Summary

Bio::Seq::RichSeq - Module implementing a sequence created from a rich
sequence database entry

Package variables

Included modules

Inherit

Bio::Seq Bio::Seq::RichSeqI

Synopsis

See Bio::Seq::RichSeqI and documentation of methods.

Description

This module implements Bio::Seq::RichSeqI, an interface for sequences
created from or created for entries from/of rich sequence databanks,
like EMBL, GenBank, and SwissProt. Methods added to the Bio::SeqI
interface therefore focus on databank-specific information. Note that
not every rich databank format may use all of the properties provided.

Methods

Methods description

 Title   : new
 Usage   : $seq    = Bio::Seq::RichSeq->new( -seq => 'ATGGGGGTGGTGGTACCCT',
                                             -id  => 'human_id',
				             -accession_number => 'AL000012',
				            );

 Function: Returns a new seq object from
           basic constructors, being a string for the sequence
           and strings for id and accession_number
 Returns : a new Bio::Seq::RichSeq object

 Title   : division
 Usage   : $obj->division($newval)
 Function: 
 Returns : value of division
 Args    : newvalue (optional)

 Title   : molecule
 Usage   : $obj->molecule($newval)
 Function: 
 Returns : type of molecule (DNA, mRNA)
 Args    : newvalue (optional)

 Title   : add_date
 Usage   : $self->add_date($datestr)
 Function: adds a date
 Example :
 Returns : a date string or an array of such strings
 Args    :

 Title   : get_dates
 Usage   :
 Function:
 Example :
 Returns : an array of date strings
 Args    :

 Title   : pid
 Usage   :
 Function: Get (and set, depending on the implementation) the PID property
           for the sequence.
 Example :
 Returns : a string
 Args    :

 Title   : accession
 Usage   : $obj->accession($newval)
 Function: Whilst the underlying sequence object does not 
           have an accession, so we need one here.

           In this implementation this is merely a synonym for
           accession_number().
 Example : 
 Returns : value of accession
 Args    : newvalue (optional)

 Title   : add_secondary_accession
 Usage   : $self->add_domment($ref)
 Function: adds a secondary_accession
 Example :
 Returns : 
 Args    : a string or an array of strings

 Title   : get_secondary_accessions
 Usage   :
 Function:
 Example :
 Returns : An array of strings
 Args    :

 Title   : seq_version
 Usage   : $obj->seq_version($newval)
 Function: 
 Example : 
 Returns : value of seq_version
 Args    : newvalue (optional)

 Title   : keywords
 Usage   : $obj->keywords($newval)
 Function: 
 Returns : value of keywords (a string)
 Args    : newvalue (optional) (a string)

Methods code

sub new {

    # standard new call..
    my($caller,@args) = @_;
    my $self = $caller->SUPER::new(@args);
    
    $self->{'_dates'} = [];
    $self->{'_secondary_accession'} = [];

    my ($dates, $xtra, $sv,
	$keywords, $pid, $mol, 
	$division ) = $self->_rearrange([qw(DATES 
					   SECONDARY_ACCESSIONS
					   SEQ_VERSION 
					   KEYWORDS
					   PID
					   MOLECULE
					   DIVISION
					   )],
				   @args);
    defined $division && $self->division($division);
    defined $mol && $self->molecule($mol);
    defined $keywords && $self->keywords($keywords);
    defined $sv && $self->seq_version($sv);
    defined $pid && $self->pid($pid);

    if( defined $dates ) {
	if( ref($dates) =~ /array/i ) {
	    foreach ( @$dates) {
		$self->add_date($_);
	    } 
	} else { 
	    $self->add_date($dates);
	}
    }

    if( defined $xtra ) {
	if( ref($xtra) =~ /array/i ) {
	    foreach ( @$xtra) {
		$self->add_secondary_accession($_);
	    } 
	} else { 
	    $self->add_secondary_accession($xtra);
	}
    }
    
    return $self;

}

sub division {

   my $obj = shift;
   if( @_ ) {
      my $value = shift;
      $obj->{'_division'} = $value;
    }
    return $obj->{'_division'};

}

sub molecule {

   my $obj = shift;
   if( @_ ) {
      my $value = shift;
      $obj->{'_molecule'} = $value;
    }
    return $obj->{'_molecule'};

}

sub add_date {

   my ($self,@dates) = @_;
   foreach my $dt ( @dates ) {
       push(@{$self->{'_dates'}},$dt);
   }

}

sub get_dates {

   my ($self) = @_;
   return @{$self->{'_dates'}};

}

sub pid {

    my ($self,$pid) = @_;
    
    if(defined($pid)) {
	$self->{'_pid'} = $pid;
    }
    return $self->{'_pid'};

}

sub accession {

   my ($obj,@args) = @_;
   return $obj->accession_number(@args);

}

sub add_secondary_accession {

   my ($self) = shift;
   foreach my $dt ( @_ ) {
       push(@{$self->{'_secondary_accession'}},$dt);
   }

}

sub get_secondary_accessions {

   my ($self,@args) = @_;
   return @{$self->{'_secondary_accession'}};

}

sub seq_version {

   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'_seq_version'} = $value;
    }
    return $obj->{'_seq_version'};

}

sub keywords {

   my $obj = shift;
   if( @_ ) {
      my $value = shift;
      $obj->{'_keywords'} = $value;
    }
    return $obj->{'_keywords'};

}

sub each_date {

   my ($self) = @_;
   $self->warn("Deprecated method... please use get_dates");
   return $self->get_dates;

}

sub each_secondary_accession {

   my ($self) = @_;
   $self->warn("each_secondary_accession - deprecated method. use get_secondary_accessions");
   return $self->get_secondary_accessions;

}

sub sv {

   my ($obj,$value) = @_;
   $obj->warn("sv - deprecated method. use seq_version");
   $obj->seq_version($value);

}

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://bio.perl.org/bioperl-bugs/

Email birney@ebi.ac.uk
Describe contact details here

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