X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=67c72c224d1fa05213375865372f336c44042540;hb=0d6e36143a2d7471edb7ef386d0b79095e0cd63e;hp=40b8ffb3fa3c0198f9fd229629f804387a9f0635;hpb=258c0056231d8a97c1d40dd665260e7814d11206;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 40b8ffb..67c72c2 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -1,31 +1,70 @@
+/*
+* 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
+*/
+
 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 jalview.gui.*;
+import jalview.datamodel.*;
+import java.util.Vector;
+import java.util.StringTokenizer;
 
 public class FileLoader
 {
+  String file;
+  String protocol;
+  String format;
+  AlignViewport viewport;
+
+  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);
+    this.file = file;
+    this.protocol = protocol;
+    this.format = format;
+
+    LoadingThread loader = new LoadingThread();
     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;
+
+    LoadingThread loader = new LoadingThread();
     loader.start();
     while (loader.isAlive())
     {
       try
       {
-        Thread.sleep(50);
+        Thread.sleep(500);
       }
       catch (Exception ex)
       {}
@@ -35,65 +74,130 @@ public class FileLoader
   }
 
 
-  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";
+
+    String historyItems = jalview.bin.Cache.getProperty(type);
+
+    StringTokenizer st;
+
+    if (historyItems != null)
+    {
+      st = new StringTokenizer(historyItems, "\t");
+
+      while (st.hasMoreTokens())
+      {
+        recent.addElement(st.nextElement().toString().trim());
+      }
+    }
 
-    if (format.equalsIgnoreCase("Jalview"))
+    if (recent.contains(file))
     {
-      af = Jalview2XML.LoadJalviewAlign(file);
+      recent.remove(file);
     }
-    else
+
+    StringBuffer newHistory = new StringBuffer(file);
+    for (int i = 0; i < recent.size() && i < 10; i++)
     {
-      if (FormatAdapter.formats.contains(format))
+      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);
+  }
+
+
+  class LoadingThread
+      extends Thread
+  {
+
+    AlignFrame af;
+
+
+
+    public void run()
+    {
+      Desktop.instance.startLoading(file);
+
+      SequenceI[] sequences = null;
+
+      if (format.equalsIgnoreCase("Jalview"))
       {
-        sequences = FormatAdapter.readFile(file, protocol, format);
+        af = new Jalview2XML().LoadJalviewAlign(file);
       }
-
-      if ( (sequences != null) && (sequences.length > 0))
+      else
       {
-        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);
+        String errorMessage = AppletFormatAdapter.SUPPORTED_FORMATS;
 
+        if (FormatAdapter.formats.contains(format))
+        {
+          try
+          {
+            sequences = new FormatAdapter().readFile(file, protocol, format);
+          }
+          catch (java.io.IOException ex)
+          {
+            errorMessage = ex.getMessage();
+          }
+        }
 
-        try
+        if ( (sequences != null) && (sequences.length > 0))
         {
-          af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+          if(viewport!=null)
+          {
+            for(int i=0; i<sequences.length; i++)
+              viewport.getAlignment().addSequence(sequences[i]);
+
+              viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+          }
+          else
+          {
+            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));
+            }
+            catch (java.beans.PropertyVetoException ex)
+            {
+            }
+          }
+
         }
-        catch (Exception ex)
+        else
         {
+          Desktop.instance.stopLoading();
+
+          JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                                "Couldn't load file " + file +
+                                                "\n"
+                                                + errorMessage,
+                                                "Error loading file",
+                                                JOptionPane.WARNING_MESSAGE);
         }
       }
-      else
+
+      if (af != null)
       {
-        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);
+        updateRecentlyOpened();
       }
+
+      Desktop.instance.stopLoading();
+
     }
   }
-}
 
 }