lib/Bio/SeqIO/xform.pm

   1 package Bio::SeqIO::xform;
   2
   3 use strict;
   4 # Object preamble - inherits from Bio::Root::Object
   5
   6 use Bio::SeqIO;
   7 use Bio::Seq::SeqFactory;
   8 use Bio::Seq::SeqFastaSpeedFactory;
   9 use UNIVERSAL qw/isa/;
  10 use base 'Bio::SeqIO';
  11 use Carp;
  12
  13 sub _initialize {
  14   my($self,@args) = @_;
  15
  16   my %a = @args; #bind em to a hash
  17
  18   ### check input ###
  19   $a{-enclose} && isa($a{-enclose},'Bio::SeqIO')
  20     or croak "Must provide SeqIO to map via -enclose";
  21
  22   ref $a{-map_next} eq 'CODE'
  23     or croak '-map_next must be a subroutine reference'
  24       if($a{-map_next});
  25
  26   ref $a{-map_write} eq 'CODE'
  27     or croak '-map_write must be a subroutine reference'
  28       if($a{-map_write});
  29
  30   @{$self}{qw/_seqio    _next      _write    /} =
  31     @a{qw/    -enclose  -map_next  -map_write/};
  32
  33   $self->SUPER::_initialize(@args);
  34 }
  35
  36
  37 =head2 enclosed
  38
  39   Ret : the enclosed SeqIO object, or undef if none set
  40
  41 =cut
  42
  43 sub enclosed {
  44   my $this = shift;
  45   UNIVERSAL::isa($this,__PACKAGE__)
  46       or croak 'improper use of enclosed(), which is a method of '.__PACKAGE__;
  47   $this->{_seqio};
  48 }
  49
  50
  51 #ret: new page number
  52 # sub _params_nextpage {
  53 #   my $self = shift;
  54 #   if ( defined $self->{_sgn_pagenum} ) {
  55 #     $self->{_sgn_pagenum}++;
  56 #   } else {
  57 #     $self->{_sgn_pagenum} = 0;
  58 #   }
  59 #   $self->params->page($self->{_sgn_pagenum});
  60 # }
  61
  62 =head2 next_seq
  63
  64  Title   : next_seq
  65  Usage   :
  66  Function: returns the next sequence in the stream
  67  Returns : Bio::Seq object
  68  Args    : NONE
  69
  70 =cut
  71
  72 sub next_seq {
  73
  74     my( $self ) = @_;
  75
  76     my $nextseq = $self->{_seqio}->next_seq;
  77     return $nextseq unless $nextseq;
  78
  79     $self->{_next} ? $self->{_next}->($nextseq) : $nextseq;
  80 }
  81
  82 =head2 write_seq
  83
  84  Title   : write_seq
  85  Usage   :
  86
  87 =cut
  88
  89 sub write_seq {
  90   my $self = shift;
  91   my @seqs = @_;
  92
  93   $self->{_seqio}->write_seq(
  94                              $self->{_write} ?
  95                                $self->{_write}->(@seqs) :
  96                                @seqs
  97                             );
  98 }
  99
 100 ###
 101 1;#do not remove
 102 ###