Loading thread moved to io.FileLoader

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index cd4608c..3da12e9 100755 (executable)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -18,8 +18,6 @@
  */\r
 package jalview.gui;\r
 \r
-import jalview.datamodel.*;\r
-\r
 import jalview.io.*;\r
 \r
 import java.awt.*;\r
@@ -146,6 +144,21 @@ public class Desktop extends jalview.jbgui.GDesktop
     public static void addInternalFrame(final JInternalFrame frame,\r
         String title, int w, int h, boolean resizable)\r
     {\r
+\r
+      frame.setTitle(title);\r
+      frame.setSize(w, h);\r
+\r
+      // THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN\r
+      // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN\r
+      // IF JALVIEW IS RUNNING HEADLESS\r
+      /////////////////////////////////////////////////\r
+      if (System.getProperty("java.awt.headless") != null\r
+          && System.getProperty("java.awt.headless").equals("true"))\r
+      {\r
+        return;\r
+      }\r
+\r
+\r
         desktop.add(frame);\r
         openFrameCount++;\r
 \r
@@ -157,8 +170,6 @@ public class Desktop extends jalview.jbgui.GDesktop
         {\r
         }\r
 \r
-        frame.setTitle(title);\r
-        frame.setSize(w, h);\r
         frame.setClosable(true);\r
         frame.setResizable(resizable);\r
         frame.setMaximizable(resizable);\r
@@ -336,32 +347,8 @@ public class Desktop extends jalview.jbgui.GDesktop
      */\r
     public void LoadFile(String file, String protocol, String format)\r
     {\r
-        LoadingThread loader = new LoadingThread(file, protocol, format);\r
-        loader.start();\r
-    }\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param file DOCUMENT ME!\r
-     * @param protocol DOCUMENT ME!\r
-     * @param format DOCUMENT ME!\r
-     */\r
-    public AlignFrame LoadFileWaitTillLoaded(String file, String protocol, String format)\r
-    {\r
-        LoadingThread loader = new LoadingThread(file, protocol, format);\r
-        loader.start();\r
-\r
-        while (loader.isAlive())\r
-        {\r
-          try\r
-          {\r
-            Thread.sleep(50);\r
-          }\r
-          catch (Exception ex)\r
-          {}\r
-        }\r
-\r
-      return loader.af;\r
+      FileLoader fileLoader = new FileLoader();\r
+      fileLoader.LoadFile(file, protocol, format);\r
     }\r
 \r
     /**\r
@@ -548,60 +535,4 @@ public class Desktop extends jalview.jbgui.GDesktop
         }\r
     }\r
 \r
-    class LoadingThread extends Thread\r
-    {\r
-        String file;\r
-        String protocol;\r
-        String format;\r
-        AlignFrame af;\r
-\r
-        public LoadingThread(String file, String protocol, String format)\r
-        {\r
-            this.file = file;\r
-            this.protocol = protocol;\r
-            this.format = format;\r
-        }\r
-\r
-        public void run()\r
-        {\r
-            SequenceI[] sequences = null;\r
-\r
-            if(format.equalsIgnoreCase("Jalview"))\r
-            {\r
-              Jalview2XML.LoadJalviewAlign(file);\r
-            }\r
-            else\r
-            {\r
-              if (FormatAdapter.formats.contains(format))\r
-              {\r
-                sequences = FormatAdapter.readFile(file, protocol, format);\r
-              }\r
-\r
-              if ( (sequences != null) && (sequences.length > 0))\r
-              {\r
-                af = new AlignFrame(new Alignment(sequences));\r
-                addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH,\r
-                                 AlignFrame.NEW_WINDOW_HEIGHT);\r
-                af.currentFileFormat = format;\r
-                af.statusBar.setText("Successfully loaded file " + file);\r
-\r
-                try\r
-                {\r
-                  af.setMaximum(Preferences.showFullscreen);\r
-                }\r
-                catch (Exception ex)\r
-                {\r
-                }\r
-              }\r
-              else\r
-              {\r
-                JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
-                    "Couldn't open file.\n" +\r
-                    "Formats currently supported are\n" +\r
-                    "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM" // JBPNote - message should be generated through FormatAdapter!\r
-                    , "Error loading file", JOptionPane.WARNING_MESSAGE);\r
-              }\r
-            }\r
-        }\r
-    }\r
 }\r