FileLoading removed from desktop

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
new file mode 100755 (executable)
index 0000000..d2d477e
--- /dev/null
+++ b/src/jalview/io/FileLoader.java
@@ -0,0 +1,99 @@
+package jalview.io;\r
+\r
+import jalview.gui.AlignFrame;\r
+import jalview.gui.Jalview2XML;\r
+import javax.swing.JOptionPane;\r
+import jalview.datamodel.Alignment;\r
+import jalview.gui.Desktop;\r
+import jalview.datamodel.SequenceI;\r
+import jalview.gui.Preferences;\r
+\r
+public class FileLoader\r
+{\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
+  public AlignFrame LoadFileWaitTillLoaded(String file, String protocol,\r
+                                                  String format)\r
+  {\r
+    LoadingThread loader = new LoadingThread(file, protocol, format);\r
+    loader.start();\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
+  }\r
+\r
+\r
+  class LoadingThread\r
+    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
+      af = 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
+        af.currentFileFormat = format;\r
+        af.statusBar.setText("Successfully loaded file " + file);\r
+\r
+        Desktop.addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH,\r
+                           AlignFrame.NEW_WINDOW_HEIGHT);\r
+\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",\r
+                                              JOptionPane.WARNING_MESSAGE);\r
+      }\r
+    }\r
+  }\r
+}\r
+\r
+}\r