From 23b7d60de931c92ba1fa462b08e8729082305825 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Tue, 11 Sep 2012 16:20:51 +0100
Subject: [PATCH] provide option to concatenate sequences or use FASTA index
---
uk/ac/sanger/artemis/io/StreamSequenceFactory.java | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/uk/ac/sanger/artemis/io/StreamSequenceFactory.java b/uk/ac/sanger/artemis/io/StreamSequenceFactory.java
index fc457ee0d..21529ca60 100644
--- a/uk/ac/sanger/artemis/io/StreamSequenceFactory.java
+++ b/uk/ac/sanger/artemis/io/StreamSequenceFactory.java
@@ -70,7 +70,11 @@ abstract public class StreamSequenceFactory
case FASTA_FORMAT:
{
if(IndexFastaStream.isIndexed(entry))
- return new IndexFastaStream(entry);
+ {
+ IndexFastaStream ifs = new IndexFastaStream(entry);
+ if(ifs.useIndex())
+ return ifs;
+ }
return new FastaStreamSequence(in_stream);
}
case GENBANK_FORMAT:
--
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