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Merge branch 'bug/JAL-4214_system_freeze_when_opening_file_using_gui_in_linux' into...
[jalview.git]
/
src
/
jalview
/
io
/
FileLoader.java
diff --git
a/src/jalview/io/FileLoader.java
b/src/jalview/io/FileLoader.java
index
7d226ed
..
49571dc
100755
(executable)
--- a/
src/jalview/io/FileLoader.java
+++ b/
src/jalview/io/FileLoader.java
@@
-96,32
+96,51
@@
public class FileLoader implements Runnable
public void LoadFile(AlignViewport viewport, Object file,
DataSourceType protocol, FileFormatI format)
{
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)
{
this.selectedFile = (File) file;
file = selectedFile.getPath();
}
this.viewport = viewport;
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)
{
}
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;
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();
+ }
}
/**
}
/**
@@
-273,6
+292,7
@@
public class FileLoader implements Runnable
? "Copied From Clipboard"
: file;
Runtime rt = Runtime.getRuntime();
? "Copied From Clipboard"
: file;
Runtime rt = Runtime.getRuntime();
+
try
{
if (Desktop.instance != null)
try
{
if (Desktop.instance != null)
@@
-301,7
+321,7
@@
public class FileLoader implements Runnable
if (format == null)
{
Desktop.instance.stopLoading();
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())
{
+ "\" has null or unidentifiable data content!");
if (!Jalview.isHeadlessMode())
{
@@
-312,7
+332,8
@@
public class FileLoader implements Runnable
MessageManager.getString("label.couldnt_read_data"),
JvOptionPane.WARNING_MESSAGE);
}
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
return;
}
// TODO: cache any stream datasources as a temporary file (eg. PDBs
@@
-333,7
+354,7
@@
public class FileLoader implements Runnable
if (source != null)
{
// Tell the user (developer?) that this is going to cause a problem
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.
}
"IMPLEMENTATION ERROR: Cannot read consecutive Jalview XML projects from a stream.");
// We read the data anyway - it might make sense.
}
@@
-380,12
+401,12
@@
public class FileLoader implements Runnable
{
if (selectedFile == null)
{
{
if (selectedFile == null)
{
- al = fa.readFile(file, protocol, format);
+ al = fa.readFile(null, file, protocol, format);
}
else
{
}
else
{
- al = fa.readFile(selectedFile, protocol, format);
+ al = fa.readFile(selectedFile, null, protocol, format);
}
source = fa.getAlignFile(); // keep reference for later if
}
source = fa.getAlignFile(); // keep reference for later if
@@
-531,7
+552,7
@@
public class FileLoader implements Runnable
}
else
{
}
else
{
- System.err.println(errorMessage);
+ jalview.bin.Console.errPrintln(errorMessage);
}
}
}
}
}
}
@@
-540,7
+561,7
@@
public class FileLoader implements Runnable
} catch (Exception er)
{
} catch (Exception er)
{
- System.err.println("Exception whilst opening file '" + file);
+ jalview.bin.Console.errPrintln("Exception whilst opening file '" + file);
er.printStackTrace();
if (raiseGUI)
{
er.printStackTrace();
if (raiseGUI)
{
@@
-580,7
+601,7
@@
public class FileLoader implements Runnable
}
});
}
}
});
}
- System.err.println("Out of memory loading file " + file + "!!");
+ jalview.bin.Console.errPrintln("Out of memory loading file " + file + "!!");
}
loadtime += System.currentTimeMillis();
}
loadtime += System.currentTimeMillis();
@@
-599,7
+620,7
@@
public class FileLoader implements Runnable
{
AlignmentI al = alignFrame.getViewport().getAlignment();
{
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)");
+ (loadtime / 1000.0) + "s, took an additional "
+ (1.0 * memused / (1024.0 * 1024.0)) + " MB ("
+ al.getHeight() + " seqs by " + al.getWidth() + " cols)");
@@
-608,7
+629,7
@@
public class FileLoader implements Runnable
{
// report that we didn't load anything probably due to an out of memory
// error
{
// 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)");
+ (loadtime / 1000.0) + "s, took an additional "
+ (1.0 * memused / (1024.0 * 1024.0))
+ " MB (alignment is null)");