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Summary

Bio::CorbaServer::PrimarySeq - PrimarySeq server bindings

Package variables

Included modules

Inherit

Bio::CorbaServer::Base POA_bsane::seqcore::AnonymousSequence

Synopsis

    # get a Bio::CorbaServer::PrimarySeq somehow
    my $seqstring = $seq->seq;

Description

This object represents the binding of the Primary Sequence
object in Bioperl to the BioCorba object. This is pretty
simple as the objects are almost identical

Methods

Methods description

 Title   : get_type
 Usage   : my $type = $self->get_type();
 Function: Return the type of the biological sequence, e.g. PROTEIN,
	   RNA, DNA,
 Returns : type [ PROTEIN, RNA, DNA]
 Args    : [optional] type to set for this sequence

 Title   : is_circular
 Usage   : $obj->is_circular()
 Function: Return whether the biological sequence is circular or linear
 Example :
 Returns : boolean
 Args    : value to set (non zero is true)

 Title   : get_length
 Usage   : my $len = $obj->get_length
 Function: returns length of biological sequence
 Returns : long
 Args    : none

 Title   : seq
 Usage   : my $seqstr = $obj->seq
 Function: biological sequence as a string
 Returns : string representing sequence contained
 Args    : none

 Title   : sub_seq
 Usage   : $self->sub_seq($begin,$end)
 Function: obtains a subsequence of the biological sequence as a string
 Returns : subseq of sequence beginning at start finishing at end
 Args    : start - start point of substring to obtain (sequence start at 1)
           end   - end point of substring to obtain

 Title   : _seq
 Usage   : get/set seq reference
 Function:
 Example : $self->_seq($new_seq)
 Returns : reference to underlying contained seq object
 Args    : [optional] new-value

 Title   : max_request_length
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

 Title   : get_id
 Usage   : my $id = $seq->accession();
 Function: Retrieve a sequence id (accession number)
 Returns : string
 Args    : none

 Title   : get_name
 Usage   : my $name = $seq->get_name();
 Function: Retrieves a sequence name
 Returns : string
 Args    : nonex

 Title   : get_description
 Usage   : my $desc = $seq->get_description();
 Function: Retrieves the description for this sequence
 Returns : string 
 Args    : none

 Title   : get_basis
 Usage   : my $basis = $seq->get_basis
 Function: Retrieves the basis this sequence is from (always experimental)
 Returns : numeric
 Args    : none

Methods code

sub new {

    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
    my ($seq) = $self->_rearrange([qw(SEQ)],@args);

    if( ! defined $seq || !ref $seq || ! $seq->isa('Bio::PrimarySeqI') ) {
	$seq = '' if( !defined $seq );
	$self->throw($class ." got a non sequence [$seq] for server object");
    }
    $self->_seq($seq);
    $self->is_circular(0);  
    return $self;

}

sub get_type {

    my $self = shift;
    # this returns a string representing the alphabet
    my $moltype = uc $self->_seq->alphabet;
    if(  $moltype eq 'DNA' ) {
	return 1;
    } elsif ( $moltype eq 'RNA' ) {
	return 2;
    } elsif ( $moltype =~ /PROT/i ) {
	return 0;
    } else { 
	return -1;
    }

}

sub is_circular {

    my ($self,$value) = @_;
    if( defined $value ) {
	$self->{'_circular'} = $value;
    }
    return defined $self->{'_circular'} && $self->{'_circular'} ? 1 : 0;

}

sub get_length {

    my $self = shift;
    return $self->_seq->length();

}

sub seq {

    my $self = shift;
    my $seqstr = $self->_seq->seq;

    return $seqstr;

}

sub sub_seq {

    my ($self,$start,$end) = @_;
    if( !defined $end || !defined $start || ($end < $start) ) {
	$start = '' if( !defined $start);
	$end = '' if( !defined $end);
	throw bsane::OutOfBounds
	    (reason=>"start is not before end ($start,$end)");
    } elsif( ($end - $start ) > $self->max_request_length ) {
	throw bsane::RequestTooLarge
	    (reason=> ($end-$start) . " is larger than max request length", 
	     suggested_size=>$self->max_request_length);
    } 

    my $seqstr;
    eval {
	$seqstr = $self->_seq->subseq($start,$end);
    };
    if( $@ ) {	
	throw bsane::OutOfRange(reason=>$@);
    } 
    
    return $seqstr;

}

sub _seq {

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

}

sub max_request_length {

   my ($self,@args) = @_;

   return 100000;

}

sub get_id {

   my ($self) = @_;
   return $self->_seq->accession || $self->_seq->display_id();

}

sub get_name {

   my ($self) = @_;
   return $self->_seq->display_id();

}

sub get_description {

   my ($self,@args) = @_;
   return $self->_seq->desc();

}

sub get_basis {

   my ($self) = @_;
   return 1; # 1 is experimental

}

1;

}

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                 - BioPerl discussion
  biocorba-l@biocorba.org               - BioCorba discussion
  http://www.bioperl.org/MailList.html  - About the BioPerl mailing list
  http://www.biocorba.org/MailList.html - About the BioCorba mailing list

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
jason@bioperl.org

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

Private Methods local to this module