+ // Replace all internal gaps with . and external spaces with ~\r
+ s[i] =new Sequence(seqs[i].getName(),seqs[i].getSequence().replace('-', '.'));\r
+\r
+ StringBuffer sb = new StringBuffer(s[i].getSequence());\r
+ for (int ii = 0; ii < sb.length(); ii++)\r
+ {\r
+ if (sb.charAt(ii) == '.')\r
+ {\r
+ sb.setCharAt(ii, '~');\r
+ }\r
+ else\r
+ break;\r
+ }\r
+\r
+ for (int ii = sb.length() - 1; ii > 0; ii--)\r
+ {\r
+ if (sb.charAt(ii) == '.')\r
+ {\r
+ sb.setCharAt(ii,'~');\r
+ }\r
+ else\r
+ break;\r
+ }\r
+\r
+ s[i].setSequence(sb.toString());\r