From dfbc97321175feae2f7bcf983a6cfba7aeb8240d Mon Sep 17 00:00:00 2001 From: gmungoc Date: Fri, 19 Feb 2016 16:45:10 +0000 Subject: [PATCH] JAL-1706 reverted setting start position as too confusing for -ve strand --- src/jalview/io/AlignFile.java | 24 ++++++------------------ 1 file changed, 6 insertions(+), 18 deletions(-) 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 { -- 1.7.10.2