X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;fp=src%2Fjalview%2Fio%2FFileLoader.java;h=870d438958e94a63449e60cdf34153d26047fefb;hb=f06554784411ddbf871d642e66c8dcb7f147d4a8;hp=73c10dfecb897bf07086f7be09977f24922e31e8;hpb=cf06ee5d732af6cc874115aece1138adafca8ad7;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 73c10df..870d438 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -268,10 +268,13 @@ public class FileLoader implements Runnable
                 + "\" has null or unidentifiable data content!");
         if (!Jalview.isHeadlessMode())
         {
-          JOptionPane.showMessageDialog(null, "The input file \"" + file
-                  + "\" has null or unidentifiable data content!",
-                  "Empty data file",
-                  JOptionPane.ERROR_MESSAGE);
+          javax.swing.JOptionPane.showInternalMessageDialog(
+                  Desktop.desktop,
+                  MessageManager.getString("label.couldnt_read_data")
+                          + " in " + file + "\n"
+                          + AppletFormatAdapter.SUPPORTED_FORMATS,
+                  MessageManager.getString("label.couldnt_read_data"),
+                  JOptionPane.WARNING_MESSAGE);
         }
         return;
       }
@@ -334,7 +337,7 @@ public class FileLoader implements Runnable
           }
         }
 
-        if ((al != null) && (al.getHeight() > 0))
+        if ((al != null) && (al.getHeight() > 0) && al.hasValidSequence())
         {
           // construct and register dataset sequences
           for (SequenceI sq : al.getSequences())
@@ -343,9 +346,9 @@ public class FileLoader implements Runnable
             {
               sq = sq.getDatasetSequence();
             }
-            if (sq.getPDBId() != null)
+            if (sq.getAllPDBEntries() != null)
             {
-              for (PDBEntry pdbe : sq.getPDBId())
+              for (PDBEntry pdbe : sq.getAllPDBEntries())
               {
                 // register PDB entries with desktop's structure selection
                 // manager