/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * 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.
- *
- * 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 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
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
package jalview.io;
-import java.util.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+import jalview.gui.Desktop;
+import jalview.gui.Jalview2XML;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
-import javax.swing.*;
+import java.util.StringTokenizer;
+import java.util.Vector;
-import jalview.datamodel.*;
-import jalview.gui.*;
+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 AlignFrame LoadFileWaitTillLoaded(FileParse source, String format)
{
this.source = source;
+
file = source.getInFile();
protocol = source.type;
this.format = format;
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"))
{
.println("IMPLEMENTATION ERROR: Cannot read consecutive Jalview XML projects from a stream.");
// We read the data anyway - it might make sense.
}
- alignFrame = new Jalview2XML(raiseGUI).LoadJalviewAlign(file);
+ alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(file);
}
else
{
// open a new source and read from it
FormatAdapter fa = new FormatAdapter();
al = fa.readFile(file, protocol, format);
- source = fa.afile; // keep reference for later if necessary.
+ source = fa.getAlignFile(); // keep reference for later if necessary.
}
} catch (java.io.IOException ex)
{
if ((al != null) && (al.getHeight() > 0))
{
- if (viewport != null)
+ for (SequenceI sq : al.getSequences())
{
- for (int i = 0; i < al.getHeight(); i++)
+ while (sq.getDatasetSequence() != null)
{
- viewport.getAlignment().addSequence(al.getSequenceAt(i));
+ sq = sq.getDatasetSequence();
}
- viewport.firePropertyChange("alignment", null, viewport
- .getAlignment().getSequences());
-
+ if (sq.getPDBId() != null)
+ {
+ for (PDBEntry pdbe : sq.getPDBId())
+ {
+ StructureSelectionManager.getStructureSelectionManager(
+ Desktop.instance).registerPDBEntry(pdbe);
+ }
+ }
+ }
+ if (viewport != null)
+ {
+ viewport.addAlignment(al, title);
}
else
{
alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
- alignFrame.statusBar.setText("Successfully loaded file "
- + title);
+ alignFrame.statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_loaded_file", new String[]
+ { title }));
if (!protocol.equals(AppletFormatAdapter.PASTE))
+ {
alignFrame.setFileName(file, format);
+ }
+ if (source instanceof HtmlFile)
+ {
+ ((HtmlFile) source).applySettingsToAlignFrame(alignFrame);
+ }
+ else if (source instanceof JSONFile)
+ {
+ ((JSONFile) source).applySettingsToAlignFrame(alignFrame);
+ }
- 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();
javax.swing.JOptionPane
.showInternalMessageDialog(
Desktop.desktop,
- "Out of memory loading file "
- + file
- + "!!"
- + "\nSee help files for increasing Java Virtual Machine memory.",
- "Out of memory",
+ MessageManager.formatMessage("warn.out_of_memory_loading_file", new String[]{file}),
+ MessageManager.getString("label.out_of_memory"),
javax.swing.JOptionPane.WARNING_MESSAGE);
}
});
}
- else
- {
- System.err.println("Out of memory loading file " + file + "!!");
- }
- }
- loadtime += System.currentTimeMillis();
+ System.err.println("Out of memory loading file " + file + "!!");
- if (Desktop.instance != null)
- {
- Desktop.instance.stopLoading();
}
+ 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
- if (alignFrame != null)
+ memused = memused
+ - (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // difference
+ // in free
+ // memory
+ // after
+ // load
+ if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
{
- if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
+ if (alignFrame != null)
{
AlignmentI al = alignFrame.getViewport().getAlignment();
+ (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 "
+ + (loadtime / 1000.0) + "s, took an additional "
+ + (1.0 * memused / (1024.0 * 1024.0))
+ + " MB (alignment is null)");
+ }
+ }
+ // remove the visual delay indicator
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.stopLoading();
}
}