initialise(vcfFile);
} catch (IOException e)
{
- System.err.println("Error opening VCF file: " + e.getMessage());
+ jalview.bin.Console.errPrintln("Error opening VCF file: " + e.getMessage());
}
// map of species!chromosome!fromAssembly!toAssembly to {fromRange, toRange}
}
} catch (Throwable e)
{
- System.err.println("Error processing VCF: " + e.getMessage());
+ jalview.bin.Console.errPrintln("Error processing VCF: " + e.getMessage());
e.printStackTrace();
if (gui != null)
{
patterns.add(Pattern.compile(token.toUpperCase(Locale.ROOT)));
} catch (PatternSyntaxException e)
{
- System.err.println("Invalid pattern ignored: " + token);
+ jalview.bin.Console.errPrintln("Invalid pattern ignored: " + token);
}
}
return patterns;