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 18ab642..65f2a57 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -22,6 +22,7 @@ package jalview.io;
 
 import jalview.api.ComplexAlignFile;
 import jalview.api.FeaturesDisplayedI;
+import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.PDBEntry;
@@ -257,6 +258,25 @@ public class FileLoader implements Runnable
         {
           format = new IdentifyFile().Identify(file, protocol);
         }
+
+      }
+
+      if (format == null || format.equalsIgnoreCase("EMPTY DATA FILE"))
+      {
+        Desktop.instance.stopLoading();
+        System.err.println("The input file \"" + file
+                + "\" has null or unidentifiable data content!");
+        if (!Jalview.isHeadlessMode())
+        {
+          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;
       }
       // TODO: cache any stream datasources as a temporary file (eg. PDBs
       // retrieved via URL)
@@ -326,9 +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