Moved comment so it doesn't break jalopy (this is not good!)

[jalview.git] / src / jalview / util / Comparison.java

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index e6aae96..03abd0c 100755 (executable)
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -8,32 +8,30 @@ public class Comparison {
   {\r
     return Comparison.compare(ii,jj,0,ii.getLength()-1);\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 = end-start;\r
-     int jlen = end-start;\r
+     int ilen = si.length()-1;\r
+     int jlen = sj.length()-1;\r
 \r
-     if ( jalview.util.Comparison.isGap( si.charAt(start+ilen)) )\r
-      {\r
+     while (jalview.util.Comparison.isGap(si.charAt(start + ilen)))\r
+     {\r
        ilen--;\r
-\r
-       while (jalview.util.Comparison.isGap( si.charAt(start+ilen)))\r
-       {\r
-         ilen--;\r
-       }\r
      }\r
 \r
-     if ( jalview.util.Comparison.isGap( sj.charAt(start+jlen)) )\r
+     while (jalview.util.Comparison.isGap(sj.charAt(start + jlen)))\r
      {\r
        jlen--;\r
-\r
-       while (jalview.util.Comparison.isGap( sj.charAt(start+jlen)))\r
-       {\r
-         jlen--;\r
-       }\r
      }\r
 \r
      int   count = 0;\r
@@ -62,8 +60,14 @@ public class Comparison {
     return pid;\r
   }\r
 \r
-  /**    */\r
-  public static float PID(Sequence s1 , Sequence s2)\r
+  /**\r
+   * this is a gapped PID calculation\r
+   *\r
+   * @param s1 SequenceI\r
+   * @param s2 SequenceI\r
+   * @return float\r
+   */\r
+  public static float PID(SequenceI s1 , SequenceI s2)\r
   {\r
     int len;\r
 \r
@@ -101,7 +105,7 @@ public class Comparison {
 \r
     return (float)100*(len-bad)/len;\r
   }\r
-\r
+  public static String GapChars = " .-";\r
   public static boolean isGap(char c)\r
   {\r
     return  (c != '.' && c != '-' && c != ' ') ? false : true;\r