// should report somewhere useful for UI if necessary
warningMessage = ((warningMessage == null) ? "" : warningMessage)
+ "Parsing error at\n" + line;
- jalview.bin.Console.outPrintln("Error parsing feature file: " + ex + "\n" + line);
+ jalview.bin.Console.outPrintln(
+ "Error parsing feature file: " + ex + "\n" + line);
ex.printStackTrace(System.err);
resetMatcher();
return false;
String[] tokens = line.split(TAB_REGEX);
if (tokens.length != 2)
{
- jalview.bin.Console.errPrintln(String.format("Invalid token count %d for %d",
- tokens.length, line));
+ jalview.bin.Console.errPrintln(String.format(
+ "Invalid token count %d for %d", tokens.length, line));
}
else
{
seq = alignment.getSequenceAt(idx);
} catch (NumberFormatException ex)
{
- jalview.bin.Console.errPrintln("Invalid sequence index: " + seqIndex);
+ jalview.bin.Console
+ .errPrintln("Invalid sequence index: " + seqIndex);
}
}
@Override
public String print(SequenceI[] sqs, boolean jvsuffix)
{
- jalview.bin.Console.outPrintln("Use printGffFormat() or printJalviewFormat()");
+ jalview.bin.Console
+ .outPrintln("Use printGffFormat() or printJalviewFormat()");
return null;
}
*/
if (gffColumns.length < 5)
{
- jalview.bin.Console.errPrintln("Ignoring GFF feature line with too few columns ("
- + gffColumns.length + ")");
+ jalview.bin.Console
+ .errPrintln("Ignoring GFF feature line with too few columns ("
+ + gffColumns.length + ")");
return null;
}
}
} catch (IOException e)
{
- jalview.bin.Console.errPrintln("GFF parsing failed with: " + e.getMessage());
+ jalview.bin.Console
+ .errPrintln("GFF parsing failed with: " + e.getMessage());
return null;
}
}