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 7387fa2..3aded05 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 +258,21 @@ 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)
           {
@@ -355,11 +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.getViewport().setShowSequenceFeatures(
                       showSeqFeatures);
+              alignFrame.getViewport().setFeaturesDisplayed(fd);
               alignFrame.changeColour(cs);
             }
             else
@@ -367,34 +388,34 @@ 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);
-          }
+            // 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[]
-                  { title }));
+            alignFrame.statusBar.setText(MessageManager.formatMessage(
+                    "label.successfully_loaded_file", new String[]
+                    { title }));
 
-          if (raiseGUI)
-          {
-            // add the window to the GUI
-            // note - this actually should happen regardless of raiseGUI
-            // status in Jalview 3
-            // TODO: define 'virtual desktop' for benefit of headless scripts
-            // that perform queries to find the 'current working alignment'
-            Desktop.addInternalFrame(alignFrame, title,
-                    AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
-          }
+            if (raiseGUI)
+            {
+              // add the window to the GUI
+              // note - this actually should happen regardless of raiseGUI
+              // status in Jalview 3
+              // TODO: define 'virtual desktop' for benefit of headless scripts
+              // that perform queries to find the 'current working alignment'
+              Desktop.addInternalFrame(alignFrame, title,
+                      AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+            }
 
-          try
-          {
-            alignFrame.setMaximum(jalview.bin.Cache.getDefault(
-                    "SHOW_FULLSCREEN", false));
-          } catch (java.beans.PropertyVetoException ex)
-          {
+            try
+            {
+              alignFrame.setMaximum(jalview.bin.Cache.getDefault(
+                      "SHOW_FULLSCREEN", false));
+            } catch (java.beans.PropertyVetoException ex)
+            {
+            }
           }
         }
         else
@@ -461,12 +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);
           }
         });
       }