Merge branch 'bug/JAL-3072scrollThread' into merge/JAL-3072_3073

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

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 1fd9e49..113fd9f 100755 (executable)
--- 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();
     }
   }
 
@@ -484,7 +485,7 @@ public class IdPanel extends JPanel
   {
     if (scrollThread != null)
     {
-      scrollThread.running = false;
+      scrollThread.stopScrolling();
     }
     MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
 
@@ -534,24 +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()
     {
@@ -559,29 +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;
         }