import java.io.PrintWriter;
import java.net.MalformedURLException;
import java.net.URI;
+import java.net.URISyntaxException;
import java.net.URL;
import java.security.AllPermission;
import java.security.CodeSource;
File imageFile = new File(file);
imageName = imageFile.getName();
HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
- htmlSVG.generateHtmlSvgOutput(new File(file));
+ htmlSVG.exportHTML(file);
System.out.println("Creating HTML image: " + file);
continue;
}
else if (format.equalsIgnoreCase("biojsmsa"))
{
- BioJsHTMLOutput.updateBioJS();
+ if (file == null)
+ {
+ System.err.println("The output html file must not be null");
+ return;
+ }
try
{
- Thread.sleep(1500);
- } catch (InterruptedException e)
+ BioJsHTMLOutput
+ .refreshVersionInfo(BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+ } catch (URISyntaxException e)
{
e.printStackTrace();
}
- BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel, af);
- bjs.exportJalviewAlignmentAsBioJsHtmlFile(file);
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
+ bjs.exportHTML(file);
System.out.println("Creating BioJS MSA Viwer HTML file: "
+ file);
continue;