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 6cb4e17..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;
@@ -95,11 +96,10 @@ public class IdPanel extends JPanel
   }
 
   /**
-   * Respond to mouse movement by constructing tooltip text for the sequence id
-   * under the mouse.
+   * Responds to mouse movement by setting tooltip text for the sequence id
+   * under the mouse (or possibly annotation label, when in wrapped mode)
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   @Override
   public void mouseMoved(MouseEvent e)
@@ -111,9 +111,12 @@ public class IdPanel extends JPanel
       /*
        * mouse is over an annotation label in wrapped mode
        */
-      AlignmentAnnotation annotation = av.getAlignment()
-              .getAlignmentAnnotation()[pos.annotationIndex];
+      AlignmentAnnotation[] anns = av.getAlignment()
+              .getAlignmentAnnotation();
+      AlignmentAnnotation annotation = anns[pos.annotationIndex];
       setToolTipText(AnnotationLabels.getTooltip(annotation));
+      alignPanel.alignFrame.setStatus(
+              AnnotationLabels.getStatusMessage(annotation, anns));
     }
     else
     {
@@ -122,10 +125,16 @@ public class IdPanel extends JPanel
       {
         SequenceI sequence = av.getAlignment().getSequenceAt(seq);
         StringBuilder tip = new StringBuilder(64);
+        tip.append(sequence.getDisplayId(true)).append(" ");
         seqAnnotReport.createTooltipAnnotationReport(tip, sequence,
                 av.isShowDBRefs(), av.isShowNPFeats(), sp.seqCanvas.fr);
-        setToolTipText(JvSwingUtils.wrapTooltip(true,
-                sequence.getDisplayId(true) + " " + tip.toString()));
+        setToolTipText(JvSwingUtils.wrapTooltip(true, tip.toString()));
+
+        StringBuilder text = new StringBuilder();
+        text.append("Sequence ").append(String.valueOf(seq + 1))
+                .append(" ID: ")
+                .append(sequence.getName());
+        alignPanel.alignFrame.setStatus(text.toString());
       }
     }
   }
@@ -220,13 +229,12 @@ public class IdPanel extends JPanel
     }
 
     MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
-    if (pos.isOverAnnotation())
+    int seq = pos.seqIndex;
+    if (pos.isOverAnnotation() || seq < 0)
     {
-      // mouse is over annotation label in wrapped mode
       return;
     }
 
-    int seq = pos.seqIndex;
     String id = av.getAlignment().getSequenceAt(seq).getName();
     String url = Preferences.sequenceUrlLinks.getPrimaryUrl(id);
 
@@ -254,7 +262,7 @@ public class IdPanel extends JPanel
   {
     if (scrollThread != null)
     {
-      scrollThread.running = false;
+      scrollThread.stopScrolling();
     }
   }
 
@@ -366,8 +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)
@@ -375,6 +386,7 @@ public class IdPanel extends JPanel
         nlinks.addAll(sf.links);
       }
     }
+    }
 
     PopupMenu pop = new PopupMenu(alignPanel, sq, features,
             Preferences.getGroupURLLinks());
@@ -423,7 +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);
   }
 
   /**
@@ -458,7 +470,7 @@ public class IdPanel extends JPanel
     for (int i = start; i <= end; i++)
     {
       av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
-              i == end);
+              false);
     }
   }
 
@@ -473,7 +485,7 @@ public class IdPanel extends JPanel
   {
     if (scrollThread != null)
     {
-      scrollThread.running = false;
+      scrollThread.stopScrolling();
     }
     MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
 
@@ -523,24 +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()
     {
@@ -548,29 +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;
         }