JAL-3438 spotless for 2.11.2.0

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

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 46e5f14..7b491e4 100755 (executable)
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -20,18 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.gui.SeqPanel.MousePos;
-import jalview.io.SequenceAnnotationReport;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.viewmodel.AlignmentViewport;
-import jalview.viewmodel.ViewportRanges;
-
 import java.awt.BorderLayout;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
@@ -48,6 +36,17 @@ import javax.swing.SwingUtilities;
 import javax.swing.Timer;
 import javax.swing.ToolTipManager;
 
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.gui.SeqPanel.MousePos;
+import jalview.io.SequenceAnnotationReport;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
+
 /**
  * This panel hosts alignment sequence ids and responds to mouse clicks on them,
  * as well as highlighting ids matched by a search from the Find menu.
@@ -66,8 +65,6 @@ public class IdPanel extends JPanel
 
   ScrollThread scrollThread = null;
 
-  String linkImageURL;
-
   int offy;
 
   // int width;
@@ -88,8 +85,7 @@ public class IdPanel extends JPanel
     this.av = av;
     alignPanel = parent;
     setIdCanvas(new IdCanvas(av));
-    linkImageURL = getClass().getResource("/images/link.gif").toString();
-    seqAnnotReport = new SequenceAnnotationReport(linkImageURL);
+    seqAnnotReport = new SequenceAnnotationReport(true);
     setLayout(new BorderLayout());
     add(getIdCanvas(), BorderLayout.CENTER);
     addMouseListener(this);
@@ -135,8 +131,7 @@ public class IdPanel extends JPanel
 
         StringBuilder text = new StringBuilder();
         text.append("Sequence ").append(String.valueOf(seq + 1))
-                .append(" ID: ")
-                .append(sequence.getName());
+                .append(" ID: ").append(sequence.getName());
         alignPanel.alignFrame.setStatus(text.toString());
       }
     }
@@ -273,6 +268,7 @@ public class IdPanel extends JPanel
     if (scrollThread != null)
     {
       scrollThread.stopScrolling();
+      scrollThread = null;
     }
   }
 
@@ -317,14 +313,7 @@ public class IdPanel extends JPanel
   void startScrolling(boolean up)
   {
     scrollThread = new ScrollThread(up);
-    if (!Platform.isJS())
-    {
-      /*
-       * Java - run in a new thread
-       */
-      scrollThread.start();
-    }
-    else
+    if (Platform.isJS())
     {
       /*
        * for JalviewJS using Swing Timer
@@ -348,13 +337,22 @@ public class IdPanel extends JPanel
         {
           if (scrollThread == null)
           {
-            // finished and nulled itself
+            // IdPanel.stopScrolling called
             t.stop();
           }
         }
       });
       t.start();
     }
+    else
+    /**
+     * Java only
+     * 
+     * @j2sIgnore
+     */
+    {
+      scrollThread.start();
+    }
   }
 
   /**
@@ -379,7 +377,7 @@ public class IdPanel extends JPanel
     }
 
     MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
-    
+
     if (e.isPopupTrigger()) // Mac reports this in mousePressed
     {
       showPopupMenu(e, pos);
@@ -433,28 +431,12 @@ public class IdPanel extends JPanel
     }
 
     Sequence sq = (Sequence) av.getAlignment().getSequenceAt(pos.seqIndex);
-
-    /*
-     *  build a new links menu based on the current links
-     *  and any non-positional features
-     */
-    List<SequenceFeature> features = null;
     if (sq != null)
     {
-    List<String> nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
-      features = sq.getFeatures().getNonPositionalFeatures();
-    for (SequenceFeature sf : features)
-    {
-      if (sf.links != null)
-      {
-        nlinks.addAll(sf.links);
-      }
-    }
+      PopupMenu pop = new PopupMenu(alignPanel, sq,
+              Preferences.getGroupURLLinks());
+      pop.show(this, e.getX(), e.getY());
     }
-
-    PopupMenu pop = new PopupMenu(alignPanel, sq, features,
-            Preferences.getGroupURLLinks());
-    pop.show(this, e.getX(), e.getY());
   }
 
   /**
@@ -549,7 +531,7 @@ public class IdPanel extends JPanel
   {
     if (scrollThread != null)
     {
-      scrollThread.stopScrolling();
+      stopScrolling();
     }
     MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
 
@@ -618,7 +600,6 @@ public class IdPanel extends JPanel
     {
       this.up = up;
       setName("IdPanel$ScrollThread$" + String.valueOf(up));
-      start();
     }
 
     /**