X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FComparison.java;h=50472a53ac0851542b951933e39c1927807f3eb5;hb=2202f8ba9f000c811358937a571c5cd4a017a403;hp=9a86696a2fdd94dd4220b2b454c31137cac98ba3;hpb=92f38d98051bc64405b16873ba33c8331afeeb1f;p=jalview.git

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index 9a86696..50472a5 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
@@ -29,215 +29,194 @@ import jalview.datamodel.*;
  */
 public class Comparison
 {
-    /** DOCUMENT ME!! */
-    public static String GapChars = " .-";
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param ii DOCUMENT ME!
-     * @param jj DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public static float compare(SequenceI ii, SequenceI jj)
+  /** DOCUMENT ME!! */
+  public static final String GapChars = " .-";
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param ii DOCUMENT ME!
+   * @param jj DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public static final float compare(SequenceI ii, SequenceI jj)
+  {
+    return Comparison.compare(ii, jj, 0, ii.getLength() - 1);
+  }
+
+  /**
+   * this was supposed to be an ungapped pid calculation
+   * @param ii SequenceI
+   * @param jj SequenceI
+   * @param start int
+   * @param end int
+   * @return float
+   */
+  public static float compare(SequenceI ii, SequenceI jj, int start, int end)
+  {
+    String si = ii.getSequenceAsString();
+    String sj = jj.getSequenceAsString();
+
+    int ilen = si.length() - 1;
+    int jlen = sj.length() - 1;
+
+    while (jalview.util.Comparison.isGap(si.charAt(start + ilen)))
     {
-        return Comparison.compare(ii, jj, 0, ii.getLength() - 1);
+      ilen--;
     }
 
-    /**
-     * this was supposed to be an ungapped pid calculation
-     * @param ii SequenceI
-     * @param jj SequenceI
-     * @param start int
-     * @param end int
-     * @return float
-     */
-    public static float compare(SequenceI ii, SequenceI jj, int start, int end)
+    while (jalview.util.Comparison.isGap(sj.charAt(start + jlen)))
     {
-        String si = ii.getSequence();
-        String sj = jj.getSequence();
+      jlen--;
+    }
 
-        int ilen = si.length() - 1;
-        int jlen = sj.length() - 1;
+    int count = 0;
+    int match = 0;
+    float pid = -1;
 
-        while (jalview.util.Comparison.isGap(si.charAt(start + ilen)))
-        {
-            ilen--;
-        }
-
-        while (jalview.util.Comparison.isGap(sj.charAt(start + jlen)))
+    if (ilen > jlen)
+    {
+      for (int j = 0; j < jlen; j++)
+      {
+        if (si.substring(start + j, start + j + 1).equals(sj.substring(start +
+            j, start + j + 1)))
         {
-            jlen--;
+          match++;
         }
 
-        int count = 0;
-        int match = 0;
-        float pid = -1;
+        count++;
+      }
 
-        if (ilen > jlen)
-        {
-            for (int j = 0; j < jlen; j++)
-            {
-                if (si.substring(start + j, start + j + 1).equals(sj.substring(start +
-                                j, start + j + 1)))
-                {
-                    match++;
-                }
-
-                count++;
-            }
-
-            pid = (float) match / (float) ilen * 100;
-        }
-        else
+      pid = (float) match / (float) ilen * 100;
+    }
+    else
+    {
+      for (int j = 0; j < jlen; j++)
+      {
+        if (si.substring(start + j, start + j + 1).equals(sj.substring(start +
+            j, start + j + 1)))
         {
-            for (int j = 0; j < jlen; j++)
-            {
-                if (si.substring(start + j, start + j + 1).equals(sj.substring(start +
-                                j, start + j + 1)))
-                {
-                    match++;
-                }
-
-                count++;
-            }
-
-            pid = (float) match / (float) jlen * 100;
+          match++;
         }
 
-        return pid;
+        count++;
+      }
+
+      pid = (float) match / (float) jlen * 100;
     }
 
-    /**
-     * this is a gapped PID calculation
-     *
-     * @param s1 SequenceI
-     * @param s2 SequenceI
-     * @return float
-     */
-    public static float PID(SequenceI s1, SequenceI s2)
-    {
-        int len;
+    return pid;
+  }
 
-        if (s1.getSequence().length() > s2.getSequence().length())
-        {
-            len = s1.getSequence().length();
-        }
-        else
-        {
-            len = s2.getSequence().length();
-        }
+  /**
+   * this is a gapped PID calculation
+   *
+   * @param s1 SequenceI
+   * @param s2 SequenceI
+   * @return float
+   */
+  public final static float PID(String seq1, String seq2)
+  {
+    return PID(seq1, seq2, 0, seq1.length());
+  }
 
-        int bad = 0;
+  static final int caseShift = 'a' - 'A';
 
-        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++;
-                }
-            }
-        }
+  // Another pid with region specification
+  public final static  float PID(String seq1, String seq2, int start, int end)
+  {
+
+    int s1len = seq1.length();
+    int s2len = seq2.length();
 
-        return ((float) 100 * (len - bad)) / len;
+    int len = Math.min(s1len, s2len);
+
+    if (end < len)
+    {
+      len = end;
     }
 
-    // Another pid with region specification
-    public static float PID(SequenceI s1, SequenceI s2, int start, int end)
+    if (len < start)
     {
-        int len;
+      start = len - 1; // we just use a single residue for the difference
+    }
 
-        if (s1.getSequence().length() > s2.getSequence().length())
-        {
-            len = s1.getSequence().length();
-        }
-        else
-        {
-            len = s2.getSequence().length();
-        }
 
-        if (end < len)
-        {
-            len = end;
-        }
+    int bad = 0;
+    char chr1;
+    char chr2;
 
-        if (len < start)
-        {
-            start = len - 1; // we just use a single residue for the difference
-        }
 
-        int bad = 0;
+    for (int i = start; i < len; i++)
+    {
+      chr1 =  seq1.charAt(i) ;
+
+      chr2 =  seq2.charAt(i) ;
+
+      if ('a' <= chr1 && chr1 <= 'z')
+      {
+        // TO UPPERCASE !!!
+        //Faster than toUpperCase
+        chr1 -= caseShift;
+      }
+      if ('a' <= chr2 && chr2 <= 'z')
+      {
+        // TO UPPERCASE !!!
+        //Faster than toUpperCase
+        chr2 -= caseShift;
+      }
+
+
+      if (chr1!=chr2 && !isGap(chr1) && !isGap(chr2) )
+      {
+          bad++;
+      }
+    }
 
-        for (int i = start; i < len; i++)
+    return ( (float) 100 * (len - bad)) / len;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param c DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public static final boolean isGap(char c)
+  {
+    return (c == '-' || c == '.' || c == ' ') ? true : false;
+  }
+
+  public static final boolean isNucleotide(SequenceI [] seqs)
+  {
+    int i = 0, iSize = seqs.length, j, jSize;
+    float nt = 0, aa = 0;
+    char c;
+    while (i < iSize)
+    {
+      jSize = seqs[i].getLength();
+      for (j = 0; j < jSize; j++)
+      {
+        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)))
         {
-            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++;
-                }
-            }
+          aa++;
         }
-
-        return ((float) 100 * (len - bad)) / len;
+      }
+      i++;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param c DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public static boolean isGap(char c)
-    {
-        return (  c=='-' || c=='.' || c==' ' ) ? true : false;
-    }
+    if ( (nt / (nt + aa)) > 0.85f)
+      return true;
+    else
+      return false;
+
+  }
 }