X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=d11d7a182175a9c9494f04d892192fa59478f81b;hb=a3af95d79b82dad26b033d8bae458d4bffe9a95c;hp=e29330ebe1246918a3e57de987b7c92befdad030;hpb=c3b91c81342d21498ffcb4639c3597a25aa2753c;p=jalview.git

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index e29330e..d11d7a1 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -30,6 +30,7 @@ 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.MouseEvent;
@@ -261,7 +262,7 @@ public class IdPanel extends JPanel
   {
     if (scrollThread != null)
     {
-      scrollThread.running = false;
+      scrollThread.stopScrolling();
     }
   }
 
@@ -373,8 +374,11 @@ public class IdPanel extends JPanel
      *  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();
-    List<SequenceFeature> features = sq.getFeatures().getNonPositionalFeatures();
+      features = sq.getFeatures().getNonPositionalFeatures();
     for (SequenceFeature sf : features)
     {
       if (sf.links != null)
@@ -382,6 +386,7 @@ public class IdPanel extends JPanel
         nlinks.addAll(sf.links);
       }
     }
+    }
 
     PopupMenu pop = new PopupMenu(alignPanel, sq, features,
             Preferences.getGroupURLLinks());
@@ -430,7 +435,7 @@ public class IdPanel extends JPanel
     lastid = seq;
 
     SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
-    av.getSelectionGroup().addOrRemove(pickedSeq, true);
+    av.getSelectionGroup().addOrRemove(pickedSeq, false);
   }
 
   /**
@@ -465,7 +470,7 @@ public class IdPanel extends JPanel
     for (int i = start; i <= end; i++)
     {
       av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
-              i == end);
+              false);
     }
   }
 
@@ -480,7 +485,7 @@ public class IdPanel extends JPanel
   {
     if (scrollThread != null)
     {
-      scrollThread.running = false;
+      scrollThread.stopScrolling();
     }
     MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
 
@@ -505,7 +510,7 @@ public class IdPanel extends JPanel
   {
     getIdCanvas().setHighlighted(list);
 
-    if (list == null)
+    if (list == null || list.isEmpty())
     {
       return;
     }
@@ -530,24 +535,42 @@ public class IdPanel extends JPanel
     this.idCanvas = idCanvas;
   }
 
-  // this class allows scrolling off the bottom of the visible alignment
+  /**
+   * Performs scrolling of the visible alignment up or down, adding newly
+   * visible sequences to the current selection
+   */
   class ScrollThread extends Thread
   {
-    boolean running = false;
+    private boolean running = false;
 
-    boolean up = true;
+    private boolean up;
 
+    /**
+     * Constructor for a thread that scrolls either up or down
+     * 
+     * @param up
+     */
     public ScrollThread(boolean up)
     {
       this.up = up;
+      setName("IdPanel$ScrollThread$" + String.valueOf(up));
       start();
     }
 
+    /**
+     * Sets a flag to stop the scrolling
+     */
     public void stopScrolling()
     {
       running = false;
     }
 
+    /**
+     * Scrolls the alignment either up or down, one row at a time, adding newly
+     * visible sequences to the current selection. Speed is limited to a maximum
+     * of ten rows per second. The thread exits when the end of the alignment is
+     * reached or a flag is set to stop it.
+     */
     @Override
     public void run()
     {
@@ -555,29 +578,20 @@ public class IdPanel extends JPanel
 
       while (running)
       {
-        if (av.getRanges().scrollUp(up))
+        ViewportRanges ranges = IdPanel.this.av.getRanges();
+        if (ranges.scrollUp(up))
         {
-          // scroll was ok, so add new sequence to selection
-          int seq = av.getRanges().getStartSeq();
-
-          if (!up)
-          {
-            seq = av.getRanges().getEndSeq();
-          }
-
-          if (seq < lastid)
-          {
-            selectSeqs(lastid - 1, seq);
-          }
-          else if (seq > lastid)
-          {
-            selectSeqs(lastid + 1, seq);
-          }
-
-          lastid = seq;
+          int toSeq = up ? ranges.getStartSeq() : ranges.getEndSeq();
+          int fromSeq = toSeq < lastid ? lastid - 1 : lastid + 1;
+          IdPanel.this.selectSeqs(fromSeq, toSeq);
+
+          lastid = toSeq;
         }
         else
         {
+          /*
+           * scroll did nothing - reached limit of visible alignment
+           */
           running = false;
         }