Bio::Tools::Run::Phylo::Hyphy::Base - Hyphy wrapping base methods
FIXME
HyPhy ([Hy]pothesis Testing Using [Phy]logenies) package of Sergei Kosakowsky
Pond, Spencer V. Muse, Simon D.W. Frost and Art Poon. See http://www.hyphy.org
for more information.
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The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
Valid and default values are listed below. The default values are always the
first one listed. These descriptions are essentially lifted from the python
wrapper or provided by the author.
Title : program_name
Usage : $factory->program_name()
Function: holds the program name
Returns: string
Args : None
Title : valid_values
Usage : $factory->valid_values()
Function: returns the possible parameters
Returns: an array holding all possible parameters (this needs to be specified per child class).
Returns an empty array in the base class.
Args : None
Title : program_dir
Usage : ->program_dir()
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :
Title : new
Usage : my $obj = Bio::Tools::Run::Phylo::Hyphy->new();
Function: Builds a new Bio::Tools::Run::Phylo::Hyphy object
Returns : Bio::Tools::Run::Phylo::Hyphy
Args : -alignment => the Bio::Align::AlignI object
-save_tempfiles => boolean to save the generated tempfiles and
NOT cleanup after onesself (default FALSE)
-tree => the Bio::Tree::TreeI object
-params => a hashref of parameters (all passed to set_parameter)
-executable => where the hyphy executable resides
See also: Bio::Tree::TreeI, Bio::Align::AlignI
Title : prepare
Usage : my $rundir = $hyphy->prepare($aln);
Function: prepare the analysis using the default or updated parameters
the alignment parameter must have been set
Returns : value of rundir
Args : L<Bio::Align::AlignI> object,
L<Bio::Tree::TreeI> object [optional]
Title : create_wrapper
Usage : $self->create_wrapper
Function: It will create the wrapper file that interfaces with the analysis bf file
Example :
Returns :
Args :
Title : run
Usage : my ($rc,$results) = $BatchFile->run();
Function: run the Hyphy analysis using the specified batchfile and its ordered parameters
Returns : Return code, Hash
Args : none
Title : error_string
Usage : $obj->error_string($newval)
Function: Where the output from the last analysus run is stored.
Returns : value of error_string
Args : newvalue (optional)
Title : alignment
Usage : $hyphy->alignment($aln);
Function: Get/Set the L<Bio::Align::AlignI> object
Returns : L<Bio::Align::AlignI> object
Comment : We could potentially add support for running directly on a file
but we shall keep it simple
See also: L<Bio::SimpleAlign>
Title : tree
Usage : $hyphy->tree($tree);
Function: Get/Set the L<Bio::Tree::TreeI> object
Returns : L<Bio::Tree::TreeI>
Args : [optional] $tree => L<Bio::Tree::TreeI>,
Comment : We could potentially add support for running directly on a file
but we shall keep it simple
See also: L<Bio::Tree::Tree>
Title : get_parameters
Usage : my %params = $self->get_parameters();
Function: returns the list of parameters as a hash
Returns : associative array keyed on parameter names
Args : none
Title : set_parameter
Usage : $hyphy->set_parameter($param,$val);
Function: Sets a hyphy parameter, will be validated against
the valid values.
The checks can be ignored if one turns off param checks like this:
$hyphy->no_param_checks(1)
Returns : boolean if set was success, if verbose is set to -1
then no warning will be reported
Args : $param => name of the parameter
$value => value to set the parameter to
See also: L<no_param_checks()>
Title : set_default_parameters
Usage : $obj->set_default_parameters();
Function: (Re)set the default parameters from the defaults
(the first value in each array in the valid_values() array)
Returns : none
Args : none
Title : update_ordered_parameters
Usage : $hyphy->update_ordered_parameters(0);
Function: (Re)set the default parameters from the defaults
(the first value in each array in the
%VALIDVALUES class variable)
Returns : none
Args : boolean: keep existing parameter values
Title : outfile_name
Usage : my $outfile = $hyphy->outfile_name();
Function: Get/Set the name of the output file for this run
(if you wanted to do something special)
Returns : string
Args : [optional] string to set value to
Title : version
Usage : $obj->version()
Function: Returns the version string from HYPHY
Returns : string
Args : none
Title : hyphy_lib_dir
Usage : $obj->hyphy_lib_dir()
Function: Returns the HYPHY_LIB_DIRECTORY from HYPHY
Returns : string
Args : none