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Add some version 3 arguments, all tests pass
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@bosborne
bosborne committed Sep 21, 2011
1 parent 4ee6c02 commit 40640a8
Showing 1 changed file with 88 additions and 40 deletions.
128 changes: 88 additions & 40 deletions lib/Bio/Tools/Run/Phylo/Phyml.pm
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Expand Up @@ -213,7 +213,8 @@ sub new {

my ($data_type, $data_format, $dataset_count, $model, $freq, $kappa, $invar,
$category_number, $alpha, $tree, $opt_topology,
$opt_lengths, $opt, $search, $rand_start, $rand_starts, $rand_seed)
$opt_lengths, $opt, $search, $rand_start, $rand_starts, $rand_seed,
$no_memory_check, $bootstrap )
= $self->_rearrange([qw( DATA_TYPE
DATA_FORMAT
DATASET_COUNT
Expand All @@ -231,6 +232,8 @@ sub new {
RAND_START
RAND_STARTS
RAND_SEED
NO_MEMORY_CHECK
BOOTSTRAP
)], %args);

$self->data_type($data_type) if $data_type;
Expand All @@ -250,7 +253,8 @@ sub new {
$self->rand_start($rand_start) if $rand_start;
$self->rand_starts($rand_starts) if $rand_starts;
$self->rand_seed($rand_seed) if $rand_seed;

$self->no_memory_check($no_memory_check) if $no_memory_check;
$self->bootstrap($bootstrap) if $bootstrap;

return $self;
}
Expand Down Expand Up @@ -831,6 +835,45 @@ sub rand_seed {
return $self->{_rand_seed} || int rand 1000000;
}

=head2 no_memory_check
Title : no_memory_check
Usage : $factory->no_memory_check(1);
Function:
Returns :
Args : None to get, integer to set.
=cut

sub no_memory_check {
my ($self, $value) = @_;
$self->throw("Not a valid parameter [no_memory_check] prior to PhyML v3") if $self->version < 3;
if (defined $value) {
die "Invalid number [$value]" unless $value =~ /^\d+$/;
$self->{_no_memory_check} = $value;
}
return $self->{_no_memory_check};
}

=head2 bootstrap
Title : bootstrap
Usage : $factory->bootstrap(100);
Function: Set number of bootstraps
Returns :
Args : None to get, integer to set.
=cut

sub bootstrap {
my ($self, $value) = @_;
$self->throw("Not a valid parameter [bootstrap] prior to PhyML v3") if $self->version < 3;
if (defined $value) {
die "Invalid number [$value]" unless $value =~ /^\d+$/;
$self->{_bootstrap} = $value;
}
return $self->{_bootstrap};
}

=head2 Internal methods
Expand Down Expand Up @@ -900,56 +943,61 @@ sub _setparams {
my $self = shift;
my $param_string;

if ($self->version >= 3 ) {
if ( $self->version >= 3 ) {

$param_string = ' -d '. $self->data_type;
$param_string .= ' -q' if $self->data_format eq 's';
$param_string .= ' -n '. $self->dataset_count if $self->dataset_count > 1;
$param_string = ' -d ' . $self->data_type;

#$param_string .= ' 0'; # no bootstap sets
$param_string .= ' -q ' if $self->data_format eq 's';
$param_string .= ' -n ' . $self->dataset_count
if $self->dataset_count > 1;
$param_string .= ' -b ' . $self->bootstrap if $self->bootstrap;

$param_string .= ' -m '. $self->model;
$param_string .= ' -f '. $self->freq if $self->freq;
# $param_string .= ' 0'; # no bootstrap sets
$param_string .= ' -m ' . $self->model;
$param_string .= ' -f ' . $self->freq if $self->freq;

if ($self->data_type eq 'dna') {
$param_string .= ' -t '. $self->kappa;
}
if ( $self->data_type eq 'dna' ) {
$param_string .= ' -t ' . $self->kappa;
}

$param_string .= ' -v '. $self->invar;
$param_string .= ' -c '. $self->category_number;
$param_string .= ' -a '. $self->alpha;
$param_string .= ' -u '. $self->tree if $self->tree ne 'BIONJ';
$param_string .= ' -o '. $self->opt if $self->opt;
$param_string .= ' -s '. $self->search;

if ($self->search eq 'SPR' ) {
$param_string .= ' --rand_start ' if $self->rand_start;
$param_string .= ' --n_rand_starts '. $self->rand_starts
if $self->rand_starts;
$param_string .= ' --r_seed '. $self->rand_seed;
}
$param_string .= ' -v ' . $self->invar;
$param_string .= ' -c ' . $self->category_number;
$param_string .= ' -a ' . $self->alpha;
$param_string .= ' -u ' . $self->tree if $self->tree ne 'BIONJ';
$param_string .= ' -o ' . $self->opt if $self->opt;
$param_string .= ' -s ' . $self->search;

if ( $self->search eq 'SPR' ) {
$param_string .= ' --rand_start ' if $self->rand_start;
$param_string .= ' --n_rand_starts ' . $self->rand_starts
if $self->rand_starts;
$param_string .= ' --r_seed ' . $self->rand_seed;
}

} else {
$param_string .= ' --no_memory_check ' if $self->no_memory_check;

$param_string = ' ' . $self->data_type;
}
else {

$param_string .= ' '. $self->data_format;
$param_string .= ' '. $self->dataset_count;
$param_string = ' ' . $self->data_type;

$param_string .= ' 0'; # no bootstap sets
$param_string .= ' ' . $self->data_format;
$param_string .= ' ' . $self->dataset_count;

$param_string .= ' '. $self->model;
$param_string .= ' 0'; # no bootstap sets

unless ($self->data_type) { # only for DNA
$param_string .= ' '. $self->kappa;
}
$param_string .= ' ' . $self->model;

unless ( $self->data_type ) { # only for DNA
$param_string .= ' ' . $self->kappa;
}

$param_string .= ' '. $self->invar;
$param_string .= ' '. $self->category_number;
$param_string .= ' '. $self->alpha;
$param_string .= ' '. $self->tree;
$param_string .= ' '. $self->opt_topology;
$param_string .= ' '. $self->opt_lengths;
$param_string .= ' ' . $self->invar;
$param_string .= ' ' . $self->category_number;
$param_string .= ' ' . $self->alpha;
$param_string .= ' ' . $self->tree;
$param_string .= ' ' . $self->opt_topology;
$param_string .= ' ' . $self->opt_lengths;

}
return $param_string;
Expand Down

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