+ protected void colorAlignmentContaining(AlignmentAnnotation currentAnn,
+ int selectedThresholdOption)
+ {
+
+ AnnotationColourGradient acg = null;
+ if (useOriginalColours.isSelected())
+ {
+ acg = new AnnotationColourGradient(currentAnn,
+ av.getGlobalColourScheme(), selectedThresholdOption);
+ }
+ else
+ {
+ acg = new AnnotationColourGradient(currentAnn,
+ minColour.getBackground(), maxColour.getBackground(),
+ selectedThresholdOption);
+ }
+ acg.setSeqAssociated(seqAssociated.isSelected());
+
+ if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
+ {
+ acg.setPredefinedColours(true);
+ }
+
+ acg.setThresholdIsMinMax(thresholdIsMin.isSelected());
+
+ this.ap.alignFrame.changeColour(acg);
+
+ if (av.getAlignment().getGroups() != null)
+ {
+
+ for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+ {
+ if (sg.cs == null)
+ {
+ continue;
+ }
+ sg.setColourScheme(acg.getInstance(av, sg));
+ }
+ }
+ }
+
+ @Override
+ protected void sliderDragReleased()
+ {
+ super.sliderDragReleased();
+ ap.paintAlignment(true, true);
+ }
+
+ /**
+ * construct and display a colourchooser for a given annotation row
+ *
+ * @param av
+ * @param ap
+ * @param alignmentAnnotation
+ * @param perseq
+ * - when true, enable per-sequence if alignment annotation is per
+ * sequence
+ */
+ public static void displayFor(AlignViewport av, AlignmentPanel ap,
+ AlignmentAnnotation alignmentAnnotation, boolean perSeq)
+ {
+ ColourSchemeI global = av.getGlobalColourScheme();
+ AnnotationColourGradient newCS = new AnnotationColourGradient(
+ alignmentAnnotation, global,
+ alignmentAnnotation.threshold != null
+ ? AnnotationColourGradient.ABOVE_THRESHOLD
+ : AnnotationColourGradient.NO_THRESHOLD);
+ if (alignmentAnnotation.sequenceRef != null)
+ {
+ newCS.setSeqAssociated(perSeq);
+ }
+ for (int i = 0; i < alignmentAnnotation.annotations.length; i++)
+ {
+ Annotation ann = alignmentAnnotation.annotations[i];
+ if (ann != null && ann.colour != null
+ && !ann.colour.equals(Color.white))
+ {
+ newCS.setPredefinedColours(true);
+ break;
+ }
+ }
+ AnnotationColourChooser achooser = new AnnotationColourChooser(av, ap,
+ newCS);
+ }