- /** DOCUMENT ME!! */\r
- public static String GapChars = " .-";\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param ii DOCUMENT ME!\r
- * @param jj DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public static float compare(SequenceI ii, SequenceI jj)\r
+ /** DOCUMENT ME!! */\r
+ public static String GapChars = " .-";\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param ii DOCUMENT ME!\r
+ * @param jj DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public static float compare(SequenceI ii, SequenceI jj)\r
+ {\r
+ return Comparison.compare(ii, jj, 0, ii.getLength() - 1);\r
+ }\r
+\r
+ /**\r
+ * this was supposed to be an ungapped pid calculation\r
+ * @param ii SequenceI\r
+ * @param jj SequenceI\r
+ * @param start int\r
+ * @param end int\r
+ * @return float\r
+ */\r
+ public static float compare(SequenceI ii, SequenceI jj, int start, int end)\r
+ {\r
+ String si = ii.getSequence();\r
+ String sj = jj.getSequence();\r
+\r
+ int ilen = si.length() - 1;\r
+ int jlen = sj.length() - 1;\r
+\r
+ while (jalview.util.Comparison.isGap(si.charAt(start + ilen)))\r