package jalview.io;
+import jalview.api.AlignmentViewPanel;
import jalview.exceptions.NoFileSelectedException;
-import jalview.gui.AlignViewport;
-import jalview.gui.AlignmentPanel;
-import jalview.gui.FeatureRenderer;
import jalview.json.binding.v1.BioJSReleasePojo;
import jalview.json.binding.v1.BioJSRepositoryPojo;
import jalview.util.MessageManager;
public class BioJsHTMLOutput
{
- private AlignViewport av;
+ private AlignmentViewPanel ap;
private static File currentBJSTemplateFile;
"biojs_template_git_repo",
"https://raw.githubusercontent.com/tcofoegbu/bjs-template/master/package.json");
- public BioJsHTMLOutput(AlignmentPanel ap, FeatureRenderer fr1)
+ public BioJsHTMLOutput(AlignmentViewPanel ap)
{
if (ap != null)
{
- this.av = ap.av;
- av.setFeatureRenderer(new FeatureRenderer(ap));
+ this.ap = ap;
}
}
try
{
String outputFile = getOutputFile();
- String jalviewAlignmentJson = JSONFile.getJSONData(av);
+ String jalviewAlignmentJson = JSONFile.getJSONData(ap);
String bioJSTemplateString = getBioJsTemplateAsString();
String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
.replaceAll(