From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 19 Feb 2016 16:45:10 +0000 (+0000)
Subject: JAL-1706 reverted setting start position as too confusing for -ve strand
X-Git-Tag: Release_2_10_0~296^2~22^2~7
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=dfbc97321175feae2f7bcf983a6cfba7aeb8240d;p=jalview.git

JAL-1706 reverted setting start position as too confusing for -ve strand
---

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 2b8f127..984eff6 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -355,24 +355,12 @@ public abstract class AlignFile extends FileParse
       String desc = id.substring(space + 1);
       seq.setDescription(desc);
 
-      if (desc.startsWith("chromosome"))
-      {
-        /*
-         * parse Ensembl style gene description e.g.
-         * chromosome:GRCh38:7:140696688:140721955:1
-         */
-        String[] tokens = desc.split(":");
-        if (tokens.length > 3)
-        {
-          try
-          {
-            seq.setStart(Integer.parseInt(tokens[3]));
-          } catch (NumberFormatException e)
-          {
-            // ignore
-          }
-        }
-      }
+      /*
+       * it is tempting to parse Ensembl style gene description e.g.
+       * chromosome:GRCh38:7:140696688:140721955:1 and set the
+       * start position of the sequence, but this causes much confusion
+       * for reverse strand feature locations
+       */
     }
     else
     {