Raw content of Bio::Tools::Phylo::PAML::Result
<![CDATA[# Result.pm,v 1.3 2002/06/20 18:50:39 amackey Exp
#
# BioPerl module for Bio::Tools::Phylo::PAML::Result
#
# Cared for by Jason Stajich <jason@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
Give standard usage here
=head1 DESCRIPTION
Describe the object here
=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/MailList.shtml - About the mailing lists
=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:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Jason Stajich, Aaron Mackey
Email jason@bioperl.org
Email amackey@virginia.edu
Describe contact details here
=head1 CONTRIBUTORS
Additional contributors names and emails here
=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 vars qw(@ISA);
use strict;
use Bio::Root::Root;
use Bio::AnalysisResultI;
@ISA = qw(Bio::Root::Root Bio::AnalysisResultI);
=head2 new
Title : new
Usage : my $obj = new Bio::Tools::Phylo::PAML::Result(%data);
Function: Builds a new Bio::Tools::Phylo::PAML::Result object
Returns : Bio::Tools::Phylo::PAML::Result
Args : -trees => array reference of L<Bio::Tree::TreeI> objects
-MLmatrix => ML matrix
.... MORE ARGUMENTS LISTED HERE BY AARON AND JASON
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($trees,$mlmat,$seqs,$ngmatrix,
$codonpos,$codonfreq,$version) = $self->_rearrange([qw(TREES MLMATRIX
SEQS NGMATRIX
CODONPOS CODONFREQ
VERSION)], @args);
$self->reset_seqs;
if( $trees ) {
if(ref($trees) !~ /ARRAY/i ) {
$self->warn("Must have provided 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 have provided a valid array reference to initialize MLmatrix");
} else {
$self->set_MLmatrix($mlmat);
}
}
if( $seqs ) {
if( ref($seqs) !~ /ARRAY/i ) {
$self->warn("Must have provided 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 have provided a valid array reference to initialize NGmatrix");
} else {
$self->set_NGmatrix($ngmatrix);
}
}
if( $codonfreq ) {
}
if( $codonpos ) {
if( ref($codonpos) !~ /ARRAY/i ) {
$self->warn("Must have provided a valid array reference to initialize codonpos");
} else {
$self->set_codon_pos_basefreq(@$codonpos);
}
}
$self->version($version) if defined $version;
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 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
=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'};
}
1;
]]>