import jalview.gui.AlignmentPanel;
import jalview.gui.FeatureRenderer;
import jalview.json.binding.v1.AlignmentPojo;
-import jalview.json.binding.v1.FeaturePojo;
+import jalview.json.binding.v1.SequenceFeaturesPojo;
import jalview.json.binding.v1.SequencePojo;
import jalview.schemes.ColourSchemeProperty;
import jalview.util.MessageManager;
{
AlignmentPojo bjsAlignment = new AlignmentPojo();
- bjsAlignment.setGlobalColorScheme(getGlobalColorScheme());
- bjsAlignment.setJalviewVersion(jalviewVersion);
- bjsAlignment.setWebStartUrl(webStartLaunchServletUrl);
+ // bjsAlignment.setGlobalColorScheme(getGlobalColorScheme());
+ // bjsAlignment.setJalviewVersion(jalviewVersion);
+ // bjsAlignment.setWebStartUrl(webStartLaunchServletUrl);
int count = 0;
for (SequenceI seq : alignment.getSequences())
SequenceFeature[] seqFeatures = seq.getSequenceFeatures();
if (seqFeatures != null)
{
- ArrayList<FeaturePojo> bjsSeqFeatures = new ArrayList<FeaturePojo>();
+ ArrayList<SequenceFeaturesPojo> bjsSeqFeatures = new ArrayList<SequenceFeaturesPojo>();
for (SequenceFeature sf : seqFeatures)
{
if (displayedFeatures != null
String featureColour = jalview.util.Format.getHexString(fr
.findFeatureColour(Color.white, seq,
seq.findIndex(sf.getBegin())));
- FeaturePojo bjsFeature = new FeaturePojo();
- bjsFeature.setFillColor(featureColour);
- bjsFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
- bjsFeature.setXend(seq.findIndex(sf.getEnd()));
- bjsFeature.setType(sf.getType());
- bjsSeqFeatures.add(bjsFeature);
+ // SequenceFeaturesPojo bjsFeature = new SequenceFeaturesPojo();
+ // bjsFeature.setFillColor(featureColour);
+ // bjsFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
+ // bjsFeature.setXend(seq.findIndex(sf.getEnd()));
+ // bjsFeature.setType(sf.getType());
+ // bjsSeqFeatures.add(bjsFeature);
}
}
- seqPojo.setFeatures(bjsSeqFeatures);
+ // seqPojo.setFeatures(bjsSeqFeatures);
}
bjsAlignment.getSeqs().add(seqPojo);
}