branch-1-6/Bio/Seq/SeqFactory.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Seq::SeqFactory
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Jason Stajich <jason@bioperl.org>
   8 #
   9 # Copyright Jason Stajich
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::Seq::SeqFactory - Instantiates a new Bio::PrimarySeqI (or derived class) through a factory
  18
  19 =head1 SYNOPSIS
  20
  21     use Bio::Seq::SeqFactory;
  22     my $factory = Bio::Seq::SeqFactory->new();
  23     my $seq = $factory->create(-seq => 'WYRAVLC',
  24                                -id  => 'name');
  25
  26     # If you want the factory to create Bio::Seq objects instead
  27     # of the default Bio::PrimarySeq objects, use the -type parameter:
  28
  29     my $factory = Bio::Seq::SeqFactory->new(-type => 'Bio::Seq');
  30
  31
  32 =head1 DESCRIPTION
  33
  34 This object will build L<Bio::PrimarySeqI> and L<Bio::SeqI> objects
  35 generically.
  36
  37 =head1 FEEDBACK
  38
  39 =head2 Mailing Lists
  40
  41 User feedback is an integral part of the evolution of this and other
  42 Bioperl modules. Send your comments and suggestions preferably to
  43 the Bioperl mailing list.  Your participation is much appreciated.
  44
  45   bioperl-l@bioperl.org                  - General discussion
  46   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  47
  48 =head2 Support
  49
  50 Please direct usage questions or support issues to the mailing list:
  51
  52 I<bioperl-l@bioperl.org>
  53
  54 rather than to the module maintainer directly. Many experienced and
  55 reponsive experts will be able look at the problem and quickly
  56 address it. Please include a thorough description of the problem
  57 with code and data examples if at all possible.
  58
  59 =head2 Reporting Bugs
  60
  61 Report bugs to the Bioperl bug tracking system to help us keep track
  62 of the bugs and their resolution. Bug reports can be submitted via the
  63 web:
  64
  65   http://bugzilla.open-bio.org/
  66
  67 =head1 AUTHOR - Jason Stajich
  68
  69 Email jason@bioperl.org
  70
  71 =head1 APPENDIX
  72
  73 The rest of the documentation details each of the object methods.
  74 Internal methods are usually preceded with a _
  75
  76 =cut
  77
  78
  79 # Let the code begin...
  80
  81
  82 package Bio::Seq::SeqFactory;
  83 use strict;
  84
  85
  86 use base qw(Bio::Root::Root Bio::Factory::SequenceFactoryI);
  87
  88 =head2 new
  89
  90  Title   : new
  91  Usage   : my $obj = Bio::Seq::SeqFactory->new();
  92  Function: Builds a new Bio::Seq::SeqFactory object
  93  Returns : Bio::Seq::SeqFactory
  94  Args    : -type => string, name of a PrimarySeqI derived class
  95                     This is optional. Default=Bio::PrimarySeq.
  96
  97 =cut
  98
  99 sub new {
 100   my($class,@args) = @_;
 101   my $self = $class->SUPER::new(@args);
 102   my ($type) = $self->_rearrange([qw(TYPE)], @args);
 103   if( ! defined $type ) {
 104       $type = 'Bio::PrimarySeq';
 105   }
 106   $self->type($type);
 107   return $self;
 108 }
 109
 110
 111 =head2 create
 112
 113  Title   : create
 114  Usage   : my $seq = $seqbuilder->create(-seq => 'CAGT', -id => 'name');
 115  Function: Instantiates new Bio::SeqI (or one of its child classes)
 116            This object allows us to genericize the instantiation of sequence
 117            objects.
 118  Returns : Bio::PrimarySeq object (default)
 119            The return type is configurable using new(-type =>"...").
 120  Args    : initialization parameters specific to the type of sequence
 121            object we want.  Typically
 122            -seq        => $str,
 123            -display_id => $name
 124
 125 =cut
 126
 127 sub create {
 128    my ($self,@args) = @_;
 129    return $self->type->new(-verbose => $self->verbose, @args);
 130 }
 131
 132 =head2 type
 133
 134  Title   : type
 135  Usage   : $obj->type($newval)
 136  Function:
 137  Returns : value of type
 138  Args    : newvalue (optional)
 139
 140
 141 =cut
 142
 143 sub type{
 144    my ($self,$value) = @_;
 145    if( defined $value) {
 146        eval "require $value";
 147        if( $@ ) { $self->throw("$@: Unrecognized Sequence type for SeqFactory '$value'");}
 148
 149        my $a = bless {},$value;
 150        unless( $a->isa('Bio::PrimarySeqI') ||
 151                $a->isa('Bio::Seq::QualI') ) {
 152            $self->throw("Must provide a valid Bio::PrimarySeqI or Bio::Seq::QualI or child class to SeqFactory Not $value");
 153        }
 154       $self->{'type'} = $value;
 155     }
 156     return $self->{'type'};
 157 }
 158
 159 1;