Clean-up code base to improve code quality

cli/src/main/java/de/jplag/cli/CLI.java

@@ -178,9 +178,8 @@ private String getResultFileBaseName() {
     private String getOffsetFileName(int offset) {
         if (offset <= 0) {
             return getResultFilePath();
-        } else {
-            return getResultFileBaseName() + "(" + offset + ")" + DEFAULT_FILE_ENDING;
         }
+        return getResultFileBaseName() + "(" + offset + ")" + DEFAULT_FILE_ENDING;
     }
 
     private String getWritableFileName() throws CliException {

cli/src/main/java/de/jplag/cli/logger/CliProgressBarProvider.java

@@ -19,17 +19,16 @@ public class CliProgressBarProvider implements ProgressBarProvider {
 
     @Override
     public ProgressBar initProgressBar(ProgressBarType type, int totalSteps) {
-        if (allowedLogLevels.contains(CollectedLogger.getLogLevel())) {
-            if (type.isIdleBar()) {
-                IdleBar idleBar = new IdleBar(type.getDefaultText());
-                idleBar.start();
-                return idleBar;
-            }
-            me.tongfei.progressbar.ProgressBar progressBar = new ProgressBarBuilder().setTaskName(type.getDefaultText()).setInitialMax(totalSteps)
-                    .setStyle(ProgressBarStyle.ASCII).build();
-            return new TongfeiProgressBar(progressBar);
-        } else {
+        if (!allowedLogLevels.contains(CollectedLogger.getLogLevel())) {
             return new VoidProgressBar();
         }
+        if (type.isIdleBar()) {
+            IdleBar idleBar = new IdleBar(type.getDefaultText());
+            idleBar.start();
+            return idleBar;
+        }
+        me.tongfei.progressbar.ProgressBar progressBar = new ProgressBarBuilder().setTaskName(type.getDefaultText()).setInitialMax(totalSteps)
+                .setStyle(ProgressBarStyle.ASCII).build();
+        return new TongfeiProgressBar(progressBar);
     }
 }

cli/src/main/java/de/jplag/cli/picocli/CliInputHandler.java

@@ -111,7 +111,7 @@ public boolean parse() throws CliException {
         try {
             this.parseResult = this.commandLine.parseArgs(args);
             if (this.parseResult.isUsageHelpRequested()
-                    || (this.parseResult.subcommand() != null && this.parseResult.subcommand().isUsageHelpRequested())) {
+                    || this.parseResult.subcommand() != null && this.parseResult.subcommand().isUsageHelpRequested()) {
                 commandLine.getExecutionStrategy().execute(this.parseResult);
                 return true;
             }

cli/src/main/java/de/jplag/cli/picocli/ParameterLabelRenderer.java

@@ -30,7 +30,7 @@ public CommandLine.Help.Ansi.Text renderParameterLabel(CommandLine.Model.ArgSpec
             List<CommandLine.Help.Ansi.IStyle> styles) {
         if (argSpec.type().isEnum()) {
             Object[] enumConstants = argSpec.type().getEnumConstants();
-            String enumValueNames = Arrays.stream(enumConstants).map(enumConstant -> (Enum.class.cast(enumConstant)).name())
+            String enumValueNames = Arrays.stream(enumConstants).map(enumConstant -> Enum.class.cast(enumConstant).name())
                     .collect(Collectors.joining(VALUE_SEPARATOR));
             return CommandLine.Help.Ansi.AUTO.text(String.format(PARAM_LABEL_PATTERN, enumValueNames));
         }

cli/src/test/java/de/jplag/cli/MinTokenMatchTest.java

@@ -33,7 +33,7 @@ void testInvalidInput() {
 
     @Test
     void testUpperBound() {
-        String higherThanMax = String.valueOf(((long) Integer.MAX_VALUE) + 1);
+        String higherThanMax = String.valueOf((long) Integer.MAX_VALUE + 1);
 
         Assertions.assertThrowsExactly(CliException.class, () -> {
             runCli(options -> options.withInvalid(CliArgument.MIN_TOKEN_MATCH, higherThanMax));

cli/src/test/java/de/jplag/cli/logger/IdleBarTest.java

@@ -64,7 +64,7 @@ private void checkIdleBarOutput(String output, int frameIndex, int numberOfSpace
 
         String[] timeParts = time.split(":");
         int seconds = Integer.parseInt(timeParts[0]) * 60 * 60 + Integer.parseInt(timeParts[1]) * 60 + Integer.parseInt(timeParts[2]);
-        int expectedTime = (int) ((IDLE_BAR_ANIMATION_DELAY * frameIndex) / 1000);
+        int expectedTime = (int) (IDLE_BAR_ANIMATION_DELAY * frameIndex / 1000);
         Assertions.assertTrue(Math.abs(seconds - expectedTime) < 1, "Frame time of by more than one second");
     }
 }

cli/src/test/java/de/jplag/cli/test/CliArgumentBuilder.java

@@ -70,12 +70,11 @@ private String[] formatArgNameAndValue(String name, Object value) {
             } else {
                 return new String[] {SHORT_OPTION_PREFIX + name, valueText};
             }
+        }
+        if (valueText.isEmpty()) {
+            return new String[] {LONG_OPTION_PREFIX + name};
         } else {
-            if (valueText.isEmpty()) {
-                return new String[] {LONG_OPTION_PREFIX + name};
-            } else {
-                return new String[] {LONG_OPTION_PREFIX + name + "=" + formatArgValue(value)};
-            }
+            return new String[] {LONG_OPTION_PREFIX + name + "=" + formatArgValue(value)};
         }
     }
 

cli/src/test/java/de/jplag/cli/test/CliTest.java

@@ -9,12 +9,16 @@
 
 import org.junit.jupiter.api.Assumptions;
 import org.junit.jupiter.api.BeforeEach;
+import org.mockito.ArgumentMatchers;
 import org.mockito.MockedStatic;
 import org.mockito.Mockito;
 import org.slf4j.event.Level;
 
 import de.jplag.JPlagResult;
-import de.jplag.cli.*;
+import de.jplag.cli.CLI;
+import de.jplag.cli.JPlagOptionsBuilder;
+import de.jplag.cli.JPlagRunner;
+import de.jplag.cli.OutputFileGenerator;
 import de.jplag.cli.logger.CollectedLogger;
 import de.jplag.cli.picocli.CliInputHandler;
 import de.jplag.exceptions.ExitException;
@@ -140,8 +144,9 @@ protected Level runCliForLogLevel(Consumer<CliArgumentBuilder> additionalOptions
     protected CliResult runCli(Consumer<CliArgumentBuilder> additionalOptionsBuilder) throws ExitException, IOException {
         try (MockedStatic<JPlagRunner> runnerMock = Mockito.mockStatic(JPlagRunner.class);
                 MockedStatic<OutputFileGenerator> generatorMock = Mockito.mockStatic(OutputFileGenerator.class)) {
-            runnerMock.when(() -> JPlagRunner.runJPlag(Mockito.any())).thenReturn(new JPlagResult(Collections.emptyList(), null, 1, null));
-            generatorMock.when(() -> OutputFileGenerator.generateJPlagResultZip(Mockito.any(), Mockito.any())).then(invocationOnMock -> null);
+            runnerMock.when(() -> JPlagRunner.runJPlag(ArgumentMatchers.any())).thenReturn(new JPlagResult(Collections.emptyList(), null, 1, null));
+            generatorMock.when(() -> OutputFileGenerator.generateJPlagResultZip(ArgumentMatchers.any(), ArgumentMatchers.any()))
+                    .then(invocationOnMock -> null);
 
             CliArgumentBuilder copy = this.defaultArgumentBuilder.copy();
             additionalOptionsBuilder.accept(copy);

core/src/main/java/de/jplag/GreedyStringTiling.java

@@ -212,22 +212,22 @@ private boolean[] calculateInitiallyMarked(Submission submission) {
         List<Token> tokens = submission.getTokenList();
         boolean[] result = new boolean[tokens.size()];
         for (int i = 0; i < result.length; i++) {
-            result[i] = tokens.get(i).getType().isExcludedFromMatching() || (baseCodeTokens != null && baseCodeTokens.contains(tokens.get(i)));
+            result[i] = tokens.get(i).getType().isExcludedFromMatching() || baseCodeTokens != null && baseCodeTokens.contains(tokens.get(i));
         }
         return result;
     }
 
     private SubsequenceHashLookupTable subsequenceHashLookupTableForSubmission(Submission submission, boolean[] marked) {
         return cachedHashLookupTables.computeIfAbsent(submission,
-                (key -> new SubsequenceHashLookupTable(minimumMatchLength, tokenValueListFromSubmission(key), marked)));
+                key -> new SubsequenceHashLookupTable(minimumMatchLength, tokenValueListFromSubmission(key), marked));
     }
 
     /**
      * Converts the tokens of the submission to a list of values.
      * @param submission The submission from which to convert the tokens.
      */
     private int[] tokenValueListFromSubmission(Submission submission) {
-        return cachedTokenValueLists.computeIfAbsent(submission, (key -> {
+        return cachedTokenValueLists.computeIfAbsent(submission, key -> {
             List<Token> tokens = key.getTokenList();
             int[] tokenValueList = new int[tokens.size()];
             for (int i = 0; i < tokens.size(); i++) {
@@ -238,7 +238,7 @@ private int[] tokenValueListFromSubmission(Submission submission) {
                 tokenValueList[i] = tokenTypeValues.get(type);
             }
             return tokenValueList;
-        }));
+        });
     }
 
     private boolean checkMark(boolean[] marks, int index, Submission submission, Submission otherSubmission) {

core/src/main/java/de/jplag/JPlagComparison.java

@@ -76,6 +76,6 @@ public String toString() {
     }
 
     private double similarity(int divisor) {
-        return (divisor == 0 ? 0.0 : (getNumberOfMatchedTokens() / (double) divisor));
+        return divisor == 0 ? 0.0 : getNumberOfMatchedTokens() / (double) divisor;
     }
 }

core/src/main/java/de/jplag/JPlagResult.java

@@ -116,7 +116,7 @@ public int[] getSimilarityDistribution() {
      * the same distribution as {@link JPlagResult#getSimilarityDistribution()}
      */
     public int[] getMaxSimilarityDistribution() {
-        return calculateDistributionFor(comparisons, (JPlagComparison::maximalSimilarity));
+        return calculateDistributionFor(comparisons, JPlagComparison::maximalSimilarity);
     }
 
     public List<ClusteringResult<Submission>> getClusteringResult() {

core/src/main/java/de/jplag/Match.java

@@ -13,17 +13,17 @@ public record Match(int startOfFirst, int startOfSecond, int length) {
      */
     public boolean overlaps(Match other) {
         if (startOfFirst < other.startOfFirst) {
-            if ((other.startOfFirst - startOfFirst) < length) {
+            if (other.startOfFirst - startOfFirst < length) {
                 return true;
             }
-        } else if ((startOfFirst - other.startOfFirst) < other.length) {
+        } else if (startOfFirst - other.startOfFirst < other.length) {
             return true;
         }
 
         if (startOfSecond < other.startOfSecond) {
-            return (other.startOfSecond - startOfSecond) < length;
+            return other.startOfSecond - startOfSecond < length;
         }
-        return (startOfSecond - other.startOfSecond) < other.length;
+        return startOfSecond - other.startOfSecond < other.length;
     }
 
     /**

core/src/main/java/de/jplag/SubmissionSet.java

@@ -172,7 +172,7 @@ private void parseSubmissions(List<Submission> submissions) throws LanguageExcep
 
         int validSubmissions = submissions.size() - errors;
         logger.debug("{} submissions parsed successfully!", validSubmissions);
-        logger.debug("{} parser error{}!", errors, (errors != 1 ? "s" : ""));
+        logger.debug("{} parser error{}!", errors, errors != 1 ? "s" : "");
     }
 
 }

core/src/main/java/de/jplag/SubmissionSetBuilder.java

@@ -70,7 +70,7 @@ public SubmissionSet buildSubmissionSet() throws ExitException {
         // For backward compatibility, don't prefix submission names with their root directory
         // if there is only one root directory.
         int numberOfRootDirectories = submissionDirectories.size() + oldSubmissionDirectories.size();
-        boolean multipleRoots = (numberOfRootDirectories > 1);
+        boolean multipleRoots = numberOfRootDirectories > 1;
 
         List<SubmissionFileData> submissionFiles = new ArrayList<>();
         for (File submissionDirectory : submissionDirectories) {
@@ -225,7 +225,7 @@ private void processSubmissionFile(SubmissionFileData file, boolean multipleRoot
         } else if (file.submissionFile().isFile() && !hasValidSuffix(file.submissionFile())) {
             logger.error("Ignore submission with invalid suffix: {}", file.submissionFile().getName());
         } else {
-            String rootDirectoryPrefix = multipleRoots ? (file.root().getName() + File.separator) : "";
+            String rootDirectoryPrefix = multipleRoots ? file.root().getName() + File.separator : "";
             String submissionName = rootDirectoryPrefix + file.submissionFile().getName();
             Submission submission = processSubmission(submissionName, file.submissionFile(), file.isNew());
             foundSubmissions.put(submission.getRoot(), submission);

core/src/main/java/de/jplag/SubsequenceHashLookupTable.java

@@ -74,7 +74,7 @@ List<Integer> startIndexesOfPossiblyMatchingSubsequencesForSubsequenceHash(int s
     private void computeSubsequenceHashes(boolean[] marked) {
         int hash = 0;
         int hashedLength = 0;
-        int factor = (windowSize != 1 ? (2 << (windowSize - 2)) : 1);
+        int factor = windowSize != 1 ? 2 << windowSize - 2 : 1;
 
         for (int windowEndIndex = 0; windowEndIndex < values.length; windowEndIndex++) {
             int windowStartIndex = windowEndIndex - windowSize;
@@ -87,7 +87,7 @@ private void computeSubsequenceHashes(boolean[] marked) {
                 }
                 hash -= factor * hashValueForValue(values[windowStartIndex]);
             }
-            hash = (2 * hash) + hashValueForValue(values[windowEndIndex]);
+            hash = 2 * hash + hashValueForValue(values[windowEndIndex]);
             if (marked[windowEndIndex]) {
                 hashedLength = 0;
             } else {

core/src/main/java/de/jplag/clustering/Cluster.java

@@ -119,7 +119,7 @@ private double averageSimilarity(BiFunction<T, T, Double> similarity) {
 
     private int connections() {
         int size = members.size();
-        return ((size - 1) * size) / 2;
+        return (size - 1) * size / 2;
     }
 
     /**

core/src/main/java/de/jplag/clustering/ClusteringResult.java

@@ -113,7 +113,7 @@ private static double calculateAverageSimilarityFor(Collection<Integer> cluster,
             }
         }
         int nMinusOne = cluster.size() - 1;
-        double numberOfComparisons = (nMinusOne * (nMinusOne + 1)) / 2.0;
+        double numberOfComparisons = nMinusOne * (nMinusOne + 1) / 2.0;
         /*
          * Use Gauss sum to calculate number of comparisons in cluster: Given cluster of size n we need Gauss sum of n-1
          * comparisons: compare first element of cluster to all other except itself: n-1 comparisons. compare second element to

core/src/main/java/de/jplag/clustering/preprocessors/CumulativeDistributionFunctionPreprocessor.java

@@ -20,7 +20,7 @@ public class CumulativeDistributionFunctionPreprocessor implements ClusteringPre
     @Override
     public double[][] preprocessSimilarities(double[][] similarityMatrix) {
         RealMatrix similarity = new Array2DRowRealMatrix(similarityMatrix, true);
-        int connections = (similarity.getColumnDimension() * (similarity.getColumnDimension() - 1)) / 2;
+        int connections = similarity.getColumnDimension() * (similarity.getColumnDimension() - 1) / 2;
         EmpiricalDistribution dist = new EmpiricalDistribution(Math.max(100, connections / 100));
         double[] allWeights = new double[connections];
         similarity.walkInOptimizedOrder(new DefaultRealMatrixPreservingVisitor() {

core/src/main/java/de/jplag/clustering/preprocessors/PercentileThresholdProcessor.java

@@ -23,7 +23,7 @@ public PercentileThresholdProcessor(double percentile) {
     public double[][] preprocessSimilarities(double[][] similarityMatrix) {
         Array2DRowRealMatrix similarity = new Array2DRowRealMatrix(similarityMatrix, false);
         Percentile percentileEstimator = new Percentile().withEstimationType(EstimationType.R_2);
-        int connections = (similarity.getColumnDimension() * (similarity.getColumnDimension() - 1)) / 2;
+        int connections = similarity.getColumnDimension() * (similarity.getColumnDimension() - 1) / 2;
         double[] allWeights = new double[connections];
         similarity.walkInOptimizedOrder(new DefaultRealMatrixPreservingVisitor() {
 

core/src/main/java/de/jplag/merging/MatchMerging.java

@@ -81,7 +81,7 @@ private List<Neighbor> computeNeighbors(List<Match> globalMatches) {
         sortedByRight.sort(Comparator.comparingInt(Match::startOfSecond));
 
         for (int i = 0; i < sortedByLeft.size() - 1; i++) {
-            if (sortedByRight.indexOf(sortedByLeft.get(i)) == (sortedByRight.indexOf(sortedByLeft.get(i + 1)) - 1)) {
+            if (sortedByRight.indexOf(sortedByLeft.get(i)) == sortedByRight.indexOf(sortedByLeft.get(i + 1)) - 1) {
                 neighbors.add(new Neighbor(sortedByLeft.get(i), sortedByLeft.get(i + 1)));
             }
         }
@@ -159,7 +159,7 @@ private boolean mergeOverlapsFiles(Submission leftSubmission, Submission rightSu
      * @return true if FILE_END is in token
      */
     private boolean containsFileEndToken(List<Token> token) {
-        return token.stream().map(Token::getType).anyMatch(it -> it.equals(SharedTokenType.FILE_END));
+        return token.stream().map(Token::getType).anyMatch(SharedTokenType.FILE_END::equals);
     }
 
     /**

core/src/main/java/de/jplag/options/JPlagOptions.java

@@ -158,7 +158,7 @@ private Integer normalizeMaximumNumberOfComparisons(Integer maximumNumberOfCompa
     }
 
     private Integer normalizeMinimumTokenMatch(Integer minimumTokenMatch) {
-        return (minimumTokenMatch != null && minimumTokenMatch < 1) ? Integer.valueOf(1) : minimumTokenMatch;
+        return minimumTokenMatch != null && minimumTokenMatch < 1 ? Integer.valueOf(1) : minimumTokenMatch;
     }
 
     /**

core/src/main/java/de/jplag/reporting/reportobject/ReportObjectFactory.java

@@ -144,7 +144,7 @@ private void writeOverview(JPlagResult result) {
         int totalComparisons = result.getAllComparisons().size();
         int numberOfMaximumComparisons = result.getOptions().maximumNumberOfComparisons();
         int shownComparisons = Math.min(totalComparisons, numberOfMaximumComparisons);
-        int missingComparisons = totalComparisons > numberOfMaximumComparisons ? (totalComparisons - numberOfMaximumComparisons) : 0;
+        int missingComparisons = totalComparisons > numberOfMaximumComparisons ? totalComparisons - numberOfMaximumComparisons : 0;
         logger.info("Total Comparisons: {}. Comparisons in Report: {}. Omitted Comparisons: {}.", totalComparisons, shownComparisons,
                 missingComparisons);
         OverviewReport overviewReport = new OverviewReport(REPORT_VIEWER_VERSION, folders.stream().map(File::getPath).toList(), // submissionFolderPath

core/src/main/java/de/jplag/strategy/AbstractComparisonStrategy.java

@@ -65,9 +65,9 @@ protected Optional<JPlagComparison> compareSubmissions(Submission first, Submiss
     private List<SubmissionTuple> buildComparisonTuples(List<Submission> submissions) {
         List<SubmissionTuple> tuples = new ArrayList<>();
 
-        for (int i = 0; i < (submissions.size() - 1); i++) {
+        for (int i = 0; i < submissions.size() - 1; i++) {
             Submission first = submissions.get(i);
-            for (int j = (i + 1); j < submissions.size(); j++) {
+            for (int j = i + 1; j < submissions.size(); j++) {
                 Submission second = submissions.get(j);
                 if (first.isNew() || second.isNew()) {
                     tuples.add(new SubmissionTuple(first, second));

core/src/test/java/de/jplag/BasicFunctionalityTest.java

@@ -68,7 +68,7 @@ void testPartialPlagiarism() throws ExitException {
 
         // All comparisons with E shall have no matches
         result.getAllComparisons().stream()
-                .filter(comparison -> comparison.secondSubmission().getName().equals("E") || comparison.firstSubmission().getName().equals("E"))
+                .filter(comparison -> "E".equals(comparison.secondSubmission().getName()) || "E".equals(comparison.firstSubmission().getName()))
                 .forEach(comparison -> assertEquals(0, comparison.similarity(), DELTA));
 
         // Hard coded assertions on selected comparisons

core/src/test/java/de/jplag/InvalidSubmissionTest.java

@@ -34,8 +34,9 @@ void testInvalidSubmissionsWithDebug() throws ExitException {
             File errorFolder = new File(Path.of("errors", "java").toString());
             assertTrue(errorFolder.exists());
             String[] errorSubmissions = errorFolder.list();
-            if (errorSubmissions != null)
+            if (errorSubmissions != null) {
                 Arrays.sort(errorSubmissions); // File systems don't promise alphabetical order.
+            }
             deleteDirectory(errorFolder.getParentFile());
             assertArrayEquals(new String[] {"A", "B"}, errorSubmissions);
         }