+ 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)