From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Tue, 8 Nov 2016 10:26:21 +0000 (+0000)
Subject: JAL-2292 updated method calls
X-Git-Tag: Release_2_10_1^2~7
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ae0940ce556aea2c6f8ffb4aa2b4351e38dfdef9;p=jalview.git

JAL-2292 updated method calls
---

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 34f09c8..783a4e2 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -147,7 +147,7 @@ public class PDBChain
         pdbpos++;
       }
 
-      boolean sameResidue = Comparison.compareChars(as.astr1.charAt(i),
+      boolean sameResidue = Comparison.isSameResidue(as.astr1.charAt(i),
               as.astr2.charAt(i), false);
       if (sameResidue)
       {
diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index f7e8f2e..86bf721 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -620,7 +620,7 @@ public class AlignSeq
       {
         if ((i + (j * len)) < astr1.length())
         {
-          boolean sameChar = Comparison.compareChars(
+          boolean sameChar = Comparison.isSameResidue(
                   astr1.charAt(i + (j * len)), astr2.charAt(i + (j * len)),
                   false);
           if (sameChar
diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index 2afcfe4..eb094da 100644
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -1005,7 +1005,7 @@ public class SiftsClient implements SiftsClientI
         {
           if ((i + (j * len)) < seqRes.length())
           {
-            boolean sameChar = Comparison.compareChars(
+            boolean sameChar = Comparison.isSameResidue(
                     seqRes.charAt(i + (j * len)),
                     strRes.charAt(i + (j * len)), false);
             if (sameChar