From: jprocter Date: Tue, 29 Jan 2008 10:17:56 +0000 (+0000) Subject: memory usage information and flag to indicate if warning dialog boxes should be raise... X-Git-Tag: Release_2_4~136 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b92eeace1b8b5237b3719a4d5b42e8a60af015e9;p=jalview.git memory usage information and flag to indicate if warning dialog boxes should be raised when problems occur. --- diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 6310cc4..3a77b73 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -26,17 +26,44 @@ import javax.swing.*; 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); @@ -59,13 +86,70 @@ public class FileLoader }); } + /** + * 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(); @@ -74,9 +158,9 @@ public class FileLoader try { Thread.sleep(500); + } catch (Exception ex) + { } - catch (Exception ex) - {} } return alignFrame; @@ -86,8 +170,8 @@ public class FileLoader { 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); @@ -125,45 +209,84 @@ public class FileLoader 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) { @@ -171,31 +294,29 @@ public class FileLoader { 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) { } } @@ -207,51 +328,115 @@ public class FileLoader 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(); + } + }