From 0afb50988743f5b902ad985793d55104e419da85 Mon Sep 17 00:00:00 2001
From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Tue, 8 Nov 2016 10:21:55 +0000
Subject: [PATCH] JAL-2292 renamed method and improved implementation as
 suggested by Kira

---
 src/jalview/util/Comparison.java      |   18 ++++++------------
 test/jalview/util/ComparisonTest.java |   14 +++++++-------
 2 files changed, 13 insertions(+), 19 deletions(-)

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index 5269d4f..1326647 100644
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -417,8 +417,8 @@ public class Comparison
   }
 
   /**
-   * Compares two chars either case sensitively or case insensitively depending
-   * on the caseSensitive flag
+   * Compares two residues either case sensitively or case insensitively
+   * depending on the caseSensitive flag
    * 
    * @param c1
    *          first char
@@ -428,18 +428,12 @@ public class Comparison
    *          if true comparison will be case sensitive otherwise its not
    * @return
    */
-  public static boolean compareChars(char c1, char c2, boolean caseSensitive)
+  public static boolean isSameResidue(char c1, char c2,
+          boolean caseSensitive)
   {
-    boolean sameCase = (Character.isUpperCase(c1) && Character
-            .isUpperCase(c2))
-            || (Character.isLowerCase(c1) && Character.isLowerCase(c2));
-    if (sameCase)
+    if (caseSensitive)
     {
-      return c1 == c2;
-    }
-    else if (caseSensitive)
-    {
-      return false;
+      return (c1 == c2);
     }
     else
     {
diff --git a/test/jalview/util/ComparisonTest.java b/test/jalview/util/ComparisonTest.java
index bce34d4..b71c270 100644
--- a/test/jalview/util/ComparisonTest.java
+++ b/test/jalview/util/ComparisonTest.java
@@ -190,14 +190,14 @@ public class ComparisonTest
   }
 
   @Test(groups = { "Functional" })
-  public void compareCharsTest()
+  public void testIsSameResidue()
   {
-    assertTrue(Comparison.compareChars('a', 'a', false));
-    assertTrue(Comparison.compareChars('a', 'a', true));
-    assertTrue(Comparison.compareChars('A', 'a', false));
-    assertTrue(Comparison.compareChars('a', 'A', false));
+    assertTrue(Comparison.isSameResidue('a', 'a', false));
+    assertTrue(Comparison.isSameResidue('a', 'a', true));
+    assertTrue(Comparison.isSameResidue('A', 'a', false));
+    assertTrue(Comparison.isSameResidue('a', 'A', false));
 
-    assertFalse(Comparison.compareChars('a', 'A', true));
-    assertFalse(Comparison.compareChars('A', 'a', true));
+    assertFalse(Comparison.isSameResidue('a', 'A', true));
+    assertFalse(Comparison.isSameResidue('A', 'a', true));
   }
 }
-- 
1.7.10.2