Check hiddenSequence before placing in tmp

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

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index e48c0ca..6c7197a 100755 (executable)
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -1,6 +1,6 @@
 /*\r
 * Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
 *\r
 * This program is free software; you can redistribute it and/or\r
 * modify it under the terms of the GNU General Public License\r
@@ -30,7 +30,7 @@ import jalview.datamodel.*;
 public class Comparison\r
 {\r
   /** DOCUMENT ME!! */\r
-  public static String GapChars = " .-";\r
+  public static final String GapChars = " .-";\r
 \r
   /**\r
    * DOCUMENT ME!\r
@@ -40,7 +40,7 @@ public class Comparison
    *\r
    * @return DOCUMENT ME!\r
    */\r
-  public static float compare(SequenceI ii, SequenceI jj)\r
+  public static final float compare(SequenceI ii, SequenceI jj)\r
   {\r
     return Comparison.compare(ii, jj, 0, ii.getLength() - 1);\r
   }\r
@@ -116,70 +116,21 @@ 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(String seq1, String 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.length());\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(String seq1, String seq2, int start, int end)\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
+    int s1len = seq1.length();\r
+    int s2len = seq2.length();\r
+\r
+    int len = Math.min(s1len, s2len);\r
 \r
     if (end < len)\r
     {\r
@@ -191,38 +142,35 @@ 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 =  seq1.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 =  seq2.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
@@ -236,12 +184,12 @@ public class Comparison
    *\r
    * @return DOCUMENT ME!\r
    */\r
-  public static boolean isGap(char c)\r
+  public static final boolean isGap(char c)\r
   {\r
     return (c == '-' || c == '.' || c == ' ') ? true : false;\r
   }\r
 \r
-  public static boolean isNucleotide(SequenceI [] seqs)\r
+  public static final boolean isNucleotide(SequenceI [] seqs)\r
   {\r
     int i = 0, iSize = seqs.length, j, jSize;\r
     float nt = 0, aa = 0;\r