JAL-819 menu options to reinstate missing auto-calculated annotation

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index fcb6572..a44df97 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -893,6 +893,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     scaleLeft.setVisible(av.getWrapAlignment());
     scaleRight.setVisible(av.getWrapAlignment());
     annotationPanelMenuItem.setState(av.isShowAnnotation());
+
     /*
      * Show/hide annotations only enabled if annotation panel is shown
      */
@@ -908,6 +909,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
     showSequenceLogo.setSelected(av.isShowSequenceLogo());
     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
+    buildAutoAnnotationMenu(av);
 
     ColourMenuHelper.setColourSelected(colourMenu,
             av.getGlobalColourScheme());
@@ -928,6 +930,168 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
+   * Adds menu items for the Autocalculated Annotation sub-menu
+   * 
+   * @param av 
+   */
+  void buildAutoAnnotationMenu(AlignViewport av)
+  {
+    autoAnnMenu.removeAll();
+    autoAnnMenu.add(showAutoFirst);
+    autoAnnMenu.add(showAutoLast);
+    autoAnnMenu.addSeparator();
+    autoAnnMenu.add(applyAutoAnnotationSettings);
+    autoAnnMenu.add(showConsensusHistogram);
+    autoAnnMenu.add(showSequenceLogo);
+    autoAnnMenu.add(normaliseSequenceLogo);
+    autoAnnMenu.addSeparator();
+
+    /*
+     * add options to reinstate any deleted auto-calculated annotations
+     */
+    boolean hasConservation = false;
+    boolean hasQuality = false;
+    boolean hasConsensus = false;
+    boolean hasOccupancy = false;
+    boolean hasRnaStruct = false;
+    AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
+    if (anns == null)
+    {
+      return;
+    }
+    for (int i = 0; i < anns.length; i++)
+    {
+      if (anns[i].autoCalculated)
+      {
+        // TODO JAL-3485 should let these strings be constants instead
+        if ("Conservation".equals(anns[i].label))
+        {
+          hasConservation = true;
+        }
+        else if ("Quality".equals(anns[i].label))
+        {
+          hasQuality = true;
+        }
+        else if ("Consensus".equals(anns[i].label))
+        {
+          hasConsensus = true;
+        }
+        else if ("Occupancy".equals(anns[i].label))
+        {
+          hasOccupancy = true;
+        }
+        else if ("StrucConsensus".equals(anns[i].label))
+        {
+          hasRnaStruct = true;
+        }
+      }
+    }
+    boolean added = false;
+
+    /*
+     * a shareable action to refresh stuff; NB action listeners
+     * get run in reverse order to that in which they are added!
+     */
+    ActionListener refresher = new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        alignPanel.adjustAnnotationHeight();
+        av.alignmentChanged(alignPanel);
+        buildAutoAnnotationMenu(av);
+      }
+    };
+
+    if (!av.isNucleotide())
+    {
+      if (!hasConservation)
+      {
+        JMenuItem mi = new JMenuItem("Conservation");
+        mi.addActionListener(refresher);
+        mi.addActionListener(new ActionListener()
+        {
+          @Override
+          public void actionPerformed(ActionEvent e)
+          {
+            av.initConservation();
+          }
+        });
+        autoAnnMenu.add(mi);
+        added = true;
+      }
+      if (!hasQuality)
+      {
+        JMenuItem mi = new JMenuItem("Quality");
+        mi.addActionListener(refresher);
+        mi.addActionListener(new ActionListener()
+        {
+          @Override
+          public void actionPerformed(ActionEvent e)
+          {
+            av.initQuality();
+          }
+        });
+        autoAnnMenu.add(mi);
+        added = true;
+      }
+    }
+    if (!hasConsensus)
+    {
+      JMenuItem mi = new JMenuItem("Consensus");
+      mi.addActionListener(refresher);
+      mi.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          av.initConsensus();
+        }
+      });
+      autoAnnMenu.add(mi);
+      added = true;
+    }
+    if (!hasOccupancy)
+    {
+      JMenuItem mi = new JMenuItem("Occupancy");
+      mi.addActionListener(refresher);
+      mi.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          av.initOccupancy();
+        }
+      });
+      autoAnnMenu.add(mi);
+      added = true;
+    }
+    if (!hasRnaStruct && av.isNucleotide()
+            && av.getAlignment().hasRNAStructure())
+    {
+      JMenuItem mi = new JMenuItem("Structure Consensus");
+      mi.addActionListener(refresher);
+      mi.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          av.initRNAStructure();
+        }
+      });
+      autoAnnMenu.add(mi);
+      added = true;
+    }
+
+    if (added)
+    {
+      autoAnnMenu.addSeparator();
+    }
+    autoAnnMenu.add(showGroupConservation);
+    autoAnnMenu.add(showGroupConsensus);
+  }
+
+  /**
    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
    * 
    * @param b