From 7a79aff7269435b0719c9cd4f30893b81fa2f7b0 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 3 Aug 2005 13:07:39 +0000
Subject: [PATCH] FileLoading removed from desktop

---
 src/jalview/io/FileLoader.java |   99 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 99 insertions(+)
 create mode 100755 src/jalview/io/FileLoader.java

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
new file mode 100755
index 0000000..d2d477e
--- /dev/null
+++ b/src/jalview/io/FileLoader.java
@@ -0,0 +1,99 @@
+package jalview.io;
+
+import jalview.gui.AlignFrame;
+import jalview.gui.Jalview2XML;
+import javax.swing.JOptionPane;
+import jalview.datamodel.Alignment;
+import jalview.gui.Desktop;
+import jalview.datamodel.SequenceI;
+import jalview.gui.Preferences;
+
+public class FileLoader
+{
+  public void LoadFile(String file, String protocol, String format)
+  {
+    LoadingThread loader = new LoadingThread(file, protocol, format);
+    loader.start();
+  }
+
+  public AlignFrame LoadFileWaitTillLoaded(String file, String protocol,
+                                                  String format)
+  {
+    LoadingThread loader = new LoadingThread(file, protocol, format);
+    loader.start();
+    while (loader.isAlive())
+    {
+      try
+      {
+        Thread.sleep(50);
+      }
+      catch (Exception ex)
+      {}
+    }
+
+    return loader.af;
+  }
+
+
+  class LoadingThread
+    extends Thread
+{
+  String file;
+  String protocol;
+  String format;
+  AlignFrame af;
+
+  public LoadingThread(String file, String protocol, String format)
+  {
+    this.file = file;
+    this.protocol = protocol;
+    this.format = format;
+  }
+
+  public void run()
+  {
+    SequenceI[] sequences = null;
+
+    if (format.equalsIgnoreCase("Jalview"))
+    {
+      af = Jalview2XML.LoadJalviewAlign(file);
+    }
+    else
+    {
+      if (FormatAdapter.formats.contains(format))
+      {
+        sequences = FormatAdapter.readFile(file, protocol, format);
+      }
+
+      if ( (sequences != null) && (sequences.length > 0))
+      {
+        af = new AlignFrame(new Alignment(sequences));
+        af.currentFileFormat = format;
+        af.statusBar.setText("Successfully loaded file " + file);
+
+        Desktop.addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH,
+                           AlignFrame.NEW_WINDOW_HEIGHT);
+
+
+        try
+        {
+          af.setMaximum(Preferences.showFullscreen);
+        }
+        catch (Exception ex)
+        {
+        }
+      }
+      else
+      {
+        JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                              "Couldn't open file.\n" +
+                                              "Formats currently supported are\n" +
+                                              "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM" // JBPNote - message should be generated through FormatAdapter!
+                                              , "Error loading file",
+                                              JOptionPane.WARNING_MESSAGE);
+      }
+    }
+  }
+}
+
+}
-- 
1.7.10.2