JAL-1517 update copyright to version 2.8.2

[jalview.git] / src / jalview / appletgui / AnnotationPanel.java

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index f4b2212..4a5fc8b 100755 (executable)
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -14,6 +14,7 @@
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
@@ -25,6 +26,7 @@ import java.awt.event.*;
 import jalview.datamodel.*;
 import jalview.renderer.AnnotationRenderer;
 import jalview.renderer.AwtRenderPanelI;
+import jalview.util.MessageManager;
 
 public class AnnotationPanel extends Panel implements AwtRenderPanelI,
         AdjustmentListener, ActionListener, MouseListener,
@@ -234,6 +236,10 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       if ((label.length() > 0) && !aa[activeRow].hasText)
       {
         aa[activeRow].hasText = true;
+        if (evt.getActionCommand().equals(STEM))
+        {
+          aa[activeRow].showAllColLabels=true;
+        }
       }
 
       for (int i = 0; i < av.getColumnSelection().size(); i++)
@@ -253,10 +259,10 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       }
     }
 
-    aa[activeRow].validateRangeAndDisplay();
+    av.getAlignment().validateAnnotation(aa[activeRow]);
 
-    adjustPanelHeight();
     ap.alignmentChanged();
+    adjustPanelHeight();
     repaint();
 
     return;
@@ -317,7 +323,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
         return;
       }
 
-      PopupMenu pop = new PopupMenu("Structure type");
+      PopupMenu pop = new PopupMenu(MessageManager.getString("label.structure_type"));
       MenuItem item;
       /*
        * Just display the needed structure options
@@ -618,7 +624,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       g.setColor(Color.black);
       if (av.validCharWidth)
       {
-        g.drawString("Alignment has no annotations", 20, 15);
+        g.drawString(MessageManager.getString("label.alignment_has_no_annotations"), 20, 15);
       }
 
       return;
@@ -630,10 +636,13 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
   int scrollOffset = 0;
 
-  public void setScrollOffset(int value)
+  public void setScrollOffset(int value, boolean repaint)
   {
     scrollOffset = value;
-    repaint();
+    if (repaint)
+    {
+      repaint();
+    }
   }
 
   @Override
@@ -657,10 +666,12 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
   @Override
   public int[] getVisibleVRange()
   {
+    if (ap!=null && ap.alabels!=null)
+    {
     int sOffset=-ap.alabels.scrollOffset;
     int visHeight = sOffset+ap.annotationPanelHolder.getHeight();
     bounds[0] = sOffset; bounds[1]=visHeight;
     return bounds;
+    } else return null;
   }
-
 }