Summary

Bio::SeqFeature::Primer - Primer Generic SeqFeature

Package variables

Included modules

Inherit

Bio::Root::Root Bio::SeqFeature::Generic

Synopsis

     A synopsis does not yet exist for this module.

Description

     A description does not yet exist for this module.

Methods

Methods description

 Title   : new()
 Usage   :
 Function:
 Example :
 Returns :
 Args    : 
Devel notes: I think that I want to accept a hash

 Title   : seq()
 Usage   : $seq = $primer->seq();
 Function: Return the _entire_ sequence associated with this Primer. 
 Returns : A Bio::Seq object
 Args    : None.
Develper Note: Do you want to be able to set the sequence associated with this
     SeqFeature?

 Title   : all_tags()
 Usage   : @tags = $primer->all_tags();
 Function: Return a list of tag names for this Primer.
 Returns : An array of strings representing the names of tags in this Primer
 Args    : None.
 Notes   : When the Bio::SeqFeature::Primer object is created, the user can
     pass in an arbitrary hash containing key->value pairs. This is allowed
     because I didn't want to assume that the user was trying to model a
     primer3 construct.

 Title   : primary_tag()
 Usage   : $tag = $feature->primary_tag();
 Function: Returns the string "Primer"
 Returns : A string.
 Args    : None.

 Title   : source_tag()
 Usage   : $tag = $feature->source_tag();
 Function: Returns the source of this tag.
 Returns : A string.
 Args    : If an argument is provided, the source of this SeqFeature
     is set to that argument.

 Title   : has_tag()
 Usage   : $true_or_false = $feature->has_tag('MELTING_TEMPERATURE');
 Function: Does this SeqFeature have this tag?
 Returns : TRUE or FALSE
 Args    : A string.

 Title   : each_tag_value()
 Usage   : $tag = $feature->each_tag_value('MELTING_TEMPERATURE');
 Function: Returns the value of this tag.
 Returns : Unknown. Whatever the value of the given tag was.
 Args    : None.

 Title   : location()
 Usage   : $tag = $feature->location();
 Function: returns a location object suitable for identifying location of
     feature on sequence or parent feature  
 Returns : a bio::locationi object.
 Args    : none.
Developer Notes: Chad has no idea how to implement this at this time.

 Title   : start()
 Usage   : $start_position = $feature->start($new_position);
 Function: Return the start position of this Primer.
 Returns : The start position of this Primer.
 Args    : If an argument is provided, the start position of this
     Primer is set to that position.

 Title   : end()
 Usage   : $end_position = $feature->end($new_position);
 Function: Return the end position of this Primer.
 Returns : The end position of this Primer.
 Args    : If an argument is provided, the end position of this
     Primer is set to that position.

 Title   : strand()
 Usage   : 
 Function: 
 Returns : 
 Args    : 
Developer Notes: Chad has no idea how to implement this at this time.

 Title   : display_id()
 Usage   : $id = $feature->display_id($new_id)
 Function: Returns the display ID for this Primer feature
 Returns : A scalar.
 Args    : If an argument is provided, the display_id of this Primer is
     set to that value.

Methods code

sub new {

     my ($class, @args) = @_;  
     my %arguments = @args;
     my $self = $class->SUPER::new(@args);
          # these are from generic.pm, with which i started
     $self->{'_parse_h'}       = {};
     $self->{'_gsf_tag_hash'}  = {}; 
          # things that belong with the primer
     my ($sequence, $primer_sequence_id, $id) = 
     $self->{'_gsf_seqname'} = $self->{primer_sequence_id};
          # i am going to keep an array of the things that have been passed
          # into the object on construction. this will aid retrieval of these
          # things later
     foreach my $argument (sort keys %arguments) {
          if ($argument eq "-SEQUENCE" || $argument eq "-sequence") {
               if (ref($arguments{$argument}) eq "Bio::Seq") {
                    $self->{seq} = $arguments{$argument};
               }
               else {
                    $self->{seq} = new Bio::Seq( -seq => $arguments{$argument},
                                                  -id => $arguments{-id});
               }
               $self->{tags}->{$argument} = "A Bio::Seq. Use seq() to get this 'tag'";
          }
          else {
               (my $fixed = $argument) =~ s/-//;
               $self->{tags}->{$fixed} = $arguments{$argument};
          }
     }
     if (!$self->{seq}) {
          $self->throw("You must pass in a sequence to construct this object.");
     }
     
               # a bunch of things now need to be set for this SeqFeature
               # things like:
                    # TARGET=513,26
                    # PRIMER_FIRST_BASE_INDEX=1
                    # PRIMER_LEFT=484,20
          return $self;

}

sub seq {

     my $self = shift;
     return $self->{seq};

}

sub all_tags {

     my $self = shift;
     my @tags = sort keys %{$self->{tags}};
     return @tags;

}

sub primary_tag {

     return "Primer";

}

sub source_tag {

     my ($self,$insource) = @_;
     if ($insource) { $self->{source} = $insource; }
     return $self->{source};

}

sub has_tag {

     my ($self,$tagname) = @_;
     if ($self->{tags}->{$tagname}) { return "TRUE"; }
     return { "FALSE" };

}

sub each_tag_value {

     my ($self,$tagname) = @_;
     return $self->{tags}->{$tagname};

}

sub location {

     my $self = shift;
     $self->warn("Chad has not written the code for this yet.");

}

sub start {

     my ($self,$new_position) = @_;
     if ($new_position) { $self->{start_position} = $new_position; }
     return $self->{start_position};

}

sub end {

     my ($self,$new_position) = @_;
     if ($new_position) { $self->{end_position} = $new_position; }
     return $self->{end_position};

}

sub strand {

     my $self = shift;
     $self->warn("Chad has not implemented this method at this time.");

}

sub display_id {

     my ($self,$newid) = @_;
     if ($newid) { $self->seq()->display_id($newid); }
     return $self->seq()->display_id();

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org          - General discussion
  http://bio.perl.org/MailList.html             - About the mailing lists

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

Chad Matsalla <bioinformatics1@dieselwurks.com>

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _