Bio::Phylo::Project - Container for related data
use Bio::Phylo::Factory; my $fac = Bio::Phylo::Factory->new; my $proj = $fac->create_project; my $taxa = $fac->create_taxa; $proj->insert($taxa); $proj->insert($fac->create_matrix->set_taxa($taxa)); $proj->insert($fac->create_forest->set_taxa($taxa)); print $proj->to_xml;
The project module is used to collect taxa blocks, tree blocks and matrices.
Project constructor.
Type : Constructor Title : merge Usage : my $project = Bio::Phylo::Project->merge( @projects ) Function: Populates a Bio::Phylo::Project object from a list of projects Returns : A Bio::Phylo::Project object. Args : A list of Bio::Phylo::Project objects to be merged
Type : Constructor Title : set_datasource Usage : $project->set_datasource( -file => $file, -format => 'nexus' ) Function: Populates a Bio::Phylo::Project object from a data source Returns : A Bio::Phylo::Project object. Args : Arguments as must be passed to Bio::Phylo::IO::parse
Resets all xml ids to default values
Type : Mutator Title : reset_xml_ids Usage : $project->reset_xml_ids Function: Resets all xml ids to default values Returns : A Bio::Phylo::Project object. Args : None
Getter for taxa objects
Type : Accessor Title : get_taxa Usage : my $taxa = $proj->get_taxa; Function: Getter for taxa objects Returns : An array reference of taxa objects Args : NONE.
Getter for forest objects
Type : Accessor Title : get_forests Usage : my $forest = $proj->get_forests; Function: Getter for forest objects Returns : An array reference of forest objects Args : NONE.
Getter for matrix objects
Type : Accessor Title : get_matrices Usage : my $matrix = $proj->get_matrices; Function: Getter for matrix objects Returns : An array reference of matrix objects Args : NONE.
Gets all items of the specified type, recursively. This method can be used to get things like all the trees in all the forest objects as one flat list (or, indeed, all nodes, all taxon objects, etc.)
Type : Accessor Title : get_items Usage : my @nodes = @{ $proj->get_items(_NODE_) }; Function: Getter for items of specified type Returns : An array reference of objects Args : A type constant as defined in Bio::Phylo::Util::CONSTANT
Type : Serializer Title : doc Usage : $proj->get_document() Function: Creates a DOM Document object, containing the present state of the project by default Returns : a Document object Args : a DOM factory object Optional: pass 1 to obtain a document node without content
Retrieves attributes for the element.
Type : Accessor Title : get_attributes Usage : my %attrs = %{ $obj->get_attributes }; Function: Gets the xml attributes for the object; Returns : A hash reference Args : None. Comments: throws ObjectMismatch if no linked taxa object can be found
By default, all XMLWritable objects are identifiable when serialized, i.e. they have a unique id attribute. However, in some cases a serialized object may not have an id attribute (governed by the nexml schema). This method indicates whether that is the case.
Type : Test Title : is_identifiable Usage : if ( $obj->is_identifiable ) { ... } Function: Indicates whether IDs are generated Returns : BOOLEAN Args : NONE
Serializes invocant to XML.
Type : XML serializer Title : to_xml Usage : my $xml = $obj->to_xml; Function: Serializes $obj to xml Returns : An xml string Args : Same arguments as can be passed to individual contained objects
Serializes invocant to NEXUS.
Type : NEXUS serializer Title : to_nexus Usage : my $nexus = $obj->to_nexus; Function: Serializes $obj to nexus Returns : An nexus string Args : Same arguments as can be passed to individual contained objects
Type : Serializer Title : to_dom Usage : $node->to_dom Function: Generates a DOM subtree from the invocant and its contained objects Returns : an XML::LibXML::Element object Args : a DOM factory object
There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.
The Bio::Phylo::Project object inherits from the Bio::Phylo::Listable object. Look there for more methods applicable to the project object.
Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com.
If you use Bio::Phylo in published research, please cite it:
Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63. http://dx.doi.org/10.1186/1471-2105-12-63
To install Bio::Phylo, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Phylo
CPAN shell
perl -MCPAN -e shell install Bio::Phylo
For more information on module installation, please visit the detailed CPAN module installation guide.