+ Annotation[] anots = new Annotation[sb.length()];\r
+ String anotString = sb.toString();\r
+ for (int i = 0; i < sb.length(); i++)\r
+ {\r
+ anots[i] = new Annotation(anotString.substring(i, i+1),\r
+ null,\r
+ ' ', 0);\r
+ }\r
+ AlignmentAnnotation aa = new AlignmentAnnotation(\r
+ seq.getName().substring(2), seq.getDescription(),\r
+ anots);\r
+\r
+ annotations.addElement(aa);\r
+ }\r
+ }\r
+ else\r
+ annotation = false;\r
+\r
+ if (!firstLine)\r
+ {\r
+ if (!annotation && !isValidProteinSequence(sb.toString().toCharArray()))\r