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##############################
#
# Bio::MAGE::ArrayDesign
#
##############################
package Bio::MAGE::ArrayDesign;
use strict;
use Carp;
use Bio::MAGE::Base;
require Exporter;
use Tie::IxHash;
use Bio::MAGE::ArrayDesign::ArrayDesign;
use Bio::MAGE::ArrayDesign::PhysicalArrayDesign;
use Bio::MAGE::ArrayDesign::ZoneLayout;
use Bio::MAGE::ArrayDesign::ZoneGroup;
use Bio::MAGE::ArrayDesign::Zone;
use Bio::MAGE::ArrayDesign::ReporterGroup;
use Bio::MAGE::ArrayDesign::FeatureGroup;
use Bio::MAGE::ArrayDesign::DesignElementGroup;
use Bio::MAGE::ArrayDesign::CompositeGroup;
use vars qw(@ISA $VERSION @EXPORT_OK %EXPORT_TAGS $__MAGEML_LISTS);
@ISA = qw(Bio::MAGE::Base Exporter);
$VERSION = q[$Id: ArrayDesign.pm,v 1.8 2002/10/13 21:56:03 jason_e_stewart Exp $];
sub initialize {
  my $self = shift;
  $self->reportergroup_list([]);
  $self->compositegroup_list([]);
  $self->arraydesign_list([]);
  $self->mageml_lists([ReporterGroup=>$self->reportergroup_list,
        CompositeGroup=>$self->compositegroup_list,
        ArrayDesign=>$self->arraydesign_list]);
  $self->tagname(q[ArrayDesign_package]);
  return 1;
}
HideShow 64 lines of Pod
=head1 NAME
Bio::MAGE::ArrayDesign - Container module for classes in the MAGE ArrayDesign package 
=head1 SYNOPSIS
  use Bio::MAGE::ArrayDesign;
=head1 DESCRIPTION
This is a I<package> module that encapsulates a number of classes in
the Bio::MAGE hierarchy. These classes belong to the
ArrayDesign package of the MAGE-OM object model.
=head1 CLASSES
The Bio::MAGE::ArrayDesign module contains the following
Bio::MAGE classes:
=over
=item * ArrayDesign
=item * PhysicalArrayDesign
=item * ZoneLayout
=item * ZoneGroup
=item * Zone
=item * ReporterGroup
=item * FeatureGroup
=item * DesignElementGroup
=item * CompositeGroup
=back
=head1 CLASS METHODS
=over
=item @class_list = Bio::MAGE::ArrayDesign::classes();
This method returns a list of non-fully qualified class names
(i.e. they do not have 'Bio::MAGE::' as a prefix) in this package.
=cut
sub classes {
  return ('ArrayDesign', 'PhysicalArrayDesign', 'ZoneLayout', 'ZoneGroup', 'Zone', 'ReporterGroup', 'FeatureGroup', 'DesignElementGroup', 'CompositeGroup');
}
HideShow 15 lines of Pod
=item $obj_ref = Bio::MAGE::ArrayDesign->new(%parameters)
=item $obj_ref_copy = $obj_ref->new()
The C<new()> method is the class constructor. If invoked with an
existing object instance, it is a copy constructor.
B<Return value>: It returns a reference to an object of class
C<Bio::MAGE::ArrayDesign>.
B<Side effects>: It invokes the C<initialize()> method if it is defined
by the class.
=cut
HideShow 17 lines of Pod
=back
=head1 INSTANCE METHODS
=over
=cut
=item $array_ref = $arraydesign->getReporterGroup_list()
This method handles the list for the C<Bio::MAGE::ARRAY(0x10499078)::ReporterGroup> class. It returns a reference to an array of the
class objects of that type associated with this package object.
This is useful when retrieving data from parsed MAGE-ML file.
=cut
sub getReporterGroup_list {
  my $self = shift;
  return $self->reportergroup_list();
}
HideShow 9 lines of Pod
=item $array_ref = $arraydesign->getCompositeGroup_list()
This method handles the list for the C<Bio::MAGE::ARRAY(0x10499078)::CompositeGroup> class. It returns a reference to an array of the
class objects of that type associated with this package object.
This is useful when retrieving data from parsed MAGE-ML file.
=cut
sub getCompositeGroup_list {
  my $self = shift;
  return $self->compositegroup_list();
}
HideShow 9 lines of Pod
=item $array_ref = $arraydesign->getArrayDesign_list()
This method handles the list for the C<Bio::MAGE::ARRAY(0x10499078)::ArrayDesign> class. It returns a reference to an array of the
class objects of that type associated with this package object.
This is useful when retrieving data from parsed MAGE-ML file.
=cut
sub getArrayDesign_list {
  my $self = shift;
  return $self->arraydesign_list();
}
#
# code for new() inherited from Base.pm
#
HideShow 15 lines of Pod
=item $obj->set_slots(%parameters)
=item $obj->set_slots(\@name_list, \@value_list)
The C<set_slots()> 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.
B<Return value>: none
B<Side effects>: will call C<croak()> if a slot_name is used that the class
does not define.
=cut
#
# code for set_slots() inherited from Base.pm
#
HideShow 11 lines of Pod
=item $obj->get_slots(@name_list)
The C<get_slots()> method is used to get the values of a number of
slots at the same time.
B<Return value>: a list of instance objects
B<Side effects>: none
=cut
#
# code for get_slots() inherited from Base.pm
#
HideShow 10 lines of Pod
=item $val = $obj->set_slot($name,$val)
The C<set_slot()> method sets the slot C<$name> to the value C<$val>
B<Return value>: the new value of the slot, i.e. C<$val>
B<Side effects>: none
=cut
#
# code for set_slot() inherited from Base.pm
#
HideShow 12 lines of Pod
=item $val = $obj->get_slot($name)
The C<get_slot()> method is used to get the values of a number of
slots at the same time.
B<Return value>: a single slot value, or undef if the slot has not been
initialized.
B<Side effects>: none
=cut
#
# code for get_slot() inherited from Base.pm
#
HideShow 12 lines of Pod
=item @names = $obj->get_slot_names()
The C<get_slot_names()> method is used to retrieve the name of all
slots defined for a given object.
B<Return value>: a single slot value, or undef if the slot has not been
initialized.
B<Side effects>: none
=cut
#
# code for get_slot_names() inherited from Base.pm
#
HideShow 19 lines of Pod
=item $val = $arraydesign->reportergroup_list()
=item $val = $arraydesign->reportergroup_list($val)
This is the unified setter/getter method for the reportergroup_list slot. If
C<$val> is specified, the setter method is invoked, with no
parameters, the getter method is invoked.
Input parameters: the optional C<$val> will invoke the setter method.
Return value: for both setter and getter the current value of the reportergroup_list
slot
Side effects: none
Exceptions: none
=cut
sub reportergroup_list {
  my $self = shift;
  if (@_) {
    $self->{__REPORTERGROUP_LIST} = shift;
  }
  return $self->{__REPORTERGROUP_LIST};
}
HideShow 19 lines of Pod
=item $val = $arraydesign->compositegroup_list()
=item $val = $arraydesign->compositegroup_list($val)
This is the unified setter/getter method for the compositegroup_list slot. If
C<$val> is specified, the setter method is invoked, with no
parameters, the getter method is invoked.
Input parameters: the optional C<$val> will invoke the setter method.
Return value: for both setter and getter the current value of the compositegroup_list
slot
Side effects: none
Exceptions: none
=cut
sub compositegroup_list {
  my $self = shift;
  if (@_) {
    $self->{__COMPOSITEGROUP_LIST} = shift;
  }
  return $self->{__COMPOSITEGROUP_LIST};
}
HideShow 19 lines of Pod
=item $val = $arraydesign->arraydesign_list()
=item $val = $arraydesign->arraydesign_list($val)
This is the unified setter/getter method for the arraydesign_list slot. If
C<$val> is specified, the setter method is invoked, with no
parameters, the getter method is invoked.
Input parameters: the optional C<$val> will invoke the setter method.
Return value: for both setter and getter the current value of the arraydesign_list
slot
Side effects: none
Exceptions: none
=cut
sub arraydesign_list {
  my $self = shift;
  if (@_) {
    $self->{__ARRAYDESIGN_LIST} = shift;
  }
  return $self->{__ARRAYDESIGN_LIST};
}
HideShow 19 lines of Pod
=item $val = $arraydesign->mageml_lists()
=item $val = $arraydesign->mageml_lists($val)
This is the unified setter/getter method for the mageml_lists slot. If
C<$val> is specified, the setter method is invoked, with no
parameters, the getter method is invoked.
Input parameters: the optional C<$val> will invoke the setter method.
Return value: for both setter and getter the current value of the mageml_lists
slot
Side effects: none
Exceptions: none
=cut
sub mageml_lists {
  my $self = shift;
  if (@_) {
    $self->{__MAGEML_LISTS} = shift;
  }
  return $self->{__MAGEML_LISTS};
}
HideShow 19 lines of Pod
=item $val = $arraydesign->tagname()
=item $val = $arraydesign->tagname($val)
This is the unified setter/getter method for the tagname slot. If
C<$val> is specified, the setter method is invoked, with no
parameters, the getter method is invoked.
Input parameters: the optional C<$val> will invoke the setter method.
Return value: for both setter and getter the current value of the tagname
slot
Side effects: none
Exceptions: none
=cut
sub tagname {
  my $self = shift;
  if (@_) {
    $self->{__TAGNAME} = shift;
  }
  return $self->{__TAGNAME};
}
HideShow 4 lines of Pod
=back
=cut
sub register {
  my ($self,$obj) = @_;
  # should we have the identifier checking code here??
  my %mageml_lists = @{$self->mageml_lists()};
  my $list_ref;
  foreach my $class (keys %mageml_lists) {
    if ($obj->isa("Bio::MAGE::ArrayDesign::$class")) {
      $list_ref = $mageml_lists{$class};
      last;
    }
  }
  return unless defined $list_ref;
  push(@{$list_ref}, $obj);
}
sub obj2mageml {
  my ($self,$writer) = @_;
  my $empty = 0;
  my $tag = $self->tagname();
  $writer->write_start_tag($tag,$empty);
  # we use IxHash because we need to preserve insertion order
  tie my %list_hash, 'Tie::IxHash', @{$self->mageml_lists()};
  foreach my $list_name (keys %list_hash) {
    if (scalar @{$list_hash{$list_name}}) {
      my $tag = $list_name . '_assnlist';
      $writer->write_start_tag($tag,$empty);
      foreach my $obj (@{$list_hash{$list_name}}) {
        # this may seem a little odd, but the writer knows how to write out 
        # the objects. Create a subclass of $OPTIONS{namespace}::XMLWriter to 
        # modify the output of the obj2mageml process
        $writer->obj2mageml($obj);
      }
      $writer->write_end_tag($tag);
    }
  }
  # and we're done
  $writer->write_end_tag($tag);
}
###############################################################################
# obj2database
###############################################################################
sub obj2database {
  my ($self,$writer) = @_;
  my $empty = 0;
  my $tag = $self->tagname();
  #$writer->write_start_tag($tag,$empty);
  # we use IxHash because we need to preserve insertion order
  tie my %list_hash, 'Tie::IxHash', @{$self->mageml_lists()};
  foreach my $list_name (keys %list_hash) {
    if (scalar @{$list_hash{$list_name}}) {
      my $tag = $list_name . '_assnlist';
      #$writer->write_start_tag($tag,$empty);
      foreach my $obj (@{$list_hash{$list_name}}) {
        # this may seem a little odd, but the writer knows how to write out
        # the objects. Create a subclass of Bio::MAGE::XMLWriter to
        # modify the output of the obj2mageml process
        $writer->obj2database($obj);
      }
      #$writer->write_end_tag($tag);
    }
  }
  # and we're done
  #$writer->write_end_tag($tag);
}
HideShow 14 lines of Pod
=head1 BUGS
Please send bug reports to mged-mage@lists.sf.net
=head1 AUTHOR
Jason E. Stewart (jason@openinformatics.com)
=head1 SEE ALSO
perl(1).
=cut
#
# End the module by returning a true value
#
1;