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 3a831d0..03abd0c 100755 (executable)
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -8,6 +8,14 @@ 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
@@ -52,7 +60,13 @@ public class Comparison {
     return pid;\r
   }\r
 \r
-  /**    */\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
@@ -91,7 +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