/ 
bioperl-1.2.3
/ Bio::Tools::Phylo::PAML::Result

NAME

Bio::Tools::Phylo::PAML::Result - A PAML result set object

SYNOPSIS

Give standard usage here

DESCRIPTION

Describe the object here

FEEDBACK

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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
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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 email or the web:

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http://bugzilla.bioperl.org/

AUTHOR - Jason Stajich, Aaron Mackey

Email jason@bioperl.org Email amackey@virginia.edu

Describe contact details here

CONTRIBUTORS

Additional contributors names and emails here

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 = 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

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>

set_MLmatrix

 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)

get_MLmatrix

Title   : get_MLmatrix
Usage   : my $mat = $result->get_MLmatrix()
Function: Get the ML matrix
Returns : 2D Array reference
Args    : none

set_NGmatrix

 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)

get_NGmatrix

Title   : get_NGmatrix
Usage   : my $mat = $result->get_NGmatrix()
Function: Get the Nei & Gojobori matrix
Returns : 2D Array reference
Args    : none

add_seq

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>

reset_seqs

Title   : reset_seqs
Usage   : $result->reset_seqs
Function: Reset the OTU seqs stored
Returns : none
Args    : none

get_seqs

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>

set_codon_pos_basefreq

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

get_codon_pos_basefreq

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

version

Title   : version
Usage   : $obj->version($newval)
Function: Get/Set version
Returns : value of version
Args    : newvalue (optional)