X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=3f0d73667f83e60537de6409005f48182d638d6c;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=3996dee7d549cfd308e1e4da3fefbfc1db5c4162;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 3996dee..3f0d736 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -75,6 +75,7 @@ import java.awt.BorderLayout;
 import java.awt.Canvas;
 import java.awt.CheckboxMenuItem;
 import java.awt.Color;
+import java.awt.FlowLayout;
 import java.awt.Font;
 import java.awt.FontMetrics;
 import java.awt.Frame;
@@ -83,6 +84,7 @@ import java.awt.Label;
 import java.awt.Menu;
 import java.awt.MenuBar;
 import java.awt.MenuItem;
+import java.awt.Panel;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.FocusEvent;
@@ -232,8 +234,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
-    showAlignmentAnnotations.setState(viewport.isShowAnnotation());
-    showSequenceAnnotations.setState(viewport.isShowAnnotation());
+    showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
+    showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
+    showAlignmentAnnotations.setState(true);
+    showSequenceAnnotations.setState(false);
 
     seqLimits.setState(viewport.getShowJVSuffix());
 
@@ -302,6 +306,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
     alignPanel.alabels.addKeyListener(this);
 
+    setAnnotationsVisibility();
+
     if (addToDisplay)
     {
       addToDisplay(embedded);
@@ -812,8 +818,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     else if (source == annotationPanelMenuItem)
     {
-      viewport.setShowAnnotation(annotationPanelMenuItem.getState());
-      alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
+      boolean showAnnotations = annotationPanelMenuItem.getState();
+      showAlignmentAnnotations.setEnabled(showAnnotations);
+      showSequenceAnnotations.setEnabled(showAnnotations);
+      viewport.setShowAnnotation(showAnnotations);
+      alignPanel.setAnnotationVisible(showAnnotations);
     }
     else if (source == sequenceFeatures)
     {
@@ -913,7 +922,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   /**
    * Set the visibility state of sequence-related and/or alignment-related
-   * annotations depending on checkbox selections. Repaint after calling.
+   * annotations depending on checkbox selections, and repaint.
    * 
    * @param visible
    */
@@ -1743,9 +1752,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
               viewport, complement);
       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
               up ? null : complement.getHiddenRepSequences(), up);
-      // TODO need to trigger a repaint of the complementary panel - how?
-      // would prefer to handle in SplitFrame but it is not overriding key
-      // listener chiz
+      getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
     }
   }
 
@@ -2059,9 +2066,32 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       seqs.addElement(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())
     {
+      boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
+              .getAlignment().getWidth()) ? true : false;
+      if (isEntireAlignWidth)
+      {
+        String title = MessageManager.getString("label.delete_all");
+        Panel infoPanel = new Panel();
+        infoPanel.setLayout(new FlowLayout());
+        infoPanel
+                .add(new Label(MessageManager.getString("warn.delete_all")));
+
+        final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
+        dialog.setMainPanel(infoPanel);
+        dialog.ok.setLabel(MessageManager.getString("action.ok"));
+        dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
+        dialog.setVisible(true);
+
+        if (!dialog.accept)
+        {
+          return;
+        }
+      }
       viewport.getColumnSelection().removeElements(sg.getStartRes(),
               sg.getEndRes() + 1);
     }
@@ -3357,8 +3387,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             MessageManager.getString("label.sort_annotations_by_label"));
     showAutoFirst = new CheckboxMenuItem(
             MessageManager.getString("label.show_first"));
+    showAutoFirst.setState(false); // pending applet parameter
+    setShowAutoCalculatedAbove(showAutoFirst.getState());
     showAutoLast = new CheckboxMenuItem(
             MessageManager.getString("label.show_last"));
+    showAutoLast.setState(!showAutoFirst.getState());
     showAlignmentAnnotations.addItemListener(this);
     showSequenceAnnotations.addItemListener(this);
     sortAnnBySequence.addItemListener(this);