JAL-3878 update branch from 2.12 merge from 2.11.2

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

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 673f04d..09624a8 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -20,6 +20,24 @@
  */
 package jalview.gui;
 
+import java.util.Locale;
+
+import jalview.analysis.AlignSeq;
+import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.workers.InformationThread;
+
 import java.awt.Color;
 import java.awt.Cursor;
 import java.awt.Dimension;
@@ -47,22 +65,6 @@ import javax.swing.JPopupMenu;
 import javax.swing.SwingUtilities;
 import javax.swing.ToolTipManager;
 
-import jalview.analysis.AlignSeq;
-import jalview.analysis.AlignmentUtils;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.io.FileFormat;
-import jalview.io.FormatAdapter;
-import jalview.util.Comparison;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.workers.InformationThread;
-
 /**
  * The panel that holds the labels for alignment annotations, providing
  * tooltips, context menus, drag to reorder rows, and drag to adjust panel
@@ -136,7 +138,7 @@ public class AnnotationLabels extends JPanel
    */
   public AnnotationLabels(AlignmentPanel ap)
   {
-         
+
     this.ap = ap;
     av = ap.av;
     ToolTipManager.sharedInstance().registerComponent(this);
@@ -292,27 +294,26 @@ public class AnnotationLabels extends JPanel
     EditNameDialog dialog = new EditNameDialog(annotation.label,
             annotation.description, name, description);
 
-    dialog.showDialog(ap.alignFrame, title,
-            new Runnable()
-            {
-              @Override
-              public void run()
-              {
-                annotation.label = dialog.getName();
-                String text = dialog.getDescription();
-                if (text != null && text.length() == 0)
-                {
-                  text = null;
-                }
-                annotation.description = text;
-                if (addNew)
-                {
-                  ap.av.getAlignment().addAnnotation(annotation);
-                  ap.av.getAlignment().setAnnotationIndex(annotation, 0);
-                }
-                ap.refresh(true);
-              }
-            });
+    dialog.showDialog(ap.alignFrame, title, new Runnable()
+    {
+      @Override
+      public void run()
+      {
+        annotation.label = dialog.getName();
+        String text = dialog.getDescription();
+        if (text != null && text.length() == 0)
+        {
+          text = null;
+        }
+        annotation.description = text;
+        if (addNew)
+        {
+          ap.av.getAlignment().addAnnotation(annotation);
+          ap.av.getAlignment().setAnnotationIndex(annotation, 0);
+        }
+        ap.refresh(true);
+      }
+    });
   }
 
   @Override
@@ -353,10 +354,8 @@ public class AnnotationLabels extends JPanel
       pop.show(this, evt.getX(), evt.getY());
       return;
     }
-
     final AlignmentAnnotation ann = aa[selectedRow];
     final boolean isSequenceAnnotation = ann.sequenceRef != null;
-
     item = new JMenuItem(EDITNAME);
     item.addActionListener(this);
     pop.add(item);
@@ -600,8 +599,7 @@ public class AnnotationLabels extends JPanel
    * @param pop
    */
   static void addConsensusMenuOptions(AlignmentPanel ap,
-          AlignmentAnnotation ann,
-          JPopupMenu pop)
+          AlignmentAnnotation ann, JPopupMenu pop)
   {
     pop.addSeparator();
 
@@ -918,12 +916,12 @@ public class AnnotationLabels extends JPanel
       // jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature
       // tooltips
       String desc = aa.getDescription(true).trim();
-      if (!desc.toLowerCase().startsWith(HTML_START_TAG))
+      if (!desc.toLowerCase(Locale.ROOT).startsWith(HTML_START_TAG))
       {
         tooltip.append(HTML_START_TAG);
         desc = desc.replace("<", "&lt;");
       }
-      else if (desc.toLowerCase().endsWith(HTML_END_TAG))
+      else if (desc.toLowerCase(Locale.ROOT).endsWith(HTML_END_TAG))
       {
         desc = desc.substring(0, desc.length() - HTML_END_TAG.length());
       }
@@ -1090,6 +1088,7 @@ public class AnnotationLabels extends JPanel
             PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
             ap.av.sendSelection();
           }
+
         }
       }
       return;
@@ -1153,6 +1152,7 @@ public class AnnotationLabels extends JPanel
   @Override
   public void paintComponent(Graphics g)
   {
+
     int width = getWidth();
     if (width == 0)
     {
@@ -1167,6 +1167,7 @@ public class AnnotationLabels extends JPanel
     }
 
     drawComponent(g2, true, width);
+
   }
 
   /**