Bio::Tools::Phylo::PAML::Result - A PAML result set object # 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; This is a container object for PAML Results.

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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/ Email jason@bioperl.org Email amackey@virginia.edu Describe contact details here Additional contributors names and emails here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $obj = new Bio::Tools::Phylo::PAML::Result(%data); Function: Builds a new Bio::Tools::Phylo::PAML::Result object Returns : Bio::Tools::Phylo::PAML::Result Args : -trees => array reference of L<Bio::Tree::TreeI> objects -MLmatrix => ML matrix -seqs => array reference of L<Bio::PrimarySeqI> objects -codonpos => array reference of codon positions -codonfreq => array reference of codon frequencies -version => version string -model => model string -patterns => hashref with the fields '-patterns', '-ns', '-ls' -stats => array ref of misc stats (optional) -aafreq => Hashref of AA frequencies (only for AAML) -aadistmat => Bio::Matrix::PhylipDist (only for AAML) -aamldistmat => Bio::Matrix::PhylipDist (only for pairwise AAML) -NSSitesresult => arrayref of PAML::ModelResult =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($trees,$mlmat,$seqs,$ngmatrix, $codonpos,$codonfreq,$version, $model,$patterns, $stats, $aafreq, $aadistmat, $aamldistmat, $NSSitesresults ) = $self->_rearrange([qw(TREES MLMATRIX SEQS NGMATRIX CODONPOS CODONFREQ VERSION MODEL PATTERNS STATS AAFREQ AADISTMAT AAMLDISTMAT NSSITESRESULTS)], @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( $codonfreq ) { if( ref($codonfreq) =~ /ARRAY/i ) { $self->set_CodonFreqs($codonfreq); } else { $self->warn("Must have provided a valid array reference to initialize 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; $self->model($model) if defined $model; if( defined $patterns ) { if( ref($patterns) =~ /HASH/i ) { $self->patterns($patterns); } else { $self->warn("Must have provided a valid array reference to initialize patterns"); } } $self->{'_aafreqs'} = {}; if( $aafreq ) { if( ref($aafreq) =~ /HASH/i ) { $self->set_AAFreqs($aafreq); } else { $self->warn("Must have provided 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 have provided 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); } } } return $self; }

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