lib/Bio/Seq/CXGNGenomic.pm

   1 package Bio::Seq::CXGNGenomic;
   2
   3 use Carp;
   4 use English;
   5 use base qw/Bio::Seq::Quality/;
   6 use Data::Dumper;
   7
   8 use Class::MethodMaker
   9   [
  10    scalar => [ +{-type => 'CXGN::Genomic::GSS'}, 'gss_object' ],
  11   ];
  12
  13 #allowed to make new CXGNGenomic seqs
  14 sub can_call_new {
  15   1;
  16 }
  17
  18 sub vector_trimmed_trunc {
  19   my $this = shift;
  20   shift && croak 'Too many arguments to trimmed_seq.';
  21
  22 #  print 'trimmed qual is '.$this->gss_object->trimmed_qual."\n";
  23
  24   __PACKAGE__->new(-display_id       => $this->display_id,
  25                    -accession_number => $this->accession_number,
  26                    -alphabet         => $this->alphabet,
  27                    -desc             => $this->desc.' (vector and quality trimmed)',
  28                    -verbose          => $this->verbose,
  29                    -primary_id       => $this->primary_id,
  30                    -seq              => $this->gss_object->trimmed_seq,
  31                    -qual             => $this->gss_object->trimmed_qual || '1',
  32                    #above strange || '1' is there to sidestep BioPerl bugzilla bug #1824
  33                   );
  34 }
  35
  36
  37
  38 ###
  39 1;# do not remove
  40 ###