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.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
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.\" ========================================================================
.\"
.IX Title "MAGE::Base 3pm"
.TH MAGE::Base 3pm "2018-10-24" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::MAGE::Base \- generic base class
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use Bio::MAGE::Base;
\&
\&  # create an empty instance
\&  my $obj = Bio::MAGE::Base\->new();
\&
\&  # create an instance and populate with data
\&  my $obj = Bio::MAGE::Base\->new(attr1=>$val1, attr2=>$val2);
\&
\&  # copy an existing instance
\&  my $obj_copy = $obj\->new();
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
The base class for all other Bio::MAGE classes
.SH "CLASS METHODS"
.IX Header "CLASS METHODS"
The following methods can all be called without first having an
instance of the class via the Namespace::Class\->\fImethodname()\fR
syntax, i.e. the class name \fBmust\fR be given as an argument to the
method.
.ie n .IP "$obj = class\->new(%params)" 4
.el .IP "\f(CW$obj\fR = class\->new(%params)" 4
.IX Item "$obj = class->new(%params)"
The \f(CW\*(C`new()\*(C'\fR method is the class constructor.
.Sp
\&\fBParameters\fR: if given a list of name/value parameters the
corresponding slots, attributes, or associations will have their
initial values set by the constructor.
.Sp
\&\fBReturn value\fR: It returns a reference to an object of the class.
.Sp
\&\fBSide effects\fR: It invokes the \f(CW\*(C`initialize()\*(C'\fR method if it is defined
by the class.
.PP
The following methods can all be called with either the
Namespace::Class\->\fImethodname()\fR and \f(CW$obj\fR\->\fImethodname()\fR syntaxes.
.ie n .IP "@names = \fIget_slot_names()\fR" 4
.el .IP "\f(CW@names\fR = \fIget_slot_names()\fR" 4
.IX Item "@names = get_slot_names()"
The \f(CW\*(C`get_slot_names()\*(C'\fR method is used to retrieve the name of all
slots defined for a given object.
.Sp
\&\fB\s-1NOTE\s0\fR: the list of names does not include attribute or association
names.
.Sp
\&\fBReturn value\fR: A list of the names of all slots defined for this class.
.Sp
\&\fBSide effects\fR: none
.ie n .IP "@name_list = \fIget_attribute_names()\fR" 4
.el .IP "\f(CW@name_list\fR = \fIget_attribute_names()\fR" 4
.IX Item "@name_list = get_attribute_names()"
returns the list of attribute data members for this class.
.ie n .IP "@name_list = \fIget_association_names()\fR" 4
.el .IP "\f(CW@name_list\fR = \fIget_association_names()\fR" 4
.IX Item "@name_list = get_association_names()"
returns the list of association data members for this class.
.ie n .IP "@class_list = \fIget_superclasses()\fR" 4
.el .IP "\f(CW@class_list\fR = \fIget_superclasses()\fR" 4
.IX Item "@class_list = get_superclasses()"
returns the list of superclasses for this class.
.ie n .IP "@class_list = \fIget_subclasses()\fR" 4
.el .IP "\f(CW@class_list\fR = \fIget_subclasses()\fR" 4
.IX Item "@class_list = get_subclasses()"
returns the list of subclasses for this class.
.ie n .IP "$name = \fIclass_name()\fR" 4
.el .IP "\f(CW$name\fR = \fIclass_name()\fR" 4
.IX Item "$name = class_name()"
Returns the full class name for this class.
.ie n .IP "$package_name = \fIpackage_name()\fR" 4
.el .IP "\f(CW$package_name\fR = \fIpackage_name()\fR" 4
.IX Item "$package_name = package_name()"
Returns the base package name (i.e. no 'namespace::') of the package
that contains this class.
.ie n .IP "%assns = \fIassociations()\fR" 4
.el .IP "\f(CW%assns\fR = \fIassociations()\fR" 4
.IX Item "%assns = associations()"
returns the association meta-information in a hash where the keys are
the association names and the values are \f(CW\*(C`Association\*(C'\fR objects that
provide the meta-information for the association.
.SH "INSTANCE METHODS"
.IX Header "INSTANCE METHODS"
These methods must be invoked with the direct object syntax using an
existing instance, i.e. \f(CW$object\fR\->\fImethod_name()\fR.
.ie n .IP "$obj_copy = $obj\->\fInew()\fR" 4
.el .IP "\f(CW$obj_copy\fR = \f(CW$obj\fR\->\fInew()\fR" 4
.IX Item "$obj_copy = $obj->new()"
When invoked with an existing object reference and not a class name,
the \f(CW\*(C`new()\*(C'\fR method acts as a copy constructor \- with the new object's
initial values set to be those of the existing object.
.Sp
\&\fBParameters\fR: No input parameters  are used in the copy  constructor,
the initial values are taken directly from the object to be copied.
.Sp
\&\fBReturn value\fR: It returns a reference to an object of the class.
.Sp
\&\fBSide effects\fR: It invokes the \f(CW\*(C`initialize()\*(C'\fR method if it is defined
by the class.
.ie n .IP "$obj\->set_slots(%parameters)" 4
.el .IP "\f(CW$obj\fR\->set_slots(%parameters)" 4
.IX Item "$obj->set_slots(%parameters)"
.PD 0
.ie n .IP "$obj\->set_slots(\e@name_list, \e@value_list)" 4
.el .IP "\f(CW$obj\fR\->set_slots(\e@name_list, \e@value_list)" 4
.IX Item "$obj->set_slots(@name_list, @value_list)"
.PD
The \f(CW\*(C`set_slots()\*(C'\fR method is used to set a number of slots at the same
time. It has two different invocation methods. The first takes a named
parameter list, and the second takes two array references.
.Sp
\&\fBReturn value\fR: none
.Sp
\&\fBSide effects\fR: will call \f(CW\*(C`croak()\*(C'\fR if a slot_name is used that the class
does not define.
.ie n .IP "$obj\->get_slots(@name_list)" 4
.el .IP "\f(CW$obj\fR\->get_slots(@name_list)" 4
.IX Item "$obj->get_slots(@name_list)"
The \f(CW\*(C`get_slots()\*(C'\fR method is used to get the values of a number of
slots at the same time.
.Sp
\&\fBReturn value\fR: a list of instance objects
.Sp
\&\fBSide effects\fR: none
.ie n .IP "$val = $obj\->set_slot($name,$val)" 4
.el .IP "\f(CW$val\fR = \f(CW$obj\fR\->set_slot($name,$val)" 4
.IX Item "$val = $obj->set_slot($name,$val)"
The \f(CW\*(C`set_slot()\*(C'\fR method sets the slot \f(CW$name\fR to the value \f(CW$val\fR
.Sp
\&\fBReturn value\fR: the new value of the slot, i.e. \f(CW$val\fR
.Sp
\&\fBSide effects\fR: none
.ie n .IP "$val = $obj\->get_slot($name)" 4
.el .IP "\f(CW$val\fR = \f(CW$obj\fR\->get_slot($name)" 4
.IX Item "$val = $obj->get_slot($name)"
The \f(CW\*(C`get_slot()\*(C'\fR method is used to get the values of a number of
slots at the same time.
.Sp
\&\fBReturn value\fR: a single slot value, or undef if the slot has not been
initialized.
.Sp
\&\fBSide effects\fR: none
.IP "throw" 4
.IX Item "throw"
.Vb 6
\& Title   : throw
\& Usage   :
\& Function:
\& Example :
\& Returns : 
\& Args    :
.Ve
.IP "throw_not_implemented" 4
.IX Item "throw_not_implemented"
.Vb 6
\& Title   : throw_not_implemented
\& Usage   :
\& Function:
\& Example :
\& Returns : 
\& Args    :
.Ve
.SH "BUGS"
.IX Header "BUGS"
Please send bug reports to the project mailing list: ()
.SH "AUTHOR"
.IX Header "AUTHOR"
.SH "SEE ALSO"
.IX Header "SEE ALSO"
\&\fIperl\fR\|(1).