#
# BioPerl module for Bio::Tools::Phylo::PAML::Result
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason-at-bioperl.org>
#
# Copyright Jason Stajich, Aaron Mackey
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Phylo::PAML::Result - A PAML result set object
=head1 SYNOPSIS
# see Bio::Tools::Phylo::PAML for example usage
use Bio::Tools::Phylo::PAML;
my $parser = Bio::Tools::Phylo::PAML->new
(-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 %input_params = $result->get_input_parameters;
my @basfreq = $result->get_codon_pos_basefreq;
my $MLmatrix = $result->get_MLmatrix; # get MaxLikelihood Matrix
my $NGmatrix = $result->get_NGmatrix; # get Nei-Gojoburi Matrix
# for AAML runs
my $AAmatrix = $result->get_AADistMatrix;
my $AAMLmatrix = $result->get_AAMLDistMatrix;
# if -dir contains an rst file get list of
# Bio::PrimarySeq ancestral state reconstructions of the sequences
my @rsts = $result->get_rst_seqs;
# if you want to print the changes on the tree
# this will print out the
# anc_aa => ANCESTRAL AMINO ACID
# anc_prob => ANCESTRAL AA PROBABILITY
# derived_aa => DERIVED AA
# derived_prob => DERIVE AA PROBABILITY (where appropriate - NA for extant/tip taxas)
# site => which codon site this in the alignment
@trees = $result->get_rst_trees;
for my $t ( @trees ) {
for my $node ( $t->get_nodes ) {
next unless $node->ancestor; # skip root node
my @changes = $node->get_tag_values('changes');
my $chgstr = '';
for my $c ( @changes ) {
for my $k ( sort keys %$c ) {
$chgstr .= "$k => $c->{$k} ";
}
$chgstr .= "\n\t";
}
printf "node:%s n=%s s=%s\n\t%s\n",
$node->id,
$node->get_tag_values('n'),
$node->get_tag_values('s'),
$chgstr;
}
}
# Persite probabilities
my $persite = $result->get_rst_persite;
# let's score site 1
$site = $persite->[2];
# so site 2, node 2 (extant node, node 2)
print $site->[2]->{'codon'}, ' ',$site->[2]->{'aa'},"\n";
# site 2, node 3
print $site->[3]->{'codon'}, ' ',$site->[3]->{'aa'}, "\n";
# ancestral node 9, codon, aa, marginal probabilities; Yang95 is listed as
# (eqn. 4 in Yang et al. 1995 Genetics 141:1641-1650) in PAML rst file.
print $site->[9]->{'codon'}, ' ',$site->[9]->{'aa'}, ' ', $site->[9]->{'prob'}, ' ',
$site->[9]->{'Yang95_aa'},' ', $site->[9]->{'Yang95_aa_prob'},"\n";
=head1 DESCRIPTION
This is a container object for PAML Results.
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=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
email or the web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Jason Stajich, Aaron Mackey
Email jason-at-bioperl-dot-org
Email amackey-at-virginia-dot-edu
=head1 CONTRIBUTORS
Albert Vilella avilella-AT-gmail-DOT-com
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Tools::Phylo::PAML::Result;
use strict;
use base qw(Bio::Root::Root Bio::AnalysisResultI);
=head2 new
Title : new
Usage : my $obj = Bio::Tools::Phylo::PAML::Result->new(%data);
Function: Builds a new Bio::Tools::Phylo::PAML::Result object
Returns : Bio::Tools::Phylo::PAML::Result
Args : -trees => array reference of Bio::Tree::TreeI objects
-MLmatrix => ML matrix
-seqs => array reference of Bio::PrimarySeqI objects
-codonpos => array reference of codon positions
-codonfreq => array reference of codon frequencies
-version => version string
-model => model string
-patterns => hashref with the fields '-patterns', '-ns', '-ls'
-stats => array ref of misc stats (optional)
-aafreq => Hashref of AA frequencies (only for AAML)
-aadistmat => Bio::Matrix::PhylipDist (only for AAML)
-aamldistmat => Bio::Matrix::PhylipDist (only for pairwise AAML)
-ntfreq => array ref of NT frequencies (only for BASEML)
-seqfile => seqfile used
-kappa_mat => Bio::Matrix::PhylipDist of kappa values (only for BASEML)
-alpha_mat => Bio::Matrix::PhylipDist of alpha values (only for BASEML)
-NSSitesresult => arrayref of PAML::ModelResult
-input_params => input params from .ctl file
-rst => array reference of Bio::PrimarySeqI objects
of ancestral state reconstruction
-rst_persite=> arrayref of persite data, this is a complicated set of AoH
-rst_trees => rst trees with changes coded on the tree
See Also: L<Bio::Tree::TreeI>, L<Bio::PrimarySeqI>, L<Bio::Matrix::PhylipDist>, L<Bio::Tools::Phylo::PAML>
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($trees,$mlmat,$seqs,$ngmatrix,
$codonpos,$codonfreq,$version,
$model,$patterns, $stats,
$aafreq, $aadistmat,
$aamldistmat,
$ntfreqs, $seqfile, $kappa_mat, $alpha_mat,
$NSSitesresults,$input_params,$rst,$rst_persite,$rst_trees ) =
$self->_rearrange([qw
(TREES MLMATRIX
SEQS NGMATRIX
CODONPOS CODONFREQ
VERSION MODEL PATTERNS
STATS AAFREQ AADISTMAT
AAMLDISTMAT
NTFREQ SEQFILE
KAPPA_DISTMAT
ALPHA_DISTMAT
NSSITESRESULTS
INPUT_PARAMS
RST RST_PERSITE RST_TREES)],
@args);
$self->reset_seqs;
if( $trees ) {
if(ref($trees) !~ /ARRAY/i ) {
$self->warn("Must provide a valid array reference to initialize trees");
} else {
foreach my $t ( @$trees ) {
$self->add_tree($t);
}
}
}
$self->{'_treeiterator'} = 0;
if( $mlmat ) {
if( ref($mlmat) !~ /ARRAY/i ) {
$self->warn("Must provide a valid array reference to initialize MLmatrix");
} else {
$self->set_MLmatrix($mlmat);
}
}
if( $seqs ) {
if( ref($seqs) !~ /ARRAY/i ) {
$self->warn("Must provide a valid array reference to initialize seqs");
} else {
foreach my $s ( @$seqs ) {
$self->add_seq($s);
}
}
}
if( $ngmatrix ) {
if( ref($ngmatrix) !~ /ARRAY/i ) {
$self->warn("Must provide a valid array reference to initialize NGmatrix");
} else {
$self->set_NGmatrix($ngmatrix);
}
}
if( $codonfreq ) {
if( ref($codonfreq) =~ /ARRAY/i ) {
$self->set_CodonFreqs($codonfreq);
} else {
$self->warn("Must provide a valid array reference to initialize codonfreq");
}
}
if( $codonpos ) {
if( ref($codonpos) !~ /ARRAY/i ) {
$self->warn("Must provide a valid array reference to initialize codonpos");
} else {
$self->set_codon_pos_basefreq(@$codonpos);
}
}
$self->version($version) if defined $version;
$self->seqfile($seqfile) if defined $seqfile;
$self->model($model) if defined $model;
if( defined $patterns ) {
if( ref($patterns) =~ /HASH/i ) {
$self->patterns($patterns);
} else {
$self->warn("Must provide a valid array reference to initialize patterns");
}
}
$self->{'_aafreqs'} = {};
if( $aafreq ) {
if( ref($aafreq) =~ /HASH/i ) {
$self->set_AAFreqs($aafreq);
} else {
$self->warn("Must provide a valid hash reference to initialize aafreq");
}
}
if( $stats ) {
if( ref($stats) =~ /HASH/i ) {
while( my ($stat,$val) = each %$stats) {
$self->add_stat($stat,$val);
}
} else {
$self->warn("Must provide a valid hash reference initialize stats");
}
}
$self->set_AADistMatrix($aadistmat) if defined $aadistmat;
$self->set_AAMLDistMatrix($aamldistmat) if defined $aamldistmat;
if( defined $NSSitesresults ) {
if( ref($NSSitesresults) !~ /ARRAY/i ) {
$self->warn("expected an arrayref for -NSSitesresults");
} else {
foreach my $m ( @$NSSitesresults ) {
$self->add_NSSite_result($m);
}
}
}
$self->{'_ntfreqs'} = {};
if( $ntfreqs ) {
if( ref($ntfreqs) =~ /HASH/i ) {
$self->set_NTFreqs($ntfreqs);
} else {
$self->warn("Must provide a valid hash reference to initialize ntfreq");
}
}
if( $kappa_mat ) {
$self->set_KappaMatrix($kappa_mat);
}
if( $alpha_mat ) {
$self->set_AlphaMatrix($alpha_mat);
}
if( $input_params ) {
if( ref($input_params) !~ /HASH/i ) {
$self->warn("Must provide a valid hash object for input_params\n");
} else {
while( my ($p,$v) = each %$input_params ) {
$self->set_input_parameter($p,$v);
}
}
}
$self->reset_rst_seqs;
if( $rst ) {
if( ref($rst) =~ /ARRAY/i ) {
for ( @$rst ) {
$self->add_rst_seq($_);
}
} else {
$self->warn("Need a valid array ref for -rst option\n");
}
}
if( defined $rst_persite ) {
$self->set_rst_persite($rst_persite);
}
$self->reset_rst_trees;
if( $rst_trees ) {
if( ref($rst_trees) =~ /ARRAY/i ) {
for ( @$rst_trees ) {
$self->add_rst_tree($_);
}
} else {
$self->warn("Need a valid array ref for -rst_trees option\n");
}
}
return $self;
}
=head2 next_tree
Title : next_tree
Usage : my $tree = $factory->next_tree;
Function: Get the next tree from the factory
Returns : L<Bio::Tree::TreeI>
Args : none
=cut
sub next_tree{
my ($self,@args) = @_;
return $self->{'_trees'}->[$self->{'_treeiterator'}++] || undef;
}
=head2 get_trees
Title : get_trees
Usage : my @trees = $result->get_trees;
Function: Get all the parsed trees as an array
Returns : Array of trees
Args : none
=cut
sub get_trees{
my ($self) = @_;
return @{$self->{'_trees'} || []};
}
=head2 rewind_tree_iterator
Title : rewind_tree_iterator
Usage : $result->rewind_tree_iterator()
Function: Rewinds the tree iterator so that next_tree can be
called again from the beginning
Returns : none
Args : none
=cut
sub rewind_tree_iterator {
shift->{'_treeiterator'} = 0;
}
=head2 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>
=cut
sub add_tree{
my ($self,$tree) = @_;
if( $tree && ref($tree) && $tree->isa('Bio::Tree::TreeI') ) {
push @{$self->{'_trees'}},$tree;
}
return scalar @{$self->{'_trees'}};
}
=head2 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)
=cut
sub set_MLmatrix{
my ($self,$mat) = @_;
return unless ( defined $mat );
if( ref($mat) !~ /ARRAY/i ) {
$self->warn("Did not provide a valid 2D Array reference for set_MLmatrix");
return;
}
$self->{'_mlmatrix'} = $mat;
}
=head2 get_MLmatrix
Title : get_MLmatrix
Usage : my $mat = $result->get_MLmatrix()
Function: Get the ML matrix
Returns : 2D Array reference
Args : none
=cut
sub get_MLmatrix{
my ($self,@args) = @_;
return $self->{'_mlmatrix'};
}
=head2 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)
=cut
sub set_NGmatrix{
my ($self,$mat) = @_;
return unless ( defined $mat );
if( ref($mat) !~ /ARRAY/i ) {
$self->warn("Did not provide a valid 2D Array reference for set_NGmatrix");
return;
}
$self->{'_ngmatrix'} = $mat;
}
=head2 get_NGmatrix
Title : get_NGmatrix
Usage : my $mat = $result->get_NGmatrix()
Function: Get the Nei & Gojobori matrix
Returns : 2D Array reference
Args : none
=cut
sub get_NGmatrix{
my ($self,@args) = @_;
return $self->{'_ngmatrix'};
}
=head2 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>
=cut
sub add_seq{
my ($self,$seq) = @_;
if( $seq ) {
unless( $seq->isa("Bio::PrimarySeqI") ) {
$self->warn("Must provide a valid Bio::PrimarySeqI to add_seq");
return;
}
push @{$self->{'_seqs'}},$seq;
}
}
=head2 reset_seqs
Title : reset_seqs
Usage : $result->reset_seqs
Function: Reset the OTU seqs stored
Returns : none
Args : none
=cut
sub reset_seqs{
my ($self) = @_;
$self->{'_seqs'} = [];
}
=head2 get_seqs
Title : get_seqs
Usage : my @otus = $result->get_seqs
Function: Get the seqs Bio::PrimarySeq (OTU = Operational Taxonomic Unit)
Returns : Array of Bio::PrimarySeq
Args : None
See also : L<Bio::PrimarySeq>
=cut
sub get_seqs{
my ($self) = @_;
return @{$self->{'_seqs'}};
}
=head2 set_codon_pos_basefreq
Title : set_codon_pos_basefreq
Usage : $result->set_codon_pos_basefreq(@freqs)
Function: Set the codon position base frequencies
Returns : none
Args : Array of length 3 where each slot has a hashref
keyed on DNA base
=cut
sub set_codon_pos_basefreq {
my ($self,@codonpos) = @_;
if( scalar @codonpos != 3 ) {
$self->warn("invalid array to set_codon_pos_basefreq, must be an array of length 3");
return;
}
foreach my $pos ( @codonpos ) {
if( ref($pos) !~ /HASH/i ||
! exists $pos->{'A'} ) {
$self->warn("invalid array to set_codon_pos_basefreq, must be an array with hashreferences keyed on DNA bases, C,A,G,T");
}
}
$self->{'_codonposbasefreq'} = [@codonpos];
}
=head2 get_codon_pos_basefreq
Title : get_codon_pos_basefreq
Usage : my @basepos = $result->get_codon_pos_basefreq;
Function: Get the codon position base frequencies
Returns : Array of length 3 (each codon position), each
slot is a hashref keyed on DNA bases, the values are
the frequency of the base at that position for all sequences
Args : none
Note : The array starts at 0 so position '1' is in position '0'
of the array
=cut
sub get_codon_pos_basefreq{
my ($self) = @_;
return @{$self->{'_codonposbasefreq'}};
}
=head2 version
Title : version
Usage : $obj->version($newval)
Function: Get/Set version
Returns : value of version
Args : newvalue (optional)
=cut
sub version{
my $self = shift;
$self->{'_version'} = shift if @_;
return $self->{'_version'};
}
=head2 seqfile
Title : seqfile
Usage : $obj->seqfile($newval)
Function: Get/Set seqfile
Returns : value of seqfile
Args : newvalue (optional)
=cut
sub seqfile{
my $self = shift;
$self->{'_seqfile'} = shift if @_;
return $self->{'_seqfile'};
}
=head2 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)
=cut
sub model{
my $self = shift;
return $self->{'_model'} = shift if @_;
return $self->{'_model'};
}
=head2 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
: }
=cut
sub patterns{
my $self = shift;
return $self->{'_patterns'} = shift if @_;
return $self->{'_patterns'};
}
=head2 set_AAFreqs
Title : set_AAFreqs
Usage : $result->set_AAFreqs(\%aafreqs);
Function: Get/Set AA freqs
Returns : none
Args : Hashref, keys are the sequence names, each points to a hashref
which in turn has keys which are the amino acids
=cut
sub set_AAFreqs{
my ($self,$aafreqs) = @_;
if( $aafreqs && ref($aafreqs) =~ /HASH/i ) {
foreach my $seqname ( keys %{$aafreqs} ) {
$self->{'_aafreqs'}->{$seqname} = $aafreqs->{$seqname};
}
}
}
=head2 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
=cut
sub get_AAFreqs{
my ($self,$seqname) = @_;
if( $seqname ) {
return $self->{'_aafreqs'}->{$seqname} || {};
} else {
return $self->{'_aafreqs'};
}
}
=head2 set_NTFreqs
Title : set_NTFreqs
Usage : $result->set_NTFreqs(\%aafreqs);
Function: Get/Set NT freqs
Returns : none
Args : Hashref, keys are the sequence names, each points to a hashref
which in turn has keys which are the amino acids
=cut
sub set_NTFreqs{
my ($self,$freqs) = @_;
if( $freqs && ref($freqs) =~ /HASH/i ) {
foreach my $seqname ( keys %{$freqs} ) {
$self->{'_ntfreqs'}->{$seqname} = $freqs->{$seqname};
}
}
}
=head2 get_NTFreqs
Title : get_NTFreqs
Usage : my %all_nt_freqs = $result->get_NTFreqs()
OR
my %seq_nt_freqs = $result->get_NTFreqs($seqname)
Function: Get the NT freqs, either for every sequence or just
for a specific sequence
The average nt freqs for the entire set are also available
for the sequence named 'Average'
Returns : Hashref
Args : (optional) sequence name to retrieve nt freqs for
=cut
sub get_NTFreqs{
my ($self,$seqname) = @_;
if( $seqname ) {
return $self->{'_ntfreqs'}->{$seqname} || {};
} else {
return $self->{'_ntfreqs'};
}
}
=head2 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
$value stat value
=cut
sub add_stat{
my ($self,$stat,$value) = @_;
return if( ! defined $stat || !defined $value );
$self->{'_stats'}->{$stat} = $value;
return;
}
=head2 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
=cut
sub get_stat{
my ($self,$statname) = @_;
return $self->{'_stats'}->{$statname};
}
=head2 get_stat_names
Title : get_stat_names
Usage : my @names = $result->get_stat_names;
Function: Get the stat names stored for the result
Returns : array of names
Args : none
=cut
sub get_stat_names{
my ($self) = @_;
return keys %{$self->{'_stats'} || {}};
}
=head2 get_AADistMatrix
Title : get_AADistMatrix
Usage : my $mat = $obj->get_AADistMatrix()
Function: Get AADistance Matrix
Returns : value of AADistMatrix (Bio::Matrix::PhylipDist)
Args : none
=cut
sub get_AADistMatrix{
my $self = shift;
return $self->{'_AADistMatix'};
}
=head2 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)
=cut
sub set_AADistMatrix{
my ($self,$d) = @_;
if( ! $d ||
! ref($d) ||
! $d->isa('Bio::Matrix::PhylipDist') ) {
$self->warn("Must provide a valid Bio::Matrix::MatrixI for set_AADistMatrix");
}
$self->{'_AADistMatix'} = $d;
return;
}
=head2 get_AAMLDistMatrix
Title : get_AAMLDistMatrix
Usage : my $mat = $obj->get_AAMLDistMatrix()
Function: Get AAMLDistance Matrix
Returns : value of AAMLDistMatrix (Bio::Matrix::PhylipDist)
Args : none
=cut
sub get_AAMLDistMatrix{
my $self = shift;
return $self->{'_AAMLDistMatix'};
}
=head2 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)
=cut
sub set_AAMLDistMatrix{
my ($self,$d) = @_;
if( ! $d ||
! ref($d) ||
! $d->isa('Bio::Matrix::PhylipDist') ) {
$self->warn("Must provide a valid Bio::Matrix::MatrixI for set_AAMLDistMatrix");
}
$self->{'_AAMLDistMatix'} = $d;
return;
}
=head2 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
=cut
sub add_NSSite_result{
my ($self,$model) = @_;
if( defined $model ) {
push @{$self->{'_nssiteresult'}}, $model;
}
return scalar @{$self->{'_nssiteresult'}};
}
=head2 get_NSSite_results
Title : get_NSSite_results
Usage : my @results = @{$self->get_NSSite_results};
Function: Get the reference to the array of NSSite_results
Returns : Array of PAML::ModelResult results
Args : none
=cut
sub get_NSSite_results{
my ($self) = @_;
return @{$self->{'_nssiteresult'} || []};
}
=head2 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)
=cut
sub set_CodonFreqs{
my $self = shift;
return $self->{'_codonfreqs'} = shift if @_;
return $self->{'_codonfreqs'};
}
=head2 get_CodonFreqs
Title : get_CodonFreqs
Usage : my @codon_freqs = $result->get_CodonFreqs()
Function: Get the Codon freqs
Returns : Array
Args : none
=cut
sub get_CodonFreqs{
my ($self) = @_;
return @{$self->{'_codonfreqs'} || []};
}
=head2 BASEML Relavent values
=cut
=head2 get_KappaMatrix
Title : get_KappaMatrix
Usage : my $mat = $obj->get_KappaMatrix()
Function: Get KappaDistance Matrix
Returns : value of KappaMatrix (Bio::Matrix::PhylipDist)
Args : none
=cut
sub get_KappaMatrix{
my $self = shift;
return $self->{'_KappaMatix'};
}
=head2 set_KappaMatrix
Title : set_KappaMatrix
Usage : $obj->set_KappaMatrix($mat);
Function: Set the KappaDistrance Matrix (Bio::Matrix::PhylipDist)
Returns : none
Args : KappaDistrance Matrix (Bio::Matrix::PhylipDist)
=cut
sub set_KappaMatrix{
my ($self,$d) = @_;
if( ! $d ||
! ref($d) ||
! $d->isa('Bio::Matrix::PhylipDist') ) {
$self->warn("Must provide a valid Bio::Matrix::MatrixI for set_NTDistMatrix");
}
$self->{'_KappaMatix'} = $d;
return;
}
=head2 get_AlphaMatrix
Title : get_AlphaMatrix
Usage : my $mat = $obj->get_AlphaMatrix()
Function: Get AlphaDistance Matrix
Returns : value of AlphaMatrix (Bio::Matrix::PhylipDist)
Args : none
=cut
sub get_AlphaMatrix{
my $self = shift;
return $self->{'_AlphaMatix'};
}
=head2 set_AlphaMatrix
Title : set_AlphaMatrix
Usage : $obj->set_AlphaMatrix($mat);
Function: Set the AlphaDistrance Matrix (Bio::Matrix::PhylipDist)
Returns : none
Args : AlphaDistrance Matrix (Bio::Matrix::PhylipDist)
=cut
sub set_AlphaMatrix{
my ($self,$d) = @_;
if( ! $d ||
! ref($d) ||
! $d->isa('Bio::Matrix::PhylipDist') ) {
$self->warn("Must provide a valid Bio::Matrix::MatrixI for set_NTDistMatrix");
}
$self->{'_AlphaMatix'} = $d;
return;
}
=head2 set_input_parameter
Title : set_input_parameter
Usage : $obj->set_input_parameter($p,$vl);
Function: Set an Input Parameter
Returns : none
Args : $parameter and $value
=cut
sub set_input_parameter{
my ($self,$p,$v) = @_;
return unless defined $p;
$self->{'_input_parameters'}->{$p} = $v;
}
=head2 get_input_parameters
Title : get_input_parameters
Usage : $obj->get_input_parameters;
Function: Get Input Parameters
Returns : Hash of key/value pairs
Args : none
=cut
sub get_input_parameters{
my ($self) = @_;
return %{$self->{'_input_parameters'} || {}};
}
=head2 reset_input_parameters
Title : reset_input_parameters
Usage : $obj->reset_input_parameters;
Function: Reset the Input Parameters hash
Returns : none
Args : none
=cut
sub reset_input_parameters{
my ($self) = @_;
$self->{'_input_parameters'} = {};
}
=head1 Reconstructed Ancestral State relevant options
=head2 add_rst_seq
Title : add_rst_seq
Usage : $obj->add_rst_seq($seq)
Function: Add a Bio::PrimarySeq to the RST Result
Returns : none
Args : Bio::PrimarySeqI
See also : L<Bio::PrimarySeqI>
=cut
sub add_rst_seq{
my ($self,$seq) = @_;
if( $seq ) {
unless( $seq->isa("Bio::PrimarySeqI") ) {
$self->warn("Must provide a valid Bio::PrimarySeqI to add_rst_seq");
return;
}
push @{$self->{'_rstseqs'}},$seq;
}
}
=head2 reset_rst_seqs
Title : reset_rst_seqs
Usage : $result->reset_rst_seqs
Function: Reset the RST seqs stored
Returns : none
Args : none
=cut
sub reset_rst_seqs{
my ($self) = @_;
$self->{'_rstseqs'} = [];
}
=head2 get_rst_seqs
Title : get_rst_seqs
Usage : my @otus = $result->get_rst_seqs
Function: Get the seqs Bio::PrimarySeq
Returns : Array of Bio::PrimarySeqI objects
Args : None
See also : L<Bio::PrimarySeq>
=cut
sub get_rst_seqs{
my ($self) = @_;
return @{$self->{'_rstseqs'} || []};
}
=head2 add_rst_tree
Title : add_rst_tree
Usage : $obj->add_rst_tree($tree)
Function: Add a Bio::Tree::TreeI to the RST Result
Returns : none
Args : Bio::Tree::TreeI
See also : L<Bio::Tree::TreeI>
=cut
sub add_rst_tree{
my ($self,$tree) = @_;
if( $tree ) {
unless( $tree->isa("Bio::Tree::TreeI") ) {
$self->warn("Must provide a valid Bio::Tree::TreeI to add_rst_tree not $tree");
return;
}
push @{$self->{'_rsttrees'}},$tree;
}
}
=head2 reset_rst_trees
Title : reset_rst_trees
Usage : $result->reset_rst_trees
Function: Reset the RST trees stored
Returns : none
Args : none
=cut
sub reset_rst_trees{
my ($self) = @_;
$self->{'_rsttrees'} = [];
}
=head2 get_rst_trees
Title : get_rst_trees
Usage : my @otus = $result->get_rst_trees
Function: Get the trees Bio::Tree::TreeI
Returns : Array of Bio::Tree::TreeI objects
Args : None
See also : L<Bio::Tree::TreeI>
=cut
sub get_rst_trees{
my ($self) = @_;
return @{$self->{'_rsttrees'} || []};
}
=head2 set_rst_persite
Title : set_rst_persite
Usage : $obj->set_rst_persite($newval)
Function: Get/Set the per-site RST values
Returns : value of set_rst_persite (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub set_rst_persite{
my $self = shift;
return $self->{'_rstpersite'} = shift if @_;
return $self->{'_rstpersite'};
}
=head2 get_rst_persite
Title : get_rst_persite
Usage : my @rst_persite = @{$result->get_rst_persite()}
Function: Get the per-site RST values
Returns : Array
Args : none
=cut
sub get_rst_persite{
my ($self) = @_;
return $self->{'_rstpersite'} || [];
}
1;