Fix some IntelliJ findings (#6204)

* Fix some IntelliJ findings

- Fix bug in TagBar (added itself instead of newTags)
- Wrong number of LOGGER paramters
- Inner class may be static
- Fix comment typo
- Bulk operation can be used instead of iteration
- Arrays.asList with only one element
- Optimized count by using numbers earlier
- Chained append for StringBuilder
- Initialize ArrayList by passing the initial contents in the constructor

* Fix checkstyle

* Revert partially "Fix some IntelliJ findings"

This partially reverts commit 167558d.

src/main/java/org/jabref/JabRefExecutorService.java

@@ -143,7 +143,7 @@ public void shutdownEverything() {
         timer.cancel();
     }
 
-    private class NamedRunnable implements Runnable {
+    private static class NamedRunnable implements Runnable {
 
         private final String name;
 

src/main/java/org/jabref/gui/SidePaneManager.java

@@ -176,7 +176,7 @@ private void updateView() {
     /**
      * Helper class for sorting visible components based on their preferred position.
      */
-    private class PreferredIndexSort implements Comparator<SidePaneComponent> {
+    private static class PreferredIndexSort implements Comparator<SidePaneComponent> {
 
         private final Map<SidePaneType, Integer> preferredPositions;
 

src/main/java/org/jabref/gui/copyfiles/CopyFilesTask.java

@@ -50,7 +50,7 @@ public CopyFilesTask(BibDatabaseContext databaseContext, List<BibEntry> entries,
         this.databaseContext = databaseContext;
         this.entries = entries;
         this.exportPath = path;
-        totalFilesCount = entries.stream().flatMap(entry -> entry.getFiles().stream()).count();
+        totalFilesCount = entries.stream().mapToLong(entry -> entry.getFiles().size()).sum();
     }
 
     @Override

src/main/java/org/jabref/gui/duplicationFinder/DuplicateSearch.java

@@ -184,7 +184,7 @@ private void handleDuplicates(DuplicateSearchResult result) {
      * Uses {@link System#identityHashCode(Object)} for identifying objects for removal, as completely identical
      * {@link BibEntry BibEntries} are equal to each other.
      */
-    class DuplicateSearchResult {
+    static class DuplicateSearchResult {
 
         private final Map<Integer, BibEntry> toRemove = new HashMap<>();
         private final List<BibEntry> toAdd = new ArrayList<>();

src/main/java/org/jabref/gui/exporter/ExportToClipboardAction.java

@@ -150,7 +150,7 @@ private String readFileToString(Path tmp) throws IOException {
         }
     }
 
-    private class ExportResult {
+    private static class ExportResult {
         final String content;
         final FileType fileType;
 

src/main/java/org/jabref/gui/groups/GroupTreeView.java

@@ -393,7 +393,7 @@ private void setupClearButtonField(CustomTextField customTextField) {
         }
     }
 
-    private class DragExpansionHandler {
+    private static class DragExpansionHandler {
         private static final long DRAG_TIME_BEFORE_EXPANDING_MS = 1000;
         private TreeItem<GroupNodeViewModel> draggedItem;
         private long dragStarted;

src/main/java/org/jabref/gui/groups/UndoableModifySubtree.java

@@ -43,9 +43,7 @@ public void undo() {
         m_modifiedSubtree.clear();
         // get node to edit
         final GroupTreeNode subtreeRoot = m_groupRoot.getDescendant(m_subtreeRootPath).get(); //TODO: NULL
-        for (GroupTreeNode child : subtreeRoot.getChildren()) {
-            m_modifiedSubtree.add(child);
-        }
+        m_modifiedSubtree.addAll(subtreeRoot.getChildren());
         // keep subtree handle, but restore everything else from backup
         subtreeRoot.removeAllChildren();
         for (GroupTreeNode child : m_subtreeBackup.getChildren()) {

src/main/java/org/jabref/gui/util/BackgroundTask.java

@@ -233,7 +233,7 @@ public BackgroundTask<V> withInitialMessage(String message) {
         return this;
     }
 
-    class BackgroundProgress {
+    static class BackgroundProgress {
 
         private final double workDone;
         private final double max;

src/main/java/org/jabref/gui/util/CurrentThreadTaskExecutor.java

@@ -74,7 +74,7 @@ public DelayTaskThrottler createThrottler(int delay) {
         return throttler;
     }
 
-    private class FailedFuture<T> implements Future<T> {
+    private static class FailedFuture<T> implements Future<T> {
         private final Throwable exception;
 
         FailedFuture(Throwable exception) {

src/main/java/org/jabref/gui/util/IconValidationDecorator.java

@@ -1,7 +1,7 @@
 package org.jabref.gui.util;
 
-import java.util.Arrays;
 import java.util.Collection;
+import java.util.Collections;
 
 import javafx.geometry.Pos;
 import javafx.scene.Node;
@@ -61,6 +61,6 @@ protected Tooltip createTooltip(ValidationMessage message) {
 
     @Override
     protected Collection<Decoration> createValidationDecorations(ValidationMessage message) {
-        return Arrays.asList(new GraphicDecoration(createDecorationNode(message), position));
+        return Collections.singletonList(new GraphicDecoration(createDecorationNode(message), position));
     }
 }

src/main/java/org/jabref/gui/util/component/TagBar.java

@@ -56,7 +56,7 @@ public ObservableList<T> getTags() {
     }
 
     public void setTags(Collection<T> newTags) {
-        this.tags.setAll(tags);
+        this.tags.setAll(newTags);
     }
 
     public ListProperty<T> tagsProperty() {

src/main/java/org/jabref/logic/bibtex/comparator/FieldComparator.java

@@ -130,13 +130,13 @@ public int compare(BibEntry e1, BibEntry e2) {
                 // Ok, parsing was successful. Update f1 and f2:
                 return i1.get().compareTo(i2.get()) * multiplier;
             } else if (i1.isPresent()) {
-                // The first one was parseable, but not the second one.
+                // The first one was parsable, but not the second one.
                 // This means we consider one < two
                 return -1 * multiplier;
             } else if (i2.isPresent()) {
-                // The second one was parseable, but not the first one.
+                // The second one was parsable, but not the first one.
                 // This means we consider one > two
-                return 1 * multiplier;
+                return multiplier;
             }
             // Else none of them were parseable, and we can fall back on comparing strings.
         }

src/main/java/org/jabref/logic/bst/VM.java

@@ -510,7 +510,7 @@ private VM(CommonTree tree) {
          */
         buildInFunctions.put("stack$", context -> {
             while (!stack.empty()) {
-                LOGGER.debug("Stack entry", stack.pop());
+                LOGGER.debug("Stack entry {}", stack.pop());
             }
         });
 
@@ -574,7 +574,7 @@ private VM(CommonTree tree) {
         /*
          * Pops and prints the top of the stack to the log file. It's useful for debugging.
          */
-        buildInFunctions.put("top$", context -> LOGGER.debug("Stack entry", stack.pop()));
+        buildInFunctions.put("top$", context -> LOGGER.debug("Stack entry {}", stack.pop()));
 
         /*
          * Pushes the current entry's type (book, article, etc.), but pushes

src/main/java/org/jabref/logic/exporter/BibTeXMLExporter.java

@@ -211,7 +211,7 @@ private <T> void parse(T entryType, BibEntry bibEntry, Entry entry) {
                         try {
                             method.invoke(entryType, new BigInteger(value));
                         } catch (NumberFormatException exception) {
-                            LOGGER.warn("The value %s of the 'number' field is not an integer and thus is ignored for the export", value);
+                            LOGGER.warn("The value {} of the 'number' field is not an integer and thus is ignored for the export", value);
                         }
                         break;
                     } else if (StandardField.MONTH.equals(key)) {

src/main/java/org/jabref/logic/exporter/TemplateExporter.java

@@ -247,7 +247,7 @@ public void export(final BibDatabaseContext databaseContext, final Path file,
             if (defLayout != null) {
                 missingFormatters.addAll(defLayout.getMissingFormatters());
                 if (!missingFormatters.isEmpty()) {
-                    LOGGER.warn("Missing formatters found ", missingFormatters);
+                    LOGGER.warn("Missing formatters found: {}", missingFormatters);
                 }
             }
             Map<EntryType, Layout> layouts = new HashMap<>();
@@ -310,10 +310,10 @@ public void export(final BibDatabaseContext databaseContext, final Path file,
             // Clear custom name formatters:
             layoutPreferences.clearCustomExportNameFormatters();
 
-            if (!missingFormatters.isEmpty()) {
+            if (!missingFormatters.isEmpty() && LOGGER.isWarnEnabled()) {
                 StringBuilder sb = new StringBuilder("The following formatters could not be found: ");
                 sb.append(String.join(", ", missingFormatters));
-                LOGGER.warn("Formatters not found", sb);
+                LOGGER.warn("Formatters {} not found", sb.toString());
             }
         }
     }

src/main/java/org/jabref/logic/importer/ImportFormatReader.java

@@ -12,7 +12,6 @@
 import org.jabref.logic.importer.fileformat.BiblioscapeImporter;
 import org.jabref.logic.importer.fileformat.BibtexImporter;
 import org.jabref.logic.importer.fileformat.CopacImporter;
-import org.jabref.logic.importer.fileformat.CustomImporter;
 import org.jabref.logic.importer.fileformat.EndnoteImporter;
 import org.jabref.logic.importer.fileformat.EndnoteXmlImporter;
 import org.jabref.logic.importer.fileformat.InspecImporter;
@@ -71,9 +70,7 @@ public void resetImportFormats(ImportFormatPreferences newImportFormatPreference
         formats.add(new SilverPlatterImporter());
 
         // Get custom import formats
-        for (CustomImporter importer : importFormatPreferences.getCustomImportList()) {
-            formats.add(importer);
-        }
+        formats.addAll(importFormatPreferences.getCustomImportList());
     }
 
     /**

src/main/java/org/jabref/logic/importer/fileformat/MrDLibImporter.java

@@ -91,7 +91,7 @@ private String convertToString(BufferedReader input) throws IOException {
     /**
      * Small pair-class to ensure the right order of the recommendations.
      */
-    private class RankedBibEntry {
+    private static class RankedBibEntry {
 
         public BibEntry entry;
         public Integer rank;

src/main/java/org/jabref/logic/layout/format/RTFChars.java

@@ -15,7 +15,7 @@
  *
  *   1.) Remove LaTeX-Command sequences.
  *
- *   2.) Replace LaTeX-Special chars with RTF aquivalents.
+ *   2.) Replace LaTeX-Special chars with RTF equivalents.
  *
  *   3.) Replace emph and textit and textbf with their RTF replacements.
  *

src/main/java/org/jabref/logic/openoffice/OpenOfficeFileSearch.java

@@ -5,6 +5,7 @@
 import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
 import java.util.Locale;
 import java.util.stream.Collectors;
@@ -67,7 +68,7 @@ private static List<Path> findWindowsOpenOfficeDirs() {
     }
 
     private static List<Path> findOSXOpenOfficeDirs() {
-        List<Path> sourceList = Arrays.asList(Paths.get("/Applications"));
+        List<Path> sourceList = Collections.singletonList(Paths.get("/Applications"));
 
         return findOpenOfficeDirectories(sourceList);
     }