import jalview.gui.AlignViewport;
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
+import jalview.gui.QuitHandler;
import jalview.json.binding.biojson.v1.ColourSchemeMapper;
import jalview.project.Jalview2XML;
import jalview.schemes.ColourSchemeI;
private File selectedFile;
+ private static boolean useDefaultFileFormat = false;
+
/**
* default constructor always raised errors in GUI dialog boxes
*/
public void LoadFile(AlignViewport viewport, Object file,
DataSourceType protocol, FileFormatI format)
{
+ LoadFile(viewport, file, protocol, format, true);
+ }
+
+ public void LoadFile(AlignViewport viewport, Object file,
+ DataSourceType protocol, FileFormatI format, boolean async)
+ {
this.viewport = viewport;
- if (file instanceof File) {
+ if (file instanceof File)
+ {
this.selectedFile = (File) file;
file = selectedFile.getPath();
}
- LoadFile(file.toString(), protocol, format);
+ LoadFile(file.toString(), protocol, format, async);
}
public void LoadFile(String file, DataSourceType protocol,
FileFormatI format)
{
+ LoadFile(file, protocol, format, true);
+ }
+
+ public void LoadFile(String file, DataSourceType protocol,
+ FileFormatI format, boolean async)
+ {
this.file = file;
this.protocol = protocol;
this.format = format;
- final Thread loader = new Thread(this);
-
- SwingUtilities.invokeLater(new Runnable()
+ if (async)
{
- @Override
- public void run()
+ final Thread loader = new Thread(this);
+
+ SwingUtilities.invokeLater(new Runnable()
{
- loader.start();
- }
- });
+ @Override
+ public void run()
+ {
+ loader.start();
+ }
+ });
+ }
+ else
+ {
+ this.run();
+ }
}
/**
? "Copied From Clipboard"
: file;
Runtime rt = Runtime.getRuntime();
+
try
{
if (Desktop.instance != null)
format = new IdentifyFile().identify(source, false);
// identify stream and rewind rather than close
}
- else if (selectedFile != null) {
+ else if (selectedFile != null)
+ {
format = new IdentifyFile().identify(selectedFile, protocol);
}
else
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);
}
+ // 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
{
file.lastIndexOf("."));
String tempStructureFileStr = createNamedJvTempFile(
urlLeafName, structExt);
-
+
// BH - switching to File object here so as to hold
// ._bytes array directly
File tempFile = new File(tempStructureFileStr);
UrlDownloadClient.download(file, tempFile);
-
- al = fa.readFile(tempFile, DataSourceType.FILE,
- format);
+
+ al = fa.readFile(tempFile, DataSourceType.FILE, format);
source = fa.getAlignFile();
}
else
{
- if (selectedFile == null) {
- al = fa.readFile(file, protocol, format);
-
- } else {
- al = fa.readFile(selectedFile, protocol, format);
- }
+ if (selectedFile == null)
+ {
+ al = fa.readFile(null, file, protocol, format);
+
+ }
+ else
+ {
+ al = fa.readFile(selectedFile, null, protocol, format);
+ }
source = fa.getAlignFile(); // keep reference for later if
-
- // necessary.
+
+ // necessary.
}
}
} catch (java.io.IOException ex)
try
{
- alignFrame.setMaximum(jalview.bin.Cache
- .getDefault("SHOW_FULLSCREEN", false));
+ alignFrame.setMaximum(
+ Cache.getDefault("SHOW_FULLSCREEN", false));
} catch (java.beans.PropertyVetoException ex)
{
}
"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)");
Desktop.instance.stopLoading();
}
+ this.setShouldBeSaved();
+ // after first file loaded we revert to assuming a default file format
+ useDefaultFileFormat = true;
}
/**
return tempStructFile.toString();
}
+ /*
+ * set whether quit should ask to save when just loaded this source
+ */
+ private void setShouldBeSaved()
+ {
+ if (protocol == null)
+ return;
+ AlignFrame af = this.alignFrame;
+ if (af == null)
+ return;
+ AlignViewport avp = af.getViewport();
+ if (avp == null)
+ return;
+ 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;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff