}
else
{
- // System.err.println("Skipping NaN - not valid value.");
+ // jalview.bin.Console.errPrintln("Skipping NaN - not valid value.");
text.append(comma + 0f);// row.annotations[j].value);
}
comma = ",";
} catch (Exception ex)
{
ex.printStackTrace();
- System.out.println("Problem reading annotation file: " + ex);
+ jalview.bin.Console.outPrintln("Problem reading annotation file: " + ex);
if (nlinesread > 0)
{
- System.out.println("Last read line " + nlinesread + ": '" + lastread
+ jalview.bin.Console.outPrintln("Last read line " + nlinesread + ": '" + lastread
+ "' (first 80 chars) ...");
}
return false;
if (refSeqIndex < 1)
{
refSeqIndex = 1;
- System.out.println(
+ jalview.bin.Console.outPrintln(
"WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");
}
} catch (Exception ex)
{
if (hidden == null)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Cannot process HIDE_INSERTIONS without an alignment view: Ignoring line: "
+ line);
}
{
// TODO: specify and implement duplication of alignment annotation
// for multiple group references.
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Ignoring 1:many group reference mappings for group name '"
+ groupRef + "'");
}
if (rowset != null && rowset.size() > 0)
{
AlignmentAnnotation alan = null;
- for (int elm = 0,
- elmSize = rowset.size(); elm < elmSize; elm++)
+ for (int elm = 0, elmSize = rowset
+ .size(); elm < elmSize; elm++)
{
alan = (AlignmentAnnotation) rowset.elementAt(elm);
alan.groupRef = theGroup;
}
else
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Couldn't combine annotations. None are added to alignment yet!");
}
}
value = Float.valueOf(nextToken);
} catch (NumberFormatException e)
{
- System.err.println("line " + nlinesread + ": Threshold '" + nextToken
+ jalview.bin.Console.errPrintln("line " + nlinesread + ": Threshold '" + nextToken
+ "' invalid, setting to zero");
}
String label = st.hasMoreTokens() ? st.nextToken() : null;
}
} catch (Exception e)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Couldn't parse Group Start or End Field as '*' or a valid column or sequence index: '"
+ rng + "' - assuming alignment width for group.");
// assume group is full width