Bio::Assembly ScaffoldI
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Summary
Bio::Assembly::ScaffoldI - Abstract Inteface of Sequence Assemblies
Package variables
No package variables defined.
Included modules
Carp
Inherit
Bio::Root::RootI
Synopsis
    # get a Bio::Assembly::ScaffoldI object somehow
foreach my $contig ($assembly->all_contigs) { # do something (see Bio::Assembly::Contig) }
Description
This interface defines the basic set of methods an object should have
to manipulate assembly data.
Methods
get_nof_contigsDescriptionCode
get_nof_singletsDescriptionCode
get_contig_idsDescriptionCode
get_singlet_idsDescriptionCode
get_contig_by_idDescriptionCode
get_singlet_by_idDescriptionCode
add_contigDescriptionCode
add_singletDescriptionCode
remove_contigsDescriptionCode
remove_singletsDescriptionCode
select_contigsDescriptionCode
select_singletsDescriptionCode
all_contigsDescriptionCode
all_singletsDescriptionCode
Methods description
get_nof_contigscode    nextTop
	Title   : get_nof_contigs
Usage : $assembly->get_nof_contigs()
Function: Get the number of contigs included in the assembly
Returns : integer
Args : none
get_nof_singletscodeprevnextTop
	Title   : get_nof_singlets
Usage : $assembly->get_nof_singlets()
Function: Get the number of singlets included in the assembly
Returns : integer
Args : none
get_contig_idscodeprevnextTop
	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
get_singlet_idscodeprevnextTop
	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
get_contig_by_idcodeprevnextTop
    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)
get_singlet_by_idcodeprevnextTop
    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
add_contigcodeprevnextTop
	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
add_singletcodeprevnextTop
	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
remove_contigscodeprevnextTop
        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
remove_singletscodeprevnextTop
        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
select_contigscodeprevnextTop
	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
select_singletscodeprevnextTop
	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
all_contigscodeprevnextTop
	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
all_singletscodeprevnextTop
    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
Methods code
get_nof_contigsdescriptionprevnextTop
sub get_nof_contigs {
    my $self = shift;

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

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

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

    $self->throw_not_implemented();
}
get_contig_by_iddescriptionprevnextTop
sub get_contig_by_id {
    my $self = shift;
    $self->throw_not_implemented();
}
get_singlet_by_iddescriptionprevnextTop
sub get_singlet_by_id {
    my $self = shift;
    $self->throw_not_implemented();
}
add_contigdescriptionprevnextTop
sub add_contig {
#---------------------
my ($self) = @_; $self->throw_not_implemented();
}
add_singletdescriptionprevnextTop
sub add_singlet {
#---------------------
my ($self) = @_; $self->throw_not_implemented();
}
remove_contigsdescriptionprevnextTop
sub remove_contigs {
#---------------------
my ($self) = @_; $self->throw_not_implemented();
}
remove_singletsdescriptionprevnextTop
sub remove_singlets {
#---------------------
my ($self) = @_; $self->throw_not_implemented();
}
select_contigsdescriptionprevnextTop
sub select_contigs {
#---------------------
my ($self) = @_; $self->throw_not_implemented();
}
select_singletsdescriptionprevnextTop
sub select_singlets {
#---------------------
my ($self) = @_; $self->throw_not_implemented();
}
all_contigsdescriptionprevnextTop
sub all_contigs {
#---------------------
my ($self) = @_; $self->throw_not_implemented();
}
all_singletsdescriptionprevnextTop
sub all_singlets {
#---------------------
my ($self) = @_; $self->throw_not_implemented(); } 1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing lists Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
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.
Reporting BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Robson Francisco de SouzaTop
Email: rfsouza@citri.iq.usp.br
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
Accessing general assembly dataTop
Modifier methodsTop
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.
Contig and singlet selection methosTop