Sarah Richardson avatar Sarah Richardson committed 2627072

removing traces of DNAssemble

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Files changed (2)

lib/Bio/GeneDesign.pm

   return $seqarr;
 }
 
-=head2 filter_uniqueness
-
-NO TEST
-
-=cut
-
-sub filter_uniqueness
-{
-  my ($self, @args) = @_;
-  
-  my ($seqs) = $self->_rearrange([qw(sequences)], @args);
-
-  $self->throw("no argument provided to filter_uniqueness")
-	  unless $seqs;
-
-  my $arrref = $self->_stripdown($seqs, 'ARRAY', 1);
-  
-  my $seqarr = _filter_uniqueness( $arrref );
-  return $seqarr;
-}
-
-=head2 filter_palindromes
-
-=cut
-
-sub filter_palindromes
-{
-  my ($self, @args) = @_;
-  
-  $self->throw("EMBOSS palindrome is not available")
-    unless $self->EMBOSS;
-
-  my ($seqobjs, $minpallen, $maxpallen, $gaplimit, $mismatches)
-    = $self->_rearrange([qw(
-        sequences
-        minpallen
-        maxpallen
-        gaplimit
-        mismatches)], @args);
-
-  $self->throw("no nucleotide sequences provided")
-	  unless $seqobjs;
-
-  $self->throw("sequences argument is not an array reference")
-    unless ref($seqobjs) eq "ARRAY";
-
-  $minpallen = $minpallen || 8;
-  $maxpallen = $maxpallen || 20;
-  my $maxlen = undef;
-  foreach my $seqobj (@$seqobjs)
-  {
-    $self->throw(ref($seqobj) . " is not a Bio::Seq object")
-      unless $seqobj->isa("Bio::Seq");
-
-    $self->throw("$seqobj is not a nucleotide sequence")
-      unless $seqobj->alphabet eq "dna";
-    my $len = $seqobj->length();
-    $maxlen = $len if (! $maxlen || $len > $maxlen);
-  }
-#  $maxpallen = sprintf "%.0f", .5 * $maxlen if ($maxpallen > .5 * $maxlen);
-  
-  my $writedir = $self->{tmp_path} || "./";
-  $gaplimit = $gaplimit  || 10;
-  $mismatches = $mismatches || 1;
-
-  my $seqarr = _filter_palindromes( $seqobjs,
-                                  $minpallen,
-                                  $maxpallen,
-                                  $gaplimit,
-                                  $mismatches,
-                                  $writedir);
-  return $seqarr;
-}
-
-=head2 filter_vmatch
-
-=cut
-
-sub filter_vmatch
-{
-  my ($self, @args) = @_;
-  
-  $self->throw("vmatch filtering is not available")
-    unless $self->vmatch;
-
-  my ($parent, $seqobjs, $mismatches, $revcom)
-    = $self->_rearrange([qw(
-        parent
-        sequences
-        mismatches
-        revcom)], @args);
-
-  $self->throw("no nucleotide sequences provided")
-	  unless $seqobjs;
-
-  $self->throw("sequences argument is not an array reference")
-    unless ref($seqobjs) eq "ARRAY";
-  
-  foreach my $seqobj (@$seqobjs)
-  {
-    $self->throw("sequence argument is not a Bio::Seq object")
-      unless $seqobj->isa("Bio::Seq");
-
-    $self->throw("$seqobj is not a nucleotide sequence")
-      unless $seqobj->alphabet eq "dna";
-  }
-  
-  $self->throw("no parent sequence provided")
-	  unless $parent;
-
-  $self->throw("parent argument is not a Bio::Seq object")
-    unless $parent->isa("Bio::Seq");
-
-  $self->throw("$parent is not a nucleotide sequence")
-    unless $parent->alphabet eq "dna";
-  
-  my $writedir = $self->{tmp_path} || "./";
-  $mismatches = $mismatches || 7;
-  $revcom = $revcom || 1;
-
-  my $seqarr = _filter_vmatch(  $parent,
-                                $seqobjs,
-                                $mismatches,
-                                $revcom,
-                                $writedir);
-  return $seqarr;
-}
-
 =head2 search_vmatch
 
 =cut

lib/Bio/GeneDesign/Oligo.pm

 
 use base qw(Exporter);
 our @EXPORT_OK = qw(
-  _filter_uniqueness
   _make_amplification_primers
   _filter_homopolymer
   _check_for_homopolymer
 
 =head1 Functions
 
-=head2 _filter_uniqueness()
-
-=cut
-
-sub _filter_uniqueness
-{
-  my ($seqarr) = @_;
-  my %hsh = ();
-  
-  $hsh{$_->seq}++ foreach (@$seqarr);
-  
-  my @newarr = grep {$hsh{$_->seq} == 1} @$seqarr;
-
-  return \@newarr;
-}
-
-
 =head2 _filter_homopolymer()
 
 =cut
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