X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=7b491e47e59ec10f8abdb2e39764bc66dff6bcb0;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=a4f79c23c547b43f7fbd01f5558896553f486188;hpb=06de78be50c3934158fa1d35ec92ad86b54e959f;p=jalview.git

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index a4f79c2..7b491e4 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -20,16 +20,9 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.io.SequenceAnnotationReport;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.viewmodel.AlignmentViewport;
-
 import java.awt.BorderLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
@@ -38,9 +31,22 @@ import java.awt.event.MouseWheelListener;
 import java.util.List;
 
 import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
 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.
@@ -59,8 +65,6 @@ public class IdPanel extends JPanel
 
   ScrollThread scrollThread = null;
 
-  String linkImageURL;
-
   int offy;
 
   // int width;
@@ -81,8 +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);
@@ -92,26 +95,45 @@ 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)
   {
     SeqPanel sp = alignPanel.getSeqPanel();
-    int seq = Math.max(0, sp.findSeq(e));
-    if (seq > -1 && seq < av.getAlignment().getHeight())
+    MousePos pos = sp.findMousePosition(e);
+    if (pos.isOverAnnotation())
+    {
+      /*
+       * mouse is over an annotation label in wrapped mode
+       */
+      AlignmentAnnotation[] anns = av.getAlignment()
+              .getAlignmentAnnotation();
+      AlignmentAnnotation annotation = anns[pos.annotationIndex];
+      setToolTipText(AnnotationLabels.getTooltip(annotation));
+      alignPanel.alignFrame.setStatus(
+              AnnotationLabels.getStatusMessage(annotation, anns));
+    }
+    else
     {
-      SequenceI sequence = av.getAlignment().getSequenceAt(seq);
-      StringBuilder tip = new StringBuilder(64);
-      seqAnnotReport.createTooltipAnnotationReport(tip, sequence,
-              av.isShowDBRefs(), av.isShowNPFeats(),
-              sp.seqCanvas.fr.getMinMax());
-      setToolTipText(JvSwingUtils.wrapTooltip(true,
-              sequence.getDisplayId(true) + " " + tip.toString()));
+      int seq = Math.max(0, pos.seqIndex);
+      if (seq < av.getAlignment().getHeight())
+      {
+        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, tip.toString()));
+
+        StringBuilder text = new StringBuilder();
+        text.append("Sequence ").append(String.valueOf(seq + 1))
+                .append(" ID: ").append(sequence.getName());
+        alignPanel.alignFrame.setStatus(text.toString());
+      }
     }
   }
 
@@ -126,7 +148,14 @@ public class IdPanel extends JPanel
   {
     mouseDragging = true;
 
-    int seq = Math.max(0, alignPanel.getSeqPanel().findSeq(e));
+    MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
+    if (pos.isOverAnnotation())
+    {
+      // mouse is over annotation label in wrapped mode
+      return;
+    }
+
+    int seq = Math.max(0, pos.seqIndex);
 
     if (seq < lastid)
     {
@@ -148,7 +177,8 @@ public class IdPanel extends JPanel
   public void mouseWheelMoved(MouseWheelEvent e)
   {
     e.consume();
-    if (e.getWheelRotation() > 0)
+    double wheelRotation = e.getPreciseWheelRotation();
+    if (wheelRotation > 0)
     {
       if (e.isShiftDown())
       {
@@ -159,7 +189,7 @@ public class IdPanel extends JPanel
         av.getRanges().scrollUp(false);
       }
     }
-    else
+    else if (wheelRotation < 0)
     {
       if (e.isShiftDown())
       {
@@ -196,7 +226,13 @@ public class IdPanel extends JPanel
       return;
     }
 
-    int seq = alignPanel.getSeqPanel().findSeq(e);
+    MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
+    int seq = pos.seqIndex;
+    if (pos.isOverAnnotation() || seq < 0)
+    {
+      return;
+    }
+
     String id = av.getAlignment().getSequenceAt(seq).getName();
     String url = Preferences.sequenceUrlLinks.getPrimaryUrl(id);
 
@@ -214,17 +250,25 @@ public class IdPanel extends JPanel
   }
 
   /**
-   * DOCUMENT ME!
+   * On (re-)entering the panel, stop any scrolling
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   @Override
   public void mouseEntered(MouseEvent e)
   {
+    stopScrolling();
+  }
+
+  /**
+   * Interrupts the scroll thread if one is running
+   */
+  void stopScrolling()
+  {
     if (scrollThread != null)
     {
-      scrollThread.running = false;
+      scrollThread.stopScrolling();
+      scrollThread = null;
     }
   }
 
@@ -242,16 +286,72 @@ public class IdPanel extends JPanel
       return;
     }
 
-    if (mouseDragging && (e.getY() < 0)
-            && (av.getRanges().getStartSeq() > 0))
+    if (mouseDragging)
     {
-      scrollThread = new ScrollThread(true);
+      /*
+       * on mouse drag above or below the panel, start 
+       * scrolling if there are more sequences to show
+       */
+      ViewportRanges ranges = av.getRanges();
+      if (e.getY() < 0 && ranges.getStartSeq() > 0)
+      {
+        startScrolling(true);
+      }
+      else if (e.getY() >= getHeight()
+              && ranges.getEndSeq() <= av.getAlignment().getHeight())
+      {
+        startScrolling(false);
+      }
     }
+  }
 
-    if (mouseDragging && (e.getY() >= getHeight())
-            && (av.getAlignment().getHeight() > av.getRanges().getEndSeq()))
+  /**
+   * Starts scrolling either up or down
+   * 
+   * @param up
+   */
+  void startScrolling(boolean up)
+  {
+    scrollThread = new ScrollThread(up);
+    if (Platform.isJS())
     {
-      scrollThread = new ScrollThread(false);
+      /*
+       * for JalviewJS using Swing Timer
+       */
+      Timer t = new Timer(20, new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          if (scrollThread != null)
+          {
+            // if (!scrollOnce() {t.stop();}) gives compiler error :-(
+            scrollThread.scrollOnce();
+          }
+        }
+      });
+      t.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          if (scrollThread == null)
+          {
+            // IdPanel.stopScrolling called
+            t.stop();
+          }
+        }
+      });
+      t.start();
+    }
+    else
+    /**
+     * Java only
+     * 
+     * @j2sIgnore
+     */
+    {
+      scrollThread.start();
     }
   }
 
@@ -276,9 +376,11 @@ public class IdPanel extends JPanel
       return;
     }
 
+    MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
+
     if (e.isPopupTrigger()) // Mac reports this in mousePressed
     {
-      showPopupMenu(e);
+      showPopupMenu(e, pos);
       return;
     }
 
@@ -287,7 +389,7 @@ public class IdPanel extends JPanel
      * (where isPopupTrigger() will answer true)
      * NB isRightMouseButton is also true for Cmd-click on Mac
      */
-    if (SwingUtilities.isRightMouseButton(e) && !Platform.isAMac())
+    if (Platform.isWinRightButton(e))
     {
       return;
     }
@@ -301,14 +403,13 @@ public class IdPanel extends JPanel
       av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);
     }
 
-    int seq = alignPanel.getSeqPanel().findSeq(e);
     if (e.isShiftDown() && (lastid != -1))
     {
-      selectSeqs(lastid, seq);
+      selectSeqs(lastid, pos.seqIndex);
     }
     else
     {
-      selectSeq(seq);
+      selectSeq(pos.seqIndex);
     }
 
     av.isSelectionGroupChanged(true);
@@ -321,30 +422,52 @@ public class IdPanel extends JPanel
    * 
    * @param e
    */
-  void showPopupMenu(MouseEvent e)
+  void showPopupMenu(MouseEvent e, MousePos pos)
   {
-    int seq2 = alignPanel.getSeqPanel().findSeq(e);
-    Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq2);
+    if (pos.isOverAnnotation())
+    {
+      showAnnotationMenu(e, pos);
+      return;
+    }
 
-    /*
-     *  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)
+    Sequence sq = (Sequence) av.getAlignment().getSequenceAt(pos.seqIndex);
+    if (sq != null)
     {
-      if (sf.links != null)
-      {
-        for (String link : sf.links)
-        {
-          nlinks.add(link);
-        }
-      }
+      PopupMenu pop = new PopupMenu(alignPanel, sq,
+              Preferences.getGroupURLLinks());
+      pop.show(this, e.getX(), e.getY());
+    }
+  }
+
+  /**
+   * On right mouse click on a Consensus annotation label, shows a limited popup
+   * menu, with options to configure the consensus calculation and rendering.
+   * 
+   * @param e
+   * @param pos
+   * @see AnnotationLabels#showPopupMenu(MouseEvent)
+   */
+  void showAnnotationMenu(MouseEvent e, MousePos pos)
+  {
+    if (pos.annotationIndex == -1)
+    {
+      return;
+    }
+    AlignmentAnnotation[] anns = this.av.getAlignment()
+            .getAlignmentAnnotation();
+    if (anns == null || pos.annotationIndex >= anns.length)
+    {
+      return;
+    }
+    AlignmentAnnotation ann = anns[pos.annotationIndex];
+    if (!ann.label.contains("Consensus"))
+    {
+      return;
     }
 
-    PopupMenu pop = new PopupMenu(alignPanel, sq, features,
-            Preferences.getGroupURLLinks());
+    JPopupMenu pop = new JPopupMenu(
+            MessageManager.getString("label.annotations"));
+    AnnotationLabels.addConsensusMenuOptions(this.alignPanel, ann, pop);
     pop.show(this, e.getX(), e.getY());
   }
 
@@ -358,7 +481,7 @@ public class IdPanel extends JPanel
     lastid = seq;
 
     SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
-    av.getSelectionGroup().addOrRemove(pickedSeq, true);
+    av.getSelectionGroup().addOrRemove(pickedSeq, false);
   }
 
   /**
@@ -393,7 +516,7 @@ public class IdPanel extends JPanel
     for (int i = start; i <= end; i++)
     {
       av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
-              i == end);
+              false);
     }
   }
 
@@ -408,8 +531,9 @@ public class IdPanel extends JPanel
   {
     if (scrollThread != null)
     {
-      scrollThread.running = false;
+      stopScrolling();
     }
+    MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
 
     mouseDragging = false;
     PaintRefresher.Refresh(this, av.getSequenceSetId());
@@ -418,7 +542,7 @@ public class IdPanel extends JPanel
 
     if (e.isPopupTrigger()) // Windows reports this in mouseReleased
     {
-      showPopupMenu(e);
+      showPopupMenu(e, pos);
     }
   }
 
@@ -432,7 +556,7 @@ public class IdPanel extends JPanel
   {
     getIdCanvas().setHighlighted(list);
 
-    if (list == null)
+    if (list == null || list.isEmpty())
     {
       return;
     }
@@ -457,24 +581,41 @@ 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;
-      start();
+      setName("IdPanel$ScrollThread$" + String.valueOf(up));
     }
 
+    /**
+     * 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 by a call to stopScrolling.
+     */
     @Override
     public void run()
     {
@@ -482,34 +623,7 @@ public class IdPanel extends JPanel
 
       while (running)
       {
-        if (av.getRanges().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;
-        }
-        else
-        {
-          running = false;
-        }
-
-        alignPanel.paintAlignment(false, false);
-
+        running = scrollOnce();
         try
         {
           Thread.sleep(100);
@@ -517,6 +631,27 @@ public class IdPanel extends JPanel
         {
         }
       }
+      IdPanel.this.scrollThread = null;
+    }
+
+    /**
+     * Scrolls one row up or down. Answers true if a scroll could be done, false
+     * if not (top or bottom of alignment reached).
+     */
+    boolean scrollOnce()
+    {
+      ViewportRanges ranges = IdPanel.this.av.getRanges();
+      if (ranges.scrollUp(up))
+      {
+        int toSeq = up ? ranges.getStartSeq() : ranges.getEndSeq();
+        int fromSeq = toSeq < lastid ? lastid - 1 : lastid + 1;
+        IdPanel.this.selectSeqs(fromSeq, toSeq);
+        lastid = toSeq;
+        alignPanel.paintAlignment(false, false);
+        return true;
+      }
+
+      return false;
     }
   }
 }