Merge branch 'develop' into features/JAL-2295setChimeraAttributes

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

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 015734f..8f7a15b 100644 (file)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -36,7 +36,8 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
-import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
 import jalview.io.SequenceAnnotationReport;
 import jalview.schemes.Blosum62ColourScheme;
 import jalview.schemes.BuriedColourScheme;
@@ -216,7 +217,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
       e.printStackTrace();
     }
 
-    for (String ff : FileFormat.getWritableFormats(true))
+    for (String ff : FileFormats.getInstance().getWritableFormats(true))
     {
       MenuItem item = new MenuItem(ff);
 
@@ -244,8 +245,12 @@ public class APopupMenu extends java.awt.PopupMenu implements
       {
         menu1.setLabel(MessageManager.getString("action.edit_group"));
         groupMenu.remove(createGroupMenuItem);
+        if (sg.cs != null)
+        {
+          abovePIDColour.setState(sg.cs.getThreshold() > 0);
+          conservationMenuItem.setState(sg.cs.conservationApplied());
+        }
       }
-
     }
     else
     {
@@ -500,23 +505,28 @@ public class APopupMenu extends java.awt.PopupMenu implements
   @Override
   public void itemStateChanged(ItemEvent evt)
   {
-    if (evt.getSource() == abovePIDColour)
+    Object source = evt.getSource();
+    if (source == abovePIDColour)
     {
       abovePIDColour_itemStateChanged();
     }
-    else if (evt.getSource() == showColourText)
+    else if (source == conservationMenuItem)
+    {
+      conservationMenuItem_itemStateChanged();
+    }
+    else if (source == showColourText)
     {
       showColourText_itemStateChanged();
     }
-    else if (evt.getSource() == showText)
+    else if (source == showText)
     {
       showText_itemStateChanged();
     }
-    else if (evt.getSource() == showBoxes)
+    else if (source == showBoxes)
     {
       showBoxes_itemStateChanged();
     }
-    else if (evt.getSource() == displayNonconserved)
+    else if (source == displayNonconserved)
     {
       this.showNonconserved_itemStateChanged();
     }
@@ -579,10 +589,6 @@ public class APopupMenu extends java.awt.PopupMenu implements
     {
       noColourmenuItem_actionPerformed();
     }
-    else if (source == conservationMenuItem)
-    {
-      conservationMenuItem_itemStateChanged();
-    }
     else if (source == unGroupMenuItem)
     {
       unGroupMenuItem_actionPerformed();
@@ -784,7 +790,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
     // now returns a full copy of sequence data
     // TODO consider using getSequenceSelection instead here
 
-    FileFormat fileFormat = FileFormat.valueOf(e.getActionCommand());
+    FileFormatI fileFormat = FileFormats.getInstance().forName(
+            e.getActionCommand());
     cap.setText(new AppletFormatAdapter().formatSequences(fileFormat,
             ap.av.getShowJVSuffix(), ap, true));