From db66b2bd5036c1d976ec38128b1d015eb2fbeb23 Mon Sep 17 00:00:00 2001
From: lapp <lapp@bioperl.org>
Date: Thu, 7 Nov 2002 23:54:23 +0000
Subject: [PATCH] Fixed the bug Mat Wiepert reported: fasta seqs lost their
 primary id.

svn path=/bioperl-live/trunk/; revision=5050
---
 Bio/Seq/SeqFastaSpeedFactory.pm | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/Bio/Seq/SeqFastaSpeedFactory.pm b/Bio/Seq/SeqFastaSpeedFactory.pm
index 0b76b4f85..01bff23b5 100644
--- a/Bio/Seq/SeqFastaSpeedFactory.pm
+++ b/Bio/Seq/SeqFastaSpeedFactory.pm
@@ -121,18 +121,16 @@ sub create {
 
     my $sequence = $param{'-seq'}  || $param{'-SEQ'};
     my $fulldesc = $param{'-desc'} || $param{'-DESC'};
-    my $id       = $param{'-id'}   || $param{'-ID'};
+    my $id       = $param{'-id'}   || $param{'-ID'} ||
+	           $param{'-primary_id'}   || $param{'-PRIMARY_ID'};
 
-
-
-    my $seq = {};
-    bless $seq,"Bio::Seq";
-    my $t_pseq = $seq->{'primary_seq'} = {};
-    bless $t_pseq,"Bio::PrimarySeq";
+    my $seq = bless {}, "Bio::Seq";
+    my $t_pseq = $seq->{'primary_seq'} = bless {}, "Bio::PrimarySeq";
     $t_pseq->{'seq'}  = $sequence;
     $t_pseq->{'desc'} = $fulldesc;
     $t_pseq->{'display_id'} = $id;
     $t_pseq->{'primary_id'} = $id;
+    $seq->{'primary_id'} = $id; # currently Bio::Seq does not delegate this
     if( $sequence ) {
 	$t_pseq->_guess_alphabet();
     }
-- 
2.11.4.GIT