X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FComparison.java;h=e48c0cac61ade1262c60ca13e062d3615977d9be;hb=9a23ee1cee6a2ef0f797fd8e1a6a950e66ef6e72;hp=d8e599ba174eaccc988ad0e47ad65ec8c835013e;hpb=8116c10ff719ac0b542b33dbabfc9051634bf5ea;p=jalview.git

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index d8e599b..e48c0ca 100755
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -1,77 +1,133 @@
+/*
+* 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
+*/
 package jalview.util;
 
 import jalview.datamodel.*;
 
-public class Comparison {
 
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+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)
   {
-    return Comparison.compare(ii,jj,0,ii.getLength()-1);
+    return Comparison.compare(ii, jj, 0, ii.getLength() - 1);
   }
-  public static float compare(SequenceI ii, SequenceI jj, int start, int end) {
 
-     String si   = ii.getSequence();
-     String sj   = jj.getSequence();
+  /**
+   * 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.getSequence();
+    String sj = jj.getSequence();
+
+    int ilen = si.length() - 1;
+    int jlen = sj.length() - 1;
+
+    while (jalview.util.Comparison.isGap(si.charAt(start + ilen)))
+    {
+      ilen--;
+    }
+
+    while (jalview.util.Comparison.isGap(sj.charAt(start + jlen)))
+    {
+      jlen--;
+    }
 
-     int ilen = end-start+1;
-     int jlen = end-start+1;
+    int count = 0;
+    int match = 0;
+    float pid = -1;
 
-     if ( jalview.util.Comparison.isGap( si.charAt(start+ilen)) )
+    if (ilen > jlen)
+    {
+      for (int j = 0; j < jlen; j++)
       {
-       ilen--;
-
-       while (jalview.util.Comparison.isGap( si.charAt(start+ilen)))
-       {
-         ilen--;
-       }
-     }
-
-     if ( jalview.util.Comparison.isGap( sj.charAt(start+jlen)) )
-     {
-       jlen--;
-
-       while (jalview.util.Comparison.isGap( sj.charAt(start+jlen)))
-       {
-         jlen--;
-       }
-     }
-
-     int   count = 0;
-     int   match = 0;
-     float pid   = -1;
-
-     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 {
-       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;
-     }
+        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
+    {
+      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;
+    }
 
     return pid;
   }
 
-  /**    */
-  public static float PID(Sequence s1 , Sequence s2)
+  /**
+   * this is a gapped PID calculation
+   *
+   * @param s1 SequenceI
+   * @param s2 SequenceI
+   * @return float
+   */
+  public static float PID(SequenceI s1, SequenceI s2)
   {
     int len;
 
     if (s1.getSequence().length() > s2.getSequence().length())
+    {
       len = s1.getSequence().length();
+    }
     else
+    {
       len = s2.getSequence().length();
-
+    }
 
     int bad = 0;
 
@@ -81,29 +137,138 @@ public class Comparison {
       char chr2;
 
       if (i < s1.getSequence().length())
-        chr1 = s1.getSequence().charAt(i);
+      {
+        chr1 = Character.toUpperCase(s1.getSequence().charAt(i));
+      }
       else
+      {
         chr1 = '.';
-
+      }
 
       if (i < s2.getSequence().length())
-        chr2 = s2.getSequence().charAt(i);
+      {
+        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;
+  }
+
+  // Another pid with region specification
+  public static float PID(SequenceI s1, SequenceI s2, int start, int end)
+  {
+    int len;
+
+    if (s1.getSequence().length() > s2.getSequence().length())
+    {
+      len = s1.getSequence().length();
+    }
+    else
+    {
+      len = s2.getSequence().length();
+    }
+
+    if (end < len)
+    {
+      len = end;
+    }
+
+    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++)
+    {
+      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 (! (jalview.util.Comparison.isGap(chr1)) &&
+          ! (jalview.util.Comparison.isGap(chr2)))
       {
-        if (chr1!=chr2)
+        if (chr1 != chr2)
+        {
           bad++;
+        }
       }
     }
 
-    return (float)100*(len-bad)/len;
+    return ( (float) 100 * (len - bad)) / len;
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param c DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
   public static boolean isGap(char c)
   {
-    return  (c != '.' && c != '-' && c != ' ') ? false : true;
+    return (c == '-' || c == '.' || c == ' ') ? true : false;
+  }
+
+  public static 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)))
+        {
+          aa++;
+        }
+      }
+      i++;
+    }
+
+    if ( (nt / (nt + aa)) > 0.85f)
+      return true;
+    else
+      return false;
+
   }
 }