edit jws2 job parameters before running job

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 96e61e9..6a457d9 100755 (executable)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -395,7 +395,7 @@ public class PopupMenu extends JPopupMenu
       {
         conservationMenuItem.setSelected(true);
       }
-      displayNonconserved.setSelected(sg.getShowunconserved());
+      displayNonconserved.setSelected(sg.getShowNonconserved());
       showText.setSelected(sg.getDisplayText());
       showColourText.setSelected(sg.getColourText());
       showBoxes.setSelected(sg.getDisplayBoxes());
@@ -1139,7 +1139,7 @@ public class PopupMenu extends JPopupMenu
 
   protected void showNonconserved_actionPerformed()
   {
-    getGroup().setShowunconserved(displayNonconserved.isSelected());
+    getGroup().setShowNonconserved(displayNonconserved.isSelected());
     refresh();
   }
 
@@ -1440,7 +1440,7 @@ public class PopupMenu extends JPopupMenu
     SequenceGroup sg = getGroup();
     EditNameDialog dialog = new EditNameDialog(sg.getName(), sg
             .getDescription(), "       Group Name ", "Group Description ",
-            "Edit Group Name/Description");
+            "Edit Group Name/Description", ap.alignFrame);
 
     if (!dialog.accept)
     {
@@ -1479,7 +1479,7 @@ public class PopupMenu extends JPopupMenu
   {
     EditNameDialog dialog = new EditNameDialog(sequence.getName(), sequence
             .getDescription(), "       Sequence Name ",
-            "Sequence Description ", "Edit Sequence Name/Description");
+            "Sequence Description ", "Edit Sequence Name/Description", ap.alignFrame);
 
     if (!dialog.accept)
     {
@@ -1698,10 +1698,12 @@ public class PopupMenu extends JPopupMenu
     omitHidden = ap.av.getViewAsString(true);
     Alignment oal = new Alignment(ap.av.getSequenceSelection());
     AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
-    for (int i = 0; i < nala.length; i++)
-    {
-      AlignmentAnnotation na = nala[i];
-      oal.addAnnotation(na);
+    if (nala!=null) {
+      for (int i = 0; i < nala.length; i++)
+      {
+        AlignmentAnnotation na = nala[i];
+        oal.addAnnotation(na);
+      }
     }
     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
             oal, omitHidden, csel, sg));
@@ -1868,7 +1870,7 @@ public class PopupMenu extends JPopupMenu
 
       EditNameDialog dialog = new EditNameDialog(sequence
               .getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1),
-              null, "Edit Sequence ", null, "Edit Sequence");
+              null, "Edit Sequence ", null, "Edit Sequence", ap.alignFrame);
 
       if (dialog.accept)
       {