JAL-3438 spotless for 2.11.2.0

[jalview.git] / src / jalview / gui / PopupMenu.java

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 1c3ab8f..fcd8171 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -359,14 +359,15 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
   }
 
   /**
-   * Constructor for a PopupMenu for a click in the alignment panel (on a residue)
+   * Constructor for a PopupMenu for a click in the alignment panel (on a
+   * residue)
    * 
    * @param ap
-   *              the panel in which the mouse is clicked
+   *          the panel in which the mouse is clicked
    * @param seq
-   *              the sequence under the mouse
+   *          the sequence under the mouse
    * @throws NullPointerException
-   *                                if seq is null
+   *           if seq is null
    */
   public PopupMenu(final AlignmentPanel ap, SequenceI seq, int column)
   {
@@ -377,13 +378,13 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
    * Constructor for a PopupMenu for a click in the sequence id panel
    * 
    * @param alignPanel
-   *                     the panel in which the mouse is clicked
+   *          the panel in which the mouse is clicked
    * @param seq
-   *                     the sequence under the mouse click
+   *          the sequence under the mouse click
    * @param groupLinks
-   *                     templates for sequence external links
+   *          templates for sequence external links
    * @throws NullPointerException
-   *                                if seq is null
+   *           if seq is null
    */
   public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq,
           List<String> groupLinks)
@@ -399,11 +400,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
    * @param alignPanel
    * @param seq
    * @param column
-   *                      aligned column position (0...)
+   *          aligned column position (0...)
    * @param groupLinks
    */
-  private PopupMenu(boolean fromIdPanel,
-          final AlignmentPanel alignPanel,
+  private PopupMenu(boolean fromIdPanel, final AlignmentPanel alignPanel,
           final SequenceI seq, final int column, List<String> groupLinks)
   {
     Objects.requireNonNull(seq);
@@ -443,9 +443,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     /*
      * And repeat for the current selection group (if there is one):
      */
-    final List<SequenceI> selectedGroup = (alignPanel.av.getSelectionGroup() == null
-            ? Collections.<SequenceI> emptyList()
-            : alignPanel.av.getSelectionGroup().getSequences());
+    final List<SequenceI> selectedGroup = (alignPanel.av
+            .getSelectionGroup() == null
+                    ? Collections.<SequenceI> emptyList()
+                    : alignPanel.av.getSelectionGroup().getSequences());
     buildAnnotationTypesMenus(groupShowAnnotationsMenu,
             groupHideAnnotationsMenu, selectedGroup);
     configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
@@ -671,7 +672,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         buildGroupURLMenu(sg, groupLinks);
       }
       // Add a 'show all structures' for the current selection
-      Hashtable<String, PDBEntry> pdbe = new Hashtable<>(), reppdb = new Hashtable<>();
+      Hashtable<String, PDBEntry> pdbe = new Hashtable<>(),
+              reppdb = new Hashtable<>();
 
       SequenceI sqass = null;
       for (SequenceI sq : alignPanel.av.getSequenceSelection())
@@ -708,7 +710,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     {
       createGroupMenuItem.setVisible(true);
       unGroupMenuItem.setVisible(false);
-      editGroupMenu.setText(MessageManager.getString("action.edit_new_group"));
+      editGroupMenu
+              .setText(MessageManager.getString("action.edit_new_group"));
     }
     else
     {
@@ -735,8 +738,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
    * <li>positional feature links (alignment panel popup menu)</li>
    * <li>feature details links (alignment panel popup menu)</li>
    * </ul>
-   * If this panel is also showed complementary (CDS/protein) features, then links
-   * to their feature details are also added.
+   * If this panel is also showed complementary (CDS/protein) features, then
+   * links to their feature details are also added.
    * 
    * @param seq
    * @param column
@@ -1144,8 +1147,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
           if (((String[]) sarray[1])[sq] == null)
           {
-            if (!e.hasMap() || (e.getMap()
-                    .locateMappedRange(start, end) != null))
+            if (!e.hasMap()
+                    || (e.getMap().locateMappedRange(start, end) != null))
             {
               ((String[]) sarray[1])[sq] = e.getAccessionId();
               ((int[]) sarray[0])[0]++;
@@ -1784,7 +1787,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         }
         inserts.and(sq.getInsertionsAsBits());
       }
-      hidden.clearAndHideColumns(inserts, ap.av.getSelectionGroup().getStartRes(),
+      hidden.clearAndHideColumns(inserts,
+              ap.av.getSelectionGroup().getStartRes(),
               ap.av.getSelectionGroup().getEndRes());
     }
 
@@ -2014,8 +2018,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
   /**
    * Shows a dialog where the sequence name and description may be edited. If a
-   * name containing spaces is entered, these are converted to underscores, with a
-   * warning message.
+   * name containing spaces is entered, these are converted to underscores, with
+   * a warning message.
    */
   void sequenceName_actionPerformed()
   {
@@ -2023,10 +2027,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
             sequence.getDescription(),
             MessageManager.getString("label.sequence_name"),
             MessageManager.getString("label.sequence_description"));
-    dialog.showDialog(ap.alignFrame,
-            MessageManager.getString(
-                    "label.edit_sequence_name_description"),
-            new Runnable()
+    dialog.showDialog(ap.alignFrame, MessageManager.getString(
+            "label.edit_sequence_name_description"), new Runnable()
             {
               @Override
               public void run()
@@ -2078,8 +2080,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
    */
   protected void outline_actionPerformed()
   {
-    String title = MessageManager
-            .getString("label.select_outline_colour");
+    String title = MessageManager.getString("label.select_outline_colour");
     ColourChooserListener listener = new ColourChooserListener()
     {
       @Override
@@ -2089,8 +2090,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         refresh();
       }
     };
-    JalviewColourChooser.showColourChooser(Desktop.getDesktop(),
-            title, Color.BLUE, listener);
+    JalviewColourChooser.showColourChooser(Desktop.getDesktop(), title,
+            Color.BLUE, listener);
   }
 
   /**