X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Futil%2FComparison.java;h=67a668a9c66b29d3e4ca6d36a530b8d4900fd901;hb=77e9dc41516acc93470931bcc5f344c67e819e70;hp=e48c0cac61ade1262c60ca13e062d3615977d9be;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index e48c0ca..67a668a 100755
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -1,26 +1,25 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.util;
 
 import jalview.datamodel.*;
 
-
 /**
  * DOCUMENT ME!
  *
@@ -30,7 +29,7 @@ import jalview.datamodel.*;
 public class Comparison
 {
   /** DOCUMENT ME!! */
-  public static String GapChars = " .-";
+  public static final String GapChars = " .-";
 
   /**
    * DOCUMENT ME!
@@ -40,7 +39,7 @@ 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);
   }
@@ -55,8 +54,8 @@ public class Comparison
    */
   public static float compare(SequenceI ii, SequenceI jj, int start, int end)
   {
-    String si = ii.getSequence();
-    String sj = jj.getSequence();
+    String si = ii.getSequenceAsString();
+    String sj = jj.getSequenceAsString();
 
     int ilen = si.length() - 1;
     int jlen = sj.length() - 1;
@@ -116,70 +115,21 @@ 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)
     {
@@ -192,37 +142,31 @@ public class Comparison
     }
 
     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++;
-        }
+        bad++;
       }
     }
 
@@ -236,12 +180,12 @@ 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;
@@ -253,11 +197,15 @@ public class Comparison
       {
         c = seqs[i].getCharAt(j);
         if ('a' <= c && c <= 'z')
+        {
           c -= ('a' - 'A');
+        }
 
         if (c == 'A' || c == 'G' || c == 'C' || c == 'T' || c == 'U')
+        {
           nt++;
-        else if (!jalview.util.Comparison.isGap( seqs[i].getCharAt(j)))
+        }
+        else if (!jalview.util.Comparison.isGap(seqs[i].getCharAt(j)))
         {
           aa++;
         }
@@ -266,9 +214,13 @@ public class Comparison
     }
 
     if ( (nt / (nt + aa)) > 0.85f)
+    {
       return true;
+    }
     else
+    {
       return false;
+    }
 
   }
 }