NAME

       Bio::Tools::Phylo::Molphy::Result - container for data parsed from a ProtML run

SYNOPSIS

         # do not use this object directly, you will get it back as part of a
         # Molphy parser
         use Bio::Tools::Phylo::Molphy;
         my $parser = Bio::Tools::Phylo::Molphy->new(-file => 'output.protml');
         while( my $r = $parser->next_result ) {
           # r is a Bio::Tools::Phylo::Molphy::Result object

           # print the model name
           print $r->model, "\n";

           # get the substitution matrix
           # this is a hash of 3letter aa codes -> 3letter aa codes representing
           # substitution rate
           my $smat = $r->substitution_matrix;
           print "Arg -> Gln substitution rate is %d\n",
                 $smat->{'Arg'}->{'Gln'}, "\n";

           # get the transition probablity matrix
           # this is a hash of 3letter aa codes -> 3letter aa codes representing
           # transition probabilty
           my $tmat = $r->transition_probability_matrix;
           print "Arg -> Gln transition probablity is %.2f\n",
                 $tmat->{'Arg'}->{'Gln'}, "\n";

           # get the frequency for each of the residues
           my $rfreqs = $r->residue_frequencies;

           foreach my $residue ( keys %{$rfreqs} ) {
              printf "residue %s  expected freq: %.2f observed freq: %.2f\n",
                     $residue,$rfreqs->{$residue}->[0], $rfreqs->{$residue}->[1];
           }

           my @trees;
           while( my $t = $r->next_tree ) {
               push @trees, $t;
           }

           print "search space is ", $r->search_space, "\n",
                 "1st tree score is ", $trees[0]->score, "\n";

           # writing to STDOUT, use -file => '>filename' to specify a file
           my $out = Bio::TreeIO->new(-format => "newick");
           $out->write_tree($trees[0]); # writing only the 1st tree
         }

DESCRIPTION

       A container for data parsed from a ProtML run.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   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 the web:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

       Email jason-at-bioperl.org

APPENDIX

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

   new
        Title   : new
        Usage   : my $obj = Bio::Tools::Phylo::Molphy::Result->new();
        Function: Builds a new Bio::Tools::Phylo::Molphy::Result object
        Returns : Bio::Tools::Phylo::Molphy::Result
        Args    :

   model
        Title   : model
        Usage   : $obj->model($newval)
        Function:
        Returns : value of model
        Args    : newvalue (optional)

   substitution_matrix
        Title   : substitution_matrix
        Usage   : my $smat = $result->subsitution_matrix;
        Function: Get the relative substitution matrix calculated in the ML procedure
        Returns : reference to hash of hashes where key is the aa/nt name and value
                  is another hash ref which contains keys for all the aa/nt
                  possibilities
        Args    : none

   transition_probability_matrix
        Title   : transition_probability_matrix
        Usage   : my $matrixref = $molphy->transition_probablity_matrix();
        Function: Gets the observed transition probability matrix
        Returns : hash of hashes of aa/nt transition to each other aa/nt
        Args    : Transition matrix type, typically
                  '1PAM-1.0e05' or '1PAM-1.0e07'

   residue_frequencies
        Title   : residue_frequencies
        Usage   : my %data = $molphy->residue_frequencies()
        Function: Get the modeled and expected frequencies for
                  each of the residues in the sequence
        Returns : hash of either aa (protml) or nt (nucml) frequencies
                  each key will point to an array reference where
                  1st slot is model's expected frequency
                  2nd slot is observed frequency in the data
                  $hash{'A'}->[0] =
        Args    : none

   next_tree
        Title   : next_tree
        Usage   : my $tree = $factory->next_tree;
        Function: Get the next tree from the factory
        Returns : L<Bio::Tree::TreeI>
        Args    : none

   rewind_tree
        Title   : rewind_tree_iterator
        Usage   : $result->rewind_tree()
        Function: Rewinds the tree iterator so that next_tree can be
                  called again from the beginning
        Returns : none
        Args    : none

   add_tree
        Title   : add_tree
        Usage   : $result->add_tree($tree);
        Function: Adds a tree
        Returns : integer which is the number of trees stored
        Args    : L<Bio::Tree::TreeI>

   search_space
        Title   : search_space
        Usage   : $obj->search_space($newval)
        Function:
        Returns : value of search_space
        Args    : newvalue (optional)