Bio/Search/Hit/HitFactory.pm

   1 #
   2 # BioPerl module for Bio::Search::Hit::HitFactory
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Jason Stajich <jason@bioperl.org>
   7 #
   8 # Copyright Jason Stajich
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::Search::Hit::HitFactory - A factory to create Bio::Search::Hit::HitI objects
  17
  18 =head1 SYNOPSIS
  19
  20     use Bio::Search::Hit::HitFactory;
  21     my $factory = Bio::Search::Hit::HitFactory->new();
  22     my $resultobj = $factory->create(@args);
  23
  24 =head1 DESCRIPTION
  25
  26 This is a general way of hiding the object creation process so that we
  27 can dynamically change the objects that are created by the SearchIO
  28 parser depending on what format report we are parsing.
  29
  30 This object is for creating new Hits.
  31
  32 =head1 FEEDBACK
  33
  34 =head2 Mailing Lists
  35
  36 User feedback is an integral part of the evolution of this and other
  37 Bioperl modules. Send your comments and suggestions preferably to
  38 the Bioperl mailing list.  Your participation is much appreciated.
  39
  40   bioperl-l@bioperl.org                  - General discussion
  41   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  42
  43 =head2 Support
  44
  45 Please direct usage questions or support issues to the mailing list:
  46
  47 I<bioperl-l@bioperl.org>
  48
  49 rather than to the module maintainer directly. Many experienced and
  50 reponsive experts will be able look at the problem and quickly
  51 address it. Please include a thorough description of the problem
  52 with code and data examples if at all possible.
  53
  54 =head2 Reporting Bugs
  55
  56 Report bugs to the Bioperl bug tracking system to help us keep track
  57 of the bugs and their resolution. Bug reports can be submitted via the
  58 web:
  59
  60   https://github.com/bioperl/bioperl-live/issues
  61
  62 =head1 AUTHOR - Jason Stajich
  63
  64 Email jason@bioperl.org
  65
  66 =head1 APPENDIX
  67
  68 The rest of the documentation details each of the object methods.
  69 Internal methods are usually preceded with a _
  70
  71 =cut
  72
  73
  74 # Let the code begin...
  75
  76
  77 package Bio::Search::Hit::HitFactory;
  78 use vars qw($DEFAULT_TYPE);
  79 use strict;
  80
  81
  82 use base qw(Bio::Root::Root Bio::Factory::ObjectFactoryI);
  83
  84 BEGIN {
  85     $DEFAULT_TYPE = 'Bio::Search::Hit::GenericHit';
  86 }
  87
  88 =head2 new
  89
  90  Title   : new
  91  Usage   : my $obj = Bio::Search::Hit::HitFactory->new();
  92  Function: Builds a new Bio::Search::Hit::HitFactory object
  93  Returns : Bio::Search::Hit::HitFactory
  94  Args    :
  95
  96
  97 =cut
  98
  99 sub new {
 100   my($class,@args) = @_;
 101
 102   my $self = $class->SUPER::new(@args);
 103   my ($type) = $self->_rearrange([qw(TYPE)],@args);
 104   $self->type($type) if defined $type;
 105   return $self;
 106 }
 107
 108 =head2 create
 109
 110  Title   : create
 111  Usage   : $factory->create(%args)
 112  Function: Create a new L<Bio::Search::Hit::HitI> object
 113  Returns : L<Bio::Search::Hit::HitI>
 114  Args    : hash of initialization parameters
 115
 116
 117 =cut
 118
 119 sub create{
 120    my ($self,@args) = @_;
 121    my $type = $self->type;
 122    eval { $self->_load_module($type) };
 123    if( $@ ) { $self->throw("Unable to load module $type"); }
 124    return $type->new(@args);
 125 }
 126
 127
 128 =head2 type
 129
 130  Title   : type
 131  Usage   : $factory->type('Bio::Search::Hit::GenericHit');
 132  Function: Get/Set the Hit creation type
 133  Returns : string
 134  Args    : [optional] string to set
 135
 136
 137 =cut
 138
 139 sub type{
 140     my ($self,$type) = @_;
 141    if( defined $type ) {
 142        # redundancy with the create method which also calls _load_module
 143        # I know - but this is not a highly called object so I am going
 144        # to leave it in
 145        eval {$self->_load_module($type) };
 146        if( $@ ){ $self->warn("Cannot find module $type, unable to set type"); }
 147        else { $self->{'_type'} = $type; }
 148    }
 149     return $self->{'_type'} || $DEFAULT_TYPE;
 150 }
 151
 152 1;