lib/Bio/Search/HSP/HSPFactory.pm

   1 #
   2 # BioPerl module for Bio::Search::HSP::HSPFactory
   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::HSP::HSPFactory - A factory to create Bio::Search::HSP::HSPI objects
  17
  18 =head1 SYNOPSIS
  19
  20     use Bio::Search::HSP::HSPFactory;
  21     my $factory = Bio::Search::HSP::HSPFactory->new();
  22     my $resultobj = $factory->create(@args);
  23
  24 =head1 DESCRIPTION
  25
  26
  27 This is a general way of hiding the object creation process so that we
  28 can dynamically change the objects that are created by the SearchIO
  29 parser depending on what format report we are parsing.
  30
  31 This object is for creating new HSPs.
  32
  33 =head1 FEEDBACK
  34
  35 =head2 Mailing Lists
  36
  37 User feedback is an integral part of the evolution of this and other
  38 Bioperl modules. Send your comments and suggestions preferably to
  39 the Bioperl mailing list.  Your participation is much appreciated.
  40
  41   bioperl-l@bioperl.org                  - General discussion
  42   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  43
  44 =head2 Support
  45
  46 Please direct usage questions or support issues to the mailing list:
  47
  48 I<bioperl-l@bioperl.org>
  49
  50 rather than to the module maintainer directly. Many experienced and
  51 reponsive experts will be able look at the problem and quickly
  52 address it. Please include a thorough description of the problem
  53 with code and data examples if at all possible.
  54
  55 =head2 Reporting Bugs
  56
  57 Report bugs to the Bioperl bug tracking system to help us keep track
  58 of the bugs and their resolution. Bug reports can be submitted via the
  59 web:
  60
  61   https://github.com/bioperl/bioperl-live/issues
  62
  63 =head1 AUTHOR - Jason Stajich
  64
  65 Email jason-at-bioperl.org
  66
  67 =head1 APPENDIX
  68
  69 The rest of the documentation details each of the object methods.
  70 Internal methods are usually preceded with a _
  71
  72 =cut
  73
  74
  75 # Let the code begin...
  76
  77
  78 package Bio::Search::HSP::HSPFactory;
  79 use vars qw($DEFAULT_TYPE);
  80 use strict;
  81
  82
  83 use base qw(Bio::Root::Root Bio::Factory::ObjectFactoryI);
  84
  85 BEGIN {
  86     $DEFAULT_TYPE = 'Bio::Search::HSP::GenericHSP';
  87 }
  88
  89 =head2 new
  90
  91  Title   : new
  92  Usage   : my $obj = Bio::Search::HSP::HSPFactory->new();
  93  Function: Builds a new Bio::Search::HSP::HSPFactory object
  94  Returns : Bio::Search::HSP::HSPFactory
  95  Args    :
  96
  97
  98 =cut
  99
 100 sub new {
 101   my($class,@args) = @_;
 102
 103   my $self = $class->SUPER::new(@args);
 104   my ($type) = $self->_rearrange([qw(TYPE)],@args);
 105   $self->type($type) if defined $type;
 106   return $self;
 107 }
 108
 109 =head2 create
 110
 111  Title   : create
 112  Usage   : $factory->create(%args)
 113  Function: Create a new L<Bio::Search::HSP::HSPI> object
 114  Returns : L<Bio::Search::HSP::HSPI>
 115  Args    : hash of initialization parameters
 116
 117
 118 =cut
 119
 120 sub create{
 121    my ($self,@args) = @_;
 122    my $type = $self->type;
 123    eval { $self->_load_module($type) };
 124    if( $@ ) { $self->throw("Unable to load module $type"); }
 125    return $type->new(@args);
 126 }
 127
 128
 129 =head2 type
 130
 131  Title   : type
 132  Usage   : $factory->type('Bio::Search::HSP::GenericHSP');
 133  Function: Get/Set the HSP creation type
 134  Returns : string
 135  Args    : [optional] string to set
 136
 137 =cut
 138
 139 sub type{
 140     my ($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;