X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=9ff3ef9cecb2f164c512069007583cbfc4e5b007;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=73c10dfecb897bf07086f7be09977f24922e31e8;hpb=72738726bce0733f652a5dbcc9db7c5a13bc2d80;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 73c10df..9ff3ef9 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
@@ -396,8 +399,8 @@ public class FileLoader implements Runnable
             }
 
             alignFrame.statusBar.setText(MessageManager.formatMessage(
-                    "label.successfully_loaded_file", new String[]
-                    { title }));
+                    "label.successfully_loaded_file",
+                    new String[] { title }));
 
             if (raiseGUI)
             {
@@ -426,8 +429,11 @@ public class FileLoader implements Runnable
             Desktop.instance.stopLoading();
           }
 
-          final String errorMessage = "Couldn't load file " + title + "\n"
-                  + error;
+          final String errorMessage = MessageManager
+                  .getString("label.couldnt_load_file")
+                  + " "
+                  + title
+                  + "\n" + error;
           // TODO: refactor FileLoader to be independent of Desktop / Applet GUI
           // bits ?
           if (raiseGUI && Desktop.desktop != null)
@@ -464,8 +470,8 @@ public class FileLoader implements Runnable
           {
             javax.swing.JOptionPane.showInternalMessageDialog(
                     Desktop.desktop, MessageManager.formatMessage(
-                            "label.problems_opening_file", new String[]
-                            { file }), MessageManager
+                            "label.problems_opening_file",
+                            new String[] { file }), MessageManager
                             .getString("label.file_open_error"),
                     javax.swing.JOptionPane.WARNING_MESSAGE);
           }