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Add program_name param

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1 parent a68cb0a commit 7ca2c8a384d12703a8a4cdd95390b12cbc47057f @bosborne bosborne committed Dec 5, 2011
Showing with 6 additions and 3 deletions.
  1. +1 −2 lib/Bio/Tools/Run/Phylo/FastTree.pm
  2. +5 −1 lib/Bio/Tools/Run/Phylo/Phyml.pm
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3 lib/Bio/Tools/Run/Phylo/FastTree.pm
@@ -18,14 +18,13 @@ Bio::Tools::Run::Phylo::FastTree
# Build a FastTree factory
$factory = Bio::Tools::Run::Phylo::FastTree->new(-quiet => 1,
-fastest => 1);
-
# Get an alignment
my $alignio = Bio::AlignIO->new(
-format => 'fasta',
-file => '219877.cdna.fasta');
my $alnobj = $alignio->next_aln;
- # Analzye the aligment and get a Tree
+ # Analyze the aligment and get a Tree
my $tree = $factory->run($alnobj);
=head1 DESCRIPTION
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6 lib/Bio/Tools/Run/Phylo/Phyml.pm
@@ -199,6 +199,7 @@ map { $models3->{'aa'}->{$_} = 1 }
-opt_lengths => boolean [1]
-no_memory_check => boolean [1]
-mpi => boolean [1]
+ -program_name => string
=cut
@@ -220,7 +221,8 @@ sub new {
$freq, $kappa, $invar, $category_number,
$alpha, $tree, $opt_topology, $opt_lengths,
$opt, $search, $rand_start, $rand_starts,
- $rand_seed, $no_memory_check, $bootstrap, $mpi
+ $rand_seed, $no_memory_check, $bootstrap, $mpi,
+ $program_name
)
= $self->_rearrange(
[
@@ -244,6 +246,7 @@ sub new {
NO_MEMORY_CHECK
BOOTSTRAP
MPI
+ PROGRAM_NAME
)
],
%args
@@ -269,6 +272,7 @@ sub new {
$self->no_memory_check($no_memory_check) if $no_memory_check;
$self->bootstrap($bootstrap) if $bootstrap;
$self->mpi($mpi) if $mpi;
+ $self->program_name($program_name) if $program_name;
return $self;
}

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