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1 # $Id: HSPFactory.pm,v 1.4 2002/10/22 07:45:17 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Search::HSP::HSPFactory
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4 #
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5 # Cared for by Jason Stajich <jason@bioperl.org>
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6 #
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7 # Copyright Jason Stajich
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8 #
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9 # You may distribute this module under the same terms as perl itself
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10
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11 # POD documentation - main docs before the code
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12
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13 =head1 NAME
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14
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15 Bio::Search::HSP::HSPFactory - A factory to create Bio::Search::HSP::HSPI objects
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16
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17 =head1 SYNOPSIS
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18
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19 use Bio::Search::HSP::HSPFactory;
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20 my $factory = new Bio::Search::HSP::HSPFactory();
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21 my $resultobj = $factory->create(@args);
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22
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23 =head1 DESCRIPTION
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24
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25
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26 This is a general way of hiding the object creation process so that we
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27 can dynamically change the objects that are created by the SearchIO
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28 parser depending on what format report we are parsing.
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29
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30 This object is for creating new HSPs.
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31
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32 =head1 FEEDBACK
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33
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34 =head2 Mailing Lists
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35
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36 User feedback is an integral part of the evolution of this and other
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37 Bioperl modules. Send your comments and suggestions preferably to
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38 the Bioperl mailing list. Your participation is much appreciated.
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39
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40 bioperl-l@bioperl.org - General discussion
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41 http://bioperl.org/MailList.shtml - About the mailing lists
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42
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43 =head2 Reporting Bugs
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44
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45 Report bugs to the Bioperl bug tracking system to help us keep track
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46 of the bugs and their resolution. Bug reports can be submitted via
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47 email or the web:
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48
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49 bioperl-bugs@bioperl.org
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50 http://bugzilla.bioperl.org/
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51
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52 =head1 AUTHOR - Jason Stajich
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53
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54 Email jason@bioperl.org
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55
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56 Describe contact details here
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57
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58 =head1 CONTRIBUTORS
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59
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60 Additional contributors names and emails here
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61
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62 =head1 APPENDIX
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63
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64 The rest of the documentation details each of the object methods.
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65 Internal methods are usually preceded with a _
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66
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67 =cut
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68
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69
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70 # Let the code begin...
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71
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72
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73 package Bio::Search::HSP::HSPFactory;
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74 use vars qw(@ISA $DEFAULT_TYPE);
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75 use strict;
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76
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77 use Bio::Root::Root;
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78 use Bio::Factory::ObjectFactoryI;
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79
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80 @ISA = qw(Bio::Root::Root Bio::Factory::ObjectFactoryI );
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81
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82 BEGIN {
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83 $DEFAULT_TYPE = 'Bio::Search::HSP::GenericHSP';
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84 }
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85
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86 =head2 new
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87
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88 Title : new
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89 Usage : my $obj = new Bio::Search::HSP::HSPFactory();
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90 Function: Builds a new Bio::Search::HSP::HSPFactory object
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91 Returns : Bio::Search::HSP::HSPFactory
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92 Args :
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93
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94
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95 =cut
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96
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97 sub new {
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98 my($class,@args) = @_;
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99
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100 my $self = $class->SUPER::new(@args);
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101 my ($type) = $self->_rearrange([qw(TYPE)],@args);
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102 $self->type($type) if defined $type;
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103 return $self;
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104 }
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105
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106 =head2 create
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107
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108 Title : create
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109 Usage : $factory->create(%args)
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110 Function: Create a new L<Bio::Search::HSP::HSPI> object
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111 Returns : L<Bio::Search::HSP::HSPI>
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112 Args : hash of initialization parameters
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113
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114
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115 =cut
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116
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117 sub create{
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118 my ($self,@args) = @_;
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119 my $type = $self->type;
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120 eval { $self->_load_module($type) };
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121 if( $@ ) { $self->throw("Unable to load module $type"); }
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122 return $type->new(@args);
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123 }
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124
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125
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126 =head2 type
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127
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128 Title : type
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129 Usage : $factory->type('Bio::Search::HSP::GenericHSP');
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130 Function: Get/Set the HSP creation type
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131 Returns : string
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132 Args : [optional] string to set
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133
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134 =cut
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135
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136 sub type{
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137 my ($self,$type) = @_;
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138 if( defined $type ) {
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139 # redundancy with the create method which also calls _load_module
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140 # I know - but this is not a highly called object so I am going
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141 # to leave it in
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142 eval {$self->_load_module($type) };
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143 if( $@ ){ $self->warn("Cannot find module $type, unable to set type") }
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144 else { $self->{'_type'} = $type; }
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145 }
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146 return $self->{'_type'} || $DEFAULT_TYPE;
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147 }
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148
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149 1;
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