+\r
+ /*\r
+ * Try to load T-Coffee score file\r
+ */\r
+ String sScoreFile = applet.getParameter("scoreFile");\r
+ if( sScoreFile != null && !"".equals(sScoreFile) ) {\r
+ try {\r
+ URL urlScore = new URL(sScoreFile);\r
+ newAlignFrame.loadScoreFile(urlScore);\r
+ //TODO check the scores matrix matches the MSA dimensions\r
+ \r
+ }\r
+ catch( Exception e ) {\r
+ // TODO error message log (shows a warning dialogbox?)\r
+ System.err.printf("Cannot read score file: '%s'. Cause: %s \n", sScoreFile, e.getMessage());\r
+ }\r
+ }\r
+ \r
+\r
+ // ///////////////////////////\r
+ // modify display of features\r
+ // we do this before any features have been loaded, ensuring any hidden groups are hidden when features first displayed\r
+ //\r
+ // hide specific groups\r
+ // \r
+ String param = applet.getParameter("hidefeaturegroups");\r
+ if (param != null)\r
+ {\r
+ newAlignFrame.setFeatureGroupState(separatorListToArray(param), false); \r
+// applet.setFeatureGroupStateOn(newAlignFrame, param, false);\r
+ }\r
+ // show specific groups\r
+ param = applet.getParameter("showfeaturegroups");\r
+ if (param != null)\r
+ {\r
+ newAlignFrame.setFeatureGroupState(separatorListToArray(param), true); \r
+// applet.setFeatureGroupStateOn(newAlignFrame, param, true);\r
+ }\r
+ // and now load features\r
+ param = applet.getParameter("features");\r