JAL-1807 explicit imports (jalview.io.*)

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

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index a27777f..1edf832 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -20,13 +20,19 @@
  */
 package jalview.io;
 
+import jalview.api.ComplexAlignFile;
+import jalview.api.FeaturesDisplayedI;
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.AlignViewport;
 import jalview.gui.Desktop;
 import jalview.gui.Jalview2XML;
+import jalview.schemes.ColourSchemeI;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 
@@ -194,7 +200,7 @@ public class FileLoader implements Runnable
     String type = protocol.equals(FormatAdapter.FILE) ? "RECENT_FILE"
             : "RECENT_URL";
 
-    String historyItems = jalview.bin.Cache.getProperty(type);
+    String historyItems = Cache.getProperty(type);
 
     StringTokenizer st;
 
@@ -220,11 +226,11 @@ public class FileLoader implements Runnable
       newHistory.append(recent.elementAt(i));
     }
 
-    jalview.bin.Cache.setProperty(type, newHistory.toString());
+    Cache.setProperty(type, newHistory.toString());
 
     if (protocol.equals(FormatAdapter.FILE))
     {
-      jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
+      Cache.setProperty("DEFAULT_FILE_FORMAT", format);
     }
   }
 
@@ -253,6 +259,21 @@ 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)
@@ -296,7 +317,8 @@ 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)
           {
@@ -314,6 +336,7 @@ 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)
@@ -324,37 +347,58 @@ 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
           {
-            alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
-                    AlignFrame.DEFAULT_HEIGHT);
+            // otherwise construct the alignFrame
 
-            alignFrame.statusBar.setText(MessageManager.formatMessage(
-                    "label.successfully_loaded_file", new String[]
-                    { title }));
-
-            if (!protocol.equals(AppletFormatAdapter.PASTE))
+            if (source instanceof ComplexAlignFile)
             {
-              alignFrame.setFileName(file, format);
+              ColumnSelection colSel = ((ComplexAlignFile) source)
+                      .getColumnSelection();
+              SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
+                      .getHiddenSequences();
+              boolean showSeqFeatures = ((ComplexAlignFile) source)
+                      .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);
             }
-            if (source instanceof HtmlFile)
+            else
             {
-              ((HtmlFile) source).applySettingsToAlignmentView(alignFrame);
+              alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+                      AlignFrame.DEFAULT_HEIGHT);
             }
-            else if (source instanceof JSONFile)
+            // add metadata and update ui
+            if (!protocol.equals(AppletFormatAdapter.PASTE))
             {
-              ((JSONFile) source).applySettingsToAlignmentView(alignFrame);
+              alignFrame.setFileName(file, format);
             }
 
+            alignFrame.statusBar.setText(MessageManager.formatMessage(
+                    "label.successfully_loaded_file", new String[]
+                    { title }));
+
             if (raiseGUI)
             {
               // add the window to the GUI
@@ -368,7 +412,7 @@ public class FileLoader implements Runnable
 
             try
             {
-              alignFrame.setMaximum(jalview.bin.Cache.getDefault(
+              alignFrame.setMaximum(Cache.getDefault(
                       "SHOW_FULLSCREEN", false));
             } catch (java.beans.PropertyVetoException ex)
             {
@@ -384,7 +428,9 @@ 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()
             {
@@ -437,12 +483,12 @@ 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);
           }
         });
       }