NAME

       Bio::Assembly::ScaffoldI - Abstract Interface of Sequence Assemblies

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.

FEEDBACK

   Mailing Lists
       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
       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 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

AUTHOR - Robson Francisco de Souza

       Email: rfsouza@citri.iq.usp.br

APPENDIX

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

Accessing general assembly data

   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

   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

   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

   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

   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)

   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

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.

   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

   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

   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

   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

Contig and singlet selection methos

   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

   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

   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

   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