVoltageBuilder() { /** * .google.protobuf.DoubleValue explicitConeVoltage = 35; */ + @Override public com.google.protobuf.DoubleValueOrBuilder getExplicitConeVoltageOrBuilder() { if (explicitConeVoltageBuilder_ != null) { return explicitConeVoltageBuilder_.getMessageOrBuilder(); @@ -13208,8 +13352,7 @@ public com.google.protobuf.DoubleValueOrBuilder getExplicitConeVoltageOrBuilder( com.google.protobuf.DoubleValue, com.google.protobuf.DoubleValue.Builder, com.google.protobuf.DoubleValueOrBuilder> getExplicitConeVoltageFieldBuilder() { if (explicitConeVoltageBuilder_ == null) { - explicitConeVoltageBuilder_ = new com.google.protobuf.SingleFieldBuilderV3< - com.google.protobuf.DoubleValue, com.google.protobuf.DoubleValue.Builder, com.google.protobuf.DoubleValueOrBuilder>( + explicitConeVoltageBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<>( getExplicitConeVoltage(), getParentForChildren(), isClean()); @@ -13225,6 +13368,7 @@ public com.google.protobuf.DoubleValueOrBuilder getExplicitConeVoltageOrBuilder( * .google.protobuf.DoubleValue explicitDeclusteringPotential = 36; * @return Whether the explicitDeclusteringPotential field is set. */ + @Override public boolean hasExplicitDeclusteringPotential() { return ((bitField1_ & 0x00000001) != 0); } @@ -13232,6 +13376,7 @@ public boolean hasExplicitDeclusteringPotential() { * .google.protobuf.DoubleValue explicitDeclusteringPotential = 36; * @return The explicitDeclusteringPotential. */ + @Override public com.google.protobuf.DoubleValue getExplicitDeclusteringPotential() { if (explicitDeclusteringPotentialBuilder_ == null) { return explicitDeclusteringPotential_ == null ? com.google.protobuf.DoubleValue.getDefaultInstance() : explicitDeclusteringPotential_; @@ -13314,6 +13459,7 @@ public com.google.protobuf.DoubleValue.Builder getExplicitDeclusteringPotentialB /** * .google.protobuf.DoubleValue explicitDeclusteringPotential = 36; */ + @Override public com.google.protobuf.DoubleValueOrBuilder getExplicitDeclusteringPotentialOrBuilder() { if (explicitDeclusteringPotentialBuilder_ != null) { return explicitDeclusteringPotentialBuilder_.getMessageOrBuilder(); @@ -13329,8 +13475,7 @@ public com.google.protobuf.DoubleValueOrBuilder getExplicitDeclusteringPotential com.google.protobuf.DoubleValue, com.google.protobuf.DoubleValue.Builder, com.google.protobuf.DoubleValueOrBuilder> getExplicitDeclusteringPotentialFieldBuilder() { if (explicitDeclusteringPotentialBuilder_ == null) { - explicitDeclusteringPotentialBuilder_ = new com.google.protobuf.SingleFieldBuilderV3< - com.google.protobuf.DoubleValue, com.google.protobuf.DoubleValue.Builder, com.google.protobuf.DoubleValueOrBuilder>( + explicitDeclusteringPotentialBuilder_ = new com.google.protobuf.SingleFieldBuilderV3<>( getExplicitDeclusteringPotential(), getParentForChildren(), isClean()); @@ -13375,7 +13520,7 @@ public Builder clearOrphanedCrosslinkIon() { java.util.Collections.emptyList(); private void ensureLinkedIonsIsMutable() { if (!((bitField1_ & 0x00000004) != 0)) { - linkedIons_ = new java.util.ArrayList(linkedIons_); + linkedIons_ = new java.util.ArrayList<>(linkedIons_); bitField1_ |= 0x00000004; } } @@ -13386,6 +13531,7 @@ private void ensureLinkedIonsIsMutable() { /** * repeated .SkylineDocumentProto.LinkedIon linkedIons = 38; */ + @Override public java.util.List getLinkedIonsList() { if (linkedIonsBuilder_ == null) { return java.util.Collections.unmodifiableList(linkedIons_); @@ -13396,6 +13542,7 @@ public java.util.Listrepeated .SkylineDocumentProto.LinkedIon linkedIons = 38; */ + @Override public int getLinkedIonsCount() { if (linkedIonsBuilder_ == null) { return linkedIons_.size(); @@ -13406,6 +13553,7 @@ public int getLinkedIonsCount() { /** * repeated .SkylineDocumentProto.LinkedIon linkedIons = 38; */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.LinkedIon getLinkedIons(int index) { if (linkedIonsBuilder_ == null) { return linkedIons_.get(index); @@ -13556,6 +13704,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.L /** * repeated .SkylineDocumentProto.LinkedIon linkedIons = 38; */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.LinkedIonOrBuilder getLinkedIonsOrBuilder( int index) { if (linkedIonsBuilder_ == null) { @@ -13566,7 +13715,8 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.L /** * repeated .SkylineDocumentProto.LinkedIon linkedIons = 38; */ - public java.util.List + @Override + public java.util.List getLinkedIonsOrBuilderList() { if (linkedIonsBuilder_ != null) { return linkedIonsBuilder_.getMessageOrBuilderList(); @@ -13600,8 +13750,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.L org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.LinkedIon, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.LinkedIon.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.LinkedIonOrBuilder> getLinkedIonsFieldBuilder() { if (linkedIonsBuilder_ == null) { - linkedIonsBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3< - org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.LinkedIon, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.LinkedIon.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.LinkedIonOrBuilder>( + linkedIonsBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<>( linkedIons_, ((bitField1_ & 0x00000004) != 0), getParentForChildren(), @@ -13637,25 +13786,34 @@ public static org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocument } private static final com.google.protobuf.Parser - PARSER = new com.google.protobuf.AbstractParser() { - @java.lang.Override - public Transition parsePartialFrom( - com.google.protobuf.CodedInputStream input, - com.google.protobuf.ExtensionRegistryLite extensionRegistry) - throws com.google.protobuf.InvalidProtocolBufferException { - Builder builder = newBuilder(); - try { - builder.mergeFrom(input, extensionRegistry); - } catch (com.google.protobuf.InvalidProtocolBufferException e) { - throw e.setUnfinishedMessage(builder.buildPartial()); - } catch (com.google.protobuf.UninitializedMessageException e) { - throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); - } catch (java.io.IOException e) { - throw new com.google.protobuf.InvalidProtocolBufferException(e) - .setUnfinishedMessage(builder.buildPartial()); + PARSER = new com.google.protobuf.AbstractParser<>() + { + @java.lang.Override + public Transition parsePartialFrom( + com.google.protobuf.CodedInputStream input, + com.google.protobuf.ExtensionRegistryLite extensionRegistry) + throws com.google.protobuf.InvalidProtocolBufferException + { + Builder builder = newBuilder(); + try + { + builder.mergeFrom(input, extensionRegistry); + } + catch (com.google.protobuf.InvalidProtocolBufferException e) + { + throw e.setUnfinishedMessage(builder.buildPartial()); + } + catch (com.google.protobuf.UninitializedMessageException e) + { + throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); + } + catch (java.io.IOException e) + { + throw new com.google.protobuf.InvalidProtocolBufferException(e) + .setUnfinishedMessage(builder.buildPartial()); + } + return builder.buildPartial(); } - return builder.buildPartial(); - } }; public static com.google.protobuf.Parser parser() { @@ -13775,12 +13933,11 @@ public boolean equals(final java.lang.Object obj) { if (obj == this) { return true; } - if (!(obj instanceof org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.OptionalInt)) { + if (!(obj instanceof OptionalInt other)) { return super.equals(obj); } - org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.OptionalInt other = (org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.OptionalInt) obj; - if (getValue() + if (getValue() != other.getValue()) return false; if (!getUnknownFields().equals(other.getUnknownFields())) return false; return true; @@ -14123,25 +14280,34 @@ public static org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocument } private static final com.google.protobuf.Parser - PARSER = new com.google.protobuf.AbstractParser() { - @java.lang.Override - public OptionalInt parsePartialFrom( - com.google.protobuf.CodedInputStream input, - com.google.protobuf.ExtensionRegistryLite extensionRegistry) - throws com.google.protobuf.InvalidProtocolBufferException { - Builder builder = newBuilder(); - try { - builder.mergeFrom(input, extensionRegistry); - } catch (com.google.protobuf.InvalidProtocolBufferException e) { - throw e.setUnfinishedMessage(builder.buildPartial()); - } catch (com.google.protobuf.UninitializedMessageException e) { - throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); - } catch (java.io.IOException e) { - throw new com.google.protobuf.InvalidProtocolBufferException(e) - .setUnfinishedMessage(builder.buildPartial()); + PARSER = new com.google.protobuf.AbstractParser<>() + { + @java.lang.Override + public OptionalInt parsePartialFrom( + com.google.protobuf.CodedInputStream input, + com.google.protobuf.ExtensionRegistryLite extensionRegistry) + throws com.google.protobuf.InvalidProtocolBufferException + { + Builder builder = newBuilder(); + try + { + builder.mergeFrom(input, extensionRegistry); + } + catch (com.google.protobuf.InvalidProtocolBufferException e) + { + throw e.setUnfinishedMessage(builder.buildPartial()); + } + catch (com.google.protobuf.UninitializedMessageException e) + { + throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); + } + catch (java.io.IOException e) + { + throw new com.google.protobuf.InvalidProtocolBufferException(e) + .setUnfinishedMessage(builder.buildPartial()); + } + return builder.buildPartial(); } - return builder.buildPartial(); - } }; public static com.google.protobuf.Parser parser() { @@ -14481,12 +14647,11 @@ public boolean equals(final java.lang.Object obj) { if (obj == this) { return true; } - if (!(obj instanceof org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionLoss)) { + if (!(obj instanceof TransitionLoss other)) { return super.equals(obj); } - org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionLoss other = (org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionLoss) obj; - if (!getFormula() + if (!getFormula() .equals(other.getFormula())) return false; if (java.lang.Double.doubleToLongBits(getMonoisotopicMass()) != java.lang.Double.doubleToLongBits( @@ -14874,6 +15039,7 @@ public Builder mergeFrom( * string formula = 1; * @return The formula. */ + @Override public java.lang.String getFormula() { java.lang.Object ref = formula_; if (!(ref instanceof java.lang.String)) { @@ -14890,6 +15056,7 @@ public java.lang.String getFormula() { * string formula = 1; * @return The bytes for formula. */ + @Override public com.google.protobuf.ByteString getFormulaBytes() { java.lang.Object ref = formula_; @@ -15063,6 +15230,7 @@ public Builder clearLossInclusion() { * string modificationName = 5; * @return The modificationName. */ + @Override public java.lang.String getModificationName() { java.lang.Object ref = modificationName_; if (!(ref instanceof java.lang.String)) { @@ -15079,6 +15247,7 @@ public java.lang.String getModificationName() { * string modificationName = 5; * @return The bytes for modificationName. */ + @Override public com.google.protobuf.ByteString getModificationNameBytes() { java.lang.Object ref = modificationName_; @@ -15220,25 +15389,34 @@ public static org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocument } private static final com.google.protobuf.Parser - PARSER = new com.google.protobuf.AbstractParser() { - @java.lang.Override - public TransitionLoss parsePartialFrom( - com.google.protobuf.CodedInputStream input, - com.google.protobuf.ExtensionRegistryLite extensionRegistry) - throws com.google.protobuf.InvalidProtocolBufferException { - Builder builder = newBuilder(); - try { - builder.mergeFrom(input, extensionRegistry); - } catch (com.google.protobuf.InvalidProtocolBufferException e) { - throw e.setUnfinishedMessage(builder.buildPartial()); - } catch (com.google.protobuf.UninitializedMessageException e) { - throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); - } catch (java.io.IOException e) { - throw new com.google.protobuf.InvalidProtocolBufferException(e) - .setUnfinishedMessage(builder.buildPartial()); + PARSER = new com.google.protobuf.AbstractParser<>() + { + @java.lang.Override + public TransitionLoss parsePartialFrom( + com.google.protobuf.CodedInputStream input, + com.google.protobuf.ExtensionRegistryLite extensionRegistry) + throws com.google.protobuf.InvalidProtocolBufferException + { + Builder builder = newBuilder(); + try + { + builder.mergeFrom(input, extensionRegistry); + } + catch (com.google.protobuf.InvalidProtocolBufferException e) + { + throw e.setUnfinishedMessage(builder.buildPartial()); + } + catch (com.google.protobuf.UninitializedMessageException e) + { + throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); + } + catch (java.io.IOException e) + { + throw new com.google.protobuf.InvalidProtocolBufferException(e) + .setUnfinishedMessage(builder.buildPartial()); + } + return builder.buildPartial(); } - return builder.buildPartial(); - } }; public static com.google.protobuf.Parser parser() { @@ -15377,12 +15555,11 @@ public boolean equals(final java.lang.Object obj) { if (obj == this) { return true; } - if (!(obj instanceof org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionLibInfo)) { + if (!(obj instanceof TransitionLibInfo other)) { return super.equals(obj); } - org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionLibInfo other = (org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionLibInfo) obj; - if (getRank() + if (getRank() != other.getRank()) return false; if (java.lang.Float.floatToIntBits(getIntensity()) != java.lang.Float.floatToIntBits( @@ -15770,25 +15947,34 @@ public static org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocument } private static final com.google.protobuf.Parser - PARSER = new com.google.protobuf.AbstractParser() { - @java.lang.Override - public TransitionLibInfo parsePartialFrom( - com.google.protobuf.CodedInputStream input, - com.google.protobuf.ExtensionRegistryLite extensionRegistry) - throws com.google.protobuf.InvalidProtocolBufferException { - Builder builder = newBuilder(); - try { - builder.mergeFrom(input, extensionRegistry); - } catch (com.google.protobuf.InvalidProtocolBufferException e) { - throw e.setUnfinishedMessage(builder.buildPartial()); - } catch (com.google.protobuf.UninitializedMessageException e) { - throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); - } catch (java.io.IOException e) { - throw new com.google.protobuf.InvalidProtocolBufferException(e) - .setUnfinishedMessage(builder.buildPartial()); + PARSER = new com.google.protobuf.AbstractParser<>() + { + @java.lang.Override + public TransitionLibInfo parsePartialFrom( + com.google.protobuf.CodedInputStream input, + com.google.protobuf.ExtensionRegistryLite extensionRegistry) + throws com.google.protobuf.InvalidProtocolBufferException + { + Builder builder = newBuilder(); + try + { + builder.mergeFrom(input, extensionRegistry); + } + catch (com.google.protobuf.InvalidProtocolBufferException e) + { + throw e.setUnfinishedMessage(builder.buildPartial()); + } + catch (com.google.protobuf.UninitializedMessageException e) + { + throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); + } + catch (java.io.IOException e) + { + throw new com.google.protobuf.InvalidProtocolBufferException(e) + .setUnfinishedMessage(builder.buildPartial()); + } + return builder.buildPartial(); } - return builder.buildPartial(); - } }; public static com.google.protobuf.Parser parser() { @@ -15952,12 +16138,11 @@ public boolean equals(final java.lang.Object obj) { if (obj == this) { return true; } - if (!(obj instanceof org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionData)) { + if (!(obj instanceof TransitionData other)) { return super.equals(obj); } - org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionData other = (org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionData) obj; - if (!getTransitionsList() + if (!getTransitionsList() .equals(other.getTransitionsList())) return false; if (!getUnknownFields().equals(other.getUnknownFields())) return false; return true; @@ -16290,7 +16475,7 @@ public Builder mergeFrom( java.util.Collections.emptyList(); private void ensureTransitionsIsMutable() { if (!((bitField0_ & 0x00000001) != 0)) { - transitions_ = new java.util.ArrayList(transitions_); + transitions_ = new java.util.ArrayList<>(transitions_); bitField0_ |= 0x00000001; } } @@ -16301,6 +16486,7 @@ private void ensureTransitionsIsMutable() { /** * repeated .SkylineDocumentProto.Transition transitions = 1; */ + @Override public java.util.List getTransitionsList() { if (transitionsBuilder_ == null) { return java.util.Collections.unmodifiableList(transitions_); @@ -16311,6 +16497,7 @@ public java.util.Listrepeated .SkylineDocumentProto.Transition transitions = 1; */ + @Override public int getTransitionsCount() { if (transitionsBuilder_ == null) { return transitions_.size(); @@ -16321,6 +16508,7 @@ public int getTransitionsCount() { /** * repeated .SkylineDocumentProto.Transition transitions = 1; */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.Transition getTransitions(int index) { if (transitionsBuilder_ == null) { return transitions_.get(index); @@ -16471,6 +16659,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.T /** * repeated .SkylineDocumentProto.Transition transitions = 1; */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionOrBuilder getTransitionsOrBuilder( int index) { if (transitionsBuilder_ == null) { @@ -16481,7 +16670,8 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.T /** * repeated .SkylineDocumentProto.Transition transitions = 1; */ - public java.util.List + @Override + public java.util.List getTransitionsOrBuilderList() { if (transitionsBuilder_ != null) { return transitionsBuilder_.getMessageOrBuilderList(); @@ -16515,8 +16705,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.T org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.Transition, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.Transition.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionOrBuilder> getTransitionsFieldBuilder() { if (transitionsBuilder_ == null) { - transitionsBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3< - org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.Transition, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.Transition.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.TransitionOrBuilder>( + transitionsBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<>( transitions_, ((bitField0_ & 0x00000001) != 0), getParentForChildren(), @@ -16552,25 +16741,34 @@ public static org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocument } private static final com.google.protobuf.Parser - PARSER = new com.google.protobuf.AbstractParser() { - @java.lang.Override - public TransitionData parsePartialFrom( - com.google.protobuf.CodedInputStream input, - com.google.protobuf.ExtensionRegistryLite extensionRegistry) - throws com.google.protobuf.InvalidProtocolBufferException { - Builder builder = newBuilder(); - try { - builder.mergeFrom(input, extensionRegistry); - } catch (com.google.protobuf.InvalidProtocolBufferException e) { - throw e.setUnfinishedMessage(builder.buildPartial()); - } catch (com.google.protobuf.UninitializedMessageException e) { - throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); - } catch (java.io.IOException e) { - throw new com.google.protobuf.InvalidProtocolBufferException(e) - .setUnfinishedMessage(builder.buildPartial()); + PARSER = new com.google.protobuf.AbstractParser<>() + { + @java.lang.Override + public TransitionData parsePartialFrom( + com.google.protobuf.CodedInputStream input, + com.google.protobuf.ExtensionRegistryLite extensionRegistry) + throws com.google.protobuf.InvalidProtocolBufferException + { + Builder builder = newBuilder(); + try + { + builder.mergeFrom(input, extensionRegistry); + } + catch (com.google.protobuf.InvalidProtocolBufferException e) + { + throw e.setUnfinishedMessage(builder.buildPartial()); + } + catch (com.google.protobuf.UninitializedMessageException e) + { + throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); + } + catch (java.io.IOException e) + { + throw new com.google.protobuf.InvalidProtocolBufferException(e) + .setUnfinishedMessage(builder.buildPartial()); + } + return builder.buildPartial(); } - return builder.buildPartial(); - } }; public static com.google.protobuf.Parser parser() { @@ -16901,12 +17099,11 @@ public boolean equals(final java.lang.Object obj) { if (obj == this) { return true; } - if (!(obj instanceof org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.LinkedIon)) { + if (!(obj instanceof LinkedIon other)) { return super.equals(obj); } - org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.LinkedIon other = (org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.LinkedIon) obj; - if (ionType_ != other.ionType_) return false; + if (ionType_ != other.ionType_) return false; if (getOrdinal() != other.getOrdinal()) return false; if (getModificationIndex() @@ -17439,6 +17636,7 @@ public Builder clearModificationIndex() { * string modificationName = 4; * @return The modificationName. */ + @Override public java.lang.String getModificationName() { java.lang.Object ref = modificationName_; if (!(ref instanceof java.lang.String)) { @@ -17455,6 +17653,7 @@ public java.lang.String getModificationName() { * string modificationName = 4; * @return The bytes for modificationName. */ + @Override public com.google.protobuf.ByteString getModificationNameBytes() { java.lang.Object ref = modificationName_; @@ -17510,7 +17709,7 @@ public Builder setModificationNameBytes( java.util.Collections.emptyList(); private void ensureChildrenIsMutable() { if (!((bitField0_ & 0x00000010) != 0)) { - children_ = new java.util.ArrayList(children_); + children_ = new java.util.ArrayList<>(children_); bitField0_ |= 0x00000010; } } @@ -17521,6 +17720,7 @@ private void ensureChildrenIsMutable() { /** * repeated .SkylineDocumentProto.LinkedIon children = 5; */ + @Override public java.util.List getChildrenList() { if (childrenBuilder_ == null) { return java.util.Collections.unmodifiableList(children_); @@ -17531,6 +17731,7 @@ public java.util.Listrepeated .SkylineDocumentProto.LinkedIon children = 5; */ + @Override public int getChildrenCount() { if (childrenBuilder_ == null) { return children_.size(); @@ -17541,6 +17742,7 @@ public int getChildrenCount() { /** * repeated .SkylineDocumentProto.LinkedIon children = 5; */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.LinkedIon getChildren(int index) { if (childrenBuilder_ == null) { return children_.get(index); @@ -17691,6 +17893,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.L /** * repeated .SkylineDocumentProto.LinkedIon children = 5; */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.LinkedIonOrBuilder getChildrenOrBuilder( int index) { if (childrenBuilder_ == null) { @@ -17701,7 +17904,8 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.L /** * repeated .SkylineDocumentProto.LinkedIon children = 5; */ - public java.util.List + @Override + public java.util.List getChildrenOrBuilderList() { if (childrenBuilder_ != null) { return childrenBuilder_.getMessageOrBuilderList(); @@ -17735,8 +17939,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.L org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.LinkedIon, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.LinkedIon.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.LinkedIonOrBuilder> getChildrenFieldBuilder() { if (childrenBuilder_ == null) { - childrenBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3< - org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.LinkedIon, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.LinkedIon.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.LinkedIonOrBuilder>( + childrenBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<>( children_, ((bitField0_ & 0x00000010) != 0), getParentForChildren(), @@ -17804,25 +18007,34 @@ public static org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocument } private static final com.google.protobuf.Parser - PARSER = new com.google.protobuf.AbstractParser() { - @java.lang.Override - public LinkedIon parsePartialFrom( - com.google.protobuf.CodedInputStream input, - com.google.protobuf.ExtensionRegistryLite extensionRegistry) - throws com.google.protobuf.InvalidProtocolBufferException { - Builder builder = newBuilder(); - try { - builder.mergeFrom(input, extensionRegistry); - } catch (com.google.protobuf.InvalidProtocolBufferException e) { - throw e.setUnfinishedMessage(builder.buildPartial()); - } catch (com.google.protobuf.UninitializedMessageException e) { - throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); - } catch (java.io.IOException e) { - throw new com.google.protobuf.InvalidProtocolBufferException(e) - .setUnfinishedMessage(builder.buildPartial()); + PARSER = new com.google.protobuf.AbstractParser<>() + { + @java.lang.Override + public LinkedIon parsePartialFrom( + com.google.protobuf.CodedInputStream input, + com.google.protobuf.ExtensionRegistryLite extensionRegistry) + throws com.google.protobuf.InvalidProtocolBufferException + { + Builder builder = newBuilder(); + try + { + builder.mergeFrom(input, extensionRegistry); + } + catch (com.google.protobuf.InvalidProtocolBufferException e) + { + throw e.setUnfinishedMessage(builder.buildPartial()); + } + catch (com.google.protobuf.UninitializedMessageException e) + { + throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); + } + catch (java.io.IOException e) + { + throw new com.google.protobuf.InvalidProtocolBufferException(e) + .setUnfinishedMessage(builder.buildPartial()); + } + return builder.buildPartial(); } - return builder.buildPartial(); - } }; public static com.google.protobuf.Parser parser() { @@ -17874,12 +18086,11 @@ public boolean equals(final java.lang.Object obj) { if (obj == this) { return true; } - if (!(obj instanceof org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto)) { + if (!(obj instanceof SkylineDocumentProto other)) { return super.equals(obj); } - org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto other = (org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto) obj; - if (!getUnknownFields().equals(other.getUnknownFields())) return false; + if (!getUnknownFields().equals(other.getUnknownFields())) return false; return true; } @@ -18162,25 +18373,34 @@ public static org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocument } private static final com.google.protobuf.Parser - PARSER = new com.google.protobuf.AbstractParser() { - @java.lang.Override - public SkylineDocumentProto parsePartialFrom( - com.google.protobuf.CodedInputStream input, - com.google.protobuf.ExtensionRegistryLite extensionRegistry) - throws com.google.protobuf.InvalidProtocolBufferException { - Builder builder = newBuilder(); - try { - builder.mergeFrom(input, extensionRegistry); - } catch (com.google.protobuf.InvalidProtocolBufferException e) { - throw e.setUnfinishedMessage(builder.buildPartial()); - } catch (com.google.protobuf.UninitializedMessageException e) { - throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); - } catch (java.io.IOException e) { - throw new com.google.protobuf.InvalidProtocolBufferException(e) - .setUnfinishedMessage(builder.buildPartial()); + PARSER = new com.google.protobuf.AbstractParser<>() + { + @java.lang.Override + public SkylineDocumentProto parsePartialFrom( + com.google.protobuf.CodedInputStream input, + com.google.protobuf.ExtensionRegistryLite extensionRegistry) + throws com.google.protobuf.InvalidProtocolBufferException + { + Builder builder = newBuilder(); + try + { + builder.mergeFrom(input, extensionRegistry); + } + catch (com.google.protobuf.InvalidProtocolBufferException e) + { + throw e.setUnfinishedMessage(builder.buildPartial()); + } + catch (com.google.protobuf.UninitializedMessageException e) + { + throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); + } + catch (java.io.IOException e) + { + throw new com.google.protobuf.InvalidProtocolBufferException(e) + .setUnfinishedMessage(builder.buildPartial()); + } + return builder.buildPartial(); } - return builder.buildPartial(); - } }; public static com.google.protobuf.Parser parser() { @@ -18440,6 +18660,7 @@ public enum KeyType public static final int crosslink_VALUE = 3; + @Override public final int getNumber() { if (this == UNRECOGNIZED) { throw new java.lang.IllegalArgumentException( @@ -18478,12 +18699,16 @@ public static KeyType forNumber(int value) { } private static final com.google.protobuf.Internal.EnumLiteMap< KeyType> internalValueMap = - new com.google.protobuf.Internal.EnumLiteMap() { - public KeyType findValueByNumber(int number) { - return KeyType.forNumber(number); - } - }; + new com.google.protobuf.Internal.EnumLiteMap<>() + { + @Override + public KeyType findValueByNumber(int number) + { + return KeyType.forNumber(number); + } + }; + @Override public final com.google.protobuf.Descriptors.EnumValueDescriptor getValueDescriptor() { if (this == UNRECOGNIZED) { @@ -18492,6 +18717,7 @@ public KeyType findValueByNumber(int number) { } return getDescriptor().getValues().get(ordinal()); } + @Override public final com.google.protobuf.Descriptors.EnumDescriptor getDescriptorForType() { return getDescriptor(); @@ -18517,7 +18743,7 @@ public static KeyType valueOf( private final int value; - private KeyType(int value) { + KeyType(int value) { this.value = value; } @@ -18727,12 +18953,11 @@ public boolean equals(final java.lang.Object obj) { if (obj == this) { return true; } - if (!(obj instanceof org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto.Crosslinker)) { + if (!(obj instanceof Crosslinker other)) { return super.equals(obj); } - org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto.Crosslinker other = (org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto.Crosslinker) obj; - if (!getName() + if (!getName() .equals(other.getName())) return false; if (!getPositionsList() .equals(other.getPositionsList())) return false; @@ -19084,6 +19309,7 @@ public Builder mergeFrom( * string name = 1; * @return The name. */ + @Override public java.lang.String getName() { java.lang.Object ref = name_; if (!(ref instanceof java.lang.String)) { @@ -19100,6 +19326,7 @@ public java.lang.String getName() { * string name = 1; * @return The bytes for name. */ + @Override public com.google.protobuf.ByteString getNameBytes() { java.lang.Object ref = name_; @@ -19155,7 +19382,7 @@ public Builder setNameBytes( java.util.Collections.emptyList(); private void ensurePositionsIsMutable() { if (!((bitField0_ & 0x00000002) != 0)) { - positions_ = new java.util.ArrayList(positions_); + positions_ = new java.util.ArrayList<>(positions_); bitField0_ |= 0x00000002; } } @@ -19166,6 +19393,7 @@ private void ensurePositionsIsMutable() { /** * repeated .LibraryKeyProto.Positions positions = 2; */ + @Override public java.util.List getPositionsList() { if (positionsBuilder_ == null) { return java.util.Collections.unmodifiableList(positions_); @@ -19176,6 +19404,7 @@ public java.util.Listrepeated .LibraryKeyProto.Positions positions = 2; */ + @Override public int getPositionsCount() { if (positionsBuilder_ == null) { return positions_.size(); @@ -19186,6 +19415,7 @@ public int getPositionsCount() { /** * repeated .LibraryKeyProto.Positions positions = 2; */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto.Positions getPositions(int index) { if (positionsBuilder_ == null) { return positions_.get(index); @@ -19336,6 +19566,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto.Positi /** * repeated .LibraryKeyProto.Positions positions = 2; */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto.PositionsOrBuilder getPositionsOrBuilder( int index) { if (positionsBuilder_ == null) { @@ -19346,7 +19577,8 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto.Positi /** * repeated .LibraryKeyProto.Positions positions = 2; */ - public java.util.List + @Override + public java.util.List getPositionsOrBuilderList() { if (positionsBuilder_ != null) { return positionsBuilder_.getMessageOrBuilderList(); @@ -19380,8 +19612,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto.Positi org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto.Positions, org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto.Positions.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto.PositionsOrBuilder> getPositionsFieldBuilder() { if (positionsBuilder_ == null) { - positionsBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3< - org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto.Positions, org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto.Positions.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto.PositionsOrBuilder>( + positionsBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<>( positions_, ((bitField0_ & 0x00000002) != 0), getParentForChildren(), @@ -19417,25 +19648,34 @@ public static org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto } private static final com.google.protobuf.Parser - PARSER = new com.google.protobuf.AbstractParser() { - @java.lang.Override - public Crosslinker parsePartialFrom( - com.google.protobuf.CodedInputStream input, - com.google.protobuf.ExtensionRegistryLite extensionRegistry) - throws com.google.protobuf.InvalidProtocolBufferException { - Builder builder = newBuilder(); - try { - builder.mergeFrom(input, extensionRegistry); - } catch (com.google.protobuf.InvalidProtocolBufferException e) { - throw e.setUnfinishedMessage(builder.buildPartial()); - } catch (com.google.protobuf.UninitializedMessageException e) { - throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); - } catch (java.io.IOException e) { - throw new com.google.protobuf.InvalidProtocolBufferException(e) - .setUnfinishedMessage(builder.buildPartial()); + PARSER = new com.google.protobuf.AbstractParser<>() + { + @java.lang.Override + public Crosslinker parsePartialFrom( + com.google.protobuf.CodedInputStream input, + com.google.protobuf.ExtensionRegistryLite extensionRegistry) + throws com.google.protobuf.InvalidProtocolBufferException + { + Builder builder = newBuilder(); + try + { + builder.mergeFrom(input, extensionRegistry); + } + catch (com.google.protobuf.InvalidProtocolBufferException e) + { + throw e.setUnfinishedMessage(builder.buildPartial()); + } + catch (com.google.protobuf.UninitializedMessageException e) + { + throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); + } + catch (java.io.IOException e) + { + throw new com.google.protobuf.InvalidProtocolBufferException(e) + .setUnfinishedMessage(builder.buildPartial()); + } + return builder.buildPartial(); } - return builder.buildPartial(); - } }; public static com.google.protobuf.Parser parser() { @@ -19528,6 +19768,7 @@ protected java.lang.Object newInstance( * repeated int32 position = 1; * @return The count of position. */ + @Override public int getPositionCount() { return position_.size(); } @@ -19536,6 +19777,7 @@ public int getPositionCount() { * @param index The index of the element to return. * @return The position at the given index. */ + @Override public int getPosition(int index) { return position_.getInt(index); } @@ -19556,7 +19798,7 @@ public final boolean isInitialized() { public void writeTo(com.google.protobuf.CodedOutputStream output) throws java.io.IOException { getSerializedSize(); - if (getPositionList().size() > 0) { + if (!getPositionList().isEmpty()) { output.writeUInt32NoTag(10); output.writeUInt32NoTag(positionMemoizedSerializedSize); } @@ -19596,12 +19838,11 @@ public boolean equals(final java.lang.Object obj) { if (obj == this) { return true; } - if (!(obj instanceof org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto.Positions)) { + if (!(obj instanceof Positions other)) { return super.equals(obj); } - org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto.Positions other = (org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto.Positions) obj; - if (!getPositionList() + if (!getPositionList() .equals(other.getPositionList())) return false; if (!getUnknownFields().equals(other.getUnknownFields())) return false; return true; @@ -19914,6 +20155,7 @@ private void ensurePositionIsMutable() { * repeated int32 position = 1; * @return A list containing the position. */ + @Override public java.util.List getPositionList() { position_.makeImmutable(); @@ -19923,6 +20165,7 @@ private void ensurePositionIsMutable() { * repeated int32 position = 1; * @return The count of position. */ + @Override public int getPositionCount() { return position_.size(); } @@ -19931,6 +20174,7 @@ public int getPositionCount() { * @param index The index of the element to return. * @return The position at the given index. */ + @Override public int getPosition(int index) { return position_.getInt(index); } @@ -20013,25 +20257,34 @@ public static org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto } private static final com.google.protobuf.Parser - PARSER = new com.google.protobuf.AbstractParser() { - @java.lang.Override - public Positions parsePartialFrom( - com.google.protobuf.CodedInputStream input, - com.google.protobuf.ExtensionRegistryLite extensionRegistry) - throws com.google.protobuf.InvalidProtocolBufferException { - Builder builder = newBuilder(); - try { - builder.mergeFrom(input, extensionRegistry); - } catch (com.google.protobuf.InvalidProtocolBufferException e) { - throw e.setUnfinishedMessage(builder.buildPartial()); - } catch (com.google.protobuf.UninitializedMessageException e) { - throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); - } catch (java.io.IOException e) { - throw new com.google.protobuf.InvalidProtocolBufferException(e) - .setUnfinishedMessage(builder.buildPartial()); + PARSER = new com.google.protobuf.AbstractParser<>() + { + @java.lang.Override + public Positions parsePartialFrom( + com.google.protobuf.CodedInputStream input, + com.google.protobuf.ExtensionRegistryLite extensionRegistry) + throws com.google.protobuf.InvalidProtocolBufferException + { + Builder builder = newBuilder(); + try + { + builder.mergeFrom(input, extensionRegistry); + } + catch (com.google.protobuf.InvalidProtocolBufferException e) + { + throw e.setUnfinishedMessage(builder.buildPartial()); + } + catch (com.google.protobuf.UninitializedMessageException e) + { + throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); + } + catch (java.io.IOException e) + { + throw new com.google.protobuf.InvalidProtocolBufferException(e) + .setUnfinishedMessage(builder.buildPartial()); + } + return builder.buildPartial(); } - return builder.buildPartial(); - } }; public static com.google.protobuf.Parser parser() { @@ -20343,6 +20596,7 @@ public double getRetentionTime() { * repeated string crosslinkedSequences = 11; * @return A list containing the crosslinkedSequences. */ + @Override public com.google.protobuf.ProtocolStringList getCrosslinkedSequencesList() { return crosslinkedSequences_; @@ -20351,6 +20605,7 @@ public double getRetentionTime() { * repeated string crosslinkedSequences = 11; * @return The count of crosslinkedSequences. */ + @Override public int getCrosslinkedSequencesCount() { return crosslinkedSequences_.size(); } @@ -20359,6 +20614,7 @@ public int getCrosslinkedSequencesCount() { * @param index The index of the element to return. * @return The crosslinkedSequences at the given index. */ + @Override public java.lang.String getCrosslinkedSequences(int index) { return crosslinkedSequences_.get(index); } @@ -20367,6 +20623,7 @@ public java.lang.String getCrosslinkedSequences(int index) { * @param index The index of the value to return. * @return The bytes of the crosslinkedSequences at the given index. */ + @Override public com.google.protobuf.ByteString getCrosslinkedSequencesBytes(int index) { return crosslinkedSequences_.getByteString(index); @@ -20528,12 +20785,11 @@ public boolean equals(final java.lang.Object obj) { if (obj == this) { return true; } - if (!(obj instanceof org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto)) { + if (!(obj instanceof LibraryKeyProto other)) { return super.equals(obj); } - org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto other = (org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto) obj; - if (keyType_ != other.keyType_) return false; + if (keyType_ != other.keyType_) return false; if (!getModifiedSequence() .equals(other.getModifiedSequence())) return false; if (getCharge() @@ -21123,6 +21379,7 @@ public Builder clearKeyType() { * string modifiedSequence = 2; * @return The modifiedSequence. */ + @Override public java.lang.String getModifiedSequence() { java.lang.Object ref = modifiedSequence_; if (!(ref instanceof java.lang.String)) { @@ -21139,6 +21396,7 @@ public java.lang.String getModifiedSequence() { * string modifiedSequence = 2; * @return The bytes for modifiedSequence. */ + @Override public com.google.protobuf.ByteString getModifiedSequenceBytes() { java.lang.Object ref = modifiedSequence_; @@ -21227,6 +21485,7 @@ public Builder clearCharge() { * string moleculeName = 4; * @return The moleculeName. */ + @Override public java.lang.String getMoleculeName() { java.lang.Object ref = moleculeName_; if (!(ref instanceof java.lang.String)) { @@ -21243,6 +21502,7 @@ public java.lang.String getMoleculeName() { * string moleculeName = 4; * @return The bytes for moleculeName. */ + @Override public com.google.protobuf.ByteString getMoleculeNameBytes() { java.lang.Object ref = moleculeName_; @@ -21299,6 +21559,7 @@ public Builder setMoleculeNameBytes( * string chemicalFormula = 5; * @return The chemicalFormula. */ + @Override public java.lang.String getChemicalFormula() { java.lang.Object ref = chemicalFormula_; if (!(ref instanceof java.lang.String)) { @@ -21315,6 +21576,7 @@ public java.lang.String getChemicalFormula() { * string chemicalFormula = 5; * @return The bytes for chemicalFormula. */ + @Override public com.google.protobuf.ByteString getChemicalFormulaBytes() { java.lang.Object ref = chemicalFormula_; @@ -21371,6 +21633,7 @@ public Builder setChemicalFormulaBytes( * string inChiKey = 6; * @return The inChiKey. */ + @Override public java.lang.String getInChiKey() { java.lang.Object ref = inChiKey_; if (!(ref instanceof java.lang.String)) { @@ -21387,6 +21650,7 @@ public java.lang.String getInChiKey() { * string inChiKey = 6; * @return The bytes for inChiKey. */ + @Override public com.google.protobuf.ByteString getInChiKeyBytes() { java.lang.Object ref = inChiKey_; @@ -21443,6 +21707,7 @@ public Builder setInChiKeyBytes( * string otherKeys = 7; * @return The otherKeys. */ + @Override public java.lang.String getOtherKeys() { java.lang.Object ref = otherKeys_; if (!(ref instanceof java.lang.String)) { @@ -21459,6 +21724,7 @@ public java.lang.String getOtherKeys() { * string otherKeys = 7; * @return The bytes for otherKeys. */ + @Override public com.google.protobuf.ByteString getOtherKeysBytes() { java.lang.Object ref = otherKeys_; @@ -21515,6 +21781,7 @@ public Builder setOtherKeysBytes( * string adduct = 8; * @return The adduct. */ + @Override public java.lang.String getAdduct() { java.lang.Object ref = adduct_; if (!(ref instanceof java.lang.String)) { @@ -21531,6 +21798,7 @@ public java.lang.String getAdduct() { * string adduct = 8; * @return The bytes for adduct. */ + @Override public com.google.protobuf.ByteString getAdductBytes() { java.lang.Object ref = adduct_; @@ -21658,6 +21926,7 @@ private void ensureCrosslinkedSequencesIsMutable() { * repeated string crosslinkedSequences = 11; * @return A list containing the crosslinkedSequences. */ + @Override public com.google.protobuf.ProtocolStringList getCrosslinkedSequencesList() { crosslinkedSequences_.makeImmutable(); @@ -21667,6 +21936,7 @@ private void ensureCrosslinkedSequencesIsMutable() { * repeated string crosslinkedSequences = 11; * @return The count of crosslinkedSequences. */ + @Override public int getCrosslinkedSequencesCount() { return crosslinkedSequences_.size(); } @@ -21675,6 +21945,7 @@ public int getCrosslinkedSequencesCount() { * @param index The index of the element to return. * @return The crosslinkedSequences at the given index. */ + @Override public java.lang.String getCrosslinkedSequences(int index) { return crosslinkedSequences_.get(index); } @@ -21683,6 +21954,7 @@ public java.lang.String getCrosslinkedSequences(int index) { * @param index The index of the value to return. * @return The bytes of the crosslinkedSequences at the given index. */ + @Override public com.google.protobuf.ByteString getCrosslinkedSequencesBytes(int index) { return crosslinkedSequences_.getByteString(index); @@ -21737,8 +22009,8 @@ public Builder addAllCrosslinkedSequences( public Builder clearCrosslinkedSequences() { crosslinkedSequences_ = com.google.protobuf.LazyStringArrayList.emptyList(); - bitField0_ = (bitField0_ & ~0x00000400);; - onChanged(); + bitField0_ = (bitField0_ & ~0x00000400); + onChanged(); return this; } /** @@ -21761,7 +22033,7 @@ public Builder addCrosslinkedSequencesBytes( java.util.Collections.emptyList(); private void ensureCrosslinkersIsMutable() { if (!((bitField0_ & 0x00000800) != 0)) { - crosslinkers_ = new java.util.ArrayList(crosslinkers_); + crosslinkers_ = new java.util.ArrayList<>(crosslinkers_); bitField0_ |= 0x00000800; } } @@ -21772,6 +22044,7 @@ private void ensureCrosslinkersIsMutable() { /** * repeated .LibraryKeyProto.Crosslinker crosslinkers = 12; */ + @Override public java.util.List getCrosslinkersList() { if (crosslinkersBuilder_ == null) { return java.util.Collections.unmodifiableList(crosslinkers_); @@ -21782,6 +22055,7 @@ public java.util.Listrepeated .LibraryKeyProto.Crosslinker crosslinkers = 12; */ + @Override public int getCrosslinkersCount() { if (crosslinkersBuilder_ == null) { return crosslinkers_.size(); @@ -21792,6 +22066,7 @@ public int getCrosslinkersCount() { /** * repeated .LibraryKeyProto.Crosslinker crosslinkers = 12; */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto.Crosslinker getCrosslinkers(int index) { if (crosslinkersBuilder_ == null) { return crosslinkers_.get(index); @@ -21942,6 +22217,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto.Crossl /** * repeated .LibraryKeyProto.Crosslinker crosslinkers = 12; */ + @Override public org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto.CrosslinkerOrBuilder getCrosslinkersOrBuilder( int index) { if (crosslinkersBuilder_ == null) { @@ -21952,7 +22228,8 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto.Crossl /** * repeated .LibraryKeyProto.Crosslinker crosslinkers = 12; */ - public java.util.List + @Override + public java.util.List getCrosslinkersOrBuilderList() { if (crosslinkersBuilder_ != null) { return crosslinkersBuilder_.getMessageOrBuilderList(); @@ -21986,8 +22263,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto.Crossl org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto.Crosslinker, org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto.Crosslinker.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto.CrosslinkerOrBuilder> getCrosslinkersFieldBuilder() { if (crosslinkersBuilder_ == null) { - crosslinkersBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3< - org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto.Crosslinker, org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto.Crosslinker.Builder, org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto.CrosslinkerOrBuilder>( + crosslinkersBuilder_ = new com.google.protobuf.RepeatedFieldBuilderV3<>( crosslinkers_, ((bitField0_ & 0x00000800) != 0), getParentForChildren(), @@ -22023,25 +22299,34 @@ public static org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto } private static final com.google.protobuf.Parser - PARSER = new com.google.protobuf.AbstractParser() { - @java.lang.Override - public LibraryKeyProto parsePartialFrom( - com.google.protobuf.CodedInputStream input, - com.google.protobuf.ExtensionRegistryLite extensionRegistry) - throws com.google.protobuf.InvalidProtocolBufferException { - Builder builder = newBuilder(); - try { - builder.mergeFrom(input, extensionRegistry); - } catch (com.google.protobuf.InvalidProtocolBufferException e) { - throw e.setUnfinishedMessage(builder.buildPartial()); - } catch (com.google.protobuf.UninitializedMessageException e) { - throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); - } catch (java.io.IOException e) { - throw new com.google.protobuf.InvalidProtocolBufferException(e) - .setUnfinishedMessage(builder.buildPartial()); + PARSER = new com.google.protobuf.AbstractParser<>() + { + @java.lang.Override + public LibraryKeyProto parsePartialFrom( + com.google.protobuf.CodedInputStream input, + com.google.protobuf.ExtensionRegistryLite extensionRegistry) + throws com.google.protobuf.InvalidProtocolBufferException + { + Builder builder = newBuilder(); + try + { + builder.mergeFrom(input, extensionRegistry); + } + catch (com.google.protobuf.InvalidProtocolBufferException e) + { + throw e.setUnfinishedMessage(builder.buildPartial()); + } + catch (com.google.protobuf.UninitializedMessageException e) + { + throw e.asInvalidProtocolBufferException().setUnfinishedMessage(builder.buildPartial()); + } + catch (java.io.IOException e) + { + throw new com.google.protobuf.InvalidProtocolBufferException(e) + .setUnfinishedMessage(builder.buildPartial()); + } + return builder.buildPartial(); } - return builder.buildPartial(); - } }; public static com.google.protobuf.Parser parser() { @@ -22140,7 +22425,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto getDef getDescriptor() { return descriptor; } - private static com.google.protobuf.Descriptors.FileDescriptor + private static final com.google.protobuf.Descriptors.FileDescriptor descriptor; static { java.lang.String[] descriptorData = { diff --git a/src/org/labkey/targetedms/parser/skyaudit/AuditLogTree.java b/src/org/labkey/targetedms/parser/skyaudit/AuditLogTree.java index 571171814..2ac567cf1 100644 --- a/src/org/labkey/targetedms/parser/skyaudit/AuditLogTree.java +++ b/src/org/labkey/targetedms/parser/skyaudit/AuditLogTree.java @@ -170,7 +170,7 @@ public Set deleteList(long versionId) entityCount.put(currentEntry.getEntryHash(), 1); } - if (currentEntry._children.size() == 0) //if this is a leaf + if (currentEntry._children.isEmpty()) //if this is a leaf { if (currentEntry._versionId == null) { diff --git a/src/org/labkey/targetedms/parser/skyaudit/UnitTestUtil.java b/src/org/labkey/targetedms/parser/skyaudit/UnitTestUtil.java index e457ae00b..812982203 100644 --- a/src/org/labkey/targetedms/parser/skyaudit/UnitTestUtil.java +++ b/src/org/labkey/targetedms/parser/skyaudit/UnitTestUtil.java @@ -47,7 +47,7 @@ public class UnitTestUtil { - private static String[] _resourcePath = {"server", "customModules", "targetedms", "resources"}; + private static final String[] _resourcePath = {"server", "customModules", "targetedms", "resources"}; public static File getSampleDataFile(String pFileName) throws IOException { @@ -69,7 +69,7 @@ private static File getTestFile(String pFileName, String[] pPathList){ //not good for production code but for testing util it should be fine) and append the //known path and file name to the Labkey root. URL r = UnitTestUtil.class.getResource("/"); - String decodedUrl = ""; + String decodedUrl; decodedUrl = URLDecoder.decode(r.getFile(), StandardCharsets.UTF_8); if(decodedUrl.startsWith("/")) decodedUrl = decodedUrl.replaceFirst("/", ""); diff --git a/src/org/labkey/targetedms/parser/skyd/CacheHeaderStruct.java b/src/org/labkey/targetedms/parser/skyd/CacheHeaderStruct.java index 597d6eb3d..bd7ce84f7 100644 --- a/src/org/labkey/targetedms/parser/skyd/CacheHeaderStruct.java +++ b/src/org/labkey/targetedms/parser/skyd/CacheHeaderStruct.java @@ -151,7 +151,7 @@ public static int getStructSize(CacheFormatVersion cacheFormatVersion) } public static StructSerializer getStructSerializer(CacheFormatVersion cacheFormatVersion) { - return new StructSerializer( + return new StructSerializer<>( CacheHeaderStruct.class, getStructSize(CacheFormatVersion.CURRENT), getStructSize(cacheFormatVersion)) { @Override diff --git a/src/org/labkey/targetedms/parser/skyd/CachedFileHeaderStruct.java b/src/org/labkey/targetedms/parser/skyd/CachedFileHeaderStruct.java index 2b6bca35b..550a51cc2 100644 --- a/src/org/labkey/targetedms/parser/skyd/CachedFileHeaderStruct.java +++ b/src/org/labkey/targetedms/parser/skyd/CachedFileHeaderStruct.java @@ -150,6 +150,6 @@ public long getLocationScanIds() public enum Flags { single_match_mz_known, single_match_mz, - has_midas_spectra; + has_midas_spectra } } diff --git a/src/org/labkey/targetedms/parser/skyd/ChromGroupHeaderInfo.java b/src/org/labkey/targetedms/parser/skyd/ChromGroupHeaderInfo.java index 6e4843c98..a9249ce9b 100644 --- a/src/org/labkey/targetedms/parser/skyd/ChromGroupHeaderInfo.java +++ b/src/org/labkey/targetedms/parser/skyd/ChromGroupHeaderInfo.java @@ -32,15 +32,15 @@ public class ChromGroupHeaderInfo // For reducing memory usage, following instance variables are commented out because of the // absence of accessors and reading from inputStream is left to correctly advance the size of the fields private int textIdIndex; - private int startTransitionIndex; + private final int startTransitionIndex; // private int startPeakIndex; // private int startScoreIndex; - private int numPoints; - private int compressedSize; - private EnumSet flagValues; - private short fileIndex; + private final int numPoints; + private final int compressedSize; + private final EnumSet flagValues; + private final short fileIndex; private short textIdLen; - private short numTransitions; + private final short numTransitions; // private byte numPeaks; // private byte maxPeakIndex; // private byte isProcessedScans; @@ -48,10 +48,10 @@ public class ChromGroupHeaderInfo // private short statusId; // private short statusRank; private double precursor; - private long locationPoints; - private int uncompressedSize; - private float startTime; - private float endTime; + private final long locationPoints; + private final int uncompressedSize; + private final float startTime; + private final float endTime; // private float collisionalCrossSection; public ChromGroupHeaderInfo(CacheFormatVersion cacheFormatVersion, LittleEndianInput dataInputStream) @@ -193,8 +193,8 @@ public enum FlagValues dda_acquisition_method(0x40, 0x800), extracted_qc_trace(0x80, 0x1000); - private int currentFlagValue; - private int legacyFlagValue; + private final int currentFlagValue; + private final int legacyFlagValue; /** * @param currentFlagValue the value that the flag has in current (skyd format 18 or greater, Skyline 23_1) skyd files. diff --git a/src/org/labkey/targetedms/parser/skyd/ChromPeak.java b/src/org/labkey/targetedms/parser/skyd/ChromPeak.java index 804430906..87735fa70 100644 --- a/src/org/labkey/targetedms/parser/skyd/ChromPeak.java +++ b/src/org/labkey/targetedms/parser/skyd/ChromPeak.java @@ -21,19 +21,19 @@ */ public class ChromPeak { - private float _retentionTime; - private float _startTime; - private float _endTime; - private float _area; - private float _backgroundArea; - private float _height; - private float _fwhm; - private int _flagBits; - private short _pointsAcross; - private float _stdDev; - private float _skewness; - private float _kurtosis; - private float _shapeCorrelation; + private final float _retentionTime; + private final float _startTime; + private final float _endTime; + private final float _area; + private final float _backgroundArea; + private final float _height; + private final float _fwhm; + private final int _flagBits; + private final short _pointsAcross; + private final float _stdDev; + private final float _skewness; + private final float _kurtosis; + private final float _shapeCorrelation; private static final int FLAGVALUE_HAS_PEAK_SHAPE = 0x80; diff --git a/src/org/labkey/targetedms/parser/speclib/BlibSpectrumReader.java b/src/org/labkey/targetedms/parser/speclib/BlibSpectrumReader.java index 70575720c..db436891a 100644 --- a/src/org/labkey/targetedms/parser/speclib/BlibSpectrumReader.java +++ b/src/org/labkey/targetedms/parser/speclib/BlibSpectrumReader.java @@ -165,12 +165,11 @@ protected List readRetentionTimes(Co return Collections.emptyList(); } - StringBuilder sql = new StringBuilder("SELECT rt.retentionTime, rt.bestSpectrum, rs.peptideModSeq, rs.precursorCharge, ssf.fileName from RetentionTimes AS rt "); - sql.append(" INNER JOIN RefSpectra AS rs ON (rt.RefSpectraID = rs.id)"); - sql.append(" INNER JOIN SpectrumSourceFiles ssf ON (rt.SpectrumSourceID = ssf.id)"); - sql.append(" WHERE rs.peptideModSeq = ?"); + String sql = "SELECT rt.retentionTime, rt.bestSpectrum, rs.peptideModSeq, rs.precursorCharge, ssf.fileName from RetentionTimes AS rt " + " INNER JOIN RefSpectra AS rs ON (rt.RefSpectraID = rs.id)" + + " INNER JOIN SpectrumSourceFiles ssf ON (rt.SpectrumSourceID = ssf.id)" + + " WHERE rs.peptideModSeq = ?"; - try(PreparedStatement stmt = conn.prepareStatement(sql.toString())) + try(PreparedStatement stmt = conn.prepareStatement(sql)) { stmt.setString(1, modifiedPeptide); List retentionTimes = new ArrayList<>(); @@ -398,11 +397,10 @@ private static byte[] getBytes(byte[] compressed, int uncompressedLength) throws private static void addRedundantSpectrumInfo(Connection conn, BlibSpectrum spectrum) throws SQLException { - StringBuilder sql = new StringBuilder("SELECT rt.*, sf.fileName "); - sql.append("FROM RetentionTimes AS rt INNER JOIN SpectrumSourceFiles AS sf ON rt.spectrumSourceID = sf.id "); - sql.append("WHERE RefSpectraID=").append(spectrum.getBlibId()); + String sql = "SELECT rt.*, sf.fileName " + "FROM RetentionTimes AS rt INNER JOIN SpectrumSourceFiles AS sf ON rt.spectrumSourceID = sf.id " + + "WHERE RefSpectraID=" + spectrum.getBlibId(); - try (Statement stmt = conn.createStatement(); ResultSet rs = stmt.executeQuery(sql.toString())) + try (Statement stmt = conn.createStatement(); ResultSet rs = stmt.executeQuery(sql)) { List redundantSpectra = new ArrayList<>(); @@ -431,11 +429,10 @@ private static void addRedundantSpectrumInfo(Connection conn, BlibSpectrum spect private static BlibSpectrum readRedundantSpectrum(Connection conn, int redundantRefSpectrumid) throws SQLException { - StringBuilder sql = new StringBuilder("SELECT rf.*, ssf.fileName FROM RefSpectra AS rf "); - sql.append("LEFT JOIN SpectrumSourceFiles AS ssf ON rf.FileID = ssf.id "); - sql.append(" WHERE rf.id=").append(redundantRefSpectrumid); + String sql = "SELECT rf.*, ssf.fileName FROM RefSpectra AS rf " + "LEFT JOIN SpectrumSourceFiles AS ssf ON rf.FileID = ssf.id " + + " WHERE rf.id=" + redundantRefSpectrumid; - try (Statement stmt = conn.createStatement(); ResultSet rs = stmt.executeQuery(sql.toString())) + try (Statement stmt = conn.createStatement(); ResultSet rs = stmt.executeQuery(sql)) { BlibSpectrum spectrum = null; diff --git a/src/org/labkey/targetedms/parser/speclib/ElibSpectrumReader.java b/src/org/labkey/targetedms/parser/speclib/ElibSpectrumReader.java index dee26224b..182839d81 100644 --- a/src/org/labkey/targetedms/parser/speclib/ElibSpectrumReader.java +++ b/src/org/labkey/targetedms/parser/speclib/ElibSpectrumReader.java @@ -103,7 +103,7 @@ private ElibSpectrum readElibSpectrum(Connection conn, SpectrumKey spectrumKey, } } - if(spectra.size() > 0) + if(!spectra.isEmpty()) { sortElibSpectra(spectra); ElibSpectrum bestSpectrum = spectra.get(0); diff --git a/src/org/labkey/targetedms/parser/speclib/LibSpectrumReader.java b/src/org/labkey/targetedms/parser/speclib/LibSpectrumReader.java index 48bb88af0..af6d489b4 100644 --- a/src/org/labkey/targetedms/parser/speclib/LibSpectrumReader.java +++ b/src/org/labkey/targetedms/parser/speclib/LibSpectrumReader.java @@ -257,7 +257,7 @@ static String findMatchingModifiedSequence(Connection conn, String modifiedSeque // Find the modified sequence representation from the library that matches List> mods = new ArrayList<>(); String unmodifiedSequence = Peptide.stripModifications(modifiedSequence, mods); - if (mods.size() == 0) { + if (mods.isEmpty()) { return modifiedSequence; } diff --git a/src/org/labkey/targetedms/pipeline/AreaProportionRecalcJob.java b/src/org/labkey/targetedms/pipeline/AreaProportionRecalcJob.java index c4a694d59..982c6a677 100644 --- a/src/org/labkey/targetedms/pipeline/AreaProportionRecalcJob.java +++ b/src/org/labkey/targetedms/pipeline/AreaProportionRecalcJob.java @@ -2,33 +2,16 @@ import org.apache.commons.lang3.mutable.MutableLong; import org.jetbrains.annotations.NotNull; -import org.labkey.api.data.Container; -import org.labkey.api.data.ContainerFilter; -import org.labkey.api.data.ContainerManager; -import org.labkey.api.data.RuntimeSQLException; -import org.labkey.api.data.SimpleFilter; -import org.labkey.api.data.Sort; import org.labkey.api.data.TableSelector; import org.labkey.api.pipeline.PipeRoot; import org.labkey.api.pipeline.PipelineJob; -import org.labkey.api.query.FieldKey; import org.labkey.api.util.FileUtil; -import org.labkey.api.util.PageFlowUtil; import org.labkey.api.util.URLHelper; import org.labkey.api.view.ViewBackgroundInfo; import org.labkey.targetedms.TargetedMSManager; import org.labkey.targetedms.TargetedMSRun; -import org.labkey.targetedms.TargetedMSSchema; -import org.labkey.targetedms.parser.Chromatogram; -import org.labkey.targetedms.parser.PrecursorChromInfo; -import org.labkey.targetedms.parser.SampleFile; -import org.labkey.targetedms.query.PrecursorManager; import java.io.File; -import java.sql.ResultSet; -import java.sql.SQLException; -import java.util.ArrayList; -import java.util.List; public class AreaProportionRecalcJob extends PipelineJob { diff --git a/src/org/labkey/targetedms/pipeline/ChromatogramCrawlerJob.java b/src/org/labkey/targetedms/pipeline/ChromatogramCrawlerJob.java index 34d47e86a..7cdd84a78 100644 --- a/src/org/labkey/targetedms/pipeline/ChromatogramCrawlerJob.java +++ b/src/org/labkey/targetedms/pipeline/ChromatogramCrawlerJob.java @@ -31,7 +31,7 @@ public class ChromatogramCrawlerJob extends PipelineJob { - private CrawlType _crawlType = CrawlType.verifyOnly; + private final CrawlType _crawlType = CrawlType.verifyOnly; /** For JSON serialization/deserialzation round-tripping * @noinspection unused*/ diff --git a/src/org/labkey/targetedms/pipeline/TargetedMSImportPipelineJob.java b/src/org/labkey/targetedms/pipeline/TargetedMSImportPipelineJob.java index 0ea696e80..80fc1c053 100644 --- a/src/org/labkey/targetedms/pipeline/TargetedMSImportPipelineJob.java +++ b/src/org/labkey/targetedms/pipeline/TargetedMSImportPipelineJob.java @@ -116,9 +116,8 @@ public RunRepresentativeDataState getRepresentative() public List compareJobs(PipelineJob job2) { List errors = super.compareJobs(job2); - if (job2 instanceof TargetedMSImportPipelineJob) + if (job2 instanceof TargetedMSImportPipelineJob copyJob2) { - TargetedMSImportPipelineJob copyJob2 = (TargetedMSImportPipelineJob)job2; if (!this._representative.equals(copyJob2._representative)) errors.add("_representative"); } diff --git a/src/org/labkey/targetedms/pipeline/TargetedMSPipelineProvider.java b/src/org/labkey/targetedms/pipeline/TargetedMSPipelineProvider.java index a9a96480b..b745b7726 100644 --- a/src/org/labkey/targetedms/pipeline/TargetedMSPipelineProvider.java +++ b/src/org/labkey/targetedms/pipeline/TargetedMSPipelineProvider.java @@ -40,7 +40,7 @@ public class TargetedMSPipelineProvider extends PipelineProvider { static String name = "Targeted MS"; - private static String ACTION_LABEL = "Import Skyline Results"; + private static final String ACTION_LABEL = "Import Skyline Results"; public TargetedMSPipelineProvider(Module owningModule) { diff --git a/src/org/labkey/targetedms/query/ConflictResultsManager.java b/src/org/labkey/targetedms/query/ConflictResultsManager.java index 9af420c5b..cf0d0fbf0 100644 --- a/src/org/labkey/targetedms/query/ConflictResultsManager.java +++ b/src/org/labkey/targetedms/query/ConflictResultsManager.java @@ -393,7 +393,7 @@ public static List getRankedTransitionsForPrecursor(l } TransitionWithAreaAndRank twr = new TransitionWithAreaAndRank(); twr.setTransition(transition); - twr.setAvgArea(transChromInfoList.size() == 0 ? 0 : totalArea / transChromInfoList.size()); + twr.setAvgArea(transChromInfoList.isEmpty() ? 0 : totalArea / transChromInfoList.size()); transWithRankList.add(twr); } diff --git a/src/org/labkey/targetedms/query/GuideSetTable.java b/src/org/labkey/targetedms/query/GuideSetTable.java index 410d4c3b8..be3c5de9f 100644 --- a/src/org/labkey/targetedms/query/GuideSetTable.java +++ b/src/org/labkey/targetedms/query/GuideSetTable.java @@ -26,7 +26,6 @@ import org.labkey.api.data.TableSelector; import org.labkey.api.query.ExprColumn; import org.labkey.api.query.FieldKey; -import org.labkey.api.query.FilteredTable; import org.labkey.api.query.QueryUpdateService; import org.labkey.api.query.RowIdQueryUpdateService; import org.labkey.api.query.SimpleUserSchema; diff --git a/src/org/labkey/targetedms/query/LibraryManager.java b/src/org/labkey/targetedms/query/LibraryManager.java index c31db02aa..53bba6f86 100644 --- a/src/org/labkey/targetedms/query/LibraryManager.java +++ b/src/org/labkey/targetedms/query/LibraryManager.java @@ -94,7 +94,7 @@ public static LinkedHashMap getLibraryFil private static LinkedHashMap getLibraryFilePaths(long runId, List libraries) { - if(libraries.size() == 0) + if(libraries.isEmpty()) return new LinkedHashMap<>(Collections.emptyMap()); Path skyFilesDir = getSkylineFilesDir(runId); diff --git a/src/org/labkey/targetedms/query/ModificationManager.java b/src/org/labkey/targetedms/query/ModificationManager.java index c8dd46bce..7b4eb20e1 100644 --- a/src/org/labkey/targetedms/query/ModificationManager.java +++ b/src/org/labkey/targetedms/query/ModificationManager.java @@ -62,7 +62,6 @@ public static IModification.IIsotopeModification getIsotopeModification(long id) } /** - * @param peptideId * @return Map of the modified amino acid index in the peptide sequence * and the mass of the modification. * ModifiedIndex -> MassDiff @@ -94,7 +93,6 @@ public static Map, Double> getPeptideStructuralModsMap(lo } /** - * @param peptideId * @return Map of the modified amino acid index in the peptide sequence * and the mass of the modification. * ModifiedIndex -> MassDiff @@ -111,7 +109,7 @@ public static Map getPeptideIsotopeModsMap(long peptideId, long "AND m.IsotopeLabelId=?"; SQLFragment sf = new SQLFragment(sql, peptideId, isotopeLabelId); - new SqlSelector(getSchema(), sf).forEach(new Selector.ForEachBlock() + new SqlSelector(getSchema(), sf).forEach(new Selector.ForEachBlock<>() { @Override public void exec(ResultSet rs) throws SQLException @@ -120,7 +118,7 @@ public void exec(ResultSet rs) throws SQLException double massDiff = rs.getDouble("MassDiff"); Double diffAtIndex = isotopeModIndexMassDiff.get(index); - if(diffAtIndex != null) + if (diffAtIndex != null) { massDiff += diffAtIndex; } @@ -136,7 +134,6 @@ public void exec(ResultSet rs) throws SQLException * that were checked in the Peptide Settings > Modifications tab in Skyline. The modifications are under * -> -> element in the .sky file. They are stored * in the targetedms.RunIsotopeModification table. - * @param runId * @return List of isotopic modifications */ public static List getIsotopeModificationsForRun(long runId) @@ -159,7 +156,6 @@ public static List getIsotopeModificatio * that were checked in the Peptide Settings > Modifications tab in Skyline. The modifications are under * -> -> element in the .sky file. They are stored * in the targetedms.RunStructuralModification table. - * @param runId * @return List of structural modifications */ public static List getStructuralModificationsForRun(long runId) @@ -179,7 +175,6 @@ public static List getStructuralModif /** * Returns a list of isotopic modifications found in at least one peptide in the run (Skyline document). - * @param runId * @return List of isotopic modifications */ public static List getIsotopeModificationsUsedInRun(long runId) @@ -191,7 +186,6 @@ public static List getIsotopeModificationsU /** * Returns a list of structural modifications found in at least one peptide in the run (Skyline document). - * @param runId * @return List of structural modifications */ public static List getStructuralModificationsUsedInRun(long runId) diff --git a/src/org/labkey/targetedms/query/MoleculeTransitionManager.java b/src/org/labkey/targetedms/query/MoleculeTransitionManager.java index 7b5f4ff96..e9663b946 100644 --- a/src/org/labkey/targetedms/query/MoleculeTransitionManager.java +++ b/src/org/labkey/targetedms/query/MoleculeTransitionManager.java @@ -26,7 +26,6 @@ import org.labkey.targetedms.TargetedMSSchema; import org.labkey.targetedms.parser.MoleculeTransition; -import java.util.Collection; import java.util.List; public class MoleculeTransitionManager diff --git a/src/org/labkey/targetedms/query/MoleculeTransitionsTableInfo.java b/src/org/labkey/targetedms/query/MoleculeTransitionsTableInfo.java index 8686b4ad8..81de81bae 100644 --- a/src/org/labkey/targetedms/query/MoleculeTransitionsTableInfo.java +++ b/src/org/labkey/targetedms/query/MoleculeTransitionsTableInfo.java @@ -18,13 +18,11 @@ import org.labkey.api.data.ContainerFilter; import org.labkey.api.data.JdbcType; import org.labkey.api.data.SQLFragment; -import org.labkey.api.data.WrappedColumn; import org.labkey.api.query.ExprColumn; import org.labkey.api.query.FieldKey; import org.labkey.api.query.QueryForeignKey; import org.labkey.targetedms.TargetedMSManager; import org.labkey.targetedms.TargetedMSSchema; -import org.labkey.targetedms.view.AnnotationUIDisplayColumn; import java.util.ArrayList; diff --git a/src/org/labkey/targetedms/query/PTMPercentsCustomizer.java b/src/org/labkey/targetedms/query/PTMPercentsCustomizer.java index 3b6b37139..8ee2ea33b 100644 --- a/src/org/labkey/targetedms/query/PTMPercentsCustomizer.java +++ b/src/org/labkey/targetedms/query/PTMPercentsCustomizer.java @@ -1,33 +1,12 @@ package org.labkey.targetedms.query; import org.apache.commons.collections4.MultiValuedMap; -import org.jetbrains.annotations.NotNull; -import org.jetbrains.annotations.Nullable; -import org.labkey.api.collections.CaseInsensitiveHashMap; -import org.labkey.api.data.ColumnInfo; -import org.labkey.api.data.CompareType; -import org.labkey.api.data.ConditionalFormat; -import org.labkey.api.data.DataColumn; -import org.labkey.api.data.DisplayColumn; -import org.labkey.api.data.DisplayColumnFactory; -import org.labkey.api.data.MutableColumnInfo; -import org.labkey.api.data.RenderContext; -import org.labkey.api.data.SQLFragment; -import org.labkey.api.data.SimpleFilter; -import org.labkey.api.data.SqlSelector; import org.labkey.api.data.TableCustomizer; import org.labkey.api.data.TableInfo; import org.labkey.api.query.FieldKey; -import org.labkey.api.util.Pair; -import org.labkey.targetedms.TargetedMSManager; -import org.labkey.targetedms.parser.Protein; import java.util.ArrayList; -import java.util.Collections; import java.util.List; -import java.util.Map; -import java.util.Optional; -import java.util.Set; /** * Customizes the set of columns available on a pivot query that operates on samples, hiding all of the pivot values diff --git a/src/org/labkey/targetedms/query/PeptideGroupManager.java b/src/org/labkey/targetedms/query/PeptideGroupManager.java index 0c9469904..aa2f41bce 100644 --- a/src/org/labkey/targetedms/query/PeptideGroupManager.java +++ b/src/org/labkey/targetedms/query/PeptideGroupManager.java @@ -129,7 +129,7 @@ public static List getPeptideGroupsForRun(long runId) public static void updateRepresentativeStatus(List peptideGroupIds, RepresentativeDataState representativeState) { - if(peptideGroupIds == null || peptideGroupIds.size() == 0) + if(peptideGroupIds == null || peptideGroupIds.isEmpty()) return; String peptideGroupIdsString = StringUtils.join(peptideGroupIds, ","); @@ -185,7 +185,7 @@ public static void updateStatusToDeprecatedOrNotRepresentative(long[] peptideGro public static void updateStatusToDeprecatedOrNotRepresentative(List peptideGroupIds) { - if(peptideGroupIds == null || peptideGroupIds.size() == 0) + if(peptideGroupIds == null || peptideGroupIds.isEmpty()) return; String peptideGroupIdsString = StringUtils.join(peptideGroupIds, ","); @@ -278,7 +278,7 @@ public static boolean ensureContainerMembership(List peptideGroupIds, Cont { pepGrpIds.append(",").append(id); } - if(pepGrpIds.length() > 0) + if(!pepGrpIds.isEmpty()) pepGrpIds.deleteCharAt(0); SQLFragment sql = new SQLFragment("SELECT COUNT(pg.Id) FROM "); sql.append(TargetedMSManager.getTableInfoPeptideGroup(), "pg"); diff --git a/src/org/labkey/targetedms/query/PrecursorManager.java b/src/org/labkey/targetedms/query/PrecursorManager.java index d66237dd5..3009b6f75 100644 --- a/src/org/labkey/targetedms/query/PrecursorManager.java +++ b/src/org/labkey/targetedms/query/PrecursorManager.java @@ -161,7 +161,7 @@ public static Set getSampleFileIdsForReplicate(long replicateId) @Nullable public static PrecursorChromInfo getBestPrecursorChromInfo(@NotNull List chromInfos) { - if(chromInfos.size() == 0) + if(chromInfos.isEmpty()) { return null; } @@ -453,7 +453,7 @@ public static int setRepresentativeState(long runId, RepresentativeDataState sta public static void updateRepresentativeStatus(List precursorIds, RepresentativeDataState representativeState) { - if(precursorIds == null || precursorIds.size() == 0) + if(precursorIds == null || precursorIds.isEmpty()) return; SQLFragment sql = new SQLFragment("UPDATE "+TargetedMSManager.getTableInfoGeneralPrecursor()); @@ -468,7 +468,7 @@ public static void updateRepresentativeStatus(List precursorIds, Represent public static void updateStatusToDeprecatedOrNotRepresentative(List precursorIds) { - if(precursorIds == null || precursorIds.size() == 0) + if(precursorIds == null || precursorIds.isEmpty()) return; SQLFragment sql = new SQLFragment("UPDATE "+TargetedMSManager.getTableInfoGeneralPrecursor()); diff --git a/src/org/labkey/targetedms/query/QCAnnotationTypeTable.java b/src/org/labkey/targetedms/query/QCAnnotationTypeTable.java index a86bcbc6c..38653e614 100644 --- a/src/org/labkey/targetedms/query/QCAnnotationTypeTable.java +++ b/src/org/labkey/targetedms/query/QCAnnotationTypeTable.java @@ -25,7 +25,6 @@ import org.labkey.api.data.DisplayColumnFactory; import org.labkey.api.data.SqlExecutor; import org.labkey.api.query.DefaultQueryUpdateService; -import org.labkey.api.query.FilteredTable; import org.labkey.api.query.InvalidKeyException; import org.labkey.api.query.QueryUpdateService; import org.labkey.api.query.QueryUpdateServiceException; diff --git a/src/org/labkey/targetedms/query/ReplicateManager.java b/src/org/labkey/targetedms/query/ReplicateManager.java index 1adb44258..fd73b32ab 100644 --- a/src/org/labkey/targetedms/query/ReplicateManager.java +++ b/src/org/labkey/targetedms/query/ReplicateManager.java @@ -19,7 +19,6 @@ import org.labkey.api.data.Container; import org.labkey.api.data.SQLFragment; import org.labkey.api.data.SimpleFilter; -import org.labkey.api.data.Sort; import org.labkey.api.data.SqlSelector; import org.labkey.api.data.Table; import org.labkey.api.data.TableSelector; diff --git a/src/org/labkey/targetedms/query/RepresentativeStateManager.java b/src/org/labkey/targetedms/query/RepresentativeStateManager.java index c1beaab66..cce203e19 100644 --- a/src/org/labkey/targetedms/query/RepresentativeStateManager.java +++ b/src/org/labkey/targetedms/query/RepresentativeStateManager.java @@ -191,7 +191,7 @@ private static int resolveRepresentativeProteinState(Container container, Target makeActiveSQL.add(RepresentativeDataState.Representative.ordinal()); makeActiveSQL.append(" WHERE RunId=? "); makeActiveSQL.add(run.getId()); - if(peptideGroupIdsToExclude.size() > 0) + if(!peptideGroupIdsToExclude.isEmpty()) { makeActiveSQL.append(" AND Id NOT IN (").append(StringUtils.join(peptideGroupIdsToExclude, ',')).append(")"); } @@ -254,7 +254,7 @@ private static int resolveRepresentativeProteinState(Container container, Target makeConflictedSQL.add(RepresentativeDataState.Conflicted.ordinal()); makeConflictedSQL.append(" WHERE RunId=?"); makeConflictedSQL.add(run.getId()); - if(peptideGroupIdsToExclude.size() > 0) + if(!peptideGroupIdsToExclude.isEmpty()) { makeConflictedSQL.append(" AND Id NOT IN (").append(StringUtils.join(peptideGroupIdsToExclude, ',')).append(")"); } @@ -268,7 +268,7 @@ private static int resolveRepresentativeProteinState(Container container, Target // If this run has "standard" proteins, mark them as being representative. // Older versions of the proteins, from previous runs, will be marked as deprecated. List standardPeptideGroupIds = getAllStandardPeptideGroups(run); - if(standardPeptideGroupIds.size() > 0) + if(!standardPeptideGroupIds.isEmpty()) { updateStandardPeptideGroups(container, standardPeptideGroupIds); } @@ -379,7 +379,7 @@ private static List getStdPrecursorIdsInRun(TargetedMSRun run) private static List getCurrentStandardPrecursorIds(Container container, List stdPrecursorIdsInRun, TableInfo precursorTable, BiFunction joinValue) { - if(stdPrecursorIdsInRun == null || stdPrecursorIdsInRun.size() == 0) + if(stdPrecursorIdsInRun == null || stdPrecursorIdsInRun.isEmpty()) { return Collections.emptyList(); } @@ -525,7 +525,7 @@ private static int resolveRepresentativeState(Container container, TargetedMSRun // If there are standard peptides in this run, we will mark them as representative. Older versions of these // peptides, from previous runs, will be marked as deprecated. List stdPrecursorIdsInRun = getStdPrecursorIdsInRun(run); - if(stdPrecursorIdsInRun.size() > 0) + if(!stdPrecursorIdsInRun.isEmpty()) { // Get a list of current representative precursors in the folder that have the same identifier and charge // as the standard precursors in the run. diff --git a/src/org/labkey/targetedms/query/SampleFileTable.java b/src/org/labkey/targetedms/query/SampleFileTable.java index f0d779491..d250ef4c0 100644 --- a/src/org/labkey/targetedms/query/SampleFileTable.java +++ b/src/org/labkey/targetedms/query/SampleFileTable.java @@ -68,8 +68,6 @@ import org.labkey.targetedms.parser.DataSettings; import org.labkey.targetedms.parser.SampleFile; -import java.io.IOException; -import java.io.Writer; import java.sql.SQLException; import java.util.ArrayList; import java.util.Arrays; diff --git a/src/org/labkey/targetedms/query/SkylineListSchema.java b/src/org/labkey/targetedms/query/SkylineListSchema.java index cbc4895d2..b7dcce9d9 100644 --- a/src/org/labkey/targetedms/query/SkylineListSchema.java +++ b/src/org/labkey/targetedms/query/SkylineListSchema.java @@ -26,7 +26,7 @@ public class SkylineListSchema extends UserSchema public static final String ID_SEPARATOR = "_"; public static final String UNION_PREFIX = "All" + ID_SEPARATOR; - private Map> _listDefinitions = new HashMap<>(); + private final Map> _listDefinitions = new HashMap<>(); static public void register(Module module) { diff --git a/src/org/labkey/targetedms/query/TargetedMSCrosstabView.java b/src/org/labkey/targetedms/query/TargetedMSCrosstabView.java index 0070238e0..c56b64a8a 100644 --- a/src/org/labkey/targetedms/query/TargetedMSCrosstabView.java +++ b/src/org/labkey/targetedms/query/TargetedMSCrosstabView.java @@ -5,7 +5,6 @@ import org.labkey.api.data.ExcelWriter; import org.labkey.api.query.CrosstabView; import org.labkey.api.query.QuerySettings; -import org.labkey.api.query.QueryView; import org.labkey.targetedms.TargetedMSSchema; import org.springframework.validation.BindException; diff --git a/src/org/labkey/targetedms/query/TargetedMSForeignKey.java b/src/org/labkey/targetedms/query/TargetedMSForeignKey.java index fb8914b7e..07c0282b4 100644 --- a/src/org/labkey/targetedms/query/TargetedMSForeignKey.java +++ b/src/org/labkey/targetedms/query/TargetedMSForeignKey.java @@ -17,7 +17,6 @@ import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; -import org.labkey.api.data.Container; import org.labkey.api.data.ContainerFilter; import org.labkey.api.data.TableInfo; import org.labkey.api.query.LookupForeignKey; diff --git a/src/org/labkey/targetedms/view/GroupComparisonView.java b/src/org/labkey/targetedms/view/GroupComparisonView.java index 1358920ca..eb20a9b55 100644 --- a/src/org/labkey/targetedms/view/GroupComparisonView.java +++ b/src/org/labkey/targetedms/view/GroupComparisonView.java @@ -37,7 +37,7 @@ public class GroupComparisonView extends QuantificationView { public static final String DATAREGION_NAME = "group_comparison"; public static final String DATAREGION_NAME_SM_MOL = DATAREGION_NAME + SMALL_MOLECULE_SUFFIX; - private GroupComparisonSettings _groupComparisonSettings; + private final GroupComparisonSettings _groupComparisonSettings; public GroupComparisonView(ViewContext ctx, TargetedMSSchema schema, Form form, boolean forExport, String dataRegionName) { diff --git a/src/org/labkey/targetedms/view/TargetedMSRunsWebPartView.java b/src/org/labkey/targetedms/view/TargetedMSRunsWebPartView.java index c3ed0b0f8..9c878864c 100644 --- a/src/org/labkey/targetedms/view/TargetedMSRunsWebPartView.java +++ b/src/org/labkey/targetedms/view/TargetedMSRunsWebPartView.java @@ -37,7 +37,7 @@ public TargetedMSRunsWebPartView(ViewContext viewContext) TargetedMSService.FolderType folderType = TargetedMSManager.getFolderType(viewContext.getContainer()); if(folderType == TargetedMSService.FolderType.Library || folderType == TargetedMSService.FolderType.LibraryProtein) { - addView(new JspView("/org/labkey/targetedms/view/conflictSummary.jsp")); + addView(new JspView<>("/org/labkey/targetedms/view/conflictSummary.jsp")); } TargetedMsRunListView runListView = TargetedMsRunListView.createView(viewContext); runListView.setFrame(WebPartView.FrameType.NONE); diff --git a/src/org/labkey/targetedms/view/TargetedMsRunListView.java b/src/org/labkey/targetedms/view/TargetedMsRunListView.java index bf1635124..74dc05676 100644 --- a/src/org/labkey/targetedms/view/TargetedMsRunListView.java +++ b/src/org/labkey/targetedms/view/TargetedMsRunListView.java @@ -52,12 +52,12 @@ public class TargetedMsRunListView extends ExperimentRunListView { private ViewType _viewType; - private boolean _hasDocVersions; - private boolean _showAllVersions; + private final boolean _hasDocVersions; + private final boolean _showAllVersions; private static final boolean DEFAULT_SHOW_ALL_VERSIONS = true; private static final String DEFAULT_VERSIONS_PARAM = DEFAULT_SHOW_ALL_VERSIONS ? "latestVersions" : "allVersions"; - public static enum ViewType + public enum ViewType { FOLDER_VIEW, EXPERIMENT_VIEW, diff --git a/src/org/labkey/targetedms/view/passport/beforeAfterReport.jsp b/src/org/labkey/targetedms/view/passport/beforeAfterReport.jsp index b83d2dac2..c8010e10d 100644 --- a/src/org/labkey/targetedms/view/passport/beforeAfterReport.jsp +++ b/src/org/labkey/targetedms/view/passport/beforeAfterReport.jsp @@ -60,7 +60,7 @@
- <%if(protein.getPep() != null && protein.getPep().size() != 0) {%> + <%if(protein.getPep() != null && !protein.getPep().isEmpty()) {%>

Filter Options

@@ -94,7 +94,7 @@
    - <%if(protein.getFeatures() != null && protein.getFeatures().size() > 0) {%> + <%if(protein.getFeatures() != null && !protein.getFeatures().isEmpty()) {%>

    Features:

    diff --git a/src/org/labkey/targetedms/view/spectrum/LibrarySpectrumMatch.java b/src/org/labkey/targetedms/view/spectrum/LibrarySpectrumMatch.java index dbb9f64be..585142f49 100644 --- a/src/org/labkey/targetedms/view/spectrum/LibrarySpectrumMatch.java +++ b/src/org/labkey/targetedms/view/spectrum/LibrarySpectrumMatch.java @@ -46,7 +46,7 @@ public class LibrarySpectrumMatch private List _libraries; // All libraries that have a match private String _lorikeetId; List _structuralModifications; - private Set _variableStructuralMods = new HashSet<>(); + private final Set _variableStructuralMods = new HashSet<>(); PeptideSettings.RunStructuralModification _ntermMod = null; PeptideSettings.RunStructuralModification _ctermMod = null; @@ -160,7 +160,7 @@ public void setMaxNeutralLosses(int maxNeutralLosses) public boolean hasRedundantSpectra() { - return _spectrum != null && _spectrum.getRedundantSpectrumList().size() > 0; + return _spectrum != null && !_spectrum.getRedundantSpectrumList().isEmpty(); } public String getPeaks() @@ -228,14 +228,14 @@ public String getStructuralModifications() return "[]"; // Example: [{modMass: 42.0, aminoAcid: 'K'}] - StringBuilder mods = new StringBuilder(); - mods.append("["); - // Return all static (not variable) structural modifications. - mods.append(appendStructuralModifications(_structuralModifications, false)); // only static mods + String mods = "[" + - mods.append("]"); - return mods.toString(); + // Return all static (not variable) structural modifications. + appendStructuralModifications(_structuralModifications, false) + // only static mods + + "]"; + return mods; } public String getVariableModifications() @@ -420,7 +420,7 @@ private static final class LossMassCalculator private static final Pattern formulaPattern = Pattern.compile("([A-Z]'*)([0-9]*)"); public static double[] getMass(String formula) { - if(formula == null || formula.trim().length() == 0) + if(formula == null || formula.trim().isEmpty()) return new double[] {0.0, 0.0}; double monoMass = 0.0; @@ -439,11 +439,11 @@ public static double[] getMass(String formula) } String atom = matcher.group(1); - int count = 0; + int count; try { String num = matcher.group(2); - if(num.length() > 0) + if(!num.isEmpty()) { count = Integer.parseInt(matcher.group(2)); } @@ -476,7 +476,7 @@ public static double[] getMass(String formula) return new double[] {monoMass, avgMass}; } - private static Map atomicMasses = new HashMap(); + private static final Map atomicMasses = new HashMap<>(); static { atomicMasses.put("H", new double[]{ 1.007825035, 1.00794}); //Unimod diff --git a/src/org/labkey/targetedms/view/spectrum/LibrarySpectrumMatchGetter.java b/src/org/labkey/targetedms/view/spectrum/LibrarySpectrumMatchGetter.java index 919a3fd67..6c894e79f 100644 --- a/src/org/labkey/targetedms/view/spectrum/LibrarySpectrumMatchGetter.java +++ b/src/org/labkey/targetedms/view/spectrum/LibrarySpectrumMatchGetter.java @@ -60,7 +60,7 @@ public class LibrarySpectrumMatchGetter { private static final int CACHE_SIZE = 10; - private static BlockingCache> _peptideIdRtsCache = + private static final BlockingCache> _peptideIdRtsCache = CacheManager.getBlockingCache(CACHE_SIZE, CacheManager.DAY, "TargetedMS peptide ID retention times", (precursor, argument) -> { if (!(argument instanceof Container)) @@ -81,7 +81,7 @@ public class LibrarySpectrumMatchGetter List rtInfos = reader.getRetentionTimes((Container) argument, libPath, precursor.getModifiedSequence()); - if (rtInfos.size() > 0) + if (!rtInfos.isEmpty()) { return rtInfos; // return matches from the first library that has a match } diff --git a/src/org/labkey/targetedms/view/spectrum/PeptideSpectrumView.java b/src/org/labkey/targetedms/view/spectrum/PeptideSpectrumView.java index 00b0dfc5b..1f96df9a0 100644 --- a/src/org/labkey/targetedms/view/spectrum/PeptideSpectrumView.java +++ b/src/org/labkey/targetedms/view/spectrum/PeptideSpectrumView.java @@ -17,7 +17,6 @@ import org.labkey.api.view.JspView; import org.labkey.targetedms.parser.PeptideSettings; -import org.springframework.validation.BindException; /** * User: vsharma diff --git a/test/src/org/labkey/test/components/targetedms/ClustergrammerDialog.java b/test/src/org/labkey/test/components/targetedms/ClustergrammerDialog.java index ece07510c..85f412355 100644 --- a/test/src/org/labkey/test/components/targetedms/ClustergrammerDialog.java +++ b/test/src/org/labkey/test/components/targetedms/ClustergrammerDialog.java @@ -84,7 +84,7 @@ protected class ElementCache extends Window.ElementCache Input reportDescriptionEditor = Input(Locator.textarea("reportDescriptionEditor" + "-inputEl"), getDriver()).findWhenNeeded(this); } - public class Confirmation extends Window + public static class Confirmation extends Window { private static final String CONFIRMATION_TITLE = "Publish to Clustergrammer"; diff --git a/test/src/org/labkey/test/components/targetedms/GuideSet.java b/test/src/org/labkey/test/components/targetedms/GuideSet.java index c177c40c0..af5609303 100644 --- a/test/src/org/labkey/test/components/targetedms/GuideSet.java +++ b/test/src/org/labkey/test/components/targetedms/GuideSet.java @@ -24,10 +24,10 @@ public class GuideSet { private int _rowId; - private String _startDate; - private String _endDate; - private String _comment; - private List _stats; + private final String _startDate; + private final String _endDate; + private final String _comment; + private final List _stats; private Integer _brushSelectedPoints; public GuideSet(String startDate, String endDate, String comment, Integer brushSelectedPoints) diff --git a/test/src/org/labkey/test/components/targetedms/GuideSetStats.java b/test/src/org/labkey/test/components/targetedms/GuideSetStats.java index 7220656f7..cf22bb73b 100644 --- a/test/src/org/labkey/test/components/targetedms/GuideSetStats.java +++ b/test/src/org/labkey/test/components/targetedms/GuideSetStats.java @@ -17,8 +17,8 @@ public class GuideSetStats { - private String _metricName; - private int _numRecords; + private final String _metricName; + private final int _numRecords; private String _precursor; private Double _mean; private Double _stdDev; diff --git a/test/src/org/labkey/test/components/targetedms/GuideSetWebPart.java b/test/src/org/labkey/test/components/targetedms/GuideSetWebPart.java index f91eaf9c7..4db77e1b7 100644 --- a/test/src/org/labkey/test/components/targetedms/GuideSetWebPart.java +++ b/test/src/org/labkey/test/components/targetedms/GuideSetWebPart.java @@ -30,7 +30,7 @@ public class GuideSetWebPart extends BodyWebPart { public static final String DEFAULT_TITLE = "Guide Set"; - private BaseWebDriverTest _test; + private final BaseWebDriverTest _test; private DataRegionTable _dataRegionTable; private String _projectName; @@ -68,7 +68,7 @@ public Integer getRowId(GuideSet guideSet) SelectRowsResponse selResp = selectCmd.execute(cn, _projectName); // guide sets created from brushing in the QC plot will not have a comment - if (selResp.getRows().size() == 0) + if (selResp.getRows().isEmpty()) { selectCmd = new SelectRowsCommand("targetedms", "GuideSet"); selectCmd.addFilter(new Filter("TrainingStart", guideSet.getStartDate())); @@ -76,7 +76,7 @@ public Integer getRowId(GuideSet guideSet) selResp = selectCmd.execute(cn, _projectName); } - if (selResp.getRows().size() > 0) + if (!selResp.getRows().isEmpty()) { String rowIdStr = selResp.getRows().get(0).get("RowId").toString(); return Integer.parseInt(rowIdStr); diff --git a/test/src/org/labkey/test/components/targetedms/LinkVersionsGrid.java b/test/src/org/labkey/test/components/targetedms/LinkVersionsGrid.java index b5f6b4d5d..34e963332 100644 --- a/test/src/org/labkey/test/components/targetedms/LinkVersionsGrid.java +++ b/test/src/org/labkey/test/components/targetedms/LinkVersionsGrid.java @@ -27,7 +27,7 @@ public class LinkVersionsGrid extends Component { - private WebDriverWrapper _test; + private final WebDriverWrapper _test; public LinkVersionsGrid(WebDriverWrapper test) { diff --git a/test/src/org/labkey/test/components/targetedms/PrecursorsWebPart.java b/test/src/org/labkey/test/components/targetedms/PrecursorsWebPart.java index 7718bf2ed..9921f8cf2 100644 --- a/test/src/org/labkey/test/components/targetedms/PrecursorsWebPart.java +++ b/test/src/org/labkey/test/components/targetedms/PrecursorsWebPart.java @@ -128,7 +128,7 @@ public enum SortBy Coefficient_of_Variation("Coefficient of Variation"), Light_heavy_ratio("Light/heavy ratio"); - private String _text; + private final String _text; SortBy(String text) { diff --git a/test/src/org/labkey/test/components/targetedms/QCAnnotationTypeWebPart.java b/test/src/org/labkey/test/components/targetedms/QCAnnotationTypeWebPart.java index 0b630b5b3..75b9f523a 100644 --- a/test/src/org/labkey/test/components/targetedms/QCAnnotationTypeWebPart.java +++ b/test/src/org/labkey/test/components/targetedms/QCAnnotationTypeWebPart.java @@ -24,7 +24,7 @@ public class QCAnnotationTypeWebPart extends BodyWebPart { public static final String DEFAULT_TITLE = "QC Annotation Type"; private DataRegionTable _dataRegionTable; - private BaseWebDriverTest _test; + private final BaseWebDriverTest _test; public QCAnnotationTypeWebPart(BaseWebDriverTest test) { diff --git a/test/src/org/labkey/test/components/targetedms/QCAnnotationWebPart.java b/test/src/org/labkey/test/components/targetedms/QCAnnotationWebPart.java index 22ceb663f..8f84f8600 100644 --- a/test/src/org/labkey/test/components/targetedms/QCAnnotationWebPart.java +++ b/test/src/org/labkey/test/components/targetedms/QCAnnotationWebPart.java @@ -24,7 +24,7 @@ public class QCAnnotationWebPart extends BodyWebPart { public static final String DEFAULT_TITLE = "QC Annotation"; private DataRegionTable _dataRegionTable; - private BaseWebDriverTest _test; + private final BaseWebDriverTest _test; public QCAnnotationWebPart(BaseWebDriverTest test) { diff --git a/test/src/org/labkey/test/components/targetedms/QCPlot.java b/test/src/org/labkey/test/components/targetedms/QCPlot.java index 6976d9d46..1ee193246 100644 --- a/test/src/org/labkey/test/components/targetedms/QCPlot.java +++ b/test/src/org/labkey/test/components/targetedms/QCPlot.java @@ -111,7 +111,7 @@ private Elements elements() return new Elements(); } - private class Elements + private static class Elements { Locator precursor = Locator.css(".labkey-wp-title-text"); Locator.CssLocator svg = Locator.css("svg"); diff --git a/test/src/org/labkey/test/pages/panoramapremium/ConfigureMetricsUIPage.java b/test/src/org/labkey/test/pages/panoramapremium/ConfigureMetricsUIPage.java index 8b45b977e..2fb30108a 100644 --- a/test/src/org/labkey/test/pages/panoramapremium/ConfigureMetricsUIPage.java +++ b/test/src/org/labkey/test/pages/panoramapremium/ConfigureMetricsUIPage.java @@ -9,7 +9,6 @@ import org.labkey.test.pages.PortalBodyPanel; import org.labkey.test.util.Ext4Helper; import org.openqa.selenium.NoSuchElementException; -import org.openqa.selenium.support.ui.ExpectedConditions; import java.util.Map; diff --git a/test/src/org/labkey/test/pages/targetedms/AnnotationInsertPage.java b/test/src/org/labkey/test/pages/targetedms/AnnotationInsertPage.java index 11fb03723..d829f8718 100644 --- a/test/src/org/labkey/test/pages/targetedms/AnnotationInsertPage.java +++ b/test/src/org/labkey/test/pages/targetedms/AnnotationInsertPage.java @@ -15,7 +15,6 @@ */ package org.labkey.test.pages.targetedms; -import org.labkey.test.BaseWebDriverTest; import org.labkey.test.Locator; import org.labkey.test.pages.InsertPage; import org.labkey.test.util.targetedms.QCHelper; diff --git a/test/src/org/labkey/test/pages/targetedms/GuideSetPage.java b/test/src/org/labkey/test/pages/targetedms/GuideSetPage.java index f32aa4aa1..f5e878b8d 100644 --- a/test/src/org/labkey/test/pages/targetedms/GuideSetPage.java +++ b/test/src/org/labkey/test/pages/targetedms/GuideSetPage.java @@ -16,7 +16,6 @@ package org.labkey.test.pages.targetedms; import org.jetbrains.annotations.Nullable; -import org.labkey.test.BaseWebDriverTest; import org.labkey.test.Locator; import org.labkey.test.components.targetedms.GuideSet; import org.labkey.test.pages.InsertPage; diff --git a/test/src/org/labkey/test/pages/targetedms/PKReportPage.java b/test/src/org/labkey/test/pages/targetedms/PKReportPage.java index 493e06e33..e737b32f0 100644 --- a/test/src/org/labkey/test/pages/targetedms/PKReportPage.java +++ b/test/src/org/labkey/test/pages/targetedms/PKReportPage.java @@ -26,7 +26,7 @@ public class PKReportPage extends LabKeyPage { - private int _totalSubgroupTimeRowCount; + private final int _totalSubgroupTimeRowCount; public PKReportPage(WebDriver driver, int totalSubgroupTimeRowCount) { diff --git a/test/src/org/labkey/test/pages/targetedms/PanoramaAnnotations.java b/test/src/org/labkey/test/pages/targetedms/PanoramaAnnotations.java index 0ae870dca..e173867a4 100644 --- a/test/src/org/labkey/test/pages/targetedms/PanoramaAnnotations.java +++ b/test/src/org/labkey/test/pages/targetedms/PanoramaAnnotations.java @@ -22,8 +22,8 @@ public class PanoramaAnnotations extends PortalBodyPanel { - private QCAnnotationWebPart _qcAnnotationWebPart; - private QCAnnotationTypeWebPart _qcAnnotationTypeWebPart; + private final QCAnnotationWebPart _qcAnnotationWebPart; + private final QCAnnotationTypeWebPart _qcAnnotationTypeWebPart; public PanoramaAnnotations(BaseWebDriverTest test) { diff --git a/test/src/org/labkey/test/pages/targetedms/ParetoPlotPage.java b/test/src/org/labkey/test/pages/targetedms/ParetoPlotPage.java index b917e66c6..f25717f5b 100644 --- a/test/src/org/labkey/test/pages/targetedms/ParetoPlotPage.java +++ b/test/src/org/labkey/test/pages/targetedms/ParetoPlotPage.java @@ -15,14 +15,13 @@ */ package org.labkey.test.pages.targetedms; -import org.labkey.test.BaseWebDriverTest; import org.labkey.test.components.targetedms.ParetoPlotsWebPart; import org.labkey.test.pages.PortalBodyPanel; import org.openqa.selenium.WebDriver; public class ParetoPlotPage extends PortalBodyPanel { - private ParetoPlotsWebPart _paretoPlotsWebPart; + private final ParetoPlotsWebPart _paretoPlotsWebPart; public ParetoPlotPage(WebDriver driver) { diff --git a/test/src/org/labkey/test/tests/panoramapremium/TargetedMSHidePeptidesAndMolecules.java b/test/src/org/labkey/test/tests/panoramapremium/TargetedMSHidePeptidesAndMolecules.java index ef5a02c73..fe09a9c61 100644 --- a/test/src/org/labkey/test/tests/panoramapremium/TargetedMSHidePeptidesAndMolecules.java +++ b/test/src/org/labkey/test/tests/panoramapremium/TargetedMSHidePeptidesAndMolecules.java @@ -30,7 +30,7 @@ public class TargetedMSHidePeptidesAndMolecules extends TargetedMSTest @BeforeClass public static void initProject() { - TargetedMSHidePeptidesAndMolecules init = (TargetedMSHidePeptidesAndMolecules) getCurrentTest(); + TargetedMSHidePeptidesAndMolecules init = getCurrentTest(); init.doInit(); } diff --git a/test/src/org/labkey/test/tests/panoramapremium/TargetedMSQCFolderImportExport.java b/test/src/org/labkey/test/tests/panoramapremium/TargetedMSQCFolderImportExport.java index 34a93d1e7..c9d1598aa 100644 --- a/test/src/org/labkey/test/tests/panoramapremium/TargetedMSQCFolderImportExport.java +++ b/test/src/org/labkey/test/tests/panoramapremium/TargetedMSQCFolderImportExport.java @@ -14,7 +14,6 @@ import org.labkey.test.util.DataRegionTable; import java.io.File; -import java.util.Arrays; import java.util.LinkedHashMap; import java.util.Map; @@ -27,7 +26,7 @@ public class TargetedMSQCFolderImportExport extends TargetedMSPremiumTest @BeforeClass public static void initProject() { - TargetedMSQCFolderImportExport init = (TargetedMSQCFolderImportExport) getCurrentTest(); + TargetedMSQCFolderImportExport init = getCurrentTest(); init.doInit(); } diff --git a/test/src/org/labkey/test/tests/panoramapremium/TargetedMSQCPremiumTest.java b/test/src/org/labkey/test/tests/panoramapremium/TargetedMSQCPremiumTest.java index 714c0ed1c..83cbca777 100644 --- a/test/src/org/labkey/test/tests/panoramapremium/TargetedMSQCPremiumTest.java +++ b/test/src/org/labkey/test/tests/panoramapremium/TargetedMSQCPremiumTest.java @@ -53,7 +53,7 @@ protected String getProjectName() @BeforeClass public static void initProject() { - TargetedMSQCPremiumTest init = (TargetedMSQCPremiumTest)getCurrentTest(); + TargetedMSQCPremiumTest init = getCurrentTest(); init.doInit(); } diff --git a/test/src/org/labkey/test/tests/panoramapremium/TargetedMSiRTMetricsTest.java b/test/src/org/labkey/test/tests/panoramapremium/TargetedMSiRTMetricsTest.java index 43101d6ec..a3f228e42 100644 --- a/test/src/org/labkey/test/tests/panoramapremium/TargetedMSiRTMetricsTest.java +++ b/test/src/org/labkey/test/tests/panoramapremium/TargetedMSiRTMetricsTest.java @@ -29,7 +29,7 @@ public class TargetedMSiRTMetricsTest extends TargetedMSPremiumTest @BeforeClass public static void initProject() { - TargetedMSiRTMetricsTest init = (TargetedMSiRTMetricsTest) getCurrentTest(); + TargetedMSiRTMetricsTest init = getCurrentTest(); init.doInit(); } diff --git a/test/src/org/labkey/test/tests/targetedms/ClustergrammerTest.java b/test/src/org/labkey/test/tests/targetedms/ClustergrammerTest.java index a45549393..6257464d4 100644 --- a/test/src/org/labkey/test/tests/targetedms/ClustergrammerTest.java +++ b/test/src/org/labkey/test/tests/targetedms/ClustergrammerTest.java @@ -42,7 +42,7 @@ protected String getProjectName() @BeforeClass public static void initProject() { - ClustergrammerTest init = (ClustergrammerTest)getCurrentTest(); + ClustergrammerTest init = getCurrentTest(); init.setupFolder(FolderType.QC); init.importData(SProCoP_FILE); } diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSAuditLogTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSAuditLogTest.java index 5bcb020d4..871d2d0ea 100644 --- a/test/src/org/labkey/test/tests/targetedms/TargetedMSAuditLogTest.java +++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSAuditLogTest.java @@ -19,7 +19,7 @@ public class TargetedMSAuditLogTest extends TargetedMSTest @BeforeClass public static void initProject() { - TargetedMSAuditLogTest init = (TargetedMSAuditLogTest) getCurrentTest(); + TargetedMSAuditLogTest init = getCurrentTest(); init.doInit(); } diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSChromatogramOptimizationTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSChromatogramOptimizationTest.java index adbb2e20c..2cbc35bbe 100644 --- a/test/src/org/labkey/test/tests/targetedms/TargetedMSChromatogramOptimizationTest.java +++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSChromatogramOptimizationTest.java @@ -30,7 +30,7 @@ public class TargetedMSChromatogramOptimizationTest extends TargetedMSTest @BeforeClass public static void setupProject() { - TargetedMSChromatogramOptimizationTest init = (TargetedMSChromatogramOptimizationTest) getCurrentTest(); + TargetedMSChromatogramOptimizationTest init = getCurrentTest(); init.setupFolder(FolderType.Library); } @@ -49,9 +49,9 @@ public void testUpload() throws Exception File downloadedClibFile = doAndWaitForDownload(() -> clickButton("Download", 0)); log("Verifying table exists"); - List tablesToVerify = new LinkedList(Arrays.asList("TransitionOptimization", "Transition", "Peptide", "Protein", "Precursor", "PrecursorRetentionTime")); + List tablesToVerify = new LinkedList<>(Arrays.asList("TransitionOptimization", "Transition", "Peptide", "Protein", "Precursor", "PrecursorRetentionTime")); List tablesNotPresent = tableExists(tablesToVerify, downloadedClibFile); - if (tablesNotPresent.size() != 0) + if (!tablesNotPresent.isEmpty()) checker().verifyTrue("Some of the tables do not exists in SQLITE file" + Arrays.toString(tablesNotPresent.toArray()), false); log("Verifying the SampleFile modifications"); diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSDocumentFormatsTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSDocumentFormatsTest.java index b32db92ae..bba9d6919 100644 --- a/test/src/org/labkey/test/tests/targetedms/TargetedMSDocumentFormatsTest.java +++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSDocumentFormatsTest.java @@ -41,7 +41,7 @@ public class TargetedMSDocumentFormatsTest extends TargetedMSTest @BeforeClass public static void setupProject() { - TargetedMSDocumentFormatsTest init = (TargetedMSDocumentFormatsTest) getCurrentTest(); + TargetedMSDocumentFormatsTest init = getCurrentTest(); init.setupFolder(FolderType.Experiment); } diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSEarlyStagePTMReportTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSEarlyStagePTMReportTest.java index 40e0d7c00..6cfe4d5b1 100644 --- a/test/src/org/labkey/test/tests/targetedms/TargetedMSEarlyStagePTMReportTest.java +++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSEarlyStagePTMReportTest.java @@ -17,7 +17,7 @@ public class TargetedMSEarlyStagePTMReportTest extends TargetedMSTest @BeforeClass public static void initProject() { - TargetedMSEarlyStagePTMReportTest init = (TargetedMSEarlyStagePTMReportTest) getCurrentTest(); + TargetedMSEarlyStagePTMReportTest init = getCurrentTest(); init.doInit(); } diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSExperimentIrtTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSExperimentIrtTest.java index 46b80ebbf..7a4c0c798 100644 --- a/test/src/org/labkey/test/tests/targetedms/TargetedMSExperimentIrtTest.java +++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSExperimentIrtTest.java @@ -38,7 +38,7 @@ public void testSteps() // For experiment folders, importing another iRT scale should create another scale and set of iRT Peptide rows. Unlike with library folders, // it doesn't matter if the new scale has a different set of standards. importData(SKY_FILE_BAD_STANDARDS, 2); - assertEquals("Incorrect total iRT peptide count.", getRowCount(), PEPTIDE_COUNT * 2 ); - assertEquals("Incorrect number of rows for iRT peptide " + UPDATE_PEPTIDE, getRowsForPeptide(UPDATE_PEPTIDE).size(), 2); + assertEquals("Incorrect total iRT peptide count.", PEPTIDE_COUNT * 2, getRowCount()); + assertEquals("Incorrect number of rows for iRT peptide " + UPDATE_PEPTIDE, 2, getRowsForPeptide(UPDATE_PEPTIDE).size()); } } diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSInstrumentNicknameTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSInstrumentNicknameTest.java index 7ee0f68e4..8a8a2b87f 100644 --- a/test/src/org/labkey/test/tests/targetedms/TargetedMSInstrumentNicknameTest.java +++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSInstrumentNicknameTest.java @@ -15,7 +15,6 @@ */ package org.labkey.test.tests.targetedms; -import org.junit.Before; import org.junit.BeforeClass; import org.junit.Test; import org.junit.experimental.categories.Category; diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSIrtTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSIrtTest.java index 4b6fcaa0a..c9defafbc 100644 --- a/test/src/org/labkey/test/tests/targetedms/TargetedMSIrtTest.java +++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSIrtTest.java @@ -18,7 +18,6 @@ import org.labkey.remoteapi.query.Filter; import org.labkey.test.Locator; import org.labkey.test.util.PipelineStatusTable; -import org.labkey.test.util.UIContainerHelper; import java.io.File; import java.util.Collections; diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSLinkVersionsTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSLinkVersionsTest.java index e23807c70..3a0dc6df6 100644 --- a/test/src/org/labkey/test/tests/targetedms/TargetedMSLinkVersionsTest.java +++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSLinkVersionsTest.java @@ -45,7 +45,7 @@ protected String getProjectName() @BeforeClass public static void initProject() { - TargetedMSLinkVersionsTest init = (TargetedMSLinkVersionsTest)getCurrentTest(); + TargetedMSLinkVersionsTest init = getCurrentTest(); init.setupFolder(FolderType.Experiment); // pre-upload the files to the pipeline root so that all of the @Test don't have to worry about it diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSMovingSKYDocAcrossFoldersTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSMovingSKYDocAcrossFoldersTest.java index e6e20eb9f..d2b6abfdd 100644 --- a/test/src/org/labkey/test/tests/targetedms/TargetedMSMovingSKYDocAcrossFoldersTest.java +++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSMovingSKYDocAcrossFoldersTest.java @@ -22,7 +22,7 @@ public class TargetedMSMovingSKYDocAcrossFoldersTest extends TargetedMSTest @BeforeClass public static void initProject() { - TargetedMSMovingSKYDocAcrossFoldersTest init = (TargetedMSMovingSKYDocAcrossFoldersTest) getCurrentTest(); + TargetedMSMovingSKYDocAcrossFoldersTest init = getCurrentTest(); init.doInit(); } diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSMultiplePeptidePlotTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSMultiplePeptidePlotTest.java index 1c674aa66..7d485b215 100644 --- a/test/src/org/labkey/test/tests/targetedms/TargetedMSMultiplePeptidePlotTest.java +++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSMultiplePeptidePlotTest.java @@ -21,7 +21,7 @@ public class TargetedMSMultiplePeptidePlotTest extends TargetedMSTest @BeforeClass public static void setupProject() { - TargetedMSMultiplePeptidePlotTest init = (TargetedMSMultiplePeptidePlotTest) getCurrentTest(); + TargetedMSMultiplePeptidePlotTest init = getCurrentTest(); init.setupFolder(FolderType.Library); } diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSMxNReproducibilityReportTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSMxNReproducibilityReportTest.java index 9bd4ae195..126cf0c67 100644 --- a/test/src/org/labkey/test/tests/targetedms/TargetedMSMxNReproducibilityReportTest.java +++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSMxNReproducibilityReportTest.java @@ -35,7 +35,7 @@ public class TargetedMSMxNReproducibilityReportTest extends TargetedMSTest @BeforeClass public static void setupProject() { - TargetedMSMxNReproducibilityReportTest init = (TargetedMSMxNReproducibilityReportTest) getCurrentTest(); + TargetedMSMxNReproducibilityReportTest init = getCurrentTest(); init.setupFolder(FolderType.Library); } diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSPeptideSummaryHeatmapTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSPeptideSummaryHeatmapTest.java index 0213c5028..8c89ebdd3 100644 --- a/test/src/org/labkey/test/tests/targetedms/TargetedMSPeptideSummaryHeatmapTest.java +++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSPeptideSummaryHeatmapTest.java @@ -23,7 +23,7 @@ public class TargetedMSPeptideSummaryHeatmapTest extends TargetedMSTest @BeforeClass public static void setupProject() { - TargetedMSPeptideSummaryHeatmapTest init = (TargetedMSPeptideSummaryHeatmapTest) getCurrentTest(); + TargetedMSPeptideSummaryHeatmapTest init = getCurrentTest(); init.doSetup(); } diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSPrecursorLevelDataTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSPrecursorLevelDataTest.java index 8c0233e87..eb9e83520 100644 --- a/test/src/org/labkey/test/tests/targetedms/TargetedMSPrecursorLevelDataTest.java +++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSPrecursorLevelDataTest.java @@ -17,10 +17,6 @@ import org.junit.After; import org.junit.Test; import org.junit.experimental.categories.Category; -import org.labkey.test.Locator; -import org.labkey.test.ModulePropertyValue; - -import java.util.Arrays; @Category({}) public class TargetedMSPrecursorLevelDataTest extends AbstractQuantificationTest diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSProteinGroupingTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSProteinGroupingTest.java index 989f1dfab..b8ad5dff4 100644 --- a/test/src/org/labkey/test/tests/targetedms/TargetedMSProteinGroupingTest.java +++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSProteinGroupingTest.java @@ -17,7 +17,7 @@ public class TargetedMSProteinGroupingTest extends TargetedMSTest @BeforeClass public static void initProject() { - TargetedMSProteinGroupingTest init = (TargetedMSProteinGroupingTest) getCurrentTest(); + TargetedMSProteinGroupingTest init = getCurrentTest(); init.doInit(); } diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSProteinSequenceViewTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSProteinSequenceViewTest.java index 4a37f860c..3f83fda4b 100644 --- a/test/src/org/labkey/test/tests/targetedms/TargetedMSProteinSequenceViewTest.java +++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSProteinSequenceViewTest.java @@ -23,7 +23,7 @@ public class TargetedMSProteinSequenceViewTest extends TargetedMSTest @BeforeClass public static void initProject() { - TargetedMSProteinSequenceViewTest init = (TargetedMSProteinSequenceViewTest) getCurrentTest(); + TargetedMSProteinSequenceViewTest init = getCurrentTest(); init.doInit(); } diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSQCConfigureMetricTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSQCConfigureMetricTest.java index d400d0be9..7761f5b87 100644 --- a/test/src/org/labkey/test/tests/targetedms/TargetedMSQCConfigureMetricTest.java +++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSQCConfigureMetricTest.java @@ -27,7 +27,7 @@ public class TargetedMSQCConfigureMetricTest extends TargetedMSPremiumTest @BeforeClass public static void setupProject() { - TargetedMSQCConfigureMetricTest init = (TargetedMSQCConfigureMetricTest) getCurrentTest(); + TargetedMSQCConfigureMetricTest init = getCurrentTest(); init.doSetup(); } diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSQCGuideSetTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSQCGuideSetTest.java index d93d0c603..d3f1fe126 100644 --- a/test/src/org/labkey/test/tests/targetedms/TargetedMSQCGuideSetTest.java +++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSQCGuideSetTest.java @@ -50,7 +50,6 @@ import java.util.List; import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertTrue; @Category({}) @BaseWebDriverTest.ClassTimeout(minutes = 25) @@ -83,7 +82,7 @@ protected String getProjectName() @BeforeClass public static void initProject() { - TargetedMSQCGuideSetTest init = (TargetedMSQCGuideSetTest)getCurrentTest(); + TargetedMSQCGuideSetTest init = getCurrentTest(); init.setupFolder(FolderType.QC); init.importData(SProCoP_FILE); diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSQCTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSQCTest.java index 778b1b83a..66f95d982 100644 --- a/test/src/org/labkey/test/tests/targetedms/TargetedMSQCTest.java +++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSQCTest.java @@ -89,13 +89,13 @@ public class TargetedMSQCTest extends TargetedMSTest private static final String QCREPLICATE_3 = "25fmol_Pepmix_spike_SRM_1601_03"; private static final String QCREPLICATE_4 = "25fmol_Pepmix_spike_SRM_1601_04"; - private static QCHelper.Annotation instrumentChange = new QCHelper.Annotation("Instrumentation Change", "We changed it", "2013-08-22 14:43:00"); - private static QCHelper.Annotation reagentChange = new QCHelper.Annotation("Reagent Change", "New reagents", "2013-08-10 15:34:00"); - private static QCHelper.Annotation technicianChange = new QCHelper.Annotation("Technician Change", "New guy on the scene", "2013-08-10 08:43:00"); - private static QCHelper.Annotation candyChange = new QCHelper.Annotation("Candy Change", "New candies!", "2013-08-21 6:57:00"); + private static final QCHelper.Annotation instrumentChange = new QCHelper.Annotation("Instrumentation Change", "We changed it", "2013-08-22 14:43:00"); + private static final QCHelper.Annotation reagentChange = new QCHelper.Annotation("Reagent Change", "New reagents", "2013-08-10 15:34:00"); + private static final QCHelper.Annotation technicianChange = new QCHelper.Annotation("Technician Change", "New guy on the scene", "2013-08-10 08:43:00"); + private static final QCHelper.Annotation candyChange = new QCHelper.Annotation("Candy Change", "New candies!", "2013-08-21 6:57:00"); - private static String longPeptideJSTest = + private static final String longPeptideJSTest = "var testVals = {\n" + " a: {fragment:'', dataType: 'Peptide', result: ''},\n" + " b: {fragment:'A', dataType: 'Peptide', result: 'A'},\n" + @@ -163,7 +163,7 @@ public class TargetedMSQCTest extends TargetedMSTest @BeforeClass public static void initProject() { - TargetedMSQCTest init = (TargetedMSQCTest) getCurrentTest(); + TargetedMSQCTest init = getCurrentTest(); init.doInit(); } diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSSampleFileChromInfoTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSSampleFileChromInfoTest.java index 9d045aacf..0fd519ca6 100644 --- a/test/src/org/labkey/test/tests/targetedms/TargetedMSSampleFileChromInfoTest.java +++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSSampleFileChromInfoTest.java @@ -34,7 +34,7 @@ public class TargetedMSSampleFileChromInfoTest extends TargetedMSTest @BeforeClass public static void setupProject() { - TargetedMSTest init = (TargetedMSTest) getCurrentTest(); + TargetedMSTest init = getCurrentTest(); init.setupFolder(FolderType.Experiment); } diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSSkydTextIdTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSSkydTextIdTest.java index dd2466a70..96db4eaed 100644 --- a/test/src/org/labkey/test/tests/targetedms/TargetedMSSkydTextIdTest.java +++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSSkydTextIdTest.java @@ -34,7 +34,7 @@ public class TargetedMSSkydTextIdTest extends TargetedMSTest @BeforeClass public static void setupProject() { - TargetedMSTest init = (TargetedMSTest) getCurrentTest(); + TargetedMSTest init = getCurrentTest(); init.setupFolder(FolderType.Experiment); } diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSTest.java index 131de3076..4253bfcfb 100644 --- a/test/src/org/labkey/test/tests/targetedms/TargetedMSTest.java +++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSTest.java @@ -69,7 +69,7 @@ protected enum SvgShapes CIRCLE_OPEN("M0-2"), TRIANGLE("M0,2L2"); - private String _pathPrefix; + private final String _pathPrefix; SvgShapes(String pathPrefix) { _pathPrefix = pathPrefix; @@ -147,7 +147,7 @@ protected String getProjectName() @BeforeClass public static void initPipeline() { - TargetedMSTest init = (TargetedMSTest)getCurrentTest(); + TargetedMSTest init = getCurrentTest(); init.doInitPipeline(); } @@ -404,8 +404,6 @@ public PanoramaDashboard goToDashboard() /** * Sets the values of the site-level module properties: "TransitionChromInfo storage limit" and "Precursor storage limit". * The values should be set back to defaults after the test completes. - * @param transitionStorageLimit - * @param precursorStorageLimit */ protected void setStorageLimitModuleProperties(String transitionStorageLimit, String precursorStorageLimit) { goToProjectHome(); diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSTrailingMeanAndCVTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSTrailingMeanAndCVTest.java index b727da238..f7085de6d 100644 --- a/test/src/org/labkey/test/tests/targetedms/TargetedMSTrailingMeanAndCVTest.java +++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSTrailingMeanAndCVTest.java @@ -23,7 +23,7 @@ public class TargetedMSTrailingMeanAndCVTest extends TargetedMSTest @BeforeClass public static void initProject() { - TargetedMSTrailingMeanAndCVTest init = (TargetedMSTrailingMeanAndCVTest) getCurrentTest(); + TargetedMSTrailingMeanAndCVTest init = getCurrentTest(); init.doInit(); } diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSTransitionChromInfoLimitTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSTransitionChromInfoLimitTest.java index f01bf7e36..1d1717f6a 100644 --- a/test/src/org/labkey/test/tests/targetedms/TargetedMSTransitionChromInfoLimitTest.java +++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSTransitionChromInfoLimitTest.java @@ -22,7 +22,7 @@ public class TargetedMSTransitionChromInfoLimitTest extends TargetedMSTest @BeforeClass public static void setupProject() { - TargetedMSTransitionChromInfoLimitTest init = (TargetedMSTransitionChromInfoLimitTest) getCurrentTest(); + TargetedMSTransitionChromInfoLimitTest init = getCurrentTest(); init.setupFolder(FolderType.Experiment); } diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSUtilizationCalendarTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSUtilizationCalendarTest.java index f38ee435f..668b27b3d 100644 --- a/test/src/org/labkey/test/tests/targetedms/TargetedMSUtilizationCalendarTest.java +++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSUtilizationCalendarTest.java @@ -27,7 +27,7 @@ public class TargetedMSUtilizationCalendarTest extends TargetedMSTest @BeforeClass public static void initProject() { - TargetedMSUtilizationCalendarTest init = (TargetedMSUtilizationCalendarTest) getCurrentTest(); + TargetedMSUtilizationCalendarTest init = getCurrentTest(); init.doInit(); } diff --git a/test/src/org/labkey/test/util/targetedms/QCHelper.java b/test/src/org/labkey/test/util/targetedms/QCHelper.java index 940c425f3..81303d8d1 100644 --- a/test/src/org/labkey/test/util/targetedms/QCHelper.java +++ b/test/src/org/labkey/test/util/targetedms/QCHelper.java @@ -28,8 +28,8 @@ public class QCHelper public static class Annotation { - private String type; - private String description; + private final String type; + private final String description; private String date; public Annotation(String type, String description, String date) @@ -88,9 +88,9 @@ public String toString() public static class AnnotationType { - private String name; + private final String name; private String description; - private String color; + private final String color; public AnnotationType(String name, String description, String color) {