+ /**
+ * false if the scheme was constructed without a minColour and maxColour used
+ * to decide if existing colours should be taken from annotation elements when
+ * they exist
+ */
+ private boolean noGradient = false;
+
+ private IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
+
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ AnnotationColourGradient acg = new AnnotationColourGradient(annotation,
+ getColourScheme(), aboveAnnotationThreshold);
+ acg.thresholdIsMinMax = thresholdIsMinMax;
+ acg.annotationThreshold = (annotationThreshold == null) ? null
+ : new GraphLine(annotationThreshold);
+ acg.redMin = redMin;
+ acg.greenMin = greenMin;
+ acg.blueMin = blueMin;
+ acg.redRange = redRange;
+ acg.greenRange = greenRange;
+ acg.blueRange = blueRange;
+ acg.predefinedColours = predefinedColours;
+ acg.seqAssociated = seqAssociated;
+ acg.noGradient = noGradient;
+ return acg;
+ }