+ StringBuilder name = new StringBuilder();
+ name.append(seq.getName()).append("/").append(seq.getStart())
+ .append("-").append(seq.getEnd());
+
+ BioJsSeqPojo seqPojo = new BioJsSeqPojo();
+ seqPojo.setId(String.valueOf(++count));
+ seqPojo.setEnd(seq.getEnd());
+ seqPojo.setStart(seq.getStart());
+ seqPojo.setName(name.toString());
+ seqPojo.setSeq(seq.getSequenceAsString());
+
+ 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);