diff variant_effect_predictor/Bio/Assembly/ScaffoldI.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Assembly/ScaffoldI.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,340 @@
+# $Id: ScaffoldI.pm,v 1.2 2002/11/11 18:16:30 lapp Exp $
+#
+#  BioPerl module for Bio::Assembly::ScaffoldI
+#
+# Copyright by Robson F. de Souza
+#
+# You may distribute this module under the same terms as perl itself
+#
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Assembly::ScaffoldI - Abstract Inteface of Sequence Assemblies
+
+=head1 SYNOPSYS
+
+    # get a Bio::Assembly::ScaffoldI object somehow
+
+    foreach my $contig ($assembly->all_contigs) {
+       # do something (see Bio::Assembly::Contig)
+    }
+
+=head1 DESCRIPTION
+
+This interface defines the basic set of methods an object should have
+to manipulate assembly data.
+
+=head1 FEEDBACK
+
+=head2 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.
+
+  [e-mail]                 - General discussion
+  http://bio.perl.org/MailList.html     - About the mailing lists
+
+=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 email
+or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Robson Francisco de Souza
+
+Email: [e-mail]
+
+=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 vars qw(@ISA);
+use Carp;
+use Bio::Root::RootI;
+
+# Inheritance
+
+@ISA = 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::PrimarySeqI 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::Align::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   : $assembly->remove_singlets(1..4)
+	Function: Remove singlet from assembly object
+	Returns : a Bio::SeqI object
+	Args    : a list of singlet IDs 
+
+    See function get_singlet_ids() above
+
+=cut
+
+#---------------------
+sub remove_singlets {
+#---------------------
+	my ($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   : $assembly->select_singlets(@list)
+	Function: Selects an array of singlets from the assembly
+	Returns : an array of Bio::SeqI objects
+	Args    : an array of singlet ids
+
+    See function get_singlet_ids() above
+
+=cut
+
+#---------------------
+sub select_singlets {
+#---------------------
+	my ($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 = $assembly->all_singlets
+    Function: Returns a list of all singlets in this assembly.
+	      Singlets are isolated reads, without non-vector
+	      matches to any other read in the assembly.
+    Returns : array of Bio::Assembly::Contig
+    Args    : none
+
+=cut
+
+#---------------------
+sub all_singlets {
+#---------------------
+	my ($self) = @_;
+	$self->throw_not_implemented();
+}
+
+1;