/dports/net/mpich2/mpich2-1.5/test/mpi/group/ |
H A D | groupnullincl.c | 16 MPI_Group group, outgroup; in main() local 28 rc = MPI_Group_incl( group, 0, 0, &outgroup ); in main() 35 rc = MPI_Group_incl( group, 0, ranks, &outgroup ); in main() 43 if (outgroup != MPI_GROUP_EMPTY) { in main() 45 rc = MPI_Group_compare( outgroup, MPI_GROUP_EMPTY, &result ); in main() 57 if (outgroup != MPI_GROUP_NULL) { in main() 58 rc = MPI_Group_free( &outgroup ); in main()
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/dports/net/mpich/mpich-3.4.3/test/mpi/group/ |
H A D | groupnullincl.c | 15 MPI_Group group, outgroup; in main() local 28 rc = MPI_Group_incl(group, 0, 0, &outgroup); in main() 35 rc = MPI_Group_incl(group, 0, ranks, &outgroup); in main() 43 if (outgroup != MPI_GROUP_EMPTY) { in main() 45 rc = MPI_Group_compare(outgroup, MPI_GROUP_EMPTY, &result); in main() 57 if (outgroup != MPI_GROUP_NULL) { in main() 58 rc = MPI_Group_free(&outgroup); in main()
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/dports/biology/py-ete3/ete3-3.1.2/ete3/tools/ |
H A D | ete_mod.py | 109 if args.outgroup and args.unroot: 111 elif args.outgroup: 112 if len(args.outgroup) > 1: 113 outgroup = t.get_common_ancestor(args.outgroup) 115 outgroup = t & args.outgroup[0] 116 t.set_outgroup(outgroup)
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/dports/math/octave-forge-control/control-3.3.1/inst/ |
H A D | __tito_dim__.m | 27 outgroup = P.outgroup; variable 30 if (! isfield (outgroup, "V")) 31 error ("%s: missing outgroup 'V'", name); 38 nmeas = numel (outgroup.V); 44 if (! isequal (outgroup.V(:), (p-nmeas+1:p)(:))) 45 error ("%s: outgroup 'V' invalid", name);
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/dports/biology/checkm/CheckM-1.0.18/scripts/genometreeworkflow/ |
H A D | rerootTree.py | 64 outgroup = [] 76 outgroup.append(t.taxon.label) 78 … if outgroup == [] or len(outgroup) == len(taxa) or not self.__isMonophyletic(tree, outgroup): 83 mrca = tree.mrca(taxon_labels=outgroup)
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/dports/biology/p5-Bio-NEXUS/Bio-NEXUS-0.78/lib/Bio/NEXUS/ |
H A D | Tree.pm | 686 my $outgroup = $tree->find($outgroup_name); 692 && $dist_back_to_newroot == $outgroup->get_length() ) 694 $newroot = $outgroup->get_parent(); 695 $outgroup->set_length($dist_back_to_newroot); 701 my $outgroup_old_parent = $outgroup->get_parent(); 704 my $newroot_siblings = $outgroup->get_siblings(); 710 $newroot->adopt( $outgroup, 1 ); 754 my ( $outgroup, $newroot, $dist_back_to_newroot ) = @_; 755 if ( $outgroup->get_length() ) { 756 my $outgroup_length = $outgroup->get_length(); [all …]
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H A D | TreesBlock.pm | 378 my ( $self, $outgroup, $root_position, $treename ) = @_; 379 if ( not defined $treename and not defined $outgroup ) { 389 push @rerooted_trees, $tree->reroot( $outgroup, $root_position ); 407 my ( $self, $outgroup, $root_position ) = @_; 411 push @rerooted_trees, $tree->reroot( $outgroup, $root_position );
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/dports/math/octave-forge-control/control-3.3.1/inst/@lti/ |
H A D | __lti_prune__.m | 37 …tmp = cellfun (@(x) __str2idx__ (lti.outgroup, lti.outname, x, "out"), out_idx, "uniformoutput", f… 45 if (numfields (lti.outgroup)) 47 …[lti.outgroup, empty] = structfun (@(x) __group_prune__ (x, out_idx, p), lti.outgroup, "uniformout… 49 fields = fieldnames (lti.outgroup); 50 lti.outgroup = rmfield (lti.outgroup, fields(empty));
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H A D | __lti_group__.m | 47 if (numfields (lti1.outgroup) || numfields (lti2.outgroup)) 49 lti2_outgroup = structfun (@(x) x + p1, lti2.outgroup, "uniformoutput", false); 50 retlti.outgroup = __merge_struct__ (lti1.outgroup, lti2_outgroup); 54 ## retlti.outgroup remains empty struct
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/dports/biology/p5-BioPerl-Run/BioPerl-Run-1.007003/t/ |
H A D | ProtPars.t | 14 my @params = ('threshold'=>10,'jumble'=>'17,10',outgroup=>2,'idlength'=>10); 30 my $outgroup = 3; 31 $tree_factory->outgroup($outgroup); 33 my $new_outgroup= $tree_factory->outgroup(); 72 @params = ('threshold'=>10,'jumble'=>'7,5',outgroup=>2,'idlength'=>10);
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H A D | Neighbor.t | 16 # 'outgroup'=>2, 34 my $outgroup= 1; 35 $tree_factory->outgroup($outgroup); 36 my $new_outgroup = $tree_factory->outgroup(); 86 $tree_factory->outgroup('ENSP000003'); 100 $tree_factory->outgroup(undef);
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/dports/biology/py-ete3/ete3-3.1.2/ete3/tools/ete_build_lib/task/ |
H A D | merger.py | 114 outgroup = partition_pairs[0][3] 115 ttree.set_outgroup(outgroup) 139 outgroup = ttree.get_common_ancestor(out_seqs) 140 if set(outgroup.get_leaf_names()) ^ out_seqs: 145 outgroup = ttree & list(out_seqs)[0] 147 ttree.set_outgroup(outgroup) 149 found_target = outgroup.get_sisters()[0] 152 outgroup.detach()
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/TreeIO/ |
H A D | lintree.pm | 214 my ($outgroup) = $treenodes[$data{'outgroup'}->[0]]; 215 if( ! defined $outgroup) { 218 $T->reroot($outgroup->ancestor);
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/dports/biology/p5-Bio-Phylo/Bio-Phylo-v2.0.1/t/ |
H A D | 21-bioperl-tree.t | 65 '-outgroup' => $n4 83 '-outgroup' => $iADHX 100 '-outgroup' => $d 108 '-outgroup' => $d 124 '-outgroup' => $d 132 '-outgroup' => $f 142 '-outgroup' => $d 145 'A,B,C are not Monophyletic w D as outgroup' 150 '-outgroup' => $i 153 'A,F,E are monophyletic with I as outgroup' [all …]
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/t/SeqIO/ |
H A D | msout.t | 175 my $outgroup = $msout->outgroup; 176 is( $outgroup, 1, "Testing msout::outgroup" ); 350 my $outgroup = $msout->outgroup; 351 is( $outgroup, 0, "Testing msout::outgroup" );
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/dports/biology/py-biopython/biopython-1.79/Bio/Phylo/ |
H A D | BaseTree.py | 844 outgroup = self.common_ancestor(outgroup_targets, *more_targets) 845 outgroup_path = self.get_path(outgroup) 850 prev_blen = outgroup.branch_length or 0.0 852 if outgroup.is_terminal() or outgroup_branch_length is not None: 854 outgroup.branch_length = outgroup_branch_length or 0.0 856 branch_length=self.root.branch_length, clades=[outgroup] 867 parent.clades.pop(parent.clades.index(outgroup)) 870 prev_blen - outgroup.branch_length, 876 new_root = outgroup 891 if outgroup in old_root.clades: [all …]
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/t/Tree/ |
H A D | Tree.t | 64 -outgroup => $n4),1,'Test Monophyly'); 77 -outgroup=> $iADHX),1, 'non-monophyletic group'); 96 -outgroup => $d),1, 'B,C are Monophyletic'); 99 -outgroup => $d),1,'A,B are Monophyletic'); 112 -outgroup => $d),1,'B,F are not Monophyletic' ); 115 -outgroup => $f),1, 'A,B are Monophyletic'); 120 -outgroup => $d), 1,'A,B,C are not Monophyletic w D as outgroup'); 123 -outgroup => $i), 1, 'A,F,E are monophyletic with I as outgroup'); 143 is($tree->reroot($a),1, 'Can re-root with A as outgroup');
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/dports/biology/py-biopython/biopython-1.79/Bio/Nexus/ |
H A D | Trees.py | 783 def root_with_outgroup(self, outgroup=None): argument 810 if outgroup is None: 812 outgroup_node = self.is_monophyletic(outgroup) 865 self, bstrees=None, constree=None, threshold=0.5, outgroup=None argument 880 if outgroup is None: 884 outgroup = self.get_taxa(smallest[1]) 888 self.root_with_outgroup(outgroup) 891 constree = consensus(bstrees, threshold=threshold, outgroup=outgroup) 895 constree.root_with_outgroup(outgroup) 903 def consensus(trees, threshold=0.5, outgroup=None): argument [all …]
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/dports/cad/qflow/qflow-1.4.98/scripts/ |
H A D | pinmanager.py.in | 863 outgroup = self.uncompress_group(group) 866 if len(outgroup['pins']) > 0: 867 … print('padgroup ' + outgroup['name'] + ' ' + outgroup['permute'], file=ofile) 868 for pin, fixed in zip(outgroup['pins'], outgroup['fixed']): 870 if outgroup['sides'] != '': 871 print('restrict side ' + outgroup['sides'], file=ofile) 872 if outgroup['start'] != 0 or outgroup['stop'] != 100: 873 fstart = str(outgroup['start'] / 100.0) 874 fstop = str(outgroup['stop'] / 100.0)
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/Tree/ |
H A D | TreeFunctionsI.pm | 898 my ($nodes,$outgroup) = $self->_rearrange([qw(NODES OUTGROUP)],@args); 900 if( ! defined $nodes || ! defined $outgroup ) { 915 my $og_ancestor = $outgroup->ancestor; 945 my ($nodes,$outgroup) = $self->_rearrange([qw(NODES OUTGROUP)],@args); 947 if( ! defined $nodes || ! defined $outgroup ) { 971 my $og_ancestor = $outgroup->ancestor;
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/dports/science/luscus/luscus_0.8.6/ |
H A D | findsym.c | 80 char *outgroup, INT outsym[], INT *ierr ) { in findsym() argument 367 find_point_group(IN_GATE,ou,&x,what0,outgroup,outsym,0); in findsym() 372 if(find_point_group(IN_GATE,ou,&x,what,outgroup,outsym,1)) in findsym() 390 find_point_group_unscrambled(IN_GATE,ou,&x,what0,outgroup,outsym,0); in findsym() 398 rank_m=mycount(outgroup,' '); in findsym() 400 rank_f=mycount(outgroup,' '); in findsym() 405 find_point_group(IN_GATE,ou,&x,what,outgroup,outsym,0); in findsym() 1144 strcpy(outgroup,"x y z"); in find_point_group_2() 1162 outgroup[0]=0; in find_point_group_2() 1169 strcat(outgroup,oplab[p[k].gen[i]]); in find_point_group_2() [all …]
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/dports/biology/graphlan/nsegata-graphlan-66ec7cfce81e/pyphlan/ |
H A D | pyphlan.py | 36 outgroup = new_root 37 outgroup_path = tree.get_path(outgroup) 41 prev_blen = outgroup.branch_length 42 if outgroup.is_terminal(): 44 outgroup.branch_length = 0.0 46 branch_length=tree.root.branch_length, clades=[outgroup]) 53 parent.clades.pop(parent.clades.index(outgroup)) 59 new_root = outgroup 74 if outgroup in old_root.clades: 76 old_root.clades.pop(old_root.clades.index(outgroup))
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/dports/biology/graphlan/nsegata-pyphlan-eae40ebc0030/ |
H A D | pyphlan.py | 36 outgroup = new_root 37 outgroup_path = tree.get_path(outgroup) 41 prev_blen = outgroup.branch_length 42 if outgroup.is_terminal(): 44 outgroup.branch_length = 0.0 46 branch_length=tree.root.branch_length, clades=[outgroup]) 53 parent.clades.pop(parent.clades.index(outgroup)) 59 new_root = outgroup 74 if outgroup in old_root.clades: 76 old_root.clades.pop(old_root.clades.index(outgroup))
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/dports/biology/graphlan/nsegata-graphlan-66ec7cfce81e/src/ |
H A D | pyphlan.py | 36 outgroup = new_root 37 outgroup_path = tree.get_path(outgroup) 41 prev_blen = outgroup.branch_length 42 if outgroup.is_terminal(): 44 outgroup.branch_length = 0.0 46 branch_length=tree.root.branch_length, clades=[outgroup]) 53 parent.clades.pop(parent.clades.index(outgroup)) 59 new_root = outgroup 74 if outgroup in old_root.clades: 76 old_root.clades.pop(old_root.clades.index(outgroup))
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/dports/www/rt50/rt-5.0.2/t/api/ |
H A D | savedsearch.t | 45 my $outgroup = RT::Group->new(RT->SystemUser); 46 $outgroup->CreateUserDefinedGroup(Name => 'searchgroup2'.$$); 47 $outgroup->AddMember(RT->SystemUser->Id); 100 ($ret, $msg) = $othersearch->Save(Privacy => 'RT::Group-' . $outgroup->Id, 110 ($ret, $msg) = $othersearch->Save(Privacy => 'RT::Group-' . $outgroup->Id,
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