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=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
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=head1 AUTHOR - Sendu Bala

Email bix@sendu.me.uk

=head1 APPENDIX

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

=cut

package Bio::Tools::Run::Phylo::Phast::PhastCons;
use strict;

use Cwd;
use File::Basename;
use Clone qw(clone);
use Bio::AlignIO;
use Bio::Tools::Run::Phylo::Phast::PhyloFit;
use Bio::FeatureIO;
use Bio::Annotation::SimpleValue;

use base qw(Bio::Tools::Run::Phylo::PhyloBase);

our $PROGRAM_NAME = 'phastCons';
our $PROGRAM_DIR = $ENV{'PHASTDIR'};

# methods and their synonyms from the phastCons args we support
our %PARAMS   = (rho => 'R',
                 nrates => 'k',
                 transitions => 't',
                 target_coverage => 'C',
                 expected_length => ['E', 'expected_lengths'],
                 lnl => 'L',
                 log => 'g',
                 max_micro_indel => 'Y',
                 indel_params => 'D',
                 lambda => 'l',
                 extrapolate => 'e',
                 hmm => 'H',
                 catmap => 'c',
                 states => 'S',
                 reflect_strand => 'U',
                 require_informative => 'M',
                 not_informative => 'F');

our %SWITCHES = (quiet => 'q',
                 indels => 'I',
                 indels_only => 'J',
                 FC => 'X',
                 coding_potential => 'p',
                 ignore_missing => 'z');

# just to be explicit, args we don't support (yet) or we handle ourselves
our %UNSUPPORTED = (estimate_trees => 'T',
                    estimate_rho => 'O',
                    gc => 'G',
                    msa_format => 'i',
                    score => 's',
                    no_post_probs => 'n',
                    seqname => 'N',
                    refidx => 'r',
                    idpref => 'P',
                    help => 'h',
                    alias => 'A',
                    most_conserved => ['V', 'viterbi']);


=head2 program_name

 Title   : program_name
 Usage   : $factory>program_name()
 Function: holds the program name
 Returns : string
 Args    : None

=cut

sub program_name {
    return $PROGRAM_NAME;
}

=head2 program_dir

 Title   : program_dir
 Usage   : $factory->program_dir(@params)
 Function: returns the program directory, obtained from ENV variable.
 Returns : string
 Args    : None

=cut

sub program_dir {
    return $PROGRAM_DIR;
}

=head2 new

 Title   : new
 Usage   : $factory = Bio::Tools::Run::Phylo::Phast::PhastCons->new(@params)
 Function: Creates a new PhastCons factory
 Returns : Bio::Tools::Run::Phylo::Phast::PhastCons
 Args    : Optionally, provide any of the following (defaults are not to use,
           see the same-named methods for information on what each option does):
           {