X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=c662ccfb380bddbaeac696b9b3348698482d816e;hb=d587f1aa61946dc14f6f089cf1dc2a3116cfb773;hp=5996d9895df54d9d9fef282e22a3a301459c4e36;hpb=771046fa14fd90393329d8ab3c1defbca37576d2;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 5996d98..c662ccf 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -1,25 +1,78 @@
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* 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
+* 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 jalview.datamodel.Alignment;
-import jalview.gui.Desktop;
-import jalview.datamodel.SequenceI;
 
-public class FileLoader
+import jalview.gui.*;
+import jalview.datamodel.*;
+import java.util.Vector;
+import java.util.StringTokenizer;
+import javax.swing.SwingUtilities;
+
+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)
+  {
+    this.viewport = viewport;
+    LoadFile(file, protocol, format);
+  }
+
+
+
   public void LoadFile(String file, String protocol, String format)
   {
-    LoadingThread loader = new LoadingThread(file, protocol, format);
-    loader.start();
+    this.file = file;
+    this.protocol = protocol;
+    this.format = format;
+
+    final Thread loader = new Thread(this);
+
+    SwingUtilities.invokeLater(new Runnable()
+    {
+      public void run()
+      {
+        loader.start();
+      }
+    });
   }
 
+
   public AlignFrame LoadFileWaitTillLoaded(String file, String protocol,
                                                   String format)
   {
-    LoadingThread loader = new LoadingThread(file, protocol, format);
+    this.file = file;
+    this.protocol = protocol;
+    this.format = format;
+
+    Thread loader = new Thread(this);
     loader.start();
+
     while (loader.isAlive())
     {
       try
@@ -30,69 +83,164 @@ public class FileLoader
       {}
     }
 
-    return loader.af;
+    return alignFrame;
   }
 
 
-  class LoadingThread
-    extends Thread
-{
-  String file;
-  String protocol;
-  String format;
-  AlignFrame af;
 
-  public LoadingThread(String file, String protocol, String format)
+  public void updateRecentlyOpened()
   {
-    this.file = file;
-    this.protocol = protocol;
-    this.format = format;
-  }
+    Vector recent = new Vector();
 
-  public void run()
-  {
-    SequenceI[] sequences = null;
+    String type = protocol.equals(FormatAdapter.FILE)
+        ? "RECENT_FILE" : "RECENT_URL";
 
-    if (format.equalsIgnoreCase("Jalview"))
-    {
-      af = Jalview2XML.LoadJalviewAlign(file);
-    }
-    else
+    String historyItems = jalview.bin.Cache.getProperty(type);
+
+    StringTokenizer st;
+
+    if (historyItems != null)
     {
-      if (FormatAdapter.formats.contains(format))
+      st = new StringTokenizer(historyItems, "\t");
+
+      while (st.hasMoreTokens())
       {
-        sequences = FormatAdapter.readFile(file, protocol, format);
+        recent.addElement(st.nextElement().toString().trim());
       }
+    }
 
-      if ( (sequences != null) && (sequences.length > 0))
-      {
-        af = new AlignFrame(new Alignment(sequences));
-        af.currentFileFormat = format;
-        af.statusBar.setText("Successfully loaded file " + file);
+    if (recent.contains(file))
+    {
+      recent.remove(file);
+    }
 
-        Desktop.addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH,
-                           AlignFrame.NEW_WINDOW_HEIGHT);
+    StringBuffer newHistory = new StringBuffer(file);
+    for (int i = 0; i < recent.size() && i < 10; i++)
+    {
+      newHistory.append("\t");
+      newHistory.append(recent.elementAt(i));
+    }
 
+    jalview.bin.Cache.setProperty(type, newHistory.toString());
 
-        try
+    if(type.equals(FormatAdapter.FILE))
+      jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
+  }
+
+    public void run()
+    {
+      try{
+        if (Desktop.instance != null)
+          Desktop.instance.startLoading(file);
+
+        SequenceI[] sequences = null;
+
+        if (format.equalsIgnoreCase("Jalview"))
         {
-          af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+          alignFrame = new Jalview2XML().LoadJalviewAlign(file);
         }
-        catch (Exception ex)
+        else
         {
+          String error = AppletFormatAdapter.SUPPORTED_FORMATS;
+
+          if (FormatAdapter.isValidFormat(format))
+          {
+            try
+            {
+              sequences = new FormatAdapter().readFile(file, protocol, format);
+            }
+            catch (java.io.IOException ex)
+            {
+              error = ex.getMessage();
+            }
+          }
+
+          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.statusBar.setText("Successfully loaded file " + file);
+              alignFrame.setFileName(file, format);
+
+
+              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);
+              }
+            });
+          }
         }
+
+         updateRecentlyOpened();
+
       }
-      else
+      catch (OutOfMemoryError er)
       {
-        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);
+
+        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);
+          }
+        });
       }
+
+     System.gc();
+     if (Desktop.instance != null)
+        Desktop.instance.stopLoading();
+
     }
-  }
-}
 
 }