if (matchInDataset != null && xref.getMap().getTo() != null
&& matchInDataset != xref.getMap().getTo())
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Implementation problem (reopen JAL-2154): CrossRef.findInDataset seems to have recovered a different sequence than the one explicitly mapped for xref."
+ "Found:" + matchInDataset + "\nExpected:"
+ xref.getMap().getTo() + "\nFor xref:"
retrieved = sftch.getSequences(sourceRefs, !fromDna);
} catch (Exception e)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Problem whilst retrieving cross references for Sequence : "
+ seq.getName());
e.printStackTrace();
String msg = "Mapping updated from " + ms.getName()
+ " to retrieved crossreference "
+ matched.getName();
- System.out.println(msg);
+ jalview.bin.Console.outPrintln(msg);
List<DBRefEntry> toRefs = map.getTo().getDBRefs();
if (toRefs != null)
cf.addMap(retrievedSequence, map.getTo(), map.getMap());
} catch (Exception e)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Exception when consolidating Mapped sequence set...");
e.printStackTrace(System.err);
}
}
if (dataset.getSequences() == null)
{
- System.err.println("Empty dataset sequence set - NO VECTOR");
+ jalview.bin.Console.errPrintln("Empty dataset sequence set - NO VECTOR");
return false;
}
List<SequenceI> ds = dataset.getSequences();
{
if (nxt.getDatasetSequence() != null)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Implementation warning: CrossRef initialised with a dataset alignment with non-dataset sequences in it! ("
+ nxt.getDisplayId(true) + " has ds reference "
+ nxt.getDatasetSequence().getDisplayId(true)