lib/Bio/SeqIO/sgn_genomic.pm

   1 package Bio::SeqIO::sgn_genomic;
   2
   3 use strict;
   4 use English;
   5
   6 # Object preamble - inherits from Bio::Root::Object
   7
   8 use Bio::SeqIO;
   9 use Bio::Seq::SeqFactory;
  10 use Bio::Seq::SeqFastaSpeedFactory;
  11 use base 'Bio::SeqIO';
  12 use Carp;
  13
  14 use Class::MethodMaker
  15   [ scalar => [+{-type=>'CXGN::Genomic::Search::GSS::Query'},  'query',
  16                +{-type=>'CXGN::Genomic::Search::GSS::Result'}, 'result',
  17                +{-type=>'CXGN::Genomic::Search::GSS'},         'search',
  18               ]
  19   ];
  20
  21
  22 sub _initialize {
  23   my($self,@args) = @_;
  24
  25   my %a = @args; #bind em to a hash
  26
  27   $a{-query} or croak "Must provide search query via -query ($a{-query})";
  28   $a{-dbconn} && UNIVERSAL::isa($a{-dbconn},'CXGN::DB::Connection')
  29     or croak 'Must provide CXGN::DB::Connection object via -dbconn';
  30
  31   $self->query($a{-query});
  32   $self->search( CXGN::Genomic::Search::GSS->new($self->query) );
  33
  34   $self->SUPER::_initialize(@args);
  35   unless ( defined $self->sequence_factory ) {
  36       $self->sequence_factory( Bio::Seq::SeqFactory->new( -type => 'Bio::Seq::CXGNGenomic' ) );
  37   }
  38
  39   #set the results object to autopage through the results
  40   $self->query->order_by(gss_id => 'asc');
  41   $self->result($self->search->new_result);
  42   $self->result->autopage($self->query,$self->search);
  43 }
  44
  45 =head2 next_seq
  46
  47  Title   : next_seq
  48  Usage   : $seq = $stream->next_seq()
  49  Function: returns the next sequence in the stream
  50  Returns : Bio::Seq object or undef if no more sequences
  51  Args    : NONE
  52
  53 =cut
  54
  55 sub next_seq {
  56     my( $self ) = @_;
  57     my $alphabet;
  58
  59     #note: initialize above put the result in autopage mode
  60     my $gss = $self->result->next_result
  61       or return undef;
  62
  63     ### at this point, $gss _must_ contain our new gss object ###
  64     $gss->isa('CXGN::Genomic::GSS')
  65       or die 'there is something wrong with this code';
  66
  67 #    print 'try gss '.$gss->gss_id." ($gss)\n";
  68 #    my $seq =
  69 #    eval {
  70     $gss->to_bio_seq( -factory => $self->sequence_factory );
  71 #     }; if($EVAL_ERROR) {
  72 #       use Data::Dumper;
  73 #       warn $EVAL_ERROR;
  74 #       die Dumper($gss);
  75 #     }
  76 #    print "got seq $seq\n";
  77 #    print "got gss ".$seq->gss_object."\n";
  78 #    return sequences$seq;
  79 }
  80
  81 =head2 write_seq
  82
  83  Title   : write_seq
  84  Usage   : this method is not implemented.  writing to the
  85            genomic database is not allowed through this interface
  86
  87 =cut
  88
  89 sub write_seq {
  90   croak 'write_seq not implemented.  Writing to the genomic database is not allowed through this interface';
  91 }
  92
  93 =head2 result
  94
  95   Accessor for this seqIO GSS results object
  96
  97 =head2 query
  98
  99   Accessor for this seqIO GSS results object
 100
 101 =head2 search
 102
 103   Accessor for this seqIO GSS results object
 104
 105 =cut
 106
 107 ###
 108 1;#do not remove
 109 ###