JAL-1432 updated copyright notices

[jalview.git] / src / jalview / io / FileLoader.java

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 6cb1212..0dddeca 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -1,20 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
- * 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 file is part of Jalview.
  * 
- * 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.
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ *  
+ * Jalview 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
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
@@ -59,7 +59,7 @@ public class FileLoader implements Runnable
    * construct a Fileloader that may raise errors non-interactively
    * 
    * @param raiseGUI
-   *                true if errors are to be raised as GUI dialog boxes
+   *          true if errors are to be raised as GUI dialog boxes
    */
   public FileLoader(boolean raiseGUI)
   {
@@ -173,7 +173,12 @@ public class FileLoader implements Runnable
   public void updateRecentlyOpened()
   {
     Vector recent = new Vector();
-
+    if (protocol.equals(FormatAdapter.PASTE))
+    {
+      // do nothing if the file was pasted in as text... there is no filename to
+      // refer to it as.
+      return;
+    }
     String type = protocol.equals(FormatAdapter.FILE) ? "RECENT_FILE"
             : "RECENT_URL";
 
@@ -237,13 +242,15 @@ public class FileLoader implements Runnable
           format = new IdentifyFile().Identify(file, protocol);
         }
       }
+      // TODO: cache any stream datasources as a temporary file (eg. PDBs
+      // retrieved via URL)
       if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
       {
         System.gc();
         memused = (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // free
-                                                                          // memory
-                                                                          // before
-                                                                          // load
+        // memory
+        // before
+        // load
       }
       loadtime = -System.currentTimeMillis();
       Alignment al = null;
@@ -297,6 +304,7 @@ public class FileLoader implements Runnable
         {
           if (viewport != null)
           {
+            // TODO: create undo object for this JAL-1101
             for (int i = 0; i < al.getHeight(); i++)
             {
               viewport.getAlignment().addSequence(al.getSequenceAt(i));
@@ -315,9 +323,14 @@ public class FileLoader implements Runnable
 
             if (!protocol.equals(AppletFormatAdapter.PASTE))
               alignFrame.setFileName(file, format);
-
-            Desktop.addInternalFrame(alignFrame, title,
-                    AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+            if (raiseGUI)
+            {
+              // add the window to the GUI
+              // note - this actually should happen regardless of raiseGUI status in Jalview 3
+              // TODO: define 'virtual desktop' for benefit of headless scripts that perform queries to find the 'current working alignment'
+              Desktop.addInternalFrame(alignFrame, title,
+                      AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+            }
 
             try
             {
@@ -408,10 +421,10 @@ public class FileLoader implements Runnable
     // System.gc();
     memused = memused
             - (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // difference
-                                                                      // in free
-                                                                      // memory
-                                                                      // after
-                                                                      // load
+    // in free
+    // memory
+    // after
+    // load
     if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
     {
       if (alignFrame != null)