From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 4 May 2017 12:56:11 +0000 (+0100)
Subject: fix for JAL-2509 - don’t replace all bracket types with ()
X-Git-Tag: Release_2_10_2~3^2~105^2^2~3
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=db1b28364c2034ea432c0668100c1ec9e0d17523;p=jalview.git

fix for JAL-2509 - don’t replace all bracket types with ()
---

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 3b0dab4..a47e1ea 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -800,9 +800,9 @@ public class StockholmFile extends AlignFile
   {
     String convert1, convert2 = null;
 
-    convert1 = OPEN_PAREN.replaceAll(annots);
-    convert2 = CLOSE_PAREN.replaceAll(convert1);
-    annots = convert2;
+    // convert1 = OPEN_PAREN.replaceAll(annots);
+    // convert2 = CLOSE_PAREN.replaceAll(convert1);
+    // annots = convert2;
 
     String type = label;
     if (label.contains("_cons"))