Raw content of Bio::Tools::Phylo::Molphy::Result # $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;