From c581ffc389af4c82c1f709cc372e158dc20e398f Mon Sep 17 00:00:00 2001
From: Vincent Liard <vincent.liard@inria.fr>
Date: Mon, 26 Jan 2015 14:23:37 +0100
Subject: [PATCH] fix overoptimization genome < promoter + terminator
The code used to be optimized to bypass phenotype computation when the
genome was smaller than the length of a promoter plus the length of a
terminator. But terminators can overlap promoters when they share a
chunk of DNA. Viruses showed that this actually happens. The condition
has thus been relaxed to bypasse genomes that are smaller than a
promoter.
---
src/libaevol/ae_genetic_unit.cpp | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/src/libaevol/ae_genetic_unit.cpp b/src/libaevol/ae_genetic_unit.cpp
index 5340b5717..09d16ee87 100644
--- a/src/libaevol/ae_genetic_unit.cpp
+++ b/src/libaevol/ae_genetic_unit.cpp
@@ -526,7 +526,9 @@ void ae_genetic_unit::do_transcription( void )
// If the genome is not long enough to bear a promoter and a terminator,
// we set all its RNAs to a length of -1
- if ( genome_length < PROM_SIZE + TERM_SIZE )
+ // (NB but a terminator can share code with the promoter, making it
+ // possible for the genome to be no longer than the promoter)
+ if ( genome_length < PROM_SIZE )
{
rna_node = _rna_list[LEADING]->get_first();
while ( rna_node != NULL )
--
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