Raw content of Bio::Tools::Phylo::Molphy::Result
<![CDATA[# $Id: Result.pm,v 1.2 2002/10/22 07:45:24 lapp Exp $
#
# BioPerl module for Bio::Tools::Phylo::Molphy::Result
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Phylo::Molphy::Result - DESCRIPTION of 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
Email jason@bioperl.org
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::Molphy::Result;
use vars qw(@ISA);
use strict;
# Object preamble - inherits from Bio::Root::Root
use Bio::Root::Root;
@ISA = qw(Bio::Root::Root );
=head2 new
Title : new
Usage : my $obj = new Bio::Tools::Phylo::Molphy::Result();
Function: Builds a new Bio::Tools::Phylo::Molphy::Result object
Returns : Bio::Tools::Phylo::Molphy::Result
Args :
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($trees,
$smat,$tmat,$freq,
$model, $sspace,
) = $self->_rearrange([qw(TREES SUBSTITUTION_MATRIX
TRANSITION_MATRIX FREQUENCIES
MODEL SEARCH_SPACE)], @args);
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);
}
}
}
# initialize things through object methods to be a good
# little OO programmer
if( ref($smat) =~ /HASH/i ) {
$self->substitution_matrix($smat);
}
if( ref($tmat) =~ /HASH/i ) {
$self->transition_probability_matrix($tmat);
}
if( ref($freq) =~ /HASH/i ) {
$self->residue_frequencies($freq);
}
$model && $self->model($model);
$sspace && $self->search_space($sspace);
$self->{'_treeiterator'} = 0;
return $self;
}
=head2 model
Title : model
Usage : $obj->model($newval)
Function:
Returns : value of model
Args : newvalue (optional)
=cut
sub model{
my ($self,$value) = @_;
if( defined $value) {
$self->{'model'} = $value;
}
return $self->{'model'};
}
=head2 substitution_matrix
Title : substitution_matrix
Usage : my $smat = $result->subsitution_matrix;
Function: Get the relative substitution matrix calculated in the ML procedure
Returns : reference to hash of hashes where key is the aa/nt name and value
is another hash ref which contains keys for all the aa/nt
possibilities
Args : none
=cut
sub substitution_matrix{
my ($self,$val) = @_;
if(defined $val ) {
if( ref($val) =~ /HASH/ ) {
foreach my $v (values %{$val} ) {
if( ref($v) !~ /HASH/i ) {
$self->warn("Must be a valid hashref of hashrefs for substition_matrix");
return undef;
}
}
$self->{'_substitution_matrix'} = $val;
} else {
$self->warn("Must be a valid hashref of hashrefs for substition_matrix");
return undef;
}
}
return $self->{'_substitution_matrix'};
}
=head2 transition_probability_matrix
Title : transition_probability_matrix
Usage : my $matrixref = $molphy->transition_probablity_matrix();
Function: Gets the observed transition probability matrix
Returns : hash of hashes of aa/nt transition to each other aa/nt
Args : none
=cut
sub transition_probability_matrix{
my ($self,$val) = @_;
if(defined $val ) {
if( ref($val) =~ /HASH/ ) {
foreach my $v (values %{$val} ) {
if( ref($v) !~ /HASH/i ) {
$self->warn("Must be a valid hashref of hashrefs for transition_probability_matrix");
return undef;
}
}
$self->{'_TPM'} = $val;
} else {
$self->warn("Must be a valid hashref of hashrefs for transition_probablity_matrix");
return undef;
}
}
# fix this for nucml where there are 2 values (one is just a transformation
# of the either, but how to represent?)
return $self->{'_TPM'};
}
=head2 residue_frequencies
Title : residue_frequencies
Usage : my %data = $molphy->residue_frequencies()
Function: Get the modeled and expected frequencies for
each of the residues in the sequence
Returns : hash of either aa (protml) or nt (nucml) frequencies
each key will point to an array reference where
1st slot is model's expected frequency
2nd slot is observed frequency in the data
$hash{'A'}->[0] =
Args : none
=cut
#'
sub residue_frequencies{
my ($self,$val) = @_;
if(defined $val ) {
if( ref($val) =~ /HASH/ ) {
$self->{'_residue_frequencies'} = $val;
} else {
$self->warn("Must be a valid hashref of hashrefs for residue_frequencies");
}
}
return %{$self->{'_residue_frequencies'}};
}
=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 search_space
Title : search_space
Usage : $obj->search_space($newval)
Function:
Returns : value of search_space
Args : newvalue (optional)
=cut
sub search_space{
my ($self,$value) = @_;
if( defined $value) {
$self->{'search_space'} = $value;
}
return $self->{'search_space'};
}
1;
]]>