.valueOf(annot.get("value").toString());
String desc = annot.get("description") == null ? null : annot
.get("description").toString();
-
- char ss = annot.get("secondaryStructure") == null ? ' ' : annot
+ char ss = annot.get("secondaryStructure") == null
+ || annot.get("secondaryStructure").toString()
+ .equalsIgnoreCase("u0000") ? ' ' : annot
.get("secondaryStructure").toString().charAt(0);
String displayChar = annot.get("displayCharacter") == null ? ""
: annot.get("displayCharacter").toString();
for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
.values())
{
- if (cs.getBioJsName().equalsIgnoreCase(bioJsColourSchemeName))
+ if (cs.getBioJsName().equalsIgnoreCase(bioJsColourSchemeName)
+ || cs.getJalviewName()
+ .equalsIgnoreCase(bioJsColourSchemeName))
{
jalviewColor = cs.getJvColourScheme();
break;