} catch (Exception e)
{
e.printStackTrace();
- jalview.bin.Console.errPrintln("Failed to read alignment using the '" + fileFormat
- + "' reader.\n" + e);
+ jalview.bin.Console.errPrintln("Failed to read alignment using the '"
+ + fileFormat + "' reader.\n" + e);
if (e.getMessage() != null
&& e.getMessage().startsWith(INVALID_CHARACTERS))
} catch (Exception e)
{
e.printStackTrace();
- jalview.bin.Console.errPrintln("Failed to read alignment using the '" + format
- + "' reader.\n" + e);
+ jalview.bin.Console.errPrintln("Failed to read alignment using the '"
+ + format + "' reader.\n" + e);
if (e.getMessage() != null
&& e.getMessage().startsWith(INVALID_CHARACTERS))
String afileresp = afile.print(seqs, jvsuffix);
if (afile.hasWarningMessage())
{
- jalview.bin.Console.errPrintln("Warning raised when writing as " + format
- + " : " + afile.getWarningMessage());
+ jalview.bin.Console.errPrintln("Warning raised when writing as "
+ + format + " : " + afile.getWarningMessage());
}
return afileresp;
} catch (Exception e)
memf += r.totalMemory() - r.freeMemory();
if (al != null)
{
- jalview.bin.Console.outPrintln("Alignment contains " + al.getHeight()
- + " sequences and " + al.getWidth() + " columns.");
+ jalview.bin.Console.outPrintln("Alignment contains "
+ + al.getHeight() + " sequences and " + al.getWidth()
+ + " columns.");
try
{
jalview.bin.Console.outPrintln(new AppletFormatAdapter()
{
jalview.bin.Console.outPrintln("Couldn't read alignment");
}
- jalview.bin.Console.outPrintln("Read took " + (t1 / 1000.0) + " seconds.");
+ jalview.bin.Console
+ .outPrintln("Read took " + (t1 / 1000.0) + " seconds.");
jalview.bin.Console.outPrintln(
"Difference between free memory now and before is "
+ (memf / (1024.0 * 1024.0) * 1.0) + " MB");
}
else
{
- jalview.bin.Console.errPrintln("Ignoring argument '" + args[i] + "' (" + i
- + "'th)- not a readable file.");
+ jalview.bin.Console.errPrintln("Ignoring argument '" + args[i]
+ + "' (" + i + "'th)- not a readable file.");
}
i++;
}
DataSourceType protocol = null;
if (debug)
{
- jalview.bin.Console.outPrintln("resolving datasource started with:\n>>file\n"
- + file + ">>endfile");
+ jalview.bin.Console
+ .outPrintln("resolving datasource started with:\n>>file\n"
+ + file + ">>endfile");
}
// This might throw a security exception in certain browsers
{
if (debug)
{
- jalview.bin.Console.errPrintln("Exception when accessing content: " + e);
+ jalview.bin.Console
+ .errPrintln("Exception when accessing content: " + e);
}
fp = null;
}
}
} catch (Exception e)
{
- jalview.bin.Console.errPrintln("Failed to access content as paste!");
+ jalview.bin.Console
+ .errPrintln("Failed to access content as paste!");
e.printStackTrace();
fp = null;
}
{
if (debug)
{
- jalview.bin.Console.outPrintln("Format not identified. Inaccessible file.");
+ jalview.bin.Console.outPrintln(
+ "Format not identified. Inaccessible file.");
}
return null;
}
{
if (debug)
{
- jalview.bin.Console.outPrintln("Protocol identified as " + protocol);
+ jalview.bin.Console
+ .outPrintln("Protocol identified as " + protocol);
}
return protocol;
}
{
if (debug)
{
- jalview.bin.Console.errPrintln("File deemed not accessible via " + protocol);
+ jalview.bin.Console
+ .errPrintln("File deemed not accessible via " + protocol);
e.printStackTrace();
}
}