From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Fri, 4 Nov 2016 15:30:28 +0000 (+0000)
Subject: JAL-2292 fix for wrong mapping output in sequence mapping output window where sequenc... 
X-Git-Tag: Release_2_10_1^2~14
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=1e943acf589b7393c666204f533d2ebce28d7471

JAL-2292 fix for wrong mapping output in sequence mapping output window where sequence residue has different case with structure residue
---

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 3ad3188..f7e8f2e 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -620,7 +620,10 @@ public class AlignSeq
       {
         if ((i + (j * len)) < astr1.length())
         {
-          if (astr1.charAt(i + (j * len)) == astr2.charAt(i + (j * len))
+          boolean sameChar = Comparison.compareChars(
+                  astr1.charAt(i + (j * len)), astr2.charAt(i + (j * len)),
+                  false);
+          if (sameChar
                   && !jalview.util.Comparison.isGap(astr1.charAt(i
                           + (j * len))))
           {
diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index 83af0e0..2afcfe4 100644
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -29,6 +29,7 @@ import jalview.datamodel.SequenceI;
 import jalview.io.StructureFile;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureMapping;
+import jalview.util.Comparison;
 import jalview.util.DBRefUtils;
 import jalview.util.Format;
 import jalview.xml.binding.sifts.Entry;
@@ -1004,8 +1005,10 @@ public class SiftsClient implements SiftsClientI
         {
           if ((i + (j * len)) < seqRes.length())
           {
-            if (seqRes.charAt(i + (j * len)) == strRes
-                    .charAt(i + (j * len))
+            boolean sameChar = Comparison.compareChars(
+                    seqRes.charAt(i + (j * len)),
+                    strRes.charAt(i + (j * len)), false);
+            if (sameChar
                     && !jalview.util.Comparison.isGap(seqRes.charAt(i
                             + (j * len))))
             {