Modware

Has_synonyms

   Modware::Has_synonyms - Mixin class, provides accessor methods for classes tha have synonyms.

  USE CASE: ADD A SYNONYM TO OBJECT

   my $gene = new Modware::Gene( -name => 'testGene' );
   $gene->add_synoym( 'new synonym' );

  
  USE CASE: PRINT A LIST OF SYNONYMS FOR OBJECT

   my $gene = new Modware::Gene( -name => 'testGene' );

   foreach $synonym ( @{ $gene->synonyms() } ) {
      print $synonym."\n";
   }

  Abstract class to provide methods for objects which carry arrays of synonyms
  Never instantiate this object, only inherit
  
  All database operations are handled in the implementing class
  for example see _get_synonyms and _update_synonyms in
  Modware::Feature::GENE
  
  _update_synonyms must be called in both the insert() and update()
  method of the implementor.

Methods description

 Title    : _get_synonyms
 Usage    : $gene->_get_synonyms();
 Function : gets the synonyms for this gene ( arrayref of strings )
 Returns  : nothing
 Args     : none

 Title    : _update_synonyms
 Function : adds/links/unlinks synonyms from this gene
          : compares list from database to current gene product list, inserts/deletes as necessary
 Returns  : nothing
 Args     : none

 Title    : add_synonym
 Usage    : $gene->add_synonym( 'test synonym' );
 Function : adds an synonym to the synonym array IF IT DOES NOT EXIST
 Returns  : nothing
 Args     : string
 TO DO    : need to add second argument (is_automated) to set the is automated property of a new gene product

 Title    : remove_synonym
 Usage    : $gene->remove_synonym( 'test product' );
 Function : removes a synonym the synonyms array if the synonym_name matches
 Returns  : nothing
 Args     : string

 Title    : synonyms
 Usage    : foreach my $synonym ( @{ $gene->synonyms() ) {
          :    print $synonym."\n";
          : }
 Function : get/set synonyms for this gene
 Returns  : reference to array of strings
 Args     : reference to array of strings ( optional )

Methods code

   my ($self) = @_;
   $self->throw_not_implemented();

   my ($self, @args) = @_;
   $self->throw_not_implemented();

   my ($self, $synonym_name ) = @_;

   $self->throw( "need synonym to add") if !$synonym_name;

   if ( !grep { $_ eq $synonym_name } @{ $self->synonyms() } ) {
      push @{ $self->synonyms }, $synonym_name;
   }

   my ($self, $synonym_name) = @_;

   $self->throw( "need synonym to remove") if !$synonym_name;

   my @synonyms = grep { $_ ne $synonym_name } @{ $self->synonyms() };

   $self->synonyms (\@ synonyms );

   my ($self, $obj) = @_;

  #
  # fetches synonyms from database (_get_synonyms) if synonyms is not yet defined
  #  and the user is not attempting to set the synonyms options
  #
   exists $self->{synonyms} || scalar @_ > 1 || $self->_get_synonyms();

   if(scalar @_ > 1) {
      $self->{synonyms} = $obj;
   }
   return $self->{synonyms};

General documentation

   Eric Just e-just@northwestern.edu

   The rest of the documentation details each of the object
   methods. Internal methods are usually preceded with a _

Copyright © 2006, Northwestern University All rights reserved.