From fe3d961f3bb67e94a11620abd93c248dd7dd997b Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Sun, 19 Sep 2010 08:13:51 +0000
Subject: [PATCH] add INDEXED_FASTA_FORMAT
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14752 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/io/StreamSequenceFactory.java | 8 +++++++-
1 file changed, 7 insertions(+), 1 deletion(-)
diff --git a/uk/ac/sanger/artemis/io/StreamSequenceFactory.java b/uk/ac/sanger/artemis/io/StreamSequenceFactory.java
index 6b09f8ed3..fc457ee0d 100644
--- a/uk/ac/sanger/artemis/io/StreamSequenceFactory.java
+++ b/uk/ac/sanger/artemis/io/StreamSequenceFactory.java
@@ -51,12 +51,14 @@ abstract public class StreamSequenceFactory
/** The tag use for sequence that is in FASTA or similar format. */
final public static int FASTA_FORMAT = 4;
+
+ final public static int INDEXED_FASTA_FORMAT = 5;
/**
* Read a StreamSequence object from a LinePushBackReader object.
**/
public static StreamSequence makeStreamSequence(final LinePushBackReader
- in_stream)
+ in_stream, Entry entry)
throws IOException
{
final int sequence_type = getSequenceType(in_stream);
@@ -66,7 +68,11 @@ abstract public class StreamSequenceFactory
case EMBL_FORMAT:
return new EmblStreamSequence(in_stream);
case FASTA_FORMAT:
+ {
+ if(IndexFastaStream.isIndexed(entry))
+ return new IndexFastaStream(entry);
return new FastaStreamSequence(in_stream);
+ }
case GENBANK_FORMAT:
return new GenbankStreamSequence(in_stream);
case RAW_FORMAT:
--
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