/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
-
package jalview.io;
-import java.util.*;
+import jalview.datamodel.AlignmentI;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+import jalview.gui.Desktop;
+import jalview.gui.Jalview2XML;
-import javax.swing.*;
+import java.util.StringTokenizer;
+import java.util.Vector;
-import jalview.datamodel.*;
-import jalview.gui.*;
+import jalview.util.MessageManager;
+import javax.swing.JOptionPane;
+import javax.swing.SwingUtilities;
public class FileLoader implements Runnable
{
long memused;
boolean raiseGUI = true;
+
/**
- * default constructor always raised errors in GUI dialog boxes
+ * default constructor always raised errors in GUI dialog boxes
*/
- public FileLoader() {
+ public FileLoader()
+ {
this(true);
}
+
/**
- * construct a Fileloader that may raise errors non-interactively
- * @param raiseGUI true if errors are to be raised as GUI dialog boxes
+ * construct a Fileloader that may raise errors non-interactively
+ *
+ * @param raiseGUI
+ * true if errors are to be raised as GUI dialog boxes
*/
public FileLoader(boolean raiseGUI)
{
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";
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
+ memused = (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // free
+ // memory
+ // before
+ // load
}
loadtime = -System.currentTimeMillis();
- Alignment al = null;
+ AlignmentI al = null;
if (format.equalsIgnoreCase("Jalview"))
{
error = format + "\n" + error;
}
}
-
+
if ((al != null) && (al.getHeight() > 0))
{
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));
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
{
public void run()
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- errorMessage, "Error loading file",
+ errorMessage, MessageManager.getString("label.error_loading_file"),
JOptionPane.WARNING_MESSAGE);
}
});
updateRecentlyOpened();
- }
- catch (Exception er)
+ } catch (Exception er)
{
- System.err.println("Exception whilst opening file '"+file);
+ System.err.println("Exception whilst opening file '" + file);
er.printStackTrace();
if (raiseGUI)
{
{
public void run()
{
- javax.swing.JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- "Encountered problems opening "
- + file
- + "!!"
- , "File open error",
- javax.swing.JOptionPane.WARNING_MESSAGE);
+ javax.swing.JOptionPane.showInternalMessageDialog(
+ Desktop.desktop, MessageManager.formatMessage("label.problems_opening_file", new String[]{file}),
+ MessageManager.getString("label.file_open_error"),
+ javax.swing.JOptionPane.WARNING_MESSAGE);
}
});
}
alignFrame = null;
- }
- catch (OutOfMemoryError er)
+ } catch (OutOfMemoryError er)
{
er.printStackTrace();
}
});
}
- else
- {
- System.err.println("Out of memory loading file " + file + "!!");
- }
+ System.err.println("Out of memory loading file " + file + "!!");
+
}
loadtime += System.currentTimeMillis();
-
+ // TODO: Estimate percentage of memory used by a newly loaded alignment -
+ // warn if more memory will be needed to work with it
// System.gc();
- memused = memused - (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // difference in free memory after load
+ memused = memused
+ - (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // difference
+ // in free
+ // memory
+ // after
+ // load
if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
{
if (alignFrame != null)
+ (loadtime / 1000.0) + "s, took an additional "
+ (1.0 * memused / (1024.0 * 1024.0)) + " MB ("
+ al.getHeight() + " seqs by " + al.getWidth() + " cols)");
- } else {
- // report that we didn't load anything probably due to an out of memory error
- System.out.println("Failed to load '"+title+"' in "
+ }
+ else
+ {
+ // report that we didn't load anything probably due to an out of memory
+ // error
+ System.out.println("Failed to load '" + title + "' in "
+ (loadtime / 1000.0) + "s, took an additional "
- + (1.0 * memused / (1024.0 * 1024.0)) + " MB (alignment is null)");
+ + (1.0 * memused / (1024.0 * 1024.0))
+ + " MB (alignment is null)");
}
}
// remove the visual delay indicator
git://source.jalview.org / jalview.git / blobdiff