Minor auto-refactor code cleanup on a massive scale

api-src/org/labkey/api/targetedms/SkylineAnnotation.java

@@ -15,17 +15,13 @@
  */
 package org.labkey.api.targetedms;
 
-import org.labkey.api.data.Container;
-
-import java.util.Date;
-
 /**
  * User: vsharma
  * Date: 8/26/2015
  * Time: 2:13 PM
  */
 public interface SkylineAnnotation
 {
-    public String getName();
-    public String getValue();
+    String getName();
+    String getValue();
 }

api-src/org/labkey/api/targetedms/TargetedMSService.java

@@ -143,26 +143,19 @@ 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);
 
     /**
      * 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.
      */

src/org/labkey/panoramapremium/PanoramaPremiumController.java

@@ -118,7 +118,7 @@ else if(isMolecule)
 
         //skip selected precursors that are already excluded
         selectedRowsKeys.forEach(id -> {
-            List<ExcludedPrecursor> prec = precursorsList.stream().filter(p -> p.getId() == id).collect(Collectors.toList());
+            List<ExcludedPrecursor> prec = precursorsList.stream().filter(p -> p.getId() == id).toList();
             ExcludedPrecursor precursor = prec.get(0);
             precursor.setIsPeptide(isPeptide);
 

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)
     {

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)
     {

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)

src/org/labkey/targetedms/SkylinePort/Irt/IRetentionScoreCalculator.java

@@ -28,7 +28,7 @@
 
 public interface IRetentionScoreCalculator
 {
-    public String getName();
+    String getName();
 
 	Double ScoreSequence(String modifiedSequence);
 

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<MeasuredRetentionTime> peptidesTimes = retentionTimes.getPeptideRetentionTimes();
             //var peptidesTimes = retentionTimes.getPeptideRetentionTimes().toArray();
-            RetentionTimeRegression regression = RetentionTimeRegression.FindThreshold(MIN_IRT_TO_TIME_CORRELATION, RetentionTimeRegression.getThresholdPrecision(), peptidesTimes, new ArrayList<MeasuredRetentionTime>(), 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<Double> listValues, int i, RefObjec
 
     private final static class CurrentCalculator extends RetentionScoreCalculatorSpec
     {
-        private LinkedHashMap<String, Double> _dictStandards = new LinkedHashMap<>();
-        private LinkedHashMap<String, Double> _dictLibrary = new LinkedHashMap<>();
+        private final LinkedHashMap<String, Double> _dictStandards = new LinkedHashMap<>();
+        private final LinkedHashMap<String, Double> _dictLibrary = new LinkedHashMap<>();
 
-        private double _unknownScore;
+        private final double _unknownScore;
 
         public CurrentCalculator(Iterable<IrtPeptide> standardPeptides, Iterable<IrtPeptide> libraryPeptides)
         {

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();

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()
     {

src/org/labkey/targetedms/SkylinePort/Irt/RetentionTimeRegression.java

@@ -306,10 +306,10 @@ private static Double GetRetentionTime(double score, IRegressionFunction convers
     */
     public RetentionTimeStatistics CalcStatistics(ArrayList<MeasuredRetentionTime> peptidesTimes, java.util.Map<String, Double> scoreCache)
     {
-        java.util.ArrayList<String> listPeptides = new java.util.ArrayList<String>();
-        java.util.ArrayList<Double> listHydroScores = new java.util.ArrayList<Double>();
-        java.util.ArrayList<Double> listPredictions = new java.util.ArrayList<Double>();
-        java.util.ArrayList<Double> listRetentionTimes = new java.util.ArrayList<Double>();
+        java.util.ArrayList<String> listPeptides = new java.util.ArrayList<>();
+        java.util.ArrayList<Double> listHydroScores = new java.util.ArrayList<>();
+        java.util.ArrayList<Double> listPredictions = new java.util.ArrayList<>();
+        java.util.ArrayList<Double> listRetentionTimes = new java.util.ArrayList<>();
 
         boolean usableCalc = getCalculator().IsUsable();
 
@@ -500,7 +500,7 @@ public static RetentionTimeRegression CalcRegression(String name, ArrayList<Rete
         RetentionScoreCalculatorSpec s = null;
         RefObject<RetentionScoreCalculatorSpec> 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<RetentionScoreCalculatorSpec> calculators, ArrayList<MeasuredRetentionTime> measuredPeptides, RetentionTimeScoreCache scoreCache, boolean allPeptides, RefObject<RetentionTimeStatistics> statistics, RefObject<RetentionScoreCalculatorSpec> 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<Rete
         // An arraylist, indexed by calculator, of actual retention times for the peptides in peptideScoresByCalc
         List<ArrayList<Double>> listRTs = new ArrayList<>(calcs);
 
-        LinkedHashMap<String, Double> dictMeasuredPeptides = new LinkedHashMap<String, Double>();
+        LinkedHashMap<String, Double> dictMeasuredPeptides = new LinkedHashMap<>();
 
         for (MeasuredRetentionTime measured : measuredPeptides)
         {
@@ -575,7 +574,7 @@ public static RetentionTimeRegression CalcRegression(String name, ArrayList<Rete
 
             try
             {
-                listRTs.set(i, new ArrayList<Double>());
+                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<RetentionTimeStatistics> tempRef_statisticsRefined = new RefObject<>(statisticsRefined);
         RefObject<LinkedHashSet<Integer>> 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<Integer>());
+        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<RetentionScoreCalculatorSpec> tempRef_s = new RefObject<RetentionScoreCalculatorSpec>(s);
+        RefObject<RetentionScoreCalculatorSpec> 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;
     }
 

src/org/labkey/targetedms/SkylinePort/Irt/RetentionTimeScoreCache.java

@@ -63,7 +63,7 @@ public void RecalculateCalcCache(RetentionScoreCalculatorSpec calculator)
         Map<String, Double> calcCache = _cache.get(calculator.getName());
         if(calcCache != null)
         {
-            LinkedHashMap<String, Double> newCalcCache = new LinkedHashMap<String, Double>();
+            LinkedHashMap<String, Double> 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<String, Double> cacheCalc = null;
+        LinkedHashMap<String, Double> cacheCalc;
         cacheCalc = _cache.get(calculator.getName());
         return CalcScore(calculator, peptide, cacheCalc);
     }

src/org/labkey/targetedms/SkylinePort/Irt/RetentionTimeStatistics.java

@@ -87,7 +87,7 @@ private void setListRetentionTimes(java.util.ArrayList<Double> value)
 
 	public java.util.Map<String, Double> getScoreCache()
 	{
-		LinkedHashMap<String, Double> scoreCache = new LinkedHashMap<String, Double>();
+		LinkedHashMap<String, Double> scoreCache = new LinkedHashMap<>();
 		for (int i = 0; i < getPeptides().size(); i++)
 		{
 			String sequence = getPeptides().get(i);

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<Double> residuals = new java.util.ArrayList<Double>();
+		java.util.ArrayList<Double> residuals = new java.util.ArrayList<>();
 		for (int i = 0; i < x.getLength(); i++)
 		{
 			residuals.add(y._list[i] - (a*x._list[i] + 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<String, Map<String, Double>> 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;

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);

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;
 

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;

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;
     }

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);