private File selectedFile;
+ private static boolean useDefaultFileFormat = false;
+
/**
* default constructor always raised errors in GUI dialog boxes
*/
if (format == null)
{
Desktop.instance.stopLoading();
- System.err.println("The input file \"" + file
+ jalview.bin.Console.errPrintln("The input file \"" + file
+ "\" has null or unidentifiable data content!");
- if (!Jalview.isHeadlessMode())
+ if (!Jalview.isHeadlessMode() && !Jalview.isBatchMode())
{
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.couldnt_read_data")
MessageManager.getString("label.couldnt_read_data"),
JvOptionPane.WARNING_MESSAGE);
}
- this.setShouldBeSaved();
+ // don't set shouldBeSaved if didn't load anything
+ // this.setShouldBeSaved();
return;
}
// TODO: cache any stream datasources as a temporary file (eg. PDBs
if (source != null)
{
// Tell the user (developer?) that this is going to cause a problem
- System.err.println(
+ jalview.bin.Console.errPrintln(
"IMPLEMENTATION ERROR: Cannot read consecutive Jalview XML projects from a stream.");
// We read the data anyway - it might make sense.
}
// BH 2018 switch to File object here instead of filename
- alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(
- selectedFile == null ? file : selectedFile);
+ alignFrame = new Jalview2XML(raiseGUI && !Jalview.isBatchMode())
+ .loadJalviewAlign(
+ selectedFile == null ? file : selectedFile);
}
else
{
"label.couldnt_load_file") + " " + title + "\n" + error;
// TODO: refactor FileLoader to be independent of Desktop / Applet GUI
// bits ?
- if (raiseGUI && Desktop.desktop != null)
+ if (raiseGUI && !Jalview.isBatchMode() && Desktop.desktop != null)
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
}
else
{
- System.err.println(errorMessage);
+ jalview.bin.Console.errPrintln(errorMessage);
}
}
}
} catch (Exception er)
{
- System.err.println("Exception whilst opening file '" + file);
+ jalview.bin.Console
+ .errPrintln("Exception whilst opening file '" + file);
er.printStackTrace();
- if (raiseGUI)
+ if (raiseGUI && !Jalview.isBatchMode())
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
er.printStackTrace();
alignFrame = null;
- if (raiseGUI)
+ if (raiseGUI && !Jalview.isBatchMode())
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
}
});
}
- System.err.println("Out of memory loading file " + file + "!!");
+ jalview.bin.Console
+ .errPrintln("Out of memory loading file " + file + "!!");
}
loadtime += System.currentTimeMillis();
{
AlignmentI al = alignFrame.getViewport().getAlignment();
- System.out.println("Loaded '" + title + "' in "
+ jalview.bin.Console.outPrintln("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)");
{
// report that we didn't load anything probably due to an out of memory
// error
- System.out.println("Failed to load '" + title + "' in "
+ jalview.bin.Console.outPrintln("Failed to load '" + title + "' in "
+ (loadtime / 1000.0) + "s, took an additional "
+ (1.0 * memused / (1024.0 * 1024.0))
+ " MB (alignment is null)");
}
this.setShouldBeSaved();
+ // after first file loaded we revert to assuming a default file format
+ useDefaultFileFormat = true;
}
/**
AlignViewport avp = af.getViewport();
if (avp == null)
return;
- avp.setSavedUpToDate(!protocol.isDynamic(),
- QuitHandler.Message.UNSAVED_ALIGNMENTS);
+ boolean upToDate = !protocol.isDynamic();
+ if (protocol.isUrl()
+ && Cache.getDefault(PROMPT_SAVE_UNCHANGED_URL_ALIGNMENTS, true))
+ {
+ upToDate = true;
+ }
+ avp.setSavedUpToDate(upToDate,
+ upToDate ? null : QuitHandler.Message.UNSAVED_ALIGNMENTS);
+ }
+
+ public static final String PROMPT_SAVE_UNCHANGED_URL_ALIGNMENTS = "PROMPT_SAVE_UNCHANGED_URL_ALIGNMENTS";
+
+ public static boolean getUseDefaultFileFormat()
+ {
+ return useDefaultFileFormat;
}
}