JAL-1506 delete all warning; JAL-1264 show/hide annotations

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 4168516..69af72b 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -334,7 +334,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     setMenusFromViewport(viewport);
     buildSortByAnnotationScoresMenu();
     buildTreeMenu();
-    buildShowHideAnnotationMenus();
     
     if (viewport.wrapAlignment)
     {
@@ -507,14 +506,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         case KeyEvent.VK_F1:
           try
           {
-            ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
-            java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
-                    "help/help");
-            javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
-
-            javax.help.HelpBroker hb = hs.createHelpBroker();
-            hb.setCurrentID("home");
-            hb.setDisplayed(true);
+            Help.showHelpWindow();
           } catch (Exception ex)
           {
             ex.printStackTrace();
@@ -731,6 +723,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     scaleLeft.setVisible(av.wrapAlignment);
     scaleRight.setVisible(av.wrapAlignment);
     annotationPanelMenuItem.setState(av.showAnnotation);
+    /*
+     * Show/hide all annotations only enabled if annotation panel is shown
+     */
+    showAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
+    hideAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
     viewBoxesMenuItem.setSelected(av.showBoxes);
     viewTextMenuItem.setSelected(av.showText);
     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
@@ -2184,17 +2181,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       return;
     }
 
-    Vector seqs = new Vector();
+    List<SequenceI> seqs = new ArrayList<SequenceI>(sg.getSize());
     SequenceI seq;
     for (int i = 0; i < sg.getSize(); i++)
     {
       seq = sg.getSequenceAt(i);
-      seqs.addElement(seq);
+      seqs.add(seq);
     }
 
-    // If the cut affects all sequences, remove highlighted columns
+    // If the cut affects all sequences, warn, remove highlighted columns
     if (sg.getSize() == viewport.getAlignment().getHeight())
     {
+      int confirm = JOptionPane.showConfirmDialog(this,
+              MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
+              MessageManager.getString("label.delete_all"), // $NON-NLS-1$
+              JOptionPane.OK_CANCEL_OPTION);
+
+      if (confirm == JOptionPane.CANCEL_OPTION
+              || confirm == JOptionPane.CLOSED_OPTION)
+      {
+        return;
+      }
       viewport.getColumnSelection().removeElements(sg.getStartRes(),
               sg.getEndRes() + 1);
     }
@@ -2202,7 +2209,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     SequenceI[] cut = new SequenceI[seqs.size()];
     for (int i = 0; i < seqs.size(); i++)
     {
-      cut[i] = (SequenceI) seqs.elementAt(i);
+      cut[i] = seqs.get(i);
     }
 
     /*
@@ -3039,16 +3046,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Action on toggle of the 'Show annotations' menu item. This shows or hides
+   * the annotations panel as a whole.
+   * 
+   * The options to show/hide all annotations should be enabled when the panel
+   * is shown, and disabled when the panel is hidden.
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   @Override
   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
-    alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
+    final boolean setVisible = annotationPanelMenuItem.isSelected();
+    viewport.setShowAnnotation(setVisible);
+    alignPanel.setAnnotationVisible(setVisible);
+    this.showAllAnnotations.setEnabled(setVisible);
+    this.hideAllAnnotations.setEnabled(setVisible);
   }
 
   @Override
@@ -5709,16 +5722,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * On menu option, open a panel to allow choice of annotation types to
-   * show/hide.
-   */
-  @Override
-  protected void chooseAnnotations_actionPerformed()
-  {
-    new AnnotationChooser(this.alignPanel);
-  }
-
-  /**
    * Get a list of unique annotation types for the alignment, optionally
    * restricted to sequence-specific annotations.
    */
@@ -5743,59 +5746,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * Action on selection of an annotation type to Show or Hide.
+   * Action on selection of menu option to Show or Hide all annotations.
    * 
-   * @param type
-   * @param doShow
+   * @param visibile
    */
   @Override
-  protected void showHideAnnotation_actionPerformed(String type, boolean doShow)
+  protected void setAllAnnotationsVisibility(boolean visible)
   {
     for (AlignmentAnnotation aa : alignPanel.getAlignment()
             .getAlignmentAnnotation())
     {
-      if (type.equals(aa.label))
-      {
-        aa.visible = doShow;
-      }
+      aa.visible = visible;
     }
     this.alignPanel.paintAlignment(true);
   }
-
-  /**
-   * Dynamically build the list of annotation types to show or hide.
-   */
-  @Override
-  protected void buildShowHideAnnotationMenus()
-  {
-    showAnnotations.removeAll();
-    hideAnnotations.removeAll();
-
-    List<String> types = getAnnotationTypes(false);
-    for (final String type : types)
-    {
-      final JMenuItem showitem = new JMenuItem(type);
-      showitem.addActionListener(new java.awt.event.ActionListener()
-      {
-        @Override
-        public void actionPerformed(ActionEvent e)
-        {
-          showHideAnnotation_actionPerformed(type, true);
-        }
-      });
-      showAnnotations.add(showitem);
-      final JMenuItem hideitem = new JMenuItem(type);
-      hideitem.addActionListener(new java.awt.event.ActionListener()
-      {
-        @Override
-        public void actionPerformed(ActionEvent e)
-        {
-          showHideAnnotation_actionPerformed(type, false);
-        }
-      });
-      hideAnnotations.add(hideitem);
-    }
-  }
 }
 
 class PrintThread extends Thread