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 3f43008..113fd9f 100755 (executable)
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -20,10 +20,12 @@
  */
 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;
@@ -39,6 +41,7 @@ import java.awt.event.MouseWheelListener;
 import java.util.List;
 
 import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
 import javax.swing.SwingUtilities;
 import javax.swing.ToolTipManager;
 
@@ -93,25 +96,46 @@ 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())
     {
-      SequenceI sequence = av.getAlignment().getSequenceAt(seq);
-      StringBuilder tip = new StringBuilder(64);
-      seqAnnotReport.createTooltipAnnotationReport(tip, sequence,
-              av.isShowDBRefs(), av.isShowNPFeats(), sp.seqCanvas.fr);
-      setToolTipText(JvSwingUtils.wrapTooltip(true,
-              sequence.getDisplayId(true) + " " + tip.toString()));
+      /*
+       * 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
+    {
+      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 +150,14 @@ 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)
     {
@@ -197,7 +228,13 @@ 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);
 
@@ -277,9 +314,11 @@ 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;
     }
 
@@ -302,14 +341,13 @@ 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);
@@ -322,27 +360,33 @@ 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;
+    }
+
+    Sequence sq = (Sequence) av.getAlignment().getSequenceAt(pos.seqIndex);
 
     /*
      *  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)
       {
-        for (String link : sf.links)
-        {
-          nlinks.add(link);
-        }
+        nlinks.addAll(sf.links);
       }
     }
+    }
 
     PopupMenu pop = new PopupMenu(alignPanel, sq, features,
             Preferences.getGroupURLLinks());
@@ -350,6 +394,38 @@ public class IdPanel extends JPanel
   }
 
   /**
+   * 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;
+    }
+
+    JPopupMenu pop = new JPopupMenu(
+            MessageManager.getString("label.annotations"));
+    AnnotationLabels.addConsensusMenuOptions(this.alignPanel, ann, pop);
+    pop.show(this, e.getX(), e.getY());
+  }
+
+  /**
    * Toggle whether the sequence is part of the current selection group.
    * 
    * @param seq
@@ -359,7 +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);
   }
 
   /**
@@ -394,7 +470,7 @@ public class IdPanel extends JPanel
     for (int i = start; i <= end; i++)
     {
       av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
-              i == end);
+              false);
     }
   }
 
@@ -411,6 +487,7 @@ public class IdPanel extends JPanel
     {
       scrollThread.stopScrolling();
     }
+    MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
 
     mouseDragging = false;
     PaintRefresher.Refresh(this, av.getSequenceSetId());
@@ -419,7 +496,7 @@ public class IdPanel extends JPanel
 
     if (e.isPopupTrigger()) // Windows reports this in mouseReleased
     {
-      showPopupMenu(e);
+      showPopupMenu(e, pos);
     }
   }