}
/*
- * configure 'full' SO model unless preferences say not to
+ * configure 'full' SO model if preferences say to,
+ * else use the default (SO Lite)
*/
- if (!Cache.getDefault("USE_SO_LITE", false))
+ if (Cache.getDefault("USE_FULL_SO", false))
{
SequenceOntologyFactory.setInstance(new SequenceOntology());
}
System.out.println("Creating HTML image: " + file);
continue;
}
+ else if (format.equalsIgnoreCase("biojsmsa"))
+ {
+ BioJsHTMLOutput.updateBioJS();
+ try
+ {
+ Thread.sleep(1500);
+ } catch (InterruptedException e)
+ {
+ e.printStackTrace();
+ }
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel, af);
+ bjs.exportJalviewAlignmentAsBioJsHtmlFile(file);
+ System.out.println("Creating BioJS MSA Viwer HTML file: "
+ + file);
+ continue;
+ }
else if (format.equalsIgnoreCase("imgMap"))
{
af.createImageMap(new File(file), imageName);
+ "-png FILE\tCreate PNG image FILE from alignment.\n"
+ "-svg FILE\tCreate SVG image FILE from alignment.\n"
+ "-html FILE\tCreate HTML file from alignment.\n"
+ + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
+ "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
+ "-eps FILE\tCreate EPS file FILE from alignment.\n"
+ "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"