X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=86c1cf4cc139ed5790de492c951682bd5842fe6c;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=40b8ffb3fa3c0198f9fd229629f804387a9f0635;hpb=258c0056231d8a97c1d40dd665260e7814d11206;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 40b8ffb..86c1cf4 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -1,99 +1,246 @@
+/*
+ * 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 jalview.datamodel.Alignment;
-import jalview.gui.Desktop;
-import jalview.datamodel.SequenceI;
-import jalview.gui.Preferences;
+import java.util.*;
+
+import javax.swing.*;
+
+import jalview.datamodel.*;
+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)
+  {
+    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)
+                                           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
       {
-        Thread.sleep(50);
+        Thread.sleep(500);
       }
       catch (Exception ex)
       {}
     }
 
-    return loader.af;
+    return alignFrame;
   }
 
+  public void updateRecentlyOpened()
+  {
+    Vector recent = new Vector();
 
-  class LoadingThread
-    extends Thread
-{
-  String file;
-  String protocol;
-  String format;
-  AlignFrame af;
+    String type = protocol.equals(FormatAdapter.FILE)
+        ? "RECENT_FILE" : "RECENT_URL";
 
-  public LoadingThread(String file, String protocol, String format)
-  {
-    this.file = file;
-    this.protocol = protocol;
-    this.format = format;
-  }
+    String historyItems = jalview.bin.Cache.getProperty(type);
 
-  public void run()
-  {
-    SequenceI[] sequences = null;
+    StringTokenizer st;
 
-    if (format.equalsIgnoreCase("Jalview"))
+    if (historyItems != null)
     {
-      af = Jalview2XML.LoadJalviewAlign(file);
+      st = new StringTokenizer(historyItems, "\t");
+
+      while (st.hasMoreTokens())
+      {
+        recent.addElement(st.nextElement().toString().trim());
+      }
     }
-    else
+
+    if (recent.contains(file))
     {
-      if (FormatAdapter.formats.contains(format))
+      recent.remove(file);
+    }
+
+    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());
+
+    if (type.equals(FormatAdapter.FILE))
+    {
+      jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
+    }
+  }
+
+  public void run()
+  {
+    try
+    {
+      if (Desktop.instance != null)
       {
-        sequences = FormatAdapter.readFile(file, protocol, format);
+        Desktop.instance.startLoading(file);
       }
 
-      if ( (sequences != null) && (sequences.length > 0))
-      {
-        af = new AlignFrame(new Alignment(sequences));
-        af.currentFileFormat = format;
-        af.statusBar.setText("Successfully loaded file " + file);
+      Alignment al = null;
 
-        Desktop.addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH,
-                           AlignFrame.NEW_WINDOW_HEIGHT);
+      if (format.equalsIgnoreCase("Jalview"))
+      {
+        alignFrame = new Jalview2XML().LoadJalviewAlign(file);
+      }
+      else
+      {
+        String error = AppletFormatAdapter.SUPPORTED_FORMATS;
 
+        if (FormatAdapter.isValidFormat(format))
+        {
+          try
+          {
+            al = new FormatAdapter().readFile(file, protocol, format);
+          }
+          catch (java.io.IOException ex)
+          {
+            error = ex.getMessage();
+          }
+        }
 
-        try
+        if ( (al != null) && (al.getHeight() > 0))
         {
-          af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+          if (viewport != null)
+          {
+            for (int i = 0; i < al.getHeight(); i++)
+            {
+              viewport.getAlignment().addSequence(al.getSequenceAt(i));
+            }
+            viewport.firePropertyChange("alignment", null,
+                                        viewport.getAlignment().getSequences());
+
+          }
+          else
+          {
+            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)
+            {
+            }
+          }
         }
-        catch (Exception 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
+
+      updateRecentlyOpened();
+
+    }
+    catch (OutOfMemoryError er)
+    {
+
+      er.printStackTrace();
+      alignFrame = null;
+
+      javax.swing.SwingUtilities.invokeLater(new Runnable()
       {
-        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);
-      }
+        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();
+    }
+
   }
-}
 
 }