Bio::Tools::Phylo::PAML
Result
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Summary
Bio::Tools::Phylo::PAML::Result - A PAML result set object
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
Give standard usage here
Description
Describe the object here
Methods
Methods description
Title : add_seq
Usage : $obj->add_seq($seq)
Function: Add a Bio::PrimarySeq to the Result
Returns : none
Args : Bio::PrimarySeqI
See also : Bio::PrimarySeqI |
Title : add_tree
Usage : $result->add_tree($tree);
Function: Adds a tree
Returns : integer which is the number of trees stored
Args : Bio::Tree::TreeI |
Title : get_MLmatrix
Usage : my $mat = $result->get_MLmatrix()
Function: Get the ML matrix
Returns : 2D Array reference
Args : none |
Title : get_NGmatrix
Usage : my $mat = $result->get_NGmatrix()
Function: Get the Nei & Gojobori matrix
Returns : 2D Array reference
Args : none |
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 |
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 : Bio::PrimarySeq |
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 Bio::Tree::TreeI objects
-MLmatrix => ML matrix
.... MORE ARGUMENTS LISTED HERE BY AARON AND JASON |
Title : next_tree
Usage : my $tree = $factory->next_tree;
Function: Get the next tree from the factory
Returns : Bio::Tree::TreeI
Args : none |
Title : reset_seqs
Usage : $result->reset_seqs
Function: Reset the OTU seqs stored
Returns : none
Args : none |
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) |
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) |
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 |
Title : version
Usage : $obj->version($newval)
Function: Get/Set version
Returns : value of version
Args : newvalue (optional) |
Methods code
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'}},$seq;
}} | sub add_tree
{ my ($self,$tree) = @_;
if( $tree && ref($tree) && $tree->isa('Bio::Tree::TreeI') ) {
push @{$self->{'_trees'}},$tree;
}
return scalar @{$self->{'_trees'}};} | sub get_MLmatrix
{ my ($self,@args) = @_;
return $self->{'_mlmatrix'};} | sub get_NGmatrix
{ my ($self,@args) = @_;
return $self->{'_ngmatrix'};} | sub get_codon_pos_basefreq
{ my ($self) = @_;
return @{$self->{'_codonposbasefreq'}};} | sub get_seqs
{ my ($self) = @_;
return @{$self->{'_seqs'}};} | sub new
{ my($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 $self;} | sub next_tree
{ my ($self,@args) = @_;
return $self->{'_trees'}->[$self->{'_treeiterator'}++] || undef;} | sub reset_seqs
{ my ($self) = @_;
$self->{'_seqs'} = [];} | sub rewind_tree_iterator
{ shift->{'_treeiterator'} = 0;} | sub set_MLmatrix
{ my ($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'} = $mat;} | sub set_NGmatrix
{ my ($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'} = $mat;} | sub set_codon_pos_basefreq
{ my ($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];} | sub version
{ my $self = shift;
$self->{'_version'} = shift if @_;
return $self->{'_version'};
}
1;} | General documentation
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
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/
| AUTHOR - Jason Stajich, Aaron Mackey | Top |
Additional contributors names and emails here
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
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