package jalview.ws.jws2;
import jalview.api.FeatureColourI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.GraphLine;
import jalview.datamodel.SequenceFeature;
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.");
+ Console.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 (vals.hasNext())
{
val = vals.next().floatValue();
- sf = new SequenceFeature(type[0], type[1],
- base + rn.from, base + rn.to, val, methodName);
+ sf = new SequenceFeature(type[0], type[1], base + rn.from,
+ base + rn.to, val, methodName);
}
else
{
- sf = new SequenceFeature(type[0], type[1],
- base + rn.from, base + rn.to, methodName);
+ sf = new SequenceFeature(type[0], type[1], base + rn.from,
+ base + rn.to, methodName);
}
dseq.addSequenceFeature(sf);
if (last != val && !Float.isNaN(last))
{
// set graduated color as fading to white for minimum, and
// autoscaling to values on alignment
- FeatureColourI ggc = new FeatureColour(Color.white,
- gc.getColour(), Float.MIN_VALUE, Float.MAX_VALUE);
+ FeatureColourI ggc = new FeatureColour(gc.getColour(),
+ Color.white, gc.getColour(), Color.white,
+ Float.MIN_VALUE, Float.MAX_VALUE);
ggc.setAutoScaled(true);
fr.setColour(ft, ggc);
}