Resolved merge conflict in EdtiCommandTest.java

[jalview.git] / src / jalview / io / AppletFormatAdapter.java

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index b235bcc..02de02e 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -26,7 +26,6 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
-import jalview.gui.AlignmentPanel;
 import jalview.util.MessageManager;
 
 import java.io.File;
@@ -146,7 +145,7 @@ public class AppletFormatAdapter
     this.viewpanel = viewpanel;
   }
 
-  public AppletFormatAdapter(AlignmentPanel alignPanel,
+  public AppletFormatAdapter(AlignmentViewPanel alignPanel,
           AlignExportSettingI settings)
   {
     viewpanel = alignPanel;
@@ -206,6 +205,10 @@ public class AppletFormatAdapter
   public static final boolean isValidFormat(String format,
           boolean forwriting)
   {
+    if (format == null)
+    {
+      return false;
+    }
     boolean valid = false;
     String[] format_list = (forwriting) ? WRITEABLE_FORMATS
             : READABLE_FORMATS;
@@ -484,7 +487,7 @@ public class AppletFormatAdapter
   private AlignmentI buildAlignmentFrom(AlignFile alignFile2)
   {
     // Standard boilerplate for creating alignment from parser
-    alignFile.configureForView(viewpanel);
+    // alignFile.configureForView(viewpanel);
 
     AlignmentI al = new Alignment(alignFile.getSeqsAsArray());
 
@@ -520,7 +523,7 @@ public class AppletFormatAdapter
         aselview.addAnnotation(aa);
       }
     }
-
+    viewpanel = ap;
     return formatSequences(format, aselview, jvsuffix);
   }
 
@@ -598,11 +601,10 @@ public class AppletFormatAdapter
       {
         throw new Exception(MessageManager.getString("error.implementation_error_unknown_file_format_string"));
       }
+
       afile.setNewlineString(newline);
       afile.addJVSuffix(jvsuffix);
-
       afile.setExportSettings(exportSettings);
-
       afile.configureForView(viewpanel);
 
       // check whether we were given a specific alignment to export, rather than