JAL-2089 patch broken merge to master for Release 2.10.0b1

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

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index e5475f8..6012c1a 100755 (executable)
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -28,6 +28,7 @@ import jalview.renderer.AwtRenderPanelI;
 import jalview.schemes.ResidueProperties;
 import jalview.util.Comparison;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 
 import java.awt.Color;
 import java.awt.Dimension;
@@ -101,7 +102,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
   public AnnotationPanel(AlignmentPanel ap)
   {
-    MAC = new jalview.util.Platform().isAMac();
+    new jalview.util.Platform();
+    MAC = Platform.isAMac();
     this.ap = ap;
     av = ap.av;
     setLayout(null);
@@ -242,7 +244,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       else if (evt.getActionCommand().equals(STEM))
       {
         type = 'S';
-        symbol = "\u03C3";
+        int column = av.getColumnSelection().getSelectedRanges().get(0)[0];
+        symbol = aa[activeRow].getDefaultRnaHelixSymbol(column);
       }
 
       if (!aa[activeRow].hasIcons)
@@ -347,7 +350,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
     if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK
             && activeRow != -1)
     {
-      if (av.getColumnSelection() == null)
+      if (av.getColumnSelection() == null
+              || av.getColumnSelection().isEmpty())
       {
         return;
       }
@@ -355,10 +359,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       PopupMenu pop = new PopupMenu(
               MessageManager.getString("label.structure_type"));
       MenuItem item;
-      /*
-       * Just display the needed structure options
-       */
-      if (av.getAlignment().isNucleotide() == true)
+
+      if (av.getAlignment().isNucleotide())
       {
         item = new MenuItem(STEM);
         item.addActionListener(this);