From 92f38d98051bc64405b16873ba33c8331afeeb1f Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 18 Aug 2005 09:33:29 +0000
Subject: [PATCH] various case sensitivity bugs fixed in residue comparison
 functions.

---
 src/jalview/analysis/AAFrequency.java  |    2 +-
 src/jalview/analysis/Conservation.java |    8 ++++----
 src/jalview/util/Comparison.java       |    8 ++++----
 3 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 0841bf2..55447d3 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -66,7 +66,7 @@ public class AAFrequency
 
                     if (sequence.length() > i)
                     {
-                        res = sequence.substring(i,i+1);
+                        res = Character.toString(Character.toUpperCase(sequence.charAt(i)));
 
                         if (jalview.util.Comparison.isGap(res.charAt(0)))
                         {
diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index d814abb..0bfb636 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -123,8 +123,8 @@ public class Conservation
 
                 for (j = 1; j <= len; j++)
                 {
-                    sqnum[j] = ((Integer) jalview.schemes.ResidueProperties.aaHash.get(new String(
-                                sq.substring(j - 1, j)))).intValue(); // yuk
+                    sqnum[j] = ((Integer) jalview.schemes.ResidueProperties.aaHash.get(Character.toString(
+                                sq.charAt(j - 1)))).intValue(); // yuk - JBPNote - case taken care of in aaHash
                 }
 
                 seqNums.setElementAt(sqnum, i);
@@ -163,7 +163,7 @@ public class Conservation
 
                     if (sequence.length() > i)
                     {
-                        res = sequence.substring(i, i + 1);
+                        res = Character.toString(Character.toUpperCase(sequence.charAt(i)));
 
                         if (residueHash.containsKey(res))
                         {
@@ -260,7 +260,7 @@ public class Conservation
                 continue;
             }
 
-            c = ((Sequence) sequences.elementAt(i)).getCharAt(j);
+            c = ((Sequence) sequences.elementAt(i)).getCharAt(j); // gaps do not have upper/lower case
 
             if (jalview.util.Comparison.isGap((c)))
             {
diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index 9b61798..9a86696 100755
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -138,7 +138,7 @@ public class Comparison
 
             if (i < s1.getSequence().length())
             {
-                chr1 = s1.getSequence().charAt(i);
+                chr1 = Character.toUpperCase(s1.getSequence().charAt(i));
             }
             else
             {
@@ -147,7 +147,7 @@ public class Comparison
 
             if (i < s2.getSequence().length())
             {
-                chr2 = s2.getSequence().charAt(i);
+                chr2 = Character.toUpperCase(s2.getSequence().charAt(i));
             }
             else
             {
@@ -200,7 +200,7 @@ public class Comparison
 
             if (i < s1.getSequence().length())
             {
-                chr1 = s1.getSequence().charAt(i);
+                chr1 = Character.toUpperCase(s1.getSequence().charAt(i));
             }
             else
             {
@@ -209,7 +209,7 @@ public class Comparison
 
             if (i < s2.getSequence().length())
             {
-                chr2 = s2.getSequence().charAt(i);
+                chr2 = Character.toUpperCase(s2.getSequence().charAt(i));
             }
             else
             {
-- 
1.7.10.2