JAL-3093 limited Consensus popup menu when in wrapped mode

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 2517a9f..739fc0f 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -376,15 +376,6 @@ public class AnnotationLabels extends JPanel
             AlignmentUtils.showOrHideSequenceAnnotations(
                     ap.av.getAlignment(), Collections.singleton(label),
                     null, false, false);
-            // for (AlignmentAnnotation ann : ap.av.getAlignment()
-            // .getAlignmentAnnotation())
-            // {
-            // if (ann.sequenceRef != null && ann.label != null
-            // && ann.label.equals(label))
-            // {
-            // ann.visible = false;
-            // }
-            // }
             ap.refresh(true);
           }
         });
@@ -423,174 +414,154 @@ public class AnnotationLabels extends JPanel
       }
       else if (label.indexOf("Consensus") > -1)
       {
-        pop.addSeparator();
-        // av and sequencegroup need to implement same interface for
-        final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
-                MessageManager.getString("label.ignore_gaps_consensus"),
-                (aa[selectedRow].groupRef != null)
-                        ? aa[selectedRow].groupRef.getIgnoreGapsConsensus()
-                        : ap.av.isIgnoreGapsConsensus());
-        final AlignmentAnnotation aaa = aa[selectedRow];
-        cbmi.addActionListener(new ActionListener()
-        {
-          @Override
-          public void actionPerformed(ActionEvent e)
-          {
-            if (aaa.groupRef != null)
-            {
-              // TODO: pass on reference to ap so the view can be updated.
-              aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
-              ap.getAnnotationPanel()
-                      .paint(ap.getAnnotationPanel().getGraphics());
-            }
-            else
-            {
-              ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
-            }
-            ap.alignmentChanged();
-          }
-        });
-        pop.add(cbmi);
-        // av and sequencegroup need to implement same interface for
+        addConsensusMenuOptions(ap, aa[selectedRow], pop);
+
+        final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
+        consclipbrd.addActionListener(this);
+        pop.add(consclipbrd);
+      }
+    }
+    pop.show(this, evt.getX(), evt.getY());
+  }
+
+  /**
+   * A helper method that adds menu options for calculation and visualisation of
+   * group and/or alignment consensus annotation to a popup menu. This is
+   * designed to be reusable for either unwrapped mode (popup menu is shown on
+   * component AnnotationLabels), or wrapped mode (popup menu is shown on
+   * IdPanel when the mouse is over an annotation label).
+   * 
+   * @param ap
+   * @param ann
+   * @param pop
+   */
+  static void addConsensusMenuOptions(AlignmentPanel ap,
+          AlignmentAnnotation ann,
+          JPopupMenu pop)
+  {
+    pop.addSeparator();
+
+    final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+            MessageManager.getString("label.ignore_gaps_consensus"),
+            (ann.groupRef != null) ? ann.groupRef.getIgnoreGapsConsensus()
+                    : ap.av.isIgnoreGapsConsensus());
+    final AlignmentAnnotation aaa = ann;
+    cbmi.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
         if (aaa.groupRef != null)
         {
-          final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
-                  MessageManager.getString("label.show_group_histogram"),
-                  aa[selectedRow].groupRef.isShowConsensusHistogram());
-          chist.addActionListener(new ActionListener()
-          {
-            @Override
-            public void actionPerformed(ActionEvent e)
-            {
-              // TODO: pass on reference
-              // to ap
-              // so the
-              // view
-              // can be
-              // updated.
-              aaa.groupRef.setShowConsensusHistogram(chist.getState());
-              ap.repaint();
-              // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
-            }
-          });
-          pop.add(chist);
-          final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
-                  MessageManager.getString("label.show_group_logo"),
-                  aa[selectedRow].groupRef.isShowSequenceLogo());
-          cprofl.addActionListener(new ActionListener()
-          {
-            @Override
-            public void actionPerformed(ActionEvent e)
-            {
-              // TODO: pass on reference
-              // to ap
-              // so the
-              // view
-              // can be
-              // updated.
-              aaa.groupRef.setshowSequenceLogo(cprofl.getState());
-              ap.repaint();
-              // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
-            }
-          });
-          pop.add(cprofl);
-          final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
-                  MessageManager.getString("label.normalise_group_logo"),
-                  aa[selectedRow].groupRef.isNormaliseSequenceLogo());
-          cproflnorm.addActionListener(new ActionListener()
-          {
-            @Override
-            public void actionPerformed(ActionEvent e)
-            {
-
-              // TODO: pass on reference
-              // to ap
-              // so the
-              // view
-              // can be
-              // updated.
-              aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState());
-              // automatically enable logo display if we're clicked
-              aaa.groupRef.setshowSequenceLogo(true);
-              ap.repaint();
-              // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
-            }
-          });
-          pop.add(cproflnorm);
+          aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
+          ap.getAnnotationPanel()
+                  .paint(ap.getAnnotationPanel().getGraphics());
         }
         else
         {
-          final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
-                  MessageManager.getString("label.show_histogram"),
-                  av.isShowConsensusHistogram());
-          chist.addActionListener(new ActionListener()
-          {
-            @Override
-            public void actionPerformed(ActionEvent e)
-            {
-              // TODO: pass on reference
-              // to ap
-              // so the
-              // view
-              // can be
-              // updated.
-              av.setShowConsensusHistogram(chist.getState());
-              ap.alignFrame.setMenusForViewport();
-              ap.repaint();
-              // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
-            }
-          });
-          pop.add(chist);
-          final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
-                  MessageManager.getString("label.show_logo"),
-                  av.isShowSequenceLogo());
-          cprof.addActionListener(new ActionListener()
-          {
-            @Override
-            public void actionPerformed(ActionEvent e)
-            {
-              // TODO: pass on reference
-              // to ap
-              // so the
-              // view
-              // can be
-              // updated.
-              av.setShowSequenceLogo(cprof.getState());
-              ap.alignFrame.setMenusForViewport();
-              ap.repaint();
-              // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
-            }
-          });
-          pop.add(cprof);
-          final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
-                  MessageManager.getString("label.normalise_logo"),
-                  av.isNormaliseSequenceLogo());
-          cprofnorm.addActionListener(new ActionListener()
-          {
-            @Override
-            public void actionPerformed(ActionEvent e)
-            {
-              // TODO: pass on reference
-              // to ap
-              // so the
-              // view
-              // can be
-              // updated.
-              av.setShowSequenceLogo(true);
-              av.setNormaliseSequenceLogo(cprofnorm.getState());
-              ap.alignFrame.setMenusForViewport();
-              ap.repaint();
-              // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
-            }
-          });
-          pop.add(cprofnorm);
+          ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
         }
-        final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
-        consclipbrd.addActionListener(this);
-        pop.add(consclipbrd);
+        ap.alignmentChanged();
       }
+    });
+    pop.add(cbmi);
+
+    if (aaa.groupRef != null)
+    {
+      /*
+       * group consensus options
+       */
+      final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+              MessageManager.getString("label.show_group_histogram"),
+              ann.groupRef.isShowConsensusHistogram());
+      chist.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          aaa.groupRef.setShowConsensusHistogram(chist.getState());
+          ap.repaint();
+        }
+      });
+      pop.add(chist);
+      final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
+              MessageManager.getString("label.show_group_logo"),
+              ann.groupRef.isShowSequenceLogo());
+      cprofl.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          aaa.groupRef.setshowSequenceLogo(cprofl.getState());
+          ap.repaint();
+        }
+      });
+      pop.add(cprofl);
+      final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
+              MessageManager.getString("label.normalise_group_logo"),
+              ann.groupRef.isNormaliseSequenceLogo());
+      cproflnorm.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState());
+          // automatically enable logo display if we're clicked
+          aaa.groupRef.setshowSequenceLogo(true);
+          ap.repaint();
+        }
+      });
+      pop.add(cproflnorm);
+    }
+    else
+    {
+      /*
+       * alignment consensus options
+       */
+      final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+              MessageManager.getString("label.show_histogram"),
+              ap.av.isShowConsensusHistogram());
+      chist.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          ap.av.setShowConsensusHistogram(chist.getState());
+          ap.alignFrame.setMenusForViewport();
+          ap.repaint();
+        }
+      });
+      pop.add(chist);
+      final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
+              MessageManager.getString("label.show_logo"),
+              ap.av.isShowSequenceLogo());
+      cprof.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          ap.av.setShowSequenceLogo(cprof.getState());
+          ap.alignFrame.setMenusForViewport();
+          ap.repaint();
+        }
+      });
+      pop.add(cprof);
+      final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
+              MessageManager.getString("label.normalise_logo"),
+              ap.av.isNormaliseSequenceLogo());
+      cprofnorm.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          ap.av.setShowSequenceLogo(true);
+          ap.av.setNormaliseSequenceLogo(cprofnorm.getState());
+          ap.alignFrame.setMenusForViewport();
+          ap.repaint();
+        }
+      });
+      pop.add(cprofnorm);
     }
-    pop.show(this, evt.getX(), evt.getY());
   }
 
   /**

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 54aeef2..6cb4e17 100755 (executable)
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -40,6 +40,7 @@ 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;
 
@@ -306,11 +307,6 @@ public class IdPanel extends JPanel
     }
 
     MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
-    if (pos.isOverAnnotation())
-    {
-      // mouse is over an annotation label in wrapped mode
-      return;
-    }
     
     if (e.isPopupTrigger()) // Mac reports this in mousePressed
     {
@@ -358,6 +354,12 @@ public class IdPanel extends JPanel
    */
   void showPopupMenu(MouseEvent e, MousePos pos)
   {
+    if (pos.isOverAnnotation())
+    {
+      showAnnotationMenu(e, pos);
+      return;
+    }
+
     Sequence sq = (Sequence) av.getAlignment().getSequenceAt(pos.seqIndex);
 
     /*
@@ -380,6 +382,38 @@ 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
@@ -442,11 +476,6 @@ public class IdPanel extends JPanel
       scrollThread.running = false;
     }
     MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
-    if (pos.isOverAnnotation())
-    {
-      // mouse is over an annotation label in wrapped mode
-      return;
-    }
 
     mouseDragging = false;
     PaintRefresher.Refresh(this, av.getSequenceSetId());