X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=86c1cf4cc139ed5790de492c951682bd5842fe6c;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=7db0b9041a6b39ea56fb06a87b1af2cb284daa7c;hpb=ca91ef118ff467dee590a67d8ea762c98451660a;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 7db0b90..86c1cf4 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -1,41 +1,42 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 
 package jalview.io;
 
-import jalview.gui.AlignFrame;
-import jalview.gui.Jalview2XML;
-import javax.swing.JOptionPane;
+import java.util.*;
+
+import javax.swing.*;
 
-import jalview.gui.*;
 import jalview.datamodel.*;
-import java.util.Vector;
-import java.util.StringTokenizer;
+import jalview.gui.*;
 
 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)
+  public void LoadFile(AlignViewport viewport, String file, String protocol,
+                       String format)
   {
     this.viewport = viewport;
     LoadFile(file, protocol, format);
@@ -47,19 +48,27 @@ public class FileLoader
     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)
+                                           String format)
   {
     this.file = file;
     this.protocol = protocol;
     this.format = format;
 
-    LoadingThread loader = new LoadingThread();
+    Thread loader = new Thread(this);
     loader.start();
+
     while (loader.isAlive())
     {
       try
@@ -70,11 +79,9 @@ public class FileLoader
       {}
     }
 
-    return loader.af;
+    return alignFrame;
   }
 
-
-
   public void updateRecentlyOpened()
   {
     Vector recent = new Vector();
@@ -110,96 +117,130 @@ public class FileLoader
 
     jalview.bin.Cache.setProperty(type, newHistory.toString());
 
-    if(type.equals(FormatAdapter.FILE))
+    if (type.equals(FormatAdapter.FILE))
+    {
       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
+    }
   }
 
-
-  class LoadingThread
-      extends Thread
+  public void run()
   {
-
-    AlignFrame af;
-
-
-
-    public void run()
+    try
     {
-      Desktop.instance.startLoading(file);
+      if (Desktop.instance != null)
+      {
+        Desktop.instance.startLoading(file);
+      }
 
-      SequenceI[] sequences = null;
+      Alignment al = null;
 
       if (format.equalsIgnoreCase("Jalview"))
       {
-        af = new Jalview2XML().LoadJalviewAlign(file);
+        alignFrame = new Jalview2XML().LoadJalviewAlign(file);
       }
       else
       {
-        String errorMessage = AppletFormatAdapter.SUPPORTED_FORMATS;
+        String error = AppletFormatAdapter.SUPPORTED_FORMATS;
 
-        if (FormatAdapter.formats.contains(format))
+        if (FormatAdapter.isValidFormat(format))
         {
           try
           {
-            sequences = new FormatAdapter().readFile(file, protocol, format);
+            al = new FormatAdapter().readFile(file, protocol, format);
           }
           catch (java.io.IOException ex)
           {
-            errorMessage = ex.getMessage();
+            error = ex.getMessage();
           }
         }
 
-        if ( (sequences != null) && (sequences.length > 0))
+        if ( (al != null) && (al.getHeight() > 0))
         {
-          if(viewport!=null)
+          if (viewport != null)
           {
-            for(int i=0; i<sequences.length; i++)
-              viewport.getAlignment().addSequence(sequences[i]);
+            for (int i = 0; i < al.getHeight(); i++)
+            {
+              viewport.getAlignment().addSequence(al.getSequenceAt(i));
+            }
+            viewport.firePropertyChange("alignment", null,
+                                        viewport.getAlignment().getSequences());
 
-              viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
           }
           else
           {
-            af = new AlignFrame(new Alignment(sequences));
-            af.currentFileFormat = format;
-            af.statusBar.setText("Successfully loaded file " + file);
+            alignFrame = new AlignFrame(al,
+                                        AlignFrame.DEFAULT_WIDTH,
+                                        AlignFrame.DEFAULT_HEIGHT);
 
-            Desktop.addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH,
-                                     AlignFrame.NEW_WINDOW_HEIGHT);
+            alignFrame.statusBar.setText("Successfully loaded file " + file);
+            alignFrame.setFileName(file, format);
+
+            Desktop.addInternalFrame(alignFrame, file,
+                                     AlignFrame.DEFAULT_WIDTH,
+                                     AlignFrame.DEFAULT_HEIGHT);
 
-            if(jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false))
-            {
-              af.wrapMenuItem.setSelected(true);
-              af.wrapMenuItem_actionPerformed(null);
-            }
             try
             {
-              af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+              alignFrame.setMaximum(jalview.bin.Cache.getDefault(
+                  "SHOW_FULLSCREEN", false));
             }
             catch (java.beans.PropertyVetoException ex)
             {
             }
           }
-
         }
         else
         {
-          JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                                "Couldn't load file " + file +
-                                                "\n"
-                                                + errorMessage,
-                                                "Error loading file",
-                                                JOptionPane.WARNING_MESSAGE);
+          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);
+            }
+          });
         }
       }
 
-      if (af != null)
+      updateRecentlyOpened();
+
+    }
+    catch (OutOfMemoryError er)
+    {
+
+      er.printStackTrace();
+      alignFrame = null;
+
+      javax.swing.SwingUtilities.invokeLater(new Runnable()
       {
-        updateRecentlyOpened();
-      }
+        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);
+        }
+      });
+    }
 
+    System.gc();
+    if (Desktop.instance != null)
+    {
       Desktop.instance.stopLoading();
     }
+
   }
 
 }