package jalview.ws.jws2;
import jalview.api.AlignCalcWorkerI;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
-
import jalview.datamodel.GraphLine;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
+
import compbio.data.sequence.Range;
import compbio.data.sequence.Score;
import compbio.data.sequence.ScoreManager.ScoreHolder;
{
seq = seq.getDatasetSequence();
}
- ;
- ScoreHolder scores = scoremanager.getAnnotationForSequence(seqId);
+ ScoreHolder scores = null;
+ try {
+ scores = scoremanager.getAnnotationForSequence(seqId);
+ } catch (Exception q)
+ {
+ Cache.log
+ .info("Couldn't recover disorder prediction for sequence "
+ + seq.getName()
+ + "(Prediction name was "
+ + seqId+")"
+ + "\nSee http://issues.jalview.org/browse/JAL-1319 for one possible reason why disorder predictions might fail.");
+ }
float last = Float.NaN, val = Float.NaN;
int lastAnnot = ourAnnot.size();
if (scores!=null && scores.scores!=null) {
end=inputSeqs.getEndRes();
- for (SequenceI sq : ((List<SequenceI>) alignment.getSequences()))
+ for (SequenceI sq : ((List<SequenceI>) inputSeqs.getSequences()))
{
if (bySequence ? sq.findPosition(end+1) -sq.findPosition(start+1) > minlen - 1 : sq.getEnd() - sq.getStart() > minlen - 1)
{