Provided by: libbio-perl-run-perl_1.7.1-3_all bug


       Bio::Tools::Run::Phylo::Hyphy::Base - Hyphy wrapping base methods




       HyPhy ([Hy]pothesis Testing Using [Phy]logenies) package of Sergei Kosakowsky Pond,
       Spencer V. Muse, Simon D.W. Frost and Art Poon.  See for more


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AUTHOR - Albert Vilella

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       Additional contributors names and emails here


       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

   Default Values
       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:
        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