lib/Bio/Seq/SeqFactory.pm

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