JAL-1759 merge from develop

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

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index e27c666..3aded05 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -20,13 +20,9 @@
  */
 package jalview.io;
 
-import java.util.StringTokenizer;
-import java.util.Vector;
-
-import javax.swing.JOptionPane;
-import javax.swing.SwingUtilities;
-
 import jalview.api.ComplexAlignFile;
+import jalview.api.FeaturesDisplayedI;
+import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.PDBEntry;
@@ -39,6 +35,12 @@ import jalview.schemes.ColourSchemeI;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import javax.swing.JOptionPane;
+import javax.swing.SwingUtilities;
+
 public class FileLoader implements Runnable
 {
   String file;
@@ -256,6 +258,21 @@ 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 no data content!");
+        if (!Jalview.isHeadlessMode())
+        {
+          JOptionPane.showMessageDialog(null, "The input file \""
+                  + file + "\" has no data content!", "Empty data file",
+                  JOptionPane.ERROR_MESSAGE);
+        }
+        return;
       }
       // TODO: cache any stream datasources as a temporary file (eg. PDBs
       // retrieved via URL)
@@ -299,7 +316,8 @@ public class FileLoader implements Runnable
               // open a new source and read from it
               FormatAdapter fa = new FormatAdapter();
               al = fa.readFile(file, protocol, format);
-              source = fa.getAlignFile(); // keep reference for later if necessary.
+              source = fa.getAlignFile(); // keep reference for later if
+                                          // necessary.
             }
           } catch (java.io.IOException ex)
           {
@@ -317,6 +335,7 @@ public class FileLoader implements Runnable
 
         if ((al != null) && (al.getHeight() > 0))
         {
+          // construct and register dataset sequences
           for (SequenceI sq : al.getSequences())
           {
             while (sq.getDatasetSequence() != null)
@@ -327,21 +346,23 @@ public class FileLoader implements Runnable
             {
               for (PDBEntry pdbe : sq.getPDBId())
               {
+                // register PDB entries with desktop's structure selection
+                // manager
                 StructureSelectionManager.getStructureSelectionManager(
                         Desktop.instance).registerPDBEntry(pdbe);
               }
             }
           }
+
           if (viewport != null)
           {
+            // append to existing alignment
             viewport.addAlignment(al, title);
           }
           else
           {
-            if (!protocol.equals(AppletFormatAdapter.PASTE))
-            {
-              alignFrame.setFileName(file, format);
-            }
+            // otherwise construct the alignFrame
+
             if (source instanceof ComplexAlignFile)
             {
               ColumnSelection colSel = ((ComplexAlignFile) source)
@@ -352,12 +373,14 @@ 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.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
 
               alignFrame.getViewport().setShowSequenceFeatures(
                       showSeqFeatures);
+              alignFrame.getViewport().setFeaturesDisplayed(fd);
               alignFrame.changeColour(cs);
             }
             else
@@ -365,6 +388,11 @@ public class FileLoader implements Runnable
               alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
                       AlignFrame.DEFAULT_HEIGHT);
             }
+            // add metadata and update ui
+            if (!protocol.equals(AppletFormatAdapter.PASTE))
+            {
+              alignFrame.setFileName(file, format);
+            }
 
             alignFrame.statusBar.setText(MessageManager.formatMessage(
                     "label.successfully_loaded_file", new String[]
@@ -399,7 +427,9 @@ public class FileLoader implements Runnable
 
           final String errorMessage = "Couldn't load file " + title + "\n"
                   + error;
-          if (raiseGUI)
+          // TODO: refactor FileLoader to be independent of Desktop / Applet GUI
+          // bits ?
+          if (raiseGUI && Desktop.desktop != null)
           {
             javax.swing.SwingUtilities.invokeLater(new Runnable()
             {
@@ -452,12 +482,12 @@ public class FileLoader implements Runnable
         {
           public void run()
           {
-            javax.swing.JOptionPane
-                    .showInternalMessageDialog(
-                            Desktop.desktop,
-                            MessageManager.formatMessage("warn.out_of_memory_loading_file", new String[]{file}),
-                            MessageManager.getString("label.out_of_memory"),
-                            javax.swing.JOptionPane.WARNING_MESSAGE);
+            javax.swing.JOptionPane.showInternalMessageDialog(
+                    Desktop.desktop, MessageManager.formatMessage(
+                            "warn.out_of_memory_loading_file", new String[]
+                            { file }), MessageManager
+                            .getString("label.out_of_memory"),
+                    javax.swing.JOptionPane.WARNING_MESSAGE);
           }
         });
       }