+\r
+ void setBelowAlignment(AlignmentI al, StringTokenizer st)\r
+ {\r
+ String token;\r
+ AlignmentAnnotation aa;\r
+ while(st.hasMoreTokens())\r
+ {\r
+ token = st.nextToken();\r
+ for(int i=0; i<al.getAlignmentAnnotation().length; i++)\r
+ {\r
+ aa = al.getAlignmentAnnotation()[i];\r
+ if(aa.sequenceRef==refSeq && aa.label.equals(token))\r
+ {\r
+ aa.belowAlignment = true;\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ void addAlignmentDetails(AlignmentI al, StringTokenizer st)\r
+ {\r
+ String keyValue, key, value;\r
+ while (st.hasMoreTokens())\r
+ {\r
+ keyValue = st.nextToken();\r
+ key = keyValue.substring(0, keyValue.indexOf("="));\r
+ value = keyValue.substring(keyValue.indexOf("=") + 1);\r
+ al.setProperty(key,value);\r
+ }\r
+ }\r