From ae0940ce556aea2c6f8ffb4aa2b4351e38dfdef9 Mon Sep 17 00:00:00 2001 From: tcofoegbu Date: Tue, 8 Nov 2016 10:26:21 +0000 Subject: [PATCH] JAL-2292 updated method calls --- src/MCview/PDBChain.java | 2 +- src/jalview/analysis/AlignSeq.java | 2 +- src/jalview/ws/sifts/SiftsClient.java | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) 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 -- 1.7.10.2