Optimised PID method

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index e48c0ca..9e0aef6 100755 (executable)
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -116,70 +116,23 @@ public class Comparison
    * @param s2 SequenceI\r
    * @return float\r
    */\r
-  public static float PID(SequenceI s1, SequenceI s2)\r
+  public final static float PID(SequenceI seq1, SequenceI seq2)\r
   {\r
-    int len;\r
-\r
-    if (s1.getSequence().length() > s2.getSequence().length())\r
-    {\r
-      len = s1.getSequence().length();\r
-    }\r
-    else\r
-    {\r
-      len = s2.getSequence().length();\r
-    }\r
-\r
-    int bad = 0;\r
-\r
-    for (int i = 0; i < len; i++)\r
-    {\r
-      char chr1;\r
-      char chr2;\r
-\r
-      if (i < s1.getSequence().length())\r
-      {\r
-        chr1 = Character.toUpperCase(s1.getSequence().charAt(i));\r
-      }\r
-      else\r
-      {\r
-        chr1 = '.';\r
-      }\r
-\r
-      if (i < s2.getSequence().length())\r
-      {\r
-        chr2 = Character.toUpperCase(s2.getSequence().charAt(i));\r
-      }\r
-      else\r
-      {\r
-        chr2 = '.';\r
-      }\r
-\r
-      if (! (jalview.util.Comparison.isGap(chr1)) &&\r
-          ! (jalview.util.Comparison.isGap(chr2)))\r
-      {\r
-        if (chr1 != chr2)\r
-        {\r
-          bad++;\r
-        }\r
-      }\r
-    }\r
-\r
-    return ( (float) 100 * (len - bad)) / len;\r
+    return PID(seq1, seq2, 0, seq1.getLength());\r
   }\r
 \r
+  static final int caseShift = 'a' - 'A';\r
+\r
   // Another pid with region specification\r
-  public static float PID(SequenceI s1, SequenceI s2, int start, int end)\r
+  public final static  float PID(SequenceI seq1, SequenceI seq2, int start, int end)\r
   {\r
-    int len;\r
+    String s1 = seq1.getSequence();//.toUpperCase();\r
+    String s2 = seq2.getSequence();//.toUpperCase();\r
+    int s1len = s1.length();\r
+    int s2len = s2.length();\r
 \r
-    if (s1.getSequence().length() > s2.getSequence().length())\r
-    {\r
-      len = s1.getSequence().length();\r
-    }\r
-    else\r
-    {\r
-      len = s2.getSequence().length();\r
-    }\r
+\r
+    int len = Math.min(s1len, s2len);\r
 \r
     if (end < len)\r
     {\r
@@ -191,38 +144,35 @@ public class Comparison
       start = len - 1; // we just use a single residue for the difference\r
     }\r
 \r
+\r
     int bad = 0;\r
+    char chr1;\r
+    char chr2;\r
+\r
 \r
     for (int i = start; i < len; i++)\r
     {\r
-      char chr1;\r
-      char chr2;\r
+      chr1 =  s1.charAt(i) ;\r
 \r
-      if (i < s1.getSequence().length())\r
-      {\r
-        chr1 = Character.toUpperCase(s1.getSequence().charAt(i));\r
-      }\r
-      else\r
-      {\r
-        chr1 = '.';\r
-      }\r
+      chr2 =  s2.charAt(i) ;\r
 \r
-      if (i < s2.getSequence().length())\r
+      if ('a' <= chr1 && chr1 <= 'z')\r
       {\r
-        chr2 = Character.toUpperCase(s2.getSequence().charAt(i));\r
+        // TO UPPERCASE !!!\r
+        //Faster than toUpperCase\r
+        chr1 -= caseShift;\r
       }\r
-      else\r
+      if ('a' <= chr2 && chr2 <= 'z')\r
       {\r
-        chr2 = '.';\r
+        // TO UPPERCASE !!!\r
+        //Faster than toUpperCase\r
+        chr2 -= caseShift;\r
       }\r
 \r
-      if (! (jalview.util.Comparison.isGap(chr1)) &&\r
-          ! (jalview.util.Comparison.isGap(chr2)))\r
+\r
+      if (chr1!=chr2 && !isGap(chr1) && !isGap(chr2) )\r
       {\r
-        if (chr1 != chr2)\r
-        {\r
           bad++;\r
-        }\r
       }\r
     }\r
 \r