X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=3ce9d4d8ac97de97188d1335ad97fb4325662e4f;hb=7634f98934b049825723fac41c8821ee38a355cd;hp=579229c06bc2d64e7881cc21e85e6e125350cc9b;hpb=fd5f6d3eed59b5f6d9a7cc09e4ddeb7e78eb2f17;p=jalview.git

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 579229c..3ce9d4d 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -20,17 +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 java.awt.BorderLayout;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
@@ -44,6 +33,17 @@ import javax.swing.JPopupMenu;
 import javax.swing.SwingUtilities;
 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.
@@ -62,8 +62,6 @@ public class IdPanel extends JPanel
 
   ScrollThread scrollThread = null;
 
-  String linkImageURL;
-
   int offy;
 
   // int width;
@@ -84,8 +82,7 @@ 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);
@@ -110,10 +107,12 @@ 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(annotation.label);
+      alignPanel.alignFrame.setStatus(
+              AnnotationLabels.getStatusMessage(annotation, anns));
     }
     else
     {
@@ -259,7 +258,7 @@ public class IdPanel extends JPanel
   {
     if (scrollThread != null)
     {
-      scrollThread.running = false;
+      scrollThread.stopScrolling();
     }
   }
 
@@ -366,24 +365,12 @@ 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<String> nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
-    List<SequenceFeature> features = sq.getFeatures().getNonPositionalFeatures();
-    for (SequenceFeature sf : features)
+    if (sq != null)
     {
-      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());
   }
 
   /**
@@ -428,7 +415,7 @@ public class IdPanel extends JPanel
     lastid = seq;
 
     SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
-    av.getSelectionGroup().addOrRemove(pickedSeq, true);
+    av.getSelectionGroup().addOrRemove(pickedSeq, false);
   }
 
   /**
@@ -463,7 +450,7 @@ public class IdPanel extends JPanel
     for (int i = start; i <= end; i++)
     {
       av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
-              i == end);
+              false);
     }
   }
 
@@ -478,7 +465,7 @@ public class IdPanel extends JPanel
   {
     if (scrollThread != null)
     {
-      scrollThread.running = false;
+      scrollThread.stopScrolling();
     }
     MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
 
@@ -503,7 +490,7 @@ public class IdPanel extends JPanel
   {
     getIdCanvas().setHighlighted(list);
 
-    if (list == null)
+    if (list == null || list.isEmpty())
     {
       return;
     }
@@ -528,24 +515,42 @@ 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()
     {
@@ -553,29 +558,20 @@ 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;
         }