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| Bio::Phylo::Project(3) | User Contributed Perl Documentation | Bio::Phylo::Project(3) |
NAME
Bio::Phylo::Project - Container for related dataSYNOPSIS
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;
DESCRIPTION
The project module is used to collect taxa blocks, tree blocks and matrices.METHODS
MUTATORS
- merge()
- 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 - set_datasource()
- Project constructor.
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 - reset_xml_ids()
- 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
ACCESSORS
- get_taxa()
- 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. - get_forests()
- 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. - get_matrices()
- 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. - get_items()
- 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 - get_document()
-
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 - get_attributes()
- 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 - is_identifiable()
- 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
SERIALIZERS
- to_xml()
- 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 - to_nexus()
- 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 - to_dom()
-
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
SEE ALSO
There is a mailing list at <https://groups.google.com/forum/#!forum/bio-phylo> for any user or developer questions and discussions.- Bio::Phylo::Listable
- The Bio::Phylo::Project object inherits from the Bio::Phylo::Listable object. Look there for more methods applicable to the project object.
- Bio::Phylo::Manual
- Also see the manual: Bio::Phylo::Manual and <http://rutgervos.blogspot.com>.
CITATION
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>
| 2017-10-30 | perl v5.32.1 |
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