import jalview.datamodel.*;
import jalview.gui.*;
-public class FileLoader
- implements Runnable
+public class FileLoader implements Runnable
{
String file;
+
String protocol;
+
String format;
+
+ FileParse source = null; // alternative specification of where data comes
+
+ // from
+
AlignViewport viewport;
+
AlignFrame alignFrame;
- public void LoadFile(AlignViewport viewport, String file, String protocol,
- String format)
+ long loadtime;
+
+ long memused;
+
+ boolean raiseGUI = true;
+ /**
+ * default constructor always raised errors in GUI dialog boxes
+ */
+ 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
+ */
+ public FileLoader(boolean raiseGUI)
+ {
+ this.raiseGUI = raiseGUI;
+ }
+
+ public void LoadFile(AlignViewport viewport, String file,
+ String protocol, String format)
{
this.viewport = viewport;
LoadFile(file, protocol, format);
});
}
+ /**
+ * Load a (file, protocol) source of unknown type
+ *
+ * @param file
+ * @param protocol
+ */
+ public void LoadFile(String file, String protocol)
+ {
+ LoadFile(file, protocol, null);
+ }
+
+ /**
+ * Load alignment from (file, protocol) and wait till loaded
+ *
+ * @param file
+ * @param protocol
+ * @return alignFrame constructed from file contents
+ */
+ public AlignFrame LoadFileWaitTillLoaded(String file, String protocol)
+ {
+ return LoadFileWaitTillLoaded(file, protocol, null);
+ }
+
+ /**
+ * Load alignment from (file, protocol) of type format and wait till loaded
+ *
+ * @param file
+ * @param protocol
+ * @param format
+ * @return alignFrame constructed from file contents
+ */
public AlignFrame LoadFileWaitTillLoaded(String file, String protocol,
- String format)
+ String format)
{
this.file = file;
this.protocol = protocol;
this.format = format;
+ return _LoadFileWaitTillLoaded();
+ }
+
+ /**
+ * Load alignment from FileParse source of type format and wait till loaded
+ *
+ * @param source
+ * @param format
+ * @return alignFrame constructed from file contents
+ */
+ public AlignFrame LoadFileWaitTillLoaded(FileParse source, String format)
+ {
+ this.source = source;
+ file = source.getInFile();
+ protocol = source.type;
+ this.format = format;
+ return _LoadFileWaitTillLoaded();
+ }
+ /**
+ * start thread and wait until finished, then return the alignFrame that's
+ * (hopefully) been read.
+ *
+ * @return
+ */
+ protected AlignFrame _LoadFileWaitTillLoaded()
+ {
Thread loader = new Thread(this);
loader.start();
try
{
Thread.sleep(500);
+ } catch (Exception ex)
+ {
}
- catch (Exception ex)
- {}
}
return alignFrame;
{
Vector recent = new Vector();
- String type = protocol.equals(FormatAdapter.FILE)
- ? "RECENT_FILE" : "RECENT_URL";
+ String type = protocol.equals(FormatAdapter.FILE) ? "RECENT_FILE"
+ : "RECENT_URL";
String historyItems = jalview.bin.Cache.getProperty(type);
public void run()
{
- String title = protocol.equals(AppletFormatAdapter.PASTE)
- ? "Copied From Clipboard" : file;
-
+ String title = protocol.equals(AppletFormatAdapter.PASTE) ? "Copied From Clipboard"
+ : file;
+ Runtime rt = Runtime.getRuntime();
try
{
if (Desktop.instance != null)
{
Desktop.instance.startLoading(file);
}
-
+ if (format == null)
+ {
+ // just in case the caller didn't identify the file for us
+ if (source != null)
+ {
+ format = new IdentifyFile().Identify(source, false); // identify
+ // stream and
+ // rewind rather
+ // than close
+ }
+ else
+ {
+ format = new IdentifyFile().Identify(file, protocol);
+ }
+ }
+ if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
+ {
+ System.gc();
+ memused = (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // free memory before load
+ }
+ loadtime = -System.currentTimeMillis();
Alignment al = null;
if (format.equalsIgnoreCase("Jalview"))
{
- alignFrame = new Jalview2XML().LoadJalviewAlign(file);
+ if (source != null)
+ {
+ // Tell the user (developer?) that this is going to cause a problem
+ System.err
+ .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);
}
else
{
String error = AppletFormatAdapter.SUPPORTED_FORMATS;
-
if (FormatAdapter.isValidFormat(format))
{
try
{
- al = new FormatAdapter().readFile(file, protocol, format);
- }
- catch (java.io.IOException ex)
+ if (source != null)
+ {
+ // read from the provided source
+ al = new FormatAdapter().readFromFile(source, format);
+ }
+ 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.
+ }
+ } catch (java.io.IOException ex)
{
error = ex.getMessage();
}
- } else {
- if (format!=null && format.length()>7)
+ }
+ else
+ {
+ if (format != null && format.length() > 7)
{
// ad hoc message in format.
- error = format +"\n"+error;
+ error = format + "\n" + error;
}
}
- if ( (al != null) && (al.getHeight() > 0))
+ if ((al != null) && (al.getHeight() > 0))
{
if (viewport != null)
{
{
viewport.getAlignment().addSequence(al.getSequenceAt(i));
}
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.firePropertyChange("alignment", null, viewport
+ .getAlignment().getSequences());
}
else
{
- alignFrame = new AlignFrame(al,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
- alignFrame.statusBar.setText("Successfully loaded file " + title);
+ alignFrame.statusBar.setText("Successfully loaded file "
+ + title);
if (!protocol.equals(AppletFormatAdapter.PASTE))
alignFrame.setFileName(file, format);
Desktop.addInternalFrame(alignFrame, title,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
try
{
alignFrame.setMaximum(jalview.bin.Cache.getDefault(
- "SHOW_FULLSCREEN", false));
- }
- catch (java.beans.PropertyVetoException ex)
+ "SHOW_FULLSCREEN", false));
+ } catch (java.beans.PropertyVetoException ex)
{
}
}
Desktop.instance.stopLoading();
}
- final String errorMessage = "Couldn't load file " + title + "\n" +
- error;
-
- javax.swing.SwingUtilities.invokeLater(new Runnable()
+ final String errorMessage = "Couldn't load file " + title + "\n"
+ + error;
+ if (raiseGUI)
{
- public void run()
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- errorMessage,
- "Error loading file",
- JOptionPane.WARNING_MESSAGE);
- }
- });
+ public void run()
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ errorMessage, "Error loading file",
+ JOptionPane.WARNING_MESSAGE);
+ }
+ });
+ }
+ else
+ {
+ System.err.println(errorMessage);
+ }
}
}
updateRecentlyOpened();
}
+ catch (Exception er)
+ {
+ System.err.println("Exception whilst opening file '"+file);
+ er.printStackTrace();
+ if (raiseGUI)
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ javax.swing.JOptionPane
+ .showInternalMessageDialog(
+ Desktop.desktop,
+ "Encountered problems opening "
+ + file
+ + "!!"
+ , "File open error",
+ javax.swing.JOptionPane.WARNING_MESSAGE);
+ }
+ });
+ }
+ alignFrame = null;
+ }
catch (OutOfMemoryError er)
{
er.printStackTrace();
alignFrame = null;
-
- javax.swing.SwingUtilities.invokeLater(new Runnable()
+ if (raiseGUI)
{
- public void run()
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
{
- 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);
- }
- });
+ 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);
+ }
+ });
+ }
+ else
+ {
+ System.err.println("Out of memory loading file " + file + "!!");
+ }
}
+ loadtime += System.currentTimeMillis();
- System.gc();
if (Desktop.instance != null)
{
Desktop.instance.stopLoading();
}
+ // System.gc();
+ memused = memused - (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // difference in free memory after load
+ if (alignFrame != null)
+ {
+ if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
+ {
+ AlignmentI al = alignFrame.getViewport().getAlignment();
+
+ System.out.println("Loaded '" + title + "' in "
+ + (loadtime / 1000.0) + "s, took an additional "
+ + (1.0 * memused / (1024.0 * 1024.0)) + " MB ("
+ + al.getHeight() + " seqs by " + al.getWidth() + " cols)");
+ }
+ }
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.lang.Object#finalize()
+ */
+ protected void finalize() throws Throwable
+ {
+ source = null;
+ alignFrame = null;
+ viewport = null;
+ super.finalize();
+ }
+
}
git://source.jalview.org / jalview.git / commitdiff