From 1dc391892e510b51e847476c67d3e09012f09550 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Wed, 21 Sep 2011 10:54:00 +0100
Subject: [PATCH] fix in handleSelenocysteine()
---
uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java | 7 ++++++-
1 file changed, 6 insertions(+), 1 deletion(-)
diff --git a/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java b/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java
index bd5b4e5e5..5e1697dd3 100644
--- a/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java
+++ b/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java
@@ -830,7 +830,12 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
nbases += seglen;
}
- String pos = sequenceloc+".."+(sequenceloc+2);
+ String pos;
+ if(f.isForwardFeature())
+ pos = sequenceloc+".."+(sequenceloc+2);
+ else
+ pos = (sequenceloc-2)+".."+sequenceloc;
+
qualifiers.add(new Qualifier("transl_except","(pos:"+pos+",aa:Sec)"));
}
--
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