From c6db7d75f1ad2ae10dab3ccaf6b2708c3192a162 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Wed, 24 Aug 2011 15:01:27 +0100
Subject: [PATCH] change handleSelenocysteine - removing complement from
position as this is not required
---
uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java | 7 +------
1 file changed, 1 insertion(+), 6 deletions(-)
diff --git a/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java b/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java
index 118145eed..376dde0b7 100644
--- a/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java
+++ b/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java
@@ -830,12 +830,7 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
nbases += seglen;
}
- String pos = "";
- if(f.isForwardFeature())
- pos = sequenceloc+".."+(sequenceloc+2);
- else
- pos = "complement("+(sequenceloc-2)+".."+sequenceloc+")";
-
+ String pos = sequenceloc+".."+(sequenceloc+2);
qualifiers.add(new Qualifier("transl_except","(pos:"+pos+",aa:Sec)"));
}
--
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