X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=7fa4fdaadb28967ca12627e2a1a2e66c21e0592f;hb=c97c8a9e4fd58a4927e040e314c5be3c5356745e;hp=7db0b9041a6b39ea56fb06a87b1af2cb284daa7c;hpb=ca91ef118ff467dee590a67d8ea762c98451660a;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 7db0b90..7fa4fda 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -1,6 +1,6 @@
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
@@ -27,13 +27,15 @@ import jalview.gui.*;
 import jalview.datamodel.*;
 import java.util.Vector;
 import java.util.StringTokenizer;
+import javax.swing.SwingUtilities;
 
-public class FileLoader
+public class FileLoader implements Runnable
 {
   String file;
   String protocol;
   String format;
   AlignViewport viewport;
+  AlignFrame alignFrame;
 
   public void LoadFile(AlignViewport viewport, String file, String protocol, String format)
   {
@@ -41,16 +43,26 @@ public class FileLoader
     LoadFile(file, protocol, format);
   }
 
+
+
   public void LoadFile(String file, String protocol, String format)
   {
     this.file = file;
     this.protocol = protocol;
     this.format = format;
 
-    LoadingThread loader = new LoadingThread();
-    loader.start();
+    final Thread loader = new Thread(this);
+
+    SwingUtilities.invokeLater(new Runnable()
+    {
+      public void run()
+      {
+        loader.start();
+      }
+    });
   }
 
+
   public AlignFrame LoadFileWaitTillLoaded(String file, String protocol,
                                                   String format)
   {
@@ -58,8 +70,9 @@ public class FileLoader
     this.protocol = protocol;
     this.format = format;
 
-    LoadingThread loader = new LoadingThread();
+    Thread loader = new Thread(this);
     loader.start();
+
     while (loader.isAlive())
     {
       try
@@ -70,7 +83,7 @@ public class FileLoader
       {}
     }
 
-    return loader.af;
+    return alignFrame;
   }
 
 
@@ -114,92 +127,120 @@ public class FileLoader
       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
   }
 
-
-  class LoadingThread
-      extends Thread
-  {
-
-    AlignFrame af;
-
-
-
     public void run()
     {
-      Desktop.instance.startLoading(file);
+      try{
+        if (Desktop.instance != null)
+          Desktop.instance.startLoading(file);
 
-      SequenceI[] sequences = null;
+        SequenceI[] sequences = null;
 
-      if (format.equalsIgnoreCase("Jalview"))
-      {
-        af = new Jalview2XML().LoadJalviewAlign(file);
-      }
-      else
-      {
-        String errorMessage = AppletFormatAdapter.SUPPORTED_FORMATS;
-
-        if (FormatAdapter.formats.contains(format))
+        if (format.equalsIgnoreCase("Jalview"))
         {
-          try
-          {
-            sequences = new FormatAdapter().readFile(file, protocol, format);
-          }
-          catch (java.io.IOException ex)
-          {
-            errorMessage = ex.getMessage();
-          }
+          alignFrame = new Jalview2XML().LoadJalviewAlign(file);
         }
-
-        if ( (sequences != null) && (sequences.length > 0))
+        else
         {
-          if(viewport!=null)
-          {
-            for(int i=0; i<sequences.length; i++)
-              viewport.getAlignment().addSequence(sequences[i]);
+          String error = AppletFormatAdapter.SUPPORTED_FORMATS;
 
-              viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
-          }
-          else
+          if (FormatAdapter.isValidFormat(format))
           {
-            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);
-
-            if(jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false))
+            try
             {
-              af.wrapMenuItem.setSelected(true);
-              af.wrapMenuItem_actionPerformed(null);
+              sequences = new FormatAdapter().readFile(file, protocol, format);
             }
-            try
+            catch (java.io.IOException ex)
             {
-              af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+              error = ex.getMessage();
             }
-            catch (java.beans.PropertyVetoException ex)
+          }
+
+          if ( (sequences != null) && (sequences.length > 0))
+          {
+            if (viewport != null)
+            {
+              for (int i = 0; i < sequences.length; i++)
+              {
+                viewport.getAlignment().addSequence(sequences[i]);
+              }
+              viewport.firePropertyChange("alignment", null,
+                                          viewport.getAlignment().getSequences());
+
+            }
+            else
             {
+              Alignment al = new Alignment(sequences);
+
+              alignFrame = new AlignFrame(al,
+                                           AlignFrame.DEFAULT_WIDTH,
+                                           AlignFrame.DEFAULT_HEIGHT);
+              alignFrame.currentFileFormat = format;
+              alignFrame.statusBar.setText("Successfully loaded file " + file);
+
+              Desktop.addInternalFrame(alignFrame, file,
+                                       AlignFrame.DEFAULT_WIDTH,
+                                       AlignFrame.DEFAULT_HEIGHT);
+
+              try
+              {
+               alignFrame.setMaximum(jalview.bin.Cache.getDefault(
+                   "SHOW_FULLSCREEN", false));
+              }
+              catch (java.beans.PropertyVetoException ex)
+              {
+              }
             }
           }
+          else
+          {
+            if (Desktop.instance != null)
+              Desktop.instance.stopLoading();
 
+            final String errorMessage = "Couldn't load file " + file + "\n" +
+                error;
+
+            javax.swing.SwingUtilities.invokeLater(new Runnable()
+            {
+              public void run()
+              {
+                JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                    errorMessage,
+                    "Error loading file",
+                    JOptionPane.WARNING_MESSAGE);
+              }
+            });
+          }
         }
-        else
+
+        if (alignFrame != null)
         {
-          JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                                "Couldn't load file " + file +
-                                                "\n"
-                                                + errorMessage,
-                                                "Error loading file",
-                                                JOptionPane.WARNING_MESSAGE);
+         updateRecentlyOpened();
         }
       }
-
-      if (af != null)
+      catch (OutOfMemoryError er)
       {
-        updateRecentlyOpened();
+
+        er.printStackTrace();
+        alignFrame = null;
+
+        javax.swing.SwingUtilities.invokeLater(new Runnable()
+        {
+          public void run()
+          {
+            javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                "Out of memory loading file "+file+"!!"
+                +
+                "\nSee help files for increasing Java Virtual Machine memory."
+                , "Out of memory",
+                javax.swing.JOptionPane.WARNING_MESSAGE);
+          }
+        });
       }
 
-      Desktop.instance.stopLoading();
+     System.gc();
+     if (Desktop.instance != null)
+        Desktop.instance.stopLoading();
+
     }
-  }
 
 }