JAL-2383 restore group conservation slider setting from project

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index d09e7c2..12b46e4 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -129,7 +129,6 @@ import java.util.jar.JarInputStream;
 import java.util.jar.JarOutputStream;
 
 import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
 import javax.swing.SwingUtilities;
 
 import org.exolab.castor.xml.Marshaller;
@@ -2638,10 +2637,10 @@ public class Jalview2XML
           @Override
           public void run()
           {
-            JOptionPane.showInternalMessageDialog(Desktop.desktop,
+            JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                     finalErrorMessage, "Error "
                             + (saving ? "saving" : "loading")
-                            + " Jalview file", JOptionPane.WARNING_MESSAGE);
+                            + " Jalview file", JvOptionPane.WARNING_MESSAGE);
           }
         });
       }
@@ -3352,6 +3351,7 @@ public class Jalview2XML
           if (cs != null)
           {
             cs.setThreshold(jGroup.getPidThreshold(), true);
+            cs.setConservationInc(jGroup.getConsThreshold());
           }
         }
 
@@ -4422,10 +4422,12 @@ public class Jalview2XML
 
     af.viewport.setShowAnnotation(view.getShowAnnotation());
     af.viewport.setAbovePIDThreshold(view.getPidSelected());
+    af.viewport.setThreshold(view.getPidThreshold());
 
     af.viewport.setColourText(view.getShowColourText());
 
     af.viewport.setConservationSelected(view.getConservationSelected());
+    af.viewport.setIncrement(view.getConsThreshold());
     af.viewport.setShowJVSuffix(view.getShowFullId());
     af.viewport.setRightAlignIds(view.getRightAlignIds());
     af.viewport.setFont(
@@ -4475,7 +4477,6 @@ public class Jalview2XML
 
       if (cs != null)
       {
-        cs.setThreshold(view.getPidThreshold(), true);
         cs.setConsensus(af.viewport.getSequenceConsensusHash());
       }
     }