+\r
+ while ( (i < seqs.length) && (seqs[i] != null))\r
+ {\r
+ // Replace all internal gaps with . and external spaces with ~\r
+ s[i] = new Sequence(seqs[i].getName(),\r
+ seqs[i].getSequenceAsString().replace('-', '.'));\r
+\r
+ StringBuffer sb = new StringBuffer();\r
+ sb.append(s[i].getSequence());\r
+\r
+ for (int ii = 0; ii < sb.length(); ii++)\r
+ {\r
+ if (sb.charAt(ii) == '.')\r
+ {\r
+ sb.setCharAt(ii, '~');\r
+ }\r
+ else\r
+ {\r
+ break;\r
+ }\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
+ {\r
+ break;\r
+ }\r
+ }\r
+\r
+ s[i].setSequence(sb.toString());\r
+\r
+ if (s[i].getSequence().length > max)\r
+ {\r
+ max = s[i].getSequence().length;\r
+ }\r
+\r
+ i++;\r
+ }\r
+\r
+ Format maxLenpad = new Format("%" + (new String("" + max)).length() +\r
+ "d");\r
+ Format maxChkpad = new Format("%" + (new String("1" + max)).length() +\r
+ "d");\r
+ i = 0;\r
+\r
+ int bigChecksum = 0;\r
+ int[] checksums = new int[s.length];\r
+ while (i < s.length)\r
+ {\r
+ checksums[i] = checkSum(s[i].getSequenceAsString());\r
+ bigChecksum += checksums[i];\r