From 2651a5db15c78afa4668124446af464dc1952c3f Mon Sep 17 00:00:00 2001 From: jason Date: Sat, 10 Jul 2004 03:51:02 +0000 Subject: [PATCH] allow alignment to be specified in run() svn path=/bioperl-run/trunk/; revision=13550 --- Bio/Tools/Run/Phylo/PAML/Codeml.pm | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/Bio/Tools/Run/Phylo/PAML/Codeml.pm b/Bio/Tools/Run/Phylo/PAML/Codeml.pm index a5bc2ca..6e46c84 100644 --- a/Bio/Tools/Run/Phylo/PAML/Codeml.pm +++ b/Bio/Tools/Run/Phylo/PAML/Codeml.pm @@ -2,7 +2,7 @@ # # BioPerl module for Bio::Tools::Run::Phylo::PAML::Codeml # -# Cared for by Jason Stajich +# Cared for by Jason Stajich # # Copyright Jason Stajich # @@ -57,15 +57,14 @@ the Bioperl mailing list. Your participation is much appreciated. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track -of the bugs and their resolution. Bug reports can be submitted via -email or the web: +of the bugs and their resolution. Bug reports can be submitted via the +web: - bioperl-bugs@bioperl.org http://bioperl.org/bioperl-bugs/ =head1 AUTHOR - Jason Stajich -Email jason@bioperl.org +Email jason-at-bioperl-dot-org =head1 CONTRIBUTORS @@ -407,12 +406,13 @@ sub new { =cut sub run{ - my ($self) = @_; + my ($self,$aln,$tree) = @_; unless ( $self->save_tempfiles ) { # brush so we don't get plaque buildup ;) $self->cleanup(); } - my ($aln,$tree) = ($self->alignment(),$self->tree); + $tree = $self->tree unless $tree; + $aln = $self->alignment unless $aln; if( ! $aln ) { $self->warn("must have supplied a valid aligment file in order to run codeml"); return 0; -- 2.11.4.GIT