view release on metacpan or  search on metacpan

Bio/Assembly/ScaffoldI.pm  view on Meta::CPAN

I<bioperl-l@bioperl.org>

rather than to the module maintainer directly. Many experienced and 
reponsive experts will be able look at the problem and quickly 
address it. Please include a thorough description of the problem 
with code and data examples if at all possible.

=head2 Reporting Bugs

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

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR - Robson Francisco de Souza

Email: rfsouza@citri.iq.usp.br

=head1 APPENDIX

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

=cut

#
# Now, let's code!


package Bio::Assembly::ScaffoldI;

use strict;
use Carp;

# Inheritance

use base qw(Bio::Root::RootI);

#
# Methods

=head1 Accessing general assembly data

=cut

=head2 get_nof_contigs

	Title   : get_nof_contigs
	Usage   : $assembly->get_nof_contigs()
	Function: Get the number of contigs included in the assembly
	Returns : integer
	Args    : none

=cut

sub get_nof_contigs {
    my $self = shift;

    $self->throw_not_implemented();
}

=head2 get_nof_singlets

	Title   : get_nof_singlets
	Usage   : $assembly->get_nof_singlets()
	Function: Get the number of singlets included in the assembly
	Returns : integer
	Args    : none

=cut

sub get_nof_singlets {
    my $self = shift;

    $self->throw_not_implemented();
}

=head2 get_contig_ids

	Title   : get_contig_ids
	Usage   : $assembly->get_contig_ids()
	Function: Access list of contig IDs from assembly
	Returns : an array if there are any contigs in the assembly.
                  undef otherwise
	Args    : an array of contig IDs

=cut

sub get_contig_ids {
    my $self = shift;

    $self->throw_not_implemented();
}

=head2 get_singlet_ids

	Title   : get_singlet_ids
	Usage   : $assembly->get_singlet_ids()
	Function: Access list of singlet IDs from assembly
	Returns : an array if there are any singlets in the assembly.
                  undef otherwise
	Args    : an array of singlet IDs

=cut

sub get_singlet_ids {
    my $self = shift;

    $self->throw_not_implemented();
}

=head2 get_contig_by_id

    Title   : get_contig_by_id
    Usage   : $assembly->get_contig_by_id($id)
    Function: Get a reference for a contig from the assembly
    Returns : a Bio::Assembly::Contig object or undef
    Args    : [string] contig unique identifier (ID)

=cut

sub get_contig_by_id {
    my $self = shift;
    $self->throw_not_implemented();
}

=head2 get_singlet_by_id

    Title   : get_singlet_by_id
    Usage   : $assembly->get_singlet_by_id()
    Function: Get a reference for a singlet from the assembly
    Returns : Bio::Assembly::Singlet object or undef
    Args    : [string] a singlet ID

=cut

sub get_singlet_by_id {
    my $self = shift;
    $self->throw_not_implemented();
}

=head1 Modifier methods

Implementation of these methods is optional in the sense that
read-only implementations may not have these. If an object implements
one of them, it should however implement all.

=cut

=head2 add_contig

	Title   : add_contig
	Usage   : $assembly->add_contig($contig)
	Function: Add another contig to the Bio::Assembly::ScaffoldI object
	Returns : 1 on success, 0 otherwise
	Args    : a Bio::Assembly:Contig object

    See Bio::Assembly::Contig for more information

=cut

#---------------------
sub add_contig {
#---------------------
	my ($self) = @_;
	$self->throw_not_implemented();
}

=head2 add_singlet

	Title   : add_singlet
	Usage   : $assembly->add_singlet($seq)
	Function: Add another singlet to the Bio::Assembly::ScaffoldI object
	Returns : 1 on success, 0 otherwise
	Args    : a Bio::Assembly::Singlet object

=cut

#---------------------
sub add_singlet {
#---------------------
	my ($self) = @_;
	$self->throw_not_implemented();
}

=head2 remove_contigs

        Title   : remove_contigs
	Usage   : $assembly->remove_contigs(1..4)
	Function: Remove contig from assembly object
	Returns : a Bio::Assembly::Contig object
	Args    : a list of contig IDs

    See function get_contig_ids() above

=cut

#---------------------
sub remove_contigs {
#---------------------
	my ($self) = @_;
	$self->throw_not_implemented();
}

=head2 remove_singlets

        Title   : remove_singlets
	Usage   : $assembly->remove_singlets(1..4)
	Function: Remove singlets from assembly object
	Returns : an array of Bio::Assembly::Singlet objects
	Args    : an array of singlet IDs 

    See function get_singlet_ids() above

=cut

#---------------------
sub remove_singlets {
#---------------------
	my ($self) = @_;
	$self->throw_not_implemented();
}

=head1 Contig and singlet selection methos

=cut

=head2 select_contigs

	Title   : select_contig
	Usage   : $assembly->select_contig
	Function: Selects an array of contigs from the assembly
	Returns : an array of Bio::Assembly::Contig objects
	Args    : an array of contig ids

    See function get_contig_ids() above

=cut

#---------------------
sub select_contigs {
#---------------------
	my ($self) = @_;
	$self->throw_not_implemented();
}

=head2 select_singlets

	Title   : select_singlets
	Usage   : $assembly->select_singlets(@list)
	Function: Selects an array of singlets from the assembly
	Returns : an array of Bio::Assembly::Singlet objects
	Args    : an array of singlet ids

    See function get_singlet_ids() above

=cut

#---------------------
sub select_singlets {
#---------------------
	my ($self) = @_;
	$self->throw_not_implemented();
}

=head2 all_contigs

	Title   : all_contigs
	Usage   : my @contigs = $assembly->all_contigs
	Function: Returns a list of all contigs in this assembly.
		  Contigs are both clusters and alignments of one
		  or more reads, with an associated consensus
		  sequence.
	Returns : array of Bio::Assembly::Contig
	Args    : none

=cut

#---------------------
sub all_contigs {
#---------------------
	my ($self) = @_;
	$self->throw_not_implemented();
}

=head2 all_singlets

    Title   : all_singlets
    Usage   : my @singlets = $assembly->all_singlets
    Function: Returns a list of all singlets in this assembly.
	      Singlets are isolated reads, without non-vector
	      matches to any other read in the assembly.
    Returns : array of Bio::Assembly::Singlet objects
    Args    : none

=cut

#---------------------
sub all_singlets {
#---------------------
	my ($self) = @_;
	$self->throw_not_implemented();
}

1;