X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=fcd81716821780f8d41c468269b439a095704b8c;hb=9c98d4bd666346f6ad3892c5394b7da3be82d93e;hp=2f77959611f9b741dba1bea97a585de7e8494c53;hpb=3af9017e1f6c6d045c6c0d41245fcd7bfdae32a6;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 2f77959..fcd8171 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -20,6 +20,8 @@
  */
 package jalview.gui;
 
+import java.util.Locale;
+
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.event.ActionEvent;
@@ -54,7 +56,7 @@ import jalview.analysis.AlignmentAnnotationUtils;
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.Conservation;
 import jalview.api.AlignViewportI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.commands.ChangeCaseCommand;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
@@ -228,13 +230,13 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         urlLink = new UrlLink(link);
       } catch (Exception foo)
       {
-        Cache.log.error("Exception for URLLink '" + link + "'", foo);
+        Console.error("Exception for URLLink '" + link + "'", foo);
         continue;
       }
 
       if (!urlLink.isValid())
       {
-        Cache.log.error(urlLink.getInvalidMessage());
+        Console.error(urlLink.getInvalidMessage());
         continue;
       }
 
@@ -357,14 +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)
   {
@@ -375,13 +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)
@@ -397,11 +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);
@@ -441,9 +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,
@@ -669,7 +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())
@@ -706,7 +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
     {
@@ -733,8 +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
@@ -837,15 +842,14 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       /*
        * show local rather than linked feature coordinates
        */
-      int[] beginRange = mf.getMappedPositions(start, start);
-      int[] endRange = mf.getMappedPositions(end, end);
-      if (beginRange == null || endRange == null)
+      int[] localRange = mf.getMappedPositions(start, end);
+      if (localRange == null)
       {
         // e.g. variant extending to stop codon so not mappable
         return;
       }
-      start = beginRange[0];
-      end = endRange[endRange.length - 1];
+      start = localRange[0];
+      end = localRange[localRange.length - 1];
     }
     StringBuilder desc = new StringBuilder();
     desc.append(sf.getType()).append(" ").append(String.valueOf(start));
@@ -1130,7 +1134,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         for (int d = 0; d < nd; d++)
         {
           DBRefEntry e = dbr.get(d);
-          String src = e.getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
+          String src = e.getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase(Locale.ROOT);
           Object[] sarray = commonDbrefs.get(src);
           if (sarray == null)
           {
@@ -1143,8 +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]++;
@@ -1164,19 +1168,19 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         urlLink = new GroupUrlLink(link);
       } catch (Exception foo)
       {
-        Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
+        Console.error("Exception for GroupURLLink '" + link + "'", foo);
         continue;
       }
       if (!urlLink.isValid())
       {
-        Cache.log.error(urlLink.getInvalidMessage());
+        Console.error(urlLink.getInvalidMessage());
         continue;
       }
       final String label = urlLink.getLabel();
       boolean usingNames = false;
       // Now see which parts of the group apply for this URL
       String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
-      Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
+      Object[] idset = commonDbrefs.get(ltarget.toUpperCase(Locale.ROOT));
       String[] seqstr, ids; // input to makeUrl
       if (idset != null)
       {
@@ -1783,7 +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());
     }
 
@@ -2013,8 +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()
   {
@@ -2022,10 +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()
@@ -2077,8 +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
@@ -2088,8 +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);
   }
 
   /**