package jalview.io;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignViewport;
import jalview.gui.AlignmentPanel;
import jalview.gui.AnnotationPanel;
-import jalview.gui.Desktop;
import jalview.gui.FeatureRenderer;
import jalview.gui.HTMLOptions;
import jalview.math.AlignmentDimension;
this.av = ap.av;
this.ap = ap;
+ av.setFeatureRenderer(new FeatureRenderer(ap));
this.annotationPanel = ap.getAnnotationPanel();
generateHtmlSvgOutput(file);
}
String titleSvgData = g1.getSVGDocument();
String alignSvgData = g2.getSVGDocument();
- String jsonData = getJSONData();
+ String jsonData = JSONFile.getJSONData(av);
String htmlData = getHtml(titleSvgData, alignSvgData, jsonData);
out.write(htmlData.getBytes());
return Printable.PAGE_EXISTS;
}
- private String getJSONData()
- {
- JSONFile jsonFile = new JSONFile();
- Alignment al = new Alignment(av.getAlignment().getSequencesArray());
- jsonFile.seqGroups = av.getAlignment().getGroups();
- // jsonFile.addAnnotations(al);
- jsonFile.setDisplayedFeatures(av.getFeaturesDisplayed());
- Desktop.setCurrentAlignFrame(av.getAlignPanel().alignFrame);
- for (SequenceI seq : av.getAlignment().getSequences())
- {
- jsonFile.seqs.add(seq);
- }
-
- // Add non auto calculated annotation to AlignFile
- for (AlignmentAnnotation annot : av.getAlignment()
- .getAlignmentAnnotation())
- {
- if (annot != null && !annot.autoCalculated)
- {
- if (annot.label.equals("PDB.CATempFactor"))
- {
- continue;
- }
- jsonFile.annotations.add(annot);
- }
- }
-
- // jsonFile.setGlobalColorScheme(av.getGlobalColourScheme());
- String jsonString = jsonFile.print();
- System.out.println(">>>>>>>>>>> JSONFile : " + jsonString);
- return jsonString;
- }
-
private String getHtml(String titleSvg, String alignmentSvg,
String jsonData)
{