GO::Model::Root(3pm) User Contributed Perl Documentation GO::Model::Root(3pm)NAME
GO::Model::Root - base class for all GO::Model objects
DESCRIPTION
base class for all GO::Model objects
Constructors
new
Constructor: Basically just calls _initialize(). Most subclasses should not need to override new, but instead should override
_initialize().
If _initialize() fails , the procedure will die
WARNING: This procedure will die if initialization is unsuccessful. Use an eval statement to catch such exceptions.
obj_factory
Usage - $obj->obj_factory->create_new_term_object($h);
Alias - apph
Returns - L<GO::ObjFactory>
Args - none
sprint_self
Prints out a description of the object to a string.
dump
dumps the object (can be read back in with eval)
namespace
Usage - print $term->namespace(); # getting the type
Usage - $term->namespace("molecular_function"); # setting the type
Alias - type
Alias - term_type
Alias - category
Alias - ontology
Returns - string representing type
Args - string represnting type [optional]
The OBO namespace for the GO::Model::Term or GO::Model::Relationship
_cleanup
Called at object destruction time. Should be overridden to perform cleanup tasks.
perl v5.14.2 2013-02-07 GO::Model::Root(3pm)
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GO::Model::Xref(3pm) User Contributed Perl Documentation GO::Model::Xref(3pm)NAME
GO::Model::Xref - cross reference to an external database
SYNOPSIS
my $xrefs = $term->dbxref_list();
foreach my $xref (@$xrefs) P
printf "Term %s has an xref %s:%s
",
$term->name, $xref->xref_key, $xref->dbname;
}
DESCRIPTION
represents a cross reference to an external database. an Xref is made up of a key (ie the accession number, or whatever the value of the
unique field being keyed off of is) and a database name. this should theorerically be enough to uniquely identify any databased entity.
NOTES
Like all the GO::Model::* classes, this uses accessor methods to get or set the attributes. by using the accessor method without any
arguments gets the value of the attribute. if you pass in an argument, then the attribuet will be set according to that argument.
for instance
# this sets the value of the attribute
$my_object->attribute_name("my value");
# this gets the value of the attribute
$my_value = $my_object->attribute_name();
xref_key
Alias - acc
Alias - accession
Usage -
Returns -
Args -
accessor: gets/sets the key/id of the cross reference
xref_keytype
Usage -
Returns -
Args -
accessor: gets/sets the key/id type of the cross reference
as_str
Usage -
Returns -
Args -
xref_dbname
Alias - dbname
Usage -
Returns -
Args -
accessor: gets/sets the database name of the cross reference
must be a valid database name
xref_desc
Alias - name
Usage -
Returns -
Args -
accessor: gets/sets the description of the accession no
useful for interpro
to_xml
Usage - print $xref->to_xml()
Returns - string
Args - indent [integer]
XML representation; you probably shouldnt call this directly, this will be called by entities that own xrefs
perl v5.14.2 2013-02-07 GO::Model::Xref(3pm)
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