Bio/Seq/SeqFastaSpeedFactory.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Seq::SeqFastaSpeedFactory
   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::SeqFastaSpeedFactory - Rapid instantiation of new Bio::SeqI objects through a factory using FASTA files.
  18
  19 =head1 SYNOPSIS
  20
  21     use Bio::Seq::SeqFastaSpeedFactory;
  22     my $factory = Bio::Seq::SeqFastaSpeedFactory->new();
  23     my $seq = $factory->create(-seq => 'WYRAVLC',
  24                                -id  => 'name');
  25
  26     # If you want the factory to create Bio::PrimarySeq objects instead
  27     # of the default Bio::Seq objects, use the -type parameter:
  28     my $factory = Bio::Seq::SeqFactory->new(-type => 'Bio::PrimarySeq');
  29
  30 =head1 DESCRIPTION
  31
  32 This factory is quick at building simple L<Bio::PrimarySeqI> and L<Bio::SeqI>
  33 objects generically derived from FASTA files (no annotations).
  34
  35 =head1 FEEDBACK
  36
  37 =head2 Mailing Lists
  38
  39 User feedback is an integral part of the evolution of this and other
  40 Bioperl modules. Send your comments and suggestions preferably to
  41 the Bioperl mailing list.  Your participation is much appreciated.
  42
  43   bioperl-l@bioperl.org                  - General discussion
  44   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  45
  46 =head2 Support
  47
  48 Please direct usage questions or support issues to the mailing list:
  49
  50 I<bioperl-l@bioperl.org>
  51
  52 rather than to the module maintainer directly. Many experienced and
  53 reponsive experts will be able look at the problem and quickly
  54 address it. Please include a thorough description of the problem
  55 with code and data examples if at all possible.
  56
  57 =head2 Reporting Bugs
  58
  59 Report bugs to the Bioperl bug tracking system to help us keep track
  60 of the bugs and their resolution. Bug reports can be submitted via the
  61 web:
  62
  63   http://bugzilla.open-bio.org/
  64
  65 =head1 AUTHOR - Jason Stajich
  66
  67 Email jason@bioperl.org
  68
  69 =head1 APPENDIX
  70
  71 The rest of the documentation details each of the object methods.
  72 Internal methods are usually preceded with a _
  73
  74 =cut
  75
  76
  77 # Let the code begin...
  78
  79
  80 package Bio::Seq::SeqFastaSpeedFactory;
  81 use strict;
  82
  83 use Bio::Seq;
  84 use Bio::PrimarySeq;
  85
  86 use base qw(Bio::Root::Root Bio::Seq::SeqFactory);
  87 # a Bio::Seq::SeqFactory is also a Bio::Factory::SequenceFactoryI
  88
  89
  90 =head2 new
  91
  92  Title   : new
  93  Usage   : my $obj = Bio::Seq::SeqFastaSpeedFactory->new();
  94  Function: Builds a new Bio::Seq::SeqFastaSpeedFactory object
  95  Returns : Bio::Seq::SeqFastaSpeedFactory
  96  Args    : -type => string, name of a PrimarySeqI derived class
  97                     This is optional. Default=Bio::Seq.
  98
  99 =cut
 100
 101 sub new {
 102   my($class,@args) = @_;
 103   my $self = $class->SUPER::new(@args);
 104   my ($type) = $self->_rearrange([qw(TYPE)], @args);
 105   $self->type($type);
 106   return $self;
 107 }
 108
 109
 110 =head2 create
 111
 112  Title   : create
 113  Usage   : my $seq = $seqbuilder->create(-seq => 'CAGT', -id => 'name');
 114  Function: Instantiates new Bio::SeqI (or one of its child classes)
 115            This object allows us to genericize the instantiation of sequence
 116            objects.
 117  Returns : Bio::Seq object (default)
 118            The return type is configurable using new(-type =>"...").
 119  Args    : initialization parameters specific to the type of sequence
 120            object we want.  Typically
 121            -seq        => $str,
 122            -id         => $name
 123
 124 =cut
 125
 126 # Overloading the 'create' method of Bio::Seq::SeqFactory
 127 sub create {
 128     my ($self,@args) = @_;
 129
 130     my %param = @args;
 131     @param{ map { lc $_ } keys %param } = values %param; # lowercase keys
 132
 133     my $sequence = $param{'-seq'};
 134     my $fulldesc = $param{'-desc'};
 135     my $id       = defined $param{'-id'} ? $param{'-id'} : $param{'-primary_id'};
 136     my $alphabet = $param{'-alphabet'};
 137
 138     # Constructing Bio::PrimarySeq object
 139     my $t_pseq = bless {}, 'Bio::PrimarySeq';
 140     $t_pseq->{'seq'}  = $sequence;
 141     $t_pseq->{'desc'} = $fulldesc;
 142     $t_pseq->{'display_id'} = $id;
 143     if( $sequence and !$alphabet ) {
 144         $t_pseq->_guess_alphabet();
 145     } elsif ( $sequence and $alphabet ) {
 146         $t_pseq->{'alphabet'} = $alphabet;
 147     }
 148
 149     my $seq;
 150     my $type = $self->type;
 151     if ($type eq 'Bio::Seq') {
 152       # Constructing Bio::Seq object
 153       $seq = bless {}, 'Bio::Seq';
 154       $seq->{'primary_seq'} = $t_pseq;
 155     } elsif ($type eq 'Bio::PrimarySeq') {
 156       # Nothing more to do for a Bio::PrimarySeq
 157       $seq = $t_pseq;
 158     } else {
 159       # Should not have any other sequence type
 160       $self->warn("Expected sequence type Bio::Seq or Bio::PrimarySeq. Got ".
 161         "$type. Defaulting to Bio::PrimarySeq\n");
 162       $self->type('Bio::PrimarySeq');
 163       $seq = $t_pseq;
 164     }
 165
 166     return $seq;
 167 }
 168
 169
 170 =head2 type
 171
 172  Title   : type
 173  Usage   : $obj->type($newval)
 174  Function:
 175  Returns : value of type
 176  Args    : newvalue (optional)
 177
 178 =cut
 179
 180 # Using the 'type' method from Bio::Seq::SeqFactory
 181
 182
 183 1;
 184