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Remove code related to MPI

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commit b047cb4de8ba6ad258b99551f526b544281bb11b 1 parent 5577f09
bosborne authored December 05, 2011

Showing 1 changed file with 1 addition and 29 deletions. Show diff stats Hide diff stats

  1. 30  lib/Bio/Tools/Run/Phylo/Phyml.pm
30  lib/Bio/Tools/Run/Phylo/Phyml.pm
@@ -198,7 +198,6 @@ map { $models3->{'aa'}->{$_} = 1 }
198 198
            -opt_topology    => boolean               [1]
199 199
            -opt_lengths     => boolean               [1]
200 200
            -no_memory_check => boolean               [1]
201  
-           -mpi             => boolean               [1]
202 201
            -program_name    => string
203 202
 
204 203
 =cut
@@ -221,8 +220,7 @@ sub new {
221 220
         $freq,      $kappa,           $invar,         $category_number,
222 221
         $alpha,     $tree,            $opt_topology,  $opt_lengths,
223 222
         $opt,       $search,          $rand_start,    $rand_starts,
224  
-        $rand_seed, $no_memory_check, $bootstrap,     $mpi,
225  
-        $program_name
  223
+        $rand_seed, $no_memory_check, $bootstrap,     $program_name
226 224
       )
227 225
       = $self->_rearrange(
228 226
         [
@@ -245,7 +243,6 @@ sub new {
245 243
               RAND_SEED
246 244
               NO_MEMORY_CHECK
247 245
               BOOTSTRAP
248  
-              MPI
249 246
               PROGRAM_NAME
250 247
               )
251 248
         ],
@@ -271,7 +268,6 @@ sub new {
271 268
     $self->rand_seed($rand_seed)             if $rand_seed;
272 269
     $self->no_memory_check($no_memory_check) if $no_memory_check;
273 270
     $self->bootstrap($bootstrap)             if $bootstrap;
274  
-    $self->mpi($mpi)                         if $mpi;
275 271
     $self->program_name($program_name)       if $program_name;
276 272
 
277 273
     return $self;
@@ -903,29 +899,6 @@ sub no_memory_check {
903 899
     return $self->{_no_memory_check} || 0;
904 900
 }
905 901
 
906  
-=head2 mpi
907  
-
908  
- Title   : mpi
909  
- Usage   : $factory->mpi(1);
910  
- Function: 
911  
- Returns : boolean (defaults to false)
912  
- Args    : None to get, integer to set. 
913  
-
914  
-=cut
915  
-
916  
-sub mpi {
917  
-    my ( $self, $value ) = @_;
918  
-    if ( defined($value) ) {
919  
-        if ($value) {
920  
-            $self->{_mpi} = 1;
921  
-        }
922  
-        else {
923  
-            $self->{_mpi} = 0;
924  
-        }
925  
-    }
926  
-    return $self->{_mpi} || 0;
927  
-}
928  
-
929 902
 =head2 bootstrap
930 903
 
931 904
  Title   : bootstrap
@@ -957,7 +930,6 @@ sub _run {
957 930
     my ( $self, $file ) = @_;
958 931
 
959 932
     my $exe = $self->executable || return;
960  
-    $exe .= '-mpi' if $self->mpi;
961 933
 
962 934
     my $command;
963 935
     my $output_stat_file;

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