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Bio::Phylo::Project(3)User Contributed Perl DocumentatioBio::Phylo::Project(3)

NAME
       Bio::Phylo::Project - Container for related data

SYNOPSIS
	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>

perl v5.32.0			  2017-10-30		Bio::Phylo::Project(3)

NAME | SYNOPSIS | DESCRIPTION | METHODS | SEE ALSO | CITATION

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