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;
String titleSvgData = g1.getSVGDocument();
String alignSvgData = g2.getSVGDocument();
- String htmlData = getHtml(titleSvgData, alignSvgData);
+ String jsonData = getJSONData();
+ String htmlData = getHtml(titleSvgData, alignSvgData, jsonData);
out.write(htmlData.getBytes());
out.flush();
return Printable.PAGE_EXISTS;
}
- private String getHtml(String titleSvg, String alignmentSvg)
+ 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)
{
StringBuilder htmlSvg = new StringBuilder();
- htmlSvg.append("<html>"
- + "<style type=\"text/css\"> "
+ htmlSvg.append("<html>\n");
+ if (jsonData != null)
+ {
+ htmlSvg.append("<input type=\"hidden\" name=\"seqData\" id=\"seqData\" value='"
+ + jsonData + "'>");
+ }
+ htmlSvg.append("\n<style type=\"text/css\"> "
+ "div.parent{ width:100%;<!-- overflow: auto; -->}\n"
+ "div.titlex{ width:11%; float: left; }\n"
+ "div.align{ width:89%; float: right; }\n"