*/
if (!trimMapping(from, to, fromRatio, toRatio))
{
- System.err.println("Ignoring mapping from " + Arrays.toString(from)
+ jalview.bin.Console.errPrintln("Ignoring mapping from " + Arrays.toString(from)
+ " to " + Arrays.toString(to) + " as counts don't match!");
return null;
}
{
from[1] += fromOverlap / toRatio;
}
- System.err.println(Arrays.toString(from));
+ jalview.bin.Console.errPrintln(Arrays.toString(from));
return true;
}
else if (fromOverlap < 0 && fromOverlap % fromRatio == 0)
{
to[1] += fromOverlap / fromRatio;
}
- System.err.println(Arrays.toString(to));
+ jalview.bin.Console.errPrintln(Arrays.toString(to));
return true;
}
return sf;
} catch (NumberFormatException nfe)
{
- System.err.println("Invalid number in gff: " + nfe.getMessage());
+ jalview.bin.Console.errPrintln("Invalid number in gff: " + nfe.getMessage());
return null;
}
}
if (!valid)
{
- System.err.println(INVALID_GFF_ATTRIBUTE_FORMAT + s);
+ jalview.bin.Console.errPrintln(INVALID_GFF_ATTRIBUTE_FORMAT + s);
return map;
}
theKey = theKey.trim();
if (theKey.isEmpty())
{
- System.err.println(INVALID_GFF_ATTRIBUTE_FORMAT + s);
+ jalview.bin.Console.errPrintln(INVALID_GFF_ATTRIBUTE_FORMAT + s);
map.clear();
return map;
}