JAL-1831 added changes to allow auto-generation of BioJSON schema from src code

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

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 3aded05..65f2a57 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -265,12 +265,16 @@ public class FileLoader implements Runnable
       {
         Desktop.instance.stopLoading();
         System.err.println("The input file \"" + file
-                + "\" has no data content!");
+                + "\" has null or unidentifiable data content!");
         if (!Jalview.isHeadlessMode())
         {
-          JOptionPane.showMessageDialog(null, "The input file \""
-                  + file + "\" has no 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;
       }
@@ -342,9 +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