X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FComparison.java;h=c779bb1e9179df755ff7d27b56316d7d6600d599;hb=b8d09897dacc7b0ad203982b4578e2c1d8929142;hp=8041d8074a4364df0ec23245f167e6bf3366924d;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index 8041d80..c779bb1 100755
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -21,10 +21,27 @@ package jalview.util;
 import jalview.datamodel.*;
 
 
-public class Comparison {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Comparison
+{
+    /** DOCUMENT ME!! */
     public static String GapChars = " .-";
 
-    public static float compare(SequenceI ii, SequenceI jj) {
+    /**
+     * 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);
     }
 
@@ -36,18 +53,21 @@ public class Comparison {
      * @param end int
      * @return float
      */
-    public static float compare(SequenceI ii, SequenceI jj, int start, int end) {
+    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))) {
+        while (jalview.util.Comparison.isGap(si.charAt(start + ilen)))
+        {
             ilen--;
         }
 
-        while (jalview.util.Comparison.isGap(sj.charAt(start + jlen))) {
+        while (jalview.util.Comparison.isGap(sj.charAt(start + jlen)))
+        {
             jlen--;
         }
 
@@ -55,10 +75,13 @@ public class Comparison {
         int match = 0;
         float pid = -1;
 
-        if (ilen > jlen) {
-            for (int j = 0; j < jlen; j++) {
+        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))) {
+                                j, start + j + 1)))
+                {
                     match++;
                 }
 
@@ -66,10 +89,14 @@ public class Comparison {
             }
 
             pid = (float) match / (float) ilen * 100;
-        } else {
-            for (int j = 0; j < jlen; j++) {
+        }
+        else
+        {
+            for (int j = 0; j < jlen; j++)
+            {
                 if (si.substring(start + j, start + j + 1).equals(sj.substring(start +
-                                j, start + j + 1))) {
+                                j, start + j + 1)))
+                {
                     match++;
                 }
 
@@ -89,36 +116,49 @@ public class Comparison {
      * @param s2 SequenceI
      * @return float
      */
-    public static float PID(SequenceI s1, SequenceI s2) {
+    public static float PID(SequenceI s1, SequenceI s2)
+    {
         int len;
 
-        if (s1.getSequence().length() > s2.getSequence().length()) {
+        if (s1.getSequence().length() > s2.getSequence().length())
+        {
             len = s1.getSequence().length();
-        } else {
+        }
+        else
+        {
             len = s2.getSequence().length();
         }
 
         int bad = 0;
 
-        for (int i = 0; i < len; i++) {
+        for (int i = 0; i < len; i++)
+        {
             char chr1;
             char chr2;
 
-            if (i < s1.getSequence().length()) {
+            if (i < s1.getSequence().length())
+            {
                 chr1 = s1.getSequence().charAt(i);
-            } else {
+            }
+            else
+            {
                 chr1 = '.';
             }
 
-            if (i < s2.getSequence().length()) {
+            if (i < s2.getSequence().length())
+            {
                 chr2 = s2.getSequence().charAt(i);
-            } else {
+            }
+            else
+            {
                 chr2 = '.';
             }
 
             if (!(jalview.util.Comparison.isGap(chr1)) &&
-                    !(jalview.util.Comparison.isGap(chr2))) {
-                if (chr1 != chr2) {
+                    !(jalview.util.Comparison.isGap(chr2)))
+            {
+                if (chr1 != chr2)
+                {
                     bad++;
                 }
             }
@@ -128,44 +168,59 @@ public class Comparison {
     }
 
     // Another pid with region specification
-    public static float PID(SequenceI s1, SequenceI s2, int start, int end) {
+    public static float PID(SequenceI s1, SequenceI s2, int start, int end)
+    {
         int len;
 
-        if (s1.getSequence().length() > s2.getSequence().length()) {
+        if (s1.getSequence().length() > s2.getSequence().length())
+        {
             len = s1.getSequence().length();
-        } else {
+        }
+        else
+        {
             len = s2.getSequence().length();
         }
 
-        if (end < len) {
+        if (end < len)
+        {
             len = end;
         }
 
-        if (len < start) {
+        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++) {
+        for (int i = start; i < len; i++)
+        {
             char chr1;
             char chr2;
 
-            if (i < s1.getSequence().length()) {
+            if (i < s1.getSequence().length())
+            {
                 chr1 = s1.getSequence().charAt(i);
-            } else {
+            }
+            else
+            {
                 chr1 = '.';
             }
 
-            if (i < s2.getSequence().length()) {
+            if (i < s2.getSequence().length())
+            {
                 chr2 = s2.getSequence().charAt(i);
-            } else {
+            }
+            else
+            {
                 chr2 = '.';
             }
 
             if (!(jalview.util.Comparison.isGap(chr1)) &&
-                    !(jalview.util.Comparison.isGap(chr2))) {
-                if (chr1 != chr2) {
+                    !(jalview.util.Comparison.isGap(chr2)))
+            {
+                if (chr1 != chr2)
+                {
                     bad++;
                 }
             }
@@ -174,7 +229,15 @@ public class Comparison {
         return ((float) 100 * (len - bad)) / len;
     }
 
-    public static boolean isGap(char c) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static boolean isGap(char c)
+    {
         return ((c != '.') && (c != '-') && (c != ' ')) ? false : true;
     }
 }