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Remove code related to MPI

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commit b047cb4de8ba6ad258b99551f526b544281bb11b 1 parent 5577f09
Brian Osborne bosborne authored
Showing with 1 addition and 29 deletions.
  1. +1 −29 lib/Bio/Tools/Run/Phylo/Phyml.pm
30 lib/Bio/Tools/Run/Phylo/Phyml.pm
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@@ -198,7 +198,6 @@ map { $models3->{'aa'}->{$_} = 1 }
-opt_topology => boolean [1]
-opt_lengths => boolean [1]
-no_memory_check => boolean [1]
- -mpi => boolean [1]
-program_name => string
=cut
@@ -221,8 +220,7 @@ 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,
- $program_name
+ $rand_seed, $no_memory_check, $bootstrap, $program_name
)
= $self->_rearrange(
[
@@ -245,7 +243,6 @@ sub new {
RAND_SEED
NO_MEMORY_CHECK
BOOTSTRAP
- MPI
PROGRAM_NAME
)
],
@@ -271,7 +268,6 @@ sub new {
$self->rand_seed($rand_seed) if $rand_seed;
$self->no_memory_check($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;
@@ -903,29 +899,6 @@ sub no_memory_check {
return $self->{_no_memory_check} || 0;
}
-=head2 mpi
-
- Title : mpi
- Usage : $factory->mpi(1);
- Function:
- Returns : boolean (defaults to false)
- Args : None to get, integer to set.
-
-=cut
-
-sub mpi {
- my ( $self, $value ) = @_;
- if ( defined($value) ) {
- if ($value) {
- $self->{_mpi} = 1;
- }
- else {
- $self->{_mpi} = 0;
- }
- }
- return $self->{_mpi} || 0;
-}
-
=head2 bootstrap
Title : bootstrap
@@ -957,7 +930,6 @@ sub _run {
my ( $self, $file ) = @_;
my $exe = $self->executable || return;
- $exe .= '-mpi' if $self->mpi;
my $command;
my $output_stat_file;
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