import jalview.datamodel.Range;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
import jalview.util.Comparison;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
updateFeatures();
/*
+ * show complement features on top (if configured to show them)
+ */
+ if (av.isShowComplementFeatures())
+ {
+ AlignViewportI complement = av.getCodingComplement();
+ AlignFrame af = Desktop.getAlignFrameFor(complement);
+ FeatureRendererModel fr2 = af.getFeatureRenderer();
+ List<SequenceFeature> features = fr2.findComplementFeaturesAtResidue(
+ seq, seq.findPosition(column));
+ // todo: ensure ordered by feature render order
+ for (SequenceFeature sf : features)
+ {
+ if (!fr2.featureGroupNotShown(sf))
+ {
+ Color col = fr2.getColour(sf);
+ if (col != null)
+ {
+ return col;
+ }
+ }
+ }
+ }
+
+ /*
* inspect features in reverse renderOrder (the last in the array is
* displayed on top) until we find one that is rendered at the position
*/