From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 5 Oct 2006 16:22:07 +0000 (+0000)
Subject: OutOfMemoryError test
X-Git-Tag: Release_2_2~318
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8e520ab1d2d745a408b3780971fa0fe92c649f32;p=jalview.git

OutOfMemoryError test
---

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index dc18cb7..7fa4fda 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -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;
   }
 
 
@@ -114,98 +127,120 @@ public class FileLoader
       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
   }
 
-
-  class LoadingThread
-      extends Thread
-  {
-
-    AlignFrame af;
-
-
-
     public void run()
     {
-      if (Desktop.instance != null)
-        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 error = AppletFormatAdapter.SUPPORTED_FORMATS;
-
-        if (FormatAdapter.isValidFormat(format))
+        if (format.equalsIgnoreCase("Jalview"))
         {
-          try
-          {
-            sequences = new FormatAdapter().readFile(file, protocol, format);
-          }
-          catch (java.io.IOException ex)
-          {
-            error = 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);
-
             try
             {
-              af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+              sequences = new FormatAdapter().readFile(file, protocol, format);
             }
-            catch (java.beans.PropertyVetoException ex)
+            catch (java.io.IOException ex)
             {
+              error = ex.getMessage();
             }
           }
-        }
-        else
-        {
-          if (Desktop.instance != null)
-            Desktop.instance.stopLoading();
-
-          final String errorMessage = "Couldn't load file "+file+"\n"+error;
 
-          javax.swing.SwingUtilities.invokeLater(new Runnable()
+          if ( (sequences != null) && (sequences.length > 0))
           {
-            public void run()
+            if (viewport != null)
             {
-              JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                                    errorMessage,
-                                                    "Error loading file",
-                                                    JOptionPane.WARNING_MESSAGE);
+              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);
+              }
+            });
+          }
         }
-      }
 
-      if (af != null)
+        if (alignFrame != null)
+        {
+         updateRecentlyOpened();
+        }
+      }
+      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);
+          }
+        });
       }
 
-      if (Desktop.instance != null)
+     System.gc();
+     if (Desktop.instance != null)
         Desktop.instance.stopLoading();
 
     }
-  }
 
 }