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1 # $Id: SeqFactory.pm,v 1.8 2002/10/25 22:49:04 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Seq::SeqFactory
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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::Seq::SeqFactory - Instantiates a new Bio::PrimarySeqI (or derived class) through a factory
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16
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17 =head1 SYNOPSIS
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18
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19 use Bio::Seq::SeqFactory;
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20 my $factory = new Bio::Seq::SeqFactory;
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21 my $seq = $factory->create(-seq => 'WYRAVLC',
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22 -id => 'name');
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23
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24 # If you want the factory to create Bio::Seq objects instead
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25 # of the default Bio::PrimarySeq objects, use the -type parameter:
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26
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27 my $factory = new Bio::Seq::SeqFactory(-type => 'Bio::Seq');
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28
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29
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30 =head1 DESCRIPTION
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31
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32 This object will build L<Bio::PrimarySeqI> and L<Bio::SeqI> objects
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33 generically.
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34
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35 =head1 FEEDBACK
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36
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37 =head2 Mailing Lists
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38
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39 User feedback is an integral part of the evolution of this and other
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40 Bioperl modules. Send your comments and suggestions preferably to
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41 the Bioperl mailing list. Your participation is much appreciated.
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42
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43 bioperl-l@bioperl.org - General discussion
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44 http://bioperl.org/MailList.shtml - About the mailing lists
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45
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46 =head2 Reporting Bugs
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47
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48 Report bugs to the Bioperl bug tracking system to help us keep track
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49 of the bugs and their resolution. Bug reports can be submitted via
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50 email or the web:
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51
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52 bioperl-bugs@bioperl.org
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53 http://bugzilla.bioperl.org/
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54
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55 =head1 AUTHOR - Jason Stajich
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56
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57 Email jason@bioperl.org
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58
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59 Describe contact details here
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60
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61 =head1 CONTRIBUTORS
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62
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63 Additional contributors names and emails here
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64
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65 =head1 APPENDIX
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66
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67 The rest of the documentation details each of the object methods.
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68 Internal methods are usually preceded with a _
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69
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70 =cut
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71
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72
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73 # Let the code begin...
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74
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75
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76 package Bio::Seq::SeqFactory;
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77 use vars qw(@ISA);
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78 use strict;
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79
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80 use Bio::Root::Root;
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81 use Bio::Factory::SequenceFactoryI;
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82
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83 @ISA = qw(Bio::Root::Root Bio::Factory::SequenceFactoryI);
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84
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85 =head2 new
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86
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87 Title : new
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88 Usage : my $obj = new Bio::Seq::SeqFactory();
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89 Function: Builds a new Bio::Seq::SeqFactory object
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90 Returns : Bio::Seq::SeqFactory
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91 Args : -type => string, name of a PrimarySeqI derived class
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92 This is optional. Default=Bio::PrimarySeq.
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93
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94 =cut
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95
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96 sub new {
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97 my($class,@args) = @_;
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98 my $self = $class->SUPER::new(@args);
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99 my ($type) = $self->_rearrange([qw(TYPE)], @args);
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100 if( ! defined $type ) {
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101 $type = 'Bio::PrimarySeq';
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102 }
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103 $self->type($type);
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104 return $self;
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105 }
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106
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107
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108 =head2 create
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109
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110 Title : create
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111 Usage : my $seq = $seqbuilder->create(-seq => 'CAGT', -id => 'name');
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112 Function: Instantiates new Bio::SeqI (or one of its child classes)
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113 This object allows us to genericize the instantiation of sequence
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114 objects.
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115 Returns : Bio::PrimarySeq object (default)
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116 The return type is configurable using new(-type =>"...").
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117 Args : initialization parameters specific to the type of sequence
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118 object we want. Typically
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119 -seq => $str,
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120 -display_id => $name
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121
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122 =cut
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123
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124 sub create {
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125 my ($self,@args) = @_;
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126 return $self->type->new(-verbose => $self->verbose, @args);
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127 }
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128
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129 =head2 type
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130
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131 Title : type
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132 Usage : $obj->type($newval)
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133 Function:
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134 Returns : value of type
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135 Args : newvalue (optional)
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136
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137
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138 =cut
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139
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140 sub type{
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141 my ($self,$value) = @_;
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142 if( defined $value) {
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143 eval "require $value";
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144 if( $@ ) { $self->throw("$@: Unrecognized Sequence type for SeqFactory '$value'");}
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145
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146 my $a = bless {},$value;
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147 unless( $a->isa('Bio::PrimarySeqI') ||
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148 $a->isa('Bio::Seq::QualI') ) {
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149 $self->throw("Must provide a valid Bio::PrimarySeqI or Bio::Seq::QualI or child class to SeqFactory Not $value");
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150 }
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151 $self->{'type'} = $value;
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152 }
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153 return $self->{'type'};
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154 }
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155
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156 1;
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