X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FComparison.java;h=6c7197ad1ed3717ca0acf0940a707c2421ed8b6f;hb=d1a58585358deed317674daeeac5fb5be66637ab;hp=e48c0cac61ade1262c60ca13e062d3615977d9be;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index e48c0ca..6c7197a 100755
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -1,6 +1,6 @@
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
@@ -30,7 +30,7 @@ import jalview.datamodel.*;
 public class Comparison
 {
   /** DOCUMENT ME!! */
-  public static String GapChars = " .-";
+  public static final String GapChars = " .-";
 
   /**
    * DOCUMENT ME!
@@ -40,7 +40,7 @@ public class Comparison
    *
    * @return DOCUMENT ME!
    */
-  public static float compare(SequenceI ii, SequenceI jj)
+  public static final float compare(SequenceI ii, SequenceI jj)
   {
     return Comparison.compare(ii, jj, 0, ii.getLength() - 1);
   }
@@ -116,70 +116,21 @@ public class Comparison
    * @param s2 SequenceI
    * @return float
    */
-  public static float PID(SequenceI s1, SequenceI s2)
+  public final static float PID(String seq1, String seq2)
   {
-    int len;
-
-    if (s1.getSequence().length() > s2.getSequence().length())
-    {
-      len = s1.getSequence().length();
-    }
-    else
-    {
-      len = s2.getSequence().length();
-    }
-
-    int bad = 0;
-
-    for (int i = 0; i < len; i++)
-    {
-      char chr1;
-      char chr2;
-
-      if (i < s1.getSequence().length())
-      {
-        chr1 = Character.toUpperCase(s1.getSequence().charAt(i));
-      }
-      else
-      {
-        chr1 = '.';
-      }
-
-      if (i < s2.getSequence().length())
-      {
-        chr2 = Character.toUpperCase(s2.getSequence().charAt(i));
-      }
-      else
-      {
-        chr2 = '.';
-      }
-
-      if (! (jalview.util.Comparison.isGap(chr1)) &&
-          ! (jalview.util.Comparison.isGap(chr2)))
-      {
-        if (chr1 != chr2)
-        {
-          bad++;
-        }
-      }
-    }
-
-    return ( (float) 100 * (len - bad)) / len;
+    return PID(seq1, seq2, 0, seq1.length());
   }
 
+  static final int caseShift = 'a' - 'A';
+
   // Another pid with region specification
-  public static float PID(SequenceI s1, SequenceI s2, int start, int end)
+  public final static  float PID(String seq1, String seq2, int start, int end)
   {
-    int len;
 
-    if (s1.getSequence().length() > s2.getSequence().length())
-    {
-      len = s1.getSequence().length();
-    }
-    else
-    {
-      len = s2.getSequence().length();
-    }
+    int s1len = seq1.length();
+    int s2len = seq2.length();
+
+    int len = Math.min(s1len, s2len);
 
     if (end < len)
     {
@@ -191,38 +142,35 @@ public class Comparison
       start = len - 1; // we just use a single residue for the difference
     }
 
+
     int bad = 0;
+    char chr1;
+    char chr2;
+
 
     for (int i = start; i < len; i++)
     {
-      char chr1;
-      char chr2;
+      chr1 =  seq1.charAt(i) ;
 
-      if (i < s1.getSequence().length())
-      {
-        chr1 = Character.toUpperCase(s1.getSequence().charAt(i));
-      }
-      else
-      {
-        chr1 = '.';
-      }
+      chr2 =  seq2.charAt(i) ;
 
-      if (i < s2.getSequence().length())
+      if ('a' <= chr1 && chr1 <= 'z')
       {
-        chr2 = Character.toUpperCase(s2.getSequence().charAt(i));
+        // TO UPPERCASE !!!
+        //Faster than toUpperCase
+        chr1 -= caseShift;
       }
-      else
+      if ('a' <= chr2 && chr2 <= 'z')
       {
-        chr2 = '.';
+        // TO UPPERCASE !!!
+        //Faster than toUpperCase
+        chr2 -= caseShift;
       }
 
-      if (! (jalview.util.Comparison.isGap(chr1)) &&
-          ! (jalview.util.Comparison.isGap(chr2)))
+
+      if (chr1!=chr2 && !isGap(chr1) && !isGap(chr2) )
       {
-        if (chr1 != chr2)
-        {
           bad++;
-        }
       }
     }
 
@@ -236,12 +184,12 @@ public class Comparison
    *
    * @return DOCUMENT ME!
    */
-  public static boolean isGap(char c)
+  public static final boolean isGap(char c)
   {
     return (c == '-' || c == '.' || c == ' ') ? true : false;
   }
 
-  public static boolean isNucleotide(SequenceI [] seqs)
+  public static final boolean isNucleotide(SequenceI [] seqs)
   {
     int i = 0, iSize = seqs.length, j, jSize;
     float nt = 0, aa = 0;