Bio::Tools::Phylo::PAML::Result - A PAML result set object
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : my $obj = new Bio::Tools::Phylo::PAML::Result(%data); Function: Builds a new Bio::Tools::Phylo::PAML::Result object Returns : Bio::Tools::Phylo::PAML::Result Args : -trees => array reference of L<Bio::Tree::TreeI> objects -MLmatrix => ML matrix .... MORE ARGUMENTS LISTED HERE BY AARON AND JASON
Title : next_tree Usage : my $tree = $factory->next_tree; Function: Get the next tree from the factory Returns : L<Bio::Tree::TreeI> Args : none
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
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>
Title : set_MLmatrix Usage : $result->set_MLmatrix($mat) Function: Set the ML Matrix Returns : none Args : Arrayref to MLmatrix (must be arrayref to 2D matrix whic is lower triangle pairwise)
Title : get_MLmatrix Usage : my $mat = $result->get_MLmatrix() Function: Get the ML matrix Returns : 2D Array reference Args : none
Title : set_NGmatrix Usage : $result->set_NGmatrix($mat) Function: Set the Nei & Gojobori Matrix Returns : none Args : Arrayref to NGmatrix (must be arrayref to 2D matrix whic is lower triangle pairwise)
Title : get_NGmatrix Usage : my $mat = $result->get_NGmatrix() Function: Get the Nei & Gojobori matrix Returns : 2D Array reference Args : none
Title : add_seq Usage : $obj->add_seq($seq) Function: Add a Bio::PrimarySeq to the Result Returns : none Args : Bio::PrimarySeqI See also : L<Bio::PrimarySeqI>
Title : reset_seqs Usage : $result->reset_seqs Function: Reset the OTU seqs stored Returns : none Args : none
Title : get_seqs Usage : my @otus = $result->get_seqs Function: Get the seqs Bio::PrimarySeq (OTU = Operational Taxonomic Unit) Returns : Array of Bio::PrimarySeq Args : None See also : L<Bio::PrimarySeq>
Title : set_codon_pos_basefreq Usage : $result->set_codon_pos_basefreq(@freqs) Function: Set the codon position base frequencies Returns : none Args : Array of length 3 where each slot has a hashref keyed on DNA base
Title : get_codon_pos_basefreq Usage : my @basepos = $result->get_codon_pos_basefreq; Function: Get the codon position base frequencies Returns : Array of length 3 (each codon position), each slot is a hashref keyed on DNA bases, the values are the frequency of the base at that position for all sequences Args : none Note : The array starts at 0 so position '1' is in position '0' of the array
Title : version Usage : $obj->version($newval) Function: Get/Set version Returns : value of version Args : newvalue (optional)
To install LocalConfig, copy and paste the appropriate command in to your terminal.
cpanm
cpanm LocalConfig
CPAN shell
perl -MCPAN -e shell install LocalConfig
For more information on module installation, please visit the detailed CPAN module installation guide.