JAL-1645 source formatting and organise imports

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

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index b11dfd5..9ff3ef9 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -21,6 +21,8 @@
 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;
@@ -256,6 +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)
@@ -316,7 +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())
@@ -325,9 +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
@@ -356,11 +377,14 @@ public class FileLoader implements Runnable
                       .isShowSeqFeatures();
               ColourSchemeI cs = ((ComplexAlignFile) source)
                       .getColourScheme();
+              FeaturesDisplayedI fd = ((ComplexAlignFile) source)
+                      .getDisplayedFeatures();
               alignFrame = new AlignFrame(al, hiddenSeqs, colSel,
                       AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
 
               alignFrame.getViewport().setShowSequenceFeatures(
                       showSeqFeatures);
+              alignFrame.getViewport().setFeaturesDisplayed(fd);
               alignFrame.changeColour(cs);
             }
             else
@@ -375,8 +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)
             {
@@ -405,8 +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)
@@ -443,8 +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);
           }