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1 # $Id: SeqFastaSpeedFactory.pm,v 1.3 2002/11/07 23:54:23 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 Bio::Seq objects generically.
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33
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34 =head1 FEEDBACK
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35
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36 =head2 Mailing Lists
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37
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38 User feedback is an integral part of the evolution of this and other
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39 Bioperl modules. Send your comments and suggestions preferably to
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40 the Bioperl mailing list. Your participation is much appreciated.
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41
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42 bioperl-l@bioperl.org - General discussion
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43 http://bioperl.org/MailList.shtml - About the mailing lists
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44
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45 =head2 Reporting Bugs
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46
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47 Report bugs to the Bioperl bug tracking system to help us keep track
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48 of the bugs and their resolution. Bug reports can be submitted via
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49 email or the web:
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50
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51 bioperl-bugs@bioperl.org
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52 http://bugzilla.bioperl.org/
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53
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54 =head1 AUTHOR - Jason Stajich
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55
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56 Email jason@bioperl.org
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57
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58 Describe contact details here
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59
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60 =head1 CONTRIBUTORS
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61
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62 Additional contributors names and emails here
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63
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64 =head1 APPENDIX
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65
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66 The rest of the documentation details each of the object methods.
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67 Internal methods are usually preceded with a _
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68
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69 =cut
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70
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71
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72 # Let the code begin...
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73
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74
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75 package Bio::Seq::SeqFastaSpeedFactory;
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76 use vars qw(@ISA);
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77 use strict;
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78
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79 use Bio::Root::Root;
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80 use Bio::Factory::SequenceFactoryI;
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81 use Bio::Seq;
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82 use Bio::PrimarySeq;
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83
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84 @ISA = qw(Bio::Root::Root Bio::Factory::SequenceFactoryI);
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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 $obj = new Bio::Seq::SeqFactory();
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90 Function: Builds a new Bio::Seq::SeqFactory object
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91 Returns : Bio::Seq::SeqFactory
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92 Args : -type => string, name of a PrimarySeqI derived class
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93 This is optional. Default=Bio::PrimarySeq.
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94
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95 =cut
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96
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97 sub new {
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98 my($class,@args) = @_;
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99 my $self = $class->SUPER::new(@args);
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100 return $self;
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101 }
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102
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103
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104 =head2 create
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105
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106 Title : create
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107 Usage : my $seq = $seqbuilder->create(-seq => 'CAGT', -id => 'name');
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108 Function: Instantiates a new Bio::Seq object, correctly built but very
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109 fast, knowing stuff about Bio::PrimarySeq and Bio::Seq
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110 Returns : Bio::Seq
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111
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112 Args : initialization parameters specific to the type of sequence
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113 object we want. Typically
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114 -seq => $str,
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115 -id => $name
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116
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117 =cut
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118
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119 sub create {
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120 my ($self,%param) = @_;
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121
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122 my $sequence = $param{'-seq'} || $param{'-SEQ'};
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123 my $fulldesc = $param{'-desc'} || $param{'-DESC'};
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124 my $id = $param{'-id'} || $param{'-ID'} ||
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125 $param{'-primary_id'} || $param{'-PRIMARY_ID'};
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126
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127 my $seq = bless {}, "Bio::Seq";
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128 my $t_pseq = $seq->{'primary_seq'} = bless {}, "Bio::PrimarySeq";
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129 $t_pseq->{'seq'} = $sequence;
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130 $t_pseq->{'desc'} = $fulldesc;
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131 $t_pseq->{'display_id'} = $id;
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132 $t_pseq->{'primary_id'} = $id;
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133 $seq->{'primary_id'} = $id; # currently Bio::Seq does not delegate this
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134 if( $sequence ) {
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135 $t_pseq->_guess_alphabet();
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136 }
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137
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138 return $seq;
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139 }
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140
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141 1;
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142
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