/ 
bioperl-1.4
/ Bio::Tools::Phylo::PAML::Result

NAME

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

SYNOPSIS

# see Bio::Tools::Phylo::PAML for example usage
use Bio::Tools::Phylo::PAML;
my $parser = new Bio::Tools::Phylo::PAML
  (-file => "./results/mlc", -dir => "./results/");

# get the first/next result; a Bio::Tools::Phylo::PAML::Result object,
# which isa Bio::SeqAnalysisResultI object.
my $result = $parser->next_result();

my @seqs       = $result->get_seqs;
my @MLmatrix   = $result->get_MLmatrix; # get MaxLikelihood Matrix
my @NGmatrix   = $result->get_NGmatrix; # get Nei-Gojoburi Matrix
my @basfreq    = $result->get_codon_pos_basefreq;

DESCRIPTION

This is a container object for PAML Results.

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/MailList.shtml  - About the mailing lists

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:

bioperl-bugs@bioperl.org
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
          -seqs      => array reference of L<Bio::PrimarySeqI> objects
          -codonpos  => array reference of codon positions 
          -codonfreq => array reference of codon frequencies
          -version   => version string
          -model     => model string
          -patterns  => hashref with the fields '-patterns', '-ns', '-ls'
          -stats     => array ref of misc stats   (optional)
          -aafreq    => Hashref of AA frequencies (only for AAML)
          -aadistmat => Bio::Matrix::PhylipDist   (only for AAML)
          -aamldistmat => Bio::Matrix::PhylipDist   (only for pairwise AAML)
          -NSSitesresult => arrayref of PAML::ModelResult

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

get_trees

Title   : get_trees
Usage   : my @trees = $result->get_trees;
Function: Get all the parsed trees as an array
Returns : Array of trees
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)

model

Title   : model
Usage   : $obj->model($newval)
Function: Get/Set model
Returns : value of model 
Args    : on set, new value (a scalar or undef, optional)

patterns

Title   : patterns
Usage   : $obj->patterns($newval)
Function: Get/Set Patterns hash
Returns : Hashref of pattern data
Args    : [optional] Hashref of patterns
        : The hashref is typically
        : { -patterns => \@arrayref
        :   -ns       => $ns
        :   -ls       => $ls
        : }

set_AAFreqs

Title   : set_AAFreqs
Usage   : $result->set_AAFreqs(\%aafreqs);
Function: Get/Set AA freqs
Returns : none
Args    : Hashref, keys are the sequence names, each points to a hashref
          which in turn has keys which are the amino acids

get_AAFreqs

Title   : get_AAFreqs
Usage   : my %all_aa_freqs = $result->get_AAFreqs() 
           OR
          my %seq_aa_freqs = $result->get_AAFreqs($seqname) 
Function: Get the AA freqs, either for every sequence or just 
          for a specific sequence
          The average aa freqs for the entire set are also available
          for the sequence named 'Average'
Returns : Hashref
Args    : (optional) sequence name to retrieve aa freqs for

add_stat

Title   : add_stat
Usage   : $result->add_stat($stat,$value);
Function: Add some misc stat valuess (key/value pairs)
Returns : none
Args    : $stat  stat name
          $value stat value

get_stat

Title   : get_stat
Usage   : my $value = $result->get_stat($name);
Function: Get the value for a stat of a given name
Returns : scalar value
Args    : name of the stat

get_stat_names

Title   : get_stat_names
Usage   : my @names = $result->get_stat_names;
Function: Get the stat names stored for the result
Returns : array of names
Args    : none

get_AADistMatrix

Title   : get_AADistMatrix
Usage   : my $mat = $obj->get_AADistMatrix()
Function: Get AADistance Matrix
Returns : value of AADistMatrix (Bio::Matrix::PhylipDist)
Args    : none

set_AADistMatrix

Title   : set_AADistMatrix
Usage   : $obj->set_AADistMatrix($mat);
Function: Set the AADistrance Matrix (Bio::Matrix::PhylipDist)
Returns : none
Args    : AADistrance Matrix (Bio::Matrix::PhylipDist)

get_AAMLDistMatrix

Title   : get_AAMLDistMatrix
Usage   : my $mat = $obj->get_AAMLDistMatrix()
Function: Get AAMLDistance Matrix
Returns : value of AAMLDistMatrix (Bio::Matrix::PhylipDist)
Args    : none

set_AAMLDistMatrix

Title   : set_AAMLDistMatrix
Usage   : $obj->set_AAMLDistMatrix($mat);
Function: Set the AA ML Distrance Matrix (Bio::Matrix::PhylipDist)
Returns : none 
Args    : AAMLDistrance Matrix (Bio::Matrix::PhylipDist)

add_NSSite_result

Title   : add_NSSite_result
Usage   : $result->add_NSSite_result($model)
Function: Add a NSsite result (PAML::ModelResult)
Returns : none
Args    : Bio::Tools::Phylo::PAML::ModelResult

get_NSSite_results

Title   : get_NSSite_results
Usage   : my @results = @{$self->get_NSSite_results};
Function: Get the reference to the array of NSSite_results
Returns : Array of PAML::ModelResult results
Args    : none

set_CodonFreqs

Title   : set_CodonFreqs
Usage   : $obj->set_CodonFreqs($newval)
Function: Get/Set the Codon Frequence table
Returns : value of set_CodonFreqs (a scalar)
Args    : on set, new value (a scalar or undef, optional)

get_CodonFreqs

Title   : get_CodonFreqs
Usage   : my @codon_freqs = $result->get_CodonFreqs() 
Function: Get the Codon freqs
Returns : Array
Args    : none