+ SequenceFeature[] seqFeatures = seq.getDatasetSequence()
+ .getSequenceFeatures();
+ if (seqFeatures != null)
+ {
+ ArrayList<BioJsFeaturePojo> bjsSeqFeatures = new ArrayList<BioJsFeaturePojo>();
+ for (SequenceFeature sf : seqFeatures)
+ {
+ if (displayedFeatures != null
+ && displayedFeatures.isVisible(sf.getType()))
+ {
+
+ // TODO: translate graduated/complex colourschemes to biojs model
+ String featureColour = jalview.util.Format.getHexString(fr
+ .findFeatureColour(Color.white, seq,
+ seq.findIndex(sf.getBegin())));
+ BioJsFeaturePojo bjsFeature = new BioJsFeaturePojo();
+ bjsFeature.setFillColor(featureColour);
+ bjsFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
+ bjsFeature.setXend(seq.findIndex(sf.getEnd()));
+ bjsFeature.setText(sf.getType());
+ bjsSeqFeatures.add(bjsFeature);
+ }
+ }
+ seqPojo.setFeatures(bjsSeqFeatures);
+ }
+ bjsAlignment.getSeqs().add(seqPojo);
+ }