X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FComparison.java;h=9a86696a2fdd94dd4220b2b454c31137cac98ba3;hb=3cc7159787bd31859f7bc27916e7ff854b895280;hp=320855ac4c0a733c905a364c3d5743e150ae89de;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index 320855a..9a86696 100755
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -16,166 +16,228 @@
 * 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 {
-
-  public static 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.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   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;
-     }
-
-    return pid;
-  }
-
-  /**
-   * 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;
-
-    for (int i = 0; i < len; i++)
-    {
-      char chr1;
-      char chr2;
-
-      if (i < s1.getSequence().length())
-        chr1 = s1.getSequence().charAt(i);
-      else
-        chr1 = '.';
-
-
-      if (i < s2.getSequence().length())
-        chr2 = s2.getSequence().charAt(i);
-      else
-        chr2 = '.';
-
 
-      if (!(jalview.util.Comparison.isGap( chr1 ))  &&  !(jalview.util.Comparison.isGap( chr2 )))
-      {
-        if (chr1!=chr2)
-          bad++;
-      }
+/**
+ * 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 (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
+    /**
+     * 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 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;
+        }
+
+        return pid;
     }
 
-    int bad = 0;
-
-    for (int i = start; i < len; i++)
+    /**
+     * this is a gapped PID calculation
+     *
+     * @param s1 SequenceI
+     * @param s2 SequenceI
+     * @return float
+     */
+    public static float PID(SequenceI s1, SequenceI s2)
     {
-      char chr1;
-      char chr2;
-
-      if (i < s1.getSequence().length())
-        chr1 = s1.getSequence().charAt(i);
-      else
-        chr1 = '.';
-
-
-      if (i < s2.getSequence().length())
-        chr2 = s2.getSequence().charAt(i);
-      else
-        chr2 = '.';
-
-
-      if (!(jalview.util.Comparison.isGap( chr1 ))  &&  !(jalview.util.Comparison.isGap( chr2 )))
-      {
-        if (chr1!=chr2)
-          bad++;
-      }
+        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 (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 (chr1 != chr2)
+                {
+                    bad++;
+                }
+            }
+        }
+
+        return ((float) 100 * (len - bad)) / len;
+    }
 
-  public static String GapChars = " .-";
-  public static boolean isGap(char c)
-  {
-    return  (c != '.' && c != '-' && c != ' ') ? false : true;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static boolean isGap(char c)
+    {
+        return (  c=='-' || c=='.' || c==' ' ) ? true : false;
+    }
 }