method parameter must be final

CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyAction.java

@@ -33,7 +33,7 @@ public class CopyAction extends CopyPasteAbstractAction {
    * @param speciesList
    *          - list of species to annotate
    */
-  public void performAnnotation(CopyPastePlugin plug, PluginListOf speciesList) {
+  public void performAnnotation(final CopyPastePlugin plug, final PluginListOf speciesList) {
     SystemClipboard sc = new SystemClipboard();
 
     int size = speciesList.size();
@@ -70,7 +70,7 @@ public class CopyAction extends CopyPasteAbstractAction {
     if (chosenElement != null) {
       try {
         sc.setClipboardContents(getCopyString(chosenElement.getAnnotationString(), chosenElement.getNotesString()));
-      } catch (InvalidXmlSchemaException e) {
+      } catch (final InvalidXmlSchemaException e) {
         logger.warn("Problem with creating copy-paste String", e);
       }
     }

CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractAction.java

@@ -40,7 +40,7 @@ public class CopyPasteAbstractAction {
    *          object to serialize
    * @return string representation of {@link MiriamData}
    */
-  protected String serialize(MiriamData md) {
+  protected String serialize(final MiriamData md) {
     return PREFIX + "\t" + md.getRelationType().getStringRepresentation() + "\t" + md.getDataType().getUris().get(0)
         + "\t" + md.getResource();
   }
@@ -53,7 +53,7 @@ public class CopyPasteAbstractAction {
    *          string representation of {@link MiriamData}
    * @return {@link MiriamData} obtained from input string
    */
-  protected MiriamData deserialize(String string) {
+  protected MiriamData deserialize(final String string) {
     if (string == null) {
       return null;
     }
@@ -88,11 +88,11 @@ public class CopyPasteAbstractAction {
    * @throws InvalidXmlSchemaException
    *           thrown when xmlString is invalid
    */
-  protected String getCopyString(String annotationString, String notesString) throws InvalidXmlSchemaException {
+  protected String getCopyString(final String annotationString, final String notesString) throws InvalidXmlSchemaException {
     XmlAnnotationParser xap = new XmlAnnotationParser();
     Set<MiriamData> set = xap.parse(annotationString, null);
     StringBuilder result = new StringBuilder();
-    for (MiriamData md : set) {
+    for (final MiriamData md : set) {
       result.append(serialize(md) + "\n");
     }
     result.append(notesString);
@@ -108,7 +108,7 @@ public class CopyPasteAbstractAction {
    * 
    * @return {@link Pair} of {@link MiriamData} set and notes string
    */
-  protected Pair<Set<MiriamData>, String> getAnnotationDataFromClipboardString(String value) {
+  protected Pair<Set<MiriamData>, String> getAnnotationDataFromClipboardString(final String value) {
     if (value == null) {
       return new Pair<Set<MiriamData>, String>(null, null);
     }

CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPastePlugin.java

@@ -65,14 +65,14 @@ public class CopyPastePlugin extends CellDesignerPlugin {
       // create keyboard listener for shortcuts
       KeyboardFocusManager.getCurrentKeyboardFocusManager().addKeyEventDispatcher(createKeyEventDispatcher());
 
-    } catch (Exception exception) {
+    } catch (final Exception exception) {
       logger.error(exception, exception);
     }
   }
 
   protected KeyEventDispatcher createKeyEventDispatcher() {
     return new KeyEventDispatcher() {
-      public boolean dispatchKeyEvent(KeyEvent e) {
+      public boolean dispatchKeyEvent(final KeyEvent e) {
         switch (e.getID()) {
         case KeyEvent.KEY_PRESSED:
           if (e.getKeyCode() == java.awt.event.KeyEvent.VK_V
@@ -101,33 +101,33 @@ public class CopyPastePlugin extends CellDesignerPlugin {
 
   // CHECKSTYLE:OFF
   @Override
-  public void SBaseAdded(PluginSBase arg0) {
+  public void SBaseAdded(final PluginSBase arg0) {
 
   }
 
   @Override
-  public void SBaseChanged(PluginSBase arg0) {
+  public void SBaseChanged(final PluginSBase arg0) {
 
   }
 
   // CHECKSTYLE:ON
 
   @Override
-  public void SBaseDeleted(PluginSBase arg0) {
+  public void SBaseDeleted(final PluginSBase arg0) {
   }
 
   @Override
-  public void modelOpened(PluginSBase arg0) {
+  public void modelOpened(final PluginSBase arg0) {
 
   }
 
   @Override
-  public void modelSelectChanged(PluginSBase arg0) {
+  public void modelSelectChanged(final PluginSBase arg0) {
 
   }
 
   @Override
-  public void modelClosed(PluginSBase arg0) {
+  public void modelClosed(final PluginSBase arg0) {
 
   }
 

CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPluginAction.java

@@ -39,17 +39,17 @@ public class CopyPluginAction extends PluginAction {
    * @param win
    *          {@link #window}
    */
-  public CopyPluginAction(CopyPastePlugin plugin, MainWindow win) {
+  public CopyPluginAction(final CopyPastePlugin plugin, final MainWindow win) {
     this.plugin = plugin;
   }
 
   @Override
-  public void myActionPerformed(ActionEvent e) {
+  public void myActionPerformed(final ActionEvent e) {
     try {
       CopyAction annotateAction = new CopyAction();
       PluginListOf list = getPlugin().getSelectedAllNode();
       annotateAction.performAnnotation(getPlugin(), list);
-    } catch (Exception ex) {
+    } catch (final Exception ex) {
       logger.error(ex, ex);
     }
   }
@@ -58,7 +58,7 @@ public class CopyPluginAction extends PluginAction {
     return plugin;
   }
 
-  protected void setPlugin(CopyPastePlugin plugin) {
+  protected void setPlugin(final CopyPastePlugin plugin) {
     this.plugin = plugin;
   }
 

CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/PasteAction.java

@@ -37,7 +37,7 @@ public class PasteAction extends CopyPasteAbstractAction {
    * @param speciesList
    *          - list of species to annotate
    */
-  public void performAnnotation(CopyPastePlugin plug, PluginListOf speciesList) {
+  public void performAnnotation(final CopyPastePlugin plug, final PluginListOf speciesList) {
     XmlAnnotationParser xap = new XmlAnnotationParser();
 
     SystemClipboard sc = new SystemClipboard();

CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/PastePluginAction.java

@@ -39,17 +39,17 @@ public class PastePluginAction extends PluginAction {
    * @param win
    *          {@link #window}
    */
-  public PastePluginAction(CopyPastePlugin plugin, MainWindow win) {
+  public PastePluginAction(final CopyPastePlugin plugin, final MainWindow win) {
     this.setPlugin(plugin);
   }
 
   @Override
-  public void myActionPerformed(ActionEvent e) {
+  public void myActionPerformed(final ActionEvent e) {
     try {
       PasteAction annotateAction = new PasteAction();
       PluginListOf list = getPlugin().getSelectedAllNode();
       annotateAction.performAnnotation(plugin, list);
-    } catch (Exception ex) {
+    } catch (final Exception ex) {
       logger.error(ex, ex);
     }
   }
@@ -58,7 +58,7 @@ public class PastePluginAction extends PluginAction {
     return plugin;
   }
 
-  protected void setPlugin(CopyPastePlugin plugin) {
+  protected void setPlugin(final CopyPastePlugin plugin) {
     this.plugin = plugin;
   }
 

CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/InfoFrame.java

@@ -136,7 +136,7 @@ public final class InfoFrame {
     JPanel controlArea = new JPanel(new GridLayout(panels, 1));
     controlArea.setLayout(new BoxLayout(controlArea, BoxLayout.Y_AXIS));
     // for every species create a panel and add it to general form
-    for (PluginSpeciesAlias sp : this.species) {
+    for (final PluginSpeciesAlias sp : this.species) {
       JPanel panel = getPanelViewForSpecies(sp);
       controlArea.add(panel);
     }
@@ -167,7 +167,7 @@ public final class InfoFrame {
    *          CellDesigner species alias
    * @return {@link JPanel} object with information about species
    */
-  private JPanel getPanelViewForSpecies(PluginSpeciesAlias species) {
+  private JPanel getPanelViewForSpecies(final PluginSpeciesAlias species) {
     JPanel result = new JPanel();
     result.setLayout(new BoxLayout(result, BoxLayout.Y_AXIS));
 
@@ -214,7 +214,7 @@ public final class InfoFrame {
    * @param visible
    *          should the frame be visible or not
    */
-  public void setVisible(boolean visible) {
+  public void setVisible(final boolean visible) {
     frame.setVisible(visible);
   }
 
@@ -224,7 +224,7 @@ public final class InfoFrame {
    * @param title
    *          title of the frame
    */
-  public void setTitle(String title) {
+  public void setTitle(final String title) {
     frame.setTitle(title);
   }
 
@@ -243,7 +243,7 @@ public final class InfoFrame {
    * @param type
    *          new {@link JFrame#defaultCloseOperation} value
    */
-  public void setDefaultCloseOperation(int type) {
+  public void setDefaultCloseOperation(final int type) {
     frame.setDefaultCloseOperation(type);
   }
 
@@ -253,7 +253,7 @@ public final class InfoFrame {
    * @param always
    *          new {@link JFrame#isAlwaysOnTop()} value
    */
-  public void setAlwaysOnTop(boolean always) {
+  public void setAlwaysOnTop(final boolean always) {
     frame.setAlwaysOnTop(always);
   }
 
@@ -267,7 +267,7 @@ public final class InfoFrame {
    * @param species
    *          - species to be shown in the form
    */
-  public void setSpecies(List<PluginSpeciesAlias> species) {
+  public void setSpecies(final List<PluginSpeciesAlias> species) {
     this.species = species;
     updateSpecies();
   }

CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/InfoPlugin.java

@@ -70,7 +70,7 @@ public class InfoPlugin extends CellDesignerPlugin {
 
       // create keyboard listener for shortcuts
       KeyboardFocusManager.getCurrentKeyboardFocusManager().addKeyEventDispatcher(new KeyEventDispatcher() {
-        public boolean dispatchKeyEvent(KeyEvent e) {
+        public boolean dispatchKeyEvent(final KeyEvent e) {
           if (KeyEvent.KEY_PRESSED == e.getID()) {
             // if someone hits CTRL+T then open/hide info window
             if (e.getKeyCode() == java.awt.event.KeyEvent.VK_T
@@ -94,7 +94,7 @@ public class InfoPlugin extends CellDesignerPlugin {
         private String selectedElementsId = "";
 
         @Override
-        public void actionPerformed(ActionEvent arg0) {
+        public void actionPerformed(final ActionEvent arg0) {
           // if there is no open model then getSelectedAllNode() will throw an
           // exception...
           List<PluginSpeciesAlias> aliasList = getListOfAlias();
@@ -113,7 +113,7 @@ public class InfoPlugin extends CellDesignerPlugin {
               selectedElementsId = newId;
               frame.setSpecies(v);
             }
-          } catch (Exception exception) {
+          } catch (final Exception exception) {
             logger.error(exception, exception);
           }
 
@@ -123,7 +123,7 @@ public class InfoPlugin extends CellDesignerPlugin {
       Timer timer = new Timer(DELAY_BETWEEN_ON_SELECT_LISTENER_CHECKS, onChangeSelectListener);
       timer.start();
 
-    } catch (Exception exception) {
+    } catch (final Exception exception) {
       logger.error("Unhandled exception. ", exception);
     }
   }
@@ -134,33 +134,33 @@ public class InfoPlugin extends CellDesignerPlugin {
 
   // CHECKSTYLE:OFF
   @Override
-  public void SBaseAdded(PluginSBase arg0) {
+  public void SBaseAdded(final PluginSBase arg0) {
 
   }
 
   @Override
-  public void SBaseChanged(PluginSBase arg0) {
+  public void SBaseChanged(final PluginSBase arg0) {
 
   }
 
   // CHECKSTYLE:ON
 
   @Override
-  public void SBaseDeleted(PluginSBase arg0) {
+  public void SBaseDeleted(final PluginSBase arg0) {
   }
 
   @Override
-  public void modelOpened(PluginSBase arg0) {
+  public void modelOpened(final PluginSBase arg0) {
 
   }
 
   @Override
-  public void modelSelectChanged(PluginSBase arg0) {
+  public void modelSelectChanged(final PluginSBase arg0) {
 
   }
 
   @Override
-  public void modelClosed(PluginSBase arg0) {
+  public void modelClosed(final PluginSBase arg0) {
 
   }
 
@@ -175,7 +175,7 @@ public class InfoPlugin extends CellDesignerPlugin {
           result.add(alias);
         }
       }
-    } catch (Exception e) {
+    } catch (final Exception e) {
     }
     return result;
   }

CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/CdPluginFunctions.java

@@ -56,7 +56,7 @@ public class CdPluginFunctions {
     return appender.getFatals();
   }
 
-  protected PluginListOf createPluginListWithSpecies(int size) {
+  protected PluginListOf createPluginListWithSpecies(final int size) {
     PluginListOf list = Mockito.mock(PluginListOf.class);
 
     Mockito.when(list.size()).thenReturn(size);
@@ -67,7 +67,7 @@ public class CdPluginFunctions {
     return list;
   }
 
-  protected PluginListOf createPluginListWithReaction(int size) {
+  protected PluginListOf createPluginListWithReaction(final int size) {
     PluginListOf list = Mockito.mock(PluginListOf.class);
 
     Mockito.when(list.size()).thenReturn(size);
@@ -78,7 +78,7 @@ public class CdPluginFunctions {
     return list;
   }
 
-  protected PluginSpeciesAlias createSpeciesAlias(String id) {
+  protected PluginSpeciesAlias createSpeciesAlias(final String id) {
     PluginSpecies species = Mockito.mock(PluginSpecies.class);
     Mockito.when(species.getId()).thenReturn(id);
     Mockito.when(species.getAnnotationString()).thenReturn(rdfString);
@@ -89,7 +89,7 @@ public class CdPluginFunctions {
     return speciesAlias;
   }
 
-  private PluginReaction createReaction(String id) {
+  private PluginReaction createReaction(final String id) {
 
     PluginReaction reaction = Mockito.mock(PluginReaction.class);
     Mockito.when(reaction.getId()).thenReturn("re" + id);

annotation/src/main/java/lcsb/mapviewer/annotation/cache/ApplicationLevelCache.java

@@ -73,26 +73,26 @@ public final class ApplicationLevelCache implements QueryCacheInterface {
   }
 
   @Override
-  public synchronized Node getXmlNodeByQuery(String query, CacheType type) {
+  public synchronized Node getXmlNodeByQuery(final String query, final CacheType type) {
     Node result = null;
     result = cachedQueryNodes.get(type.getId() + "\n" + query);
     return result;
   }
 
   @Override
-  public synchronized String getStringByQuery(String query, CacheType type) {
+  public synchronized String getStringByQuery(final String query, final CacheType type) {
     String result = null;
     result = cachedQueryString.get(type.getId() + "\n" + query);
     return result;
   }
 
   @Override
-  public synchronized void setCachedQuery(String query, CacheType type, Object object) {
+  public synchronized void setCachedQuery(final String query, final CacheType type, final Object object) {
     setCachedQuery(query, type, object, 0);
   }
 
   @Override
-  public synchronized void setCachedQuery(String query, CacheType type, Object object, int validDays) {
+  public synchronized void setCachedQuery(final String query, final CacheType type, final Object object, final int validDays) {
     performMemoryBalance();
 
     if (object instanceof String) {
@@ -114,13 +114,13 @@ public final class ApplicationLevelCache implements QueryCacheInterface {
   }
 
   @Override
-  public synchronized void removeByQuery(String query, CacheType type) {
+  public synchronized void removeByQuery(final String query, final CacheType type) {
     cachedQueryString.remove(type.getId() + "\n" + query);
     cachedQueryNodes.remove(type.getId() + "\n" + query);
   }
 
   @Override
-  public void invalidateByQuery(String query, CacheType type) {
+  public void invalidateByQuery(final String query, final CacheType type) {
     removeByQuery(query, type);
   }
 
@@ -146,7 +146,7 @@ public final class ApplicationLevelCache implements QueryCacheInterface {
         System.gc();
         try {
           Thread.sleep(1000);
-        } catch (InterruptedException e) {
+        } catch (final InterruptedException e) {
           // TODO Auto-generated catch block
           e.printStackTrace();
         }

annotation/src/main/java/lcsb/mapviewer/annotation/cache/BigFileCache.java

@@ -96,7 +96,7 @@ public class BigFileCache {
    * Constructor.
    */
   @Autowired
-  public BigFileCache(BigFileEntryDao bigFileEntryDao, ConfigurationDao configurationDao, DbUtils dbUtils) {
+  public BigFileCache(final BigFileEntryDao bigFileEntryDao, final ConfigurationDao configurationDao, final DbUtils dbUtils) {
     this.bigFileEntryDao = bigFileEntryDao;
     this.configurationDao = configurationDao;
     this.dbUtils = dbUtils;
@@ -104,7 +104,7 @@ public class BigFileCache {
     // when the main program exits
     asyncExecutorService = Executors.newScheduledThreadPool(10, new ThreadFactory() {
       @Override
-      public Thread newThread(Runnable r) {
+      public Thread newThread(final Runnable r) {
         Thread t = new Thread(r);
         t.setDaemon(true);
         return t;
@@ -112,7 +112,7 @@ public class BigFileCache {
     });
     syncExecutorService = Executors.newScheduledThreadPool(1, new ThreadFactory() {
       @Override
-      public Thread newThread(Runnable r) {
+      public Thread newThread(final Runnable r) {
         Thread t = new Thread(r);
         t.setDaemon(true);
         return t;
@@ -145,7 +145,7 @@ public class BigFileCache {
    *           thrown when file should be in file system, but couldn't be found
    *           there (somebody manually removed it)
    */
-  public String getAbsolutePathForFile(String url) throws FileNotFoundException {
+  public String getAbsolutePathForFile(final String url) throws FileNotFoundException {
     BigFileEntry entry = bigFileEntryDao.getByUrl(url);
     if (entry == null) {
       return null;
@@ -172,7 +172,7 @@ public class BigFileCache {
    *           thrown when file should be in file system, but couldn't be found
    *           there (somebody manually removed it)
    */
-  public String getLocalPathForFile(String url) throws FileNotFoundException {
+  public String getLocalPathForFile(final String url) throws FileNotFoundException {
     BigFileEntry entry = bigFileEntryDao.getByUrl(url);
     if (entry == null) {
       return null;
@@ -204,7 +204,7 @@ public class BigFileCache {
    * @throws URISyntaxException
    *           thrown when url is invalid
    */
-  public void downloadFile(String url, boolean async, IProgressUpdater updater) throws IOException, URISyntaxException {
+  public void downloadFile(final String url, final boolean async, final IProgressUpdater updater) throws IOException, URISyntaxException {
     Callable<Void> computations = null;
     if (url.toLowerCase().startsWith("ftp:")) {
       computations = new GetFtpFileTask(url, updater);
@@ -232,7 +232,7 @@ public class BigFileCache {
    *           thrown when url is invalid
    * @throws IOException
    */
-  private BigFileEntry createEntryForBigFile(String url) throws URISyntaxException, IOException {
+  private BigFileEntry createEntryForBigFile(final String url) throws URISyntaxException, IOException {
     String localPath = configurationDao.getValueByType(ConfigurationElementType.BIG_FILE_STORAGE_DIR);
     BigFileEntry entry = new BigFileEntry();
     entry.setDownloadDate(Calendar.getInstance());
@@ -271,7 +271,7 @@ public class BigFileCache {
    * @throws IOException
    *           thrown when there is a problem with accessing local or remote file
    */
-  public boolean isLocalFileUpToDate(String url) throws URISyntaxException, IOException {
+  public boolean isLocalFileUpToDate(final String url) throws URISyntaxException, IOException {
     if (url.toLowerCase().startsWith("ftp")) {
       return isLocalFtpFileUpToDate(url);
     } else if (url.toLowerCase().startsWith("http")) {
@@ -294,7 +294,7 @@ public class BigFileCache {
    * @throws IOException
    *           thrown when there is a problem with connection to remote server
    */
-  public boolean isLocalFtpFileUpToDate(String url) throws FileNotFoundException, IOException, URISyntaxException {
+  public boolean isLocalFtpFileUpToDate(final String url) throws FileNotFoundException, IOException, URISyntaxException {
     boolean result = false;
     BigFileEntry entry = bigFileEntryDao.getByUrl(url);
     if (entry == null) {
@@ -349,7 +349,7 @@ public class BigFileCache {
    *           thrown when local file cannot be found or there is a problem with
    *           accessing remote file
    */
-  public boolean isLocalHttpFileUpToDate(String url) throws IOException {
+  public boolean isLocalHttpFileUpToDate(final String url) throws IOException {
     boolean result = false;
     BigFileEntry entry = bigFileEntryDao.getByUrl(url);
     if (entry == null) {
@@ -377,7 +377,7 @@ public class BigFileCache {
    * @throws IOException
    *           thrown when there is a problem with accessing remote file
    */
-  long getRemoteHttpFileSize(String url) throws IOException {
+  long getRemoteHttpFileSize(final String url) throws IOException {
     long remoteSize = -1;
     HttpURLConnection conn = null;
     try {
@@ -402,9 +402,9 @@ public class BigFileCache {
    * @throws IOException
    *           thrown when there is a problem with deleting file
    */
-  public void removeFile(String url) throws IOException {
+  public void removeFile(final String url) throws IOException {
     List<BigFileEntry> entries = bigFileEntryDao.getAllByUrl(url);
-    for (BigFileEntry entry : entries) {
+    for (final BigFileEntry entry : entries) {
       String path = Configuration.getWebAppDir() + entry.getLocalPath();
       File f = new File(path);
       if (!f.exists()) {
@@ -432,7 +432,7 @@ public class BigFileCache {
    * @throws URISyntaxException
    *           thrown when url is invalid
    */
-  public void updateFile(String url, boolean async) throws URISyntaxException, IOException {
+  public void updateFile(final String url, final boolean async) throws URISyntaxException, IOException {
     if (isLocalFileUpToDate(url)) {
       logger.warn("File is up to date. Skipping...");
       return;
@@ -456,12 +456,12 @@ public class BigFileCache {
    * @throws IOException
    *           thrown when task finished with {@link IOException}
    */
-  void executeTask(Future<?> task) throws URISyntaxException, IOException {
+  void executeTask(final Future<?> task) throws URISyntaxException, IOException {
     try {
       task.get();
-    } catch (InterruptedException e) {
+    } catch (final InterruptedException