import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.exceptions.NoFileSelectedException;
-import jalview.gui.AlignViewport;
import jalview.gui.AlignmentPanel;
import jalview.gui.FeatureRenderer;
-import jalview.json.binding.v1.BioJsAlignmentPojo;
-import jalview.json.binding.v1.BioJsFeaturePojo;
-import jalview.json.binding.v1.BioJsSeqPojo;
+import jalview.json.binding.v1.AlignmentPojo;
+import jalview.json.binding.v1.SequenceFeaturesPojo;
+import jalview.json.binding.v1.SequencePojo;
import jalview.schemes.ColourSchemeProperty;
import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
import java.awt.Color;
import java.io.BufferedReader;
public class BioJsHTMLOutput
{
- private AlignViewport av;
+ private AlignmentViewport av;
private jalview.api.FeatureRenderer fr;
public String getJalviewAlignmentAsJsonString(AlignmentI alignment)
throws IOException, JSONException
{
- BioJsAlignmentPojo bjsAlignment = new BioJsAlignmentPojo();
+ 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())
name.append(seq.getName()).append("/").append(seq.getStart())
.append("-").append(seq.getEnd());
- BioJsSeqPojo seqPojo = new BioJsSeqPojo();
+ SequencePojo seqPojo = new SequencePojo();
seqPojo.setId(String.valueOf(++count));
seqPojo.setEnd(seq.getEnd());
seqPojo.setStart(seq.getStart());
SequenceFeature[] seqFeatures = seq.getSequenceFeatures();
if (seqFeatures != null)
{
- ArrayList<BioJsFeaturePojo> bjsSeqFeatures = new ArrayList<BioJsFeaturePojo>();
+ 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())));
- 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);
+ // 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);
}