comparison variant_effect_predictor/Bio/LiveSeq/ChainI.pm @ 0:1f6dce3d34e0

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# $Id: ChainI.pm,v 1.9 2002/10/22 07:38:34 lapp Exp $
#
# bioperl module for Bio::LiveSeq::ChainI
#
# Cared for by Joseph Insana <[e-mail]> <[e-mail]>
#
# Copyright Joseph Insana
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code

=head1 NAME

Bio::LiveSeq::ChainI - Double linked chain data structure

=head1 SYNOPSIS

  #documentation needed

=head1 DESCRIPTION

This class generates and manipulates generic double linked list, chain,
that can be used to manage biological sequences.

The advantages over strings or plain arrays is the ease of tracking
changes (mutations) in the elements (sequence). The other side of the
coin is that these structures need consideraly more memory, but that
is cheap and constantly inceasing resource in computers.

=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 one
of 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 - Joseph A.L. Insana

Email:  [e-mail], [e-mail]
Address: 

     EMBL Outstation, European Bioinformatics Institute
     Wellcome Trust Genome Campus, Hinxton
     Cambs. CB10 1SD, United Kingdom 

=head1 APPENDIX

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

=cut

# Let the code begin...

package Bio::LiveSeq::ChainI;
$VERSION=1.9;
# Version history:
# Thu Mar 16 01:38:25 GMT 2000 v.1.4 1st wraparound of methods complete
#                                    tested with chainseq_asobj_test.pl
# Thu Mar 16 19:03:56 GMT 2000 v.1.5 decided to stick with same names as Chain
# Fri Mar 17 05:08:15 GMT 2000 v.1.6 in sync with Chain 2.4
# Fri Mar 17 15:47:23 GMT 2000 v.1.7 added pos_of_label, enforced down_ or up_
# Fri Mar 17 20:12:27 GMT 2000 v.1.8 NAMING change: index->label everywhere
# Mon Mar 20 19:20:17 GMT 2000 v.1.81 minor addings, Chain 2.52
# Mon Mar 20 23:15:09 GMT 2000 v.1.82 in sync with Chain 2.6
# Tue Mar 21 01:36:29 GMT 2000 v.1.83 added default strand if new(DNA)
# Tue Mar 21 14:19:17 GMT 2000 v.1.9 moved new(DNA) to DNA, added chain2string()

use Carp qw(croak);
use strict; # this will be moved before when strict enforced in Chain.pm

use Bio::LiveSeq::Chain 2.6; # package where all the subroutines are defined


=head2 new
    
  Title   : new
  Usage   : $chain = Bio::LiveSeq::ChainI->new(-string => "thequickbrownfoxjumpsoverthelazydog",
					     -offset => 3 );
         OR $chain = Bio::LiveSeq::ChainI->new(-array => \@array,
					     -offset => 3 );
  Function: generates a new Bio::LiveSeq:ChainI
  Returns : a new Chain
  Args    : string
         OR arrayreference
        AND optional offset to create element labels
=cut

sub new {
  my ($thing, %args) = @_;
  my $class = ref($thing) || $thing;
  my $obj;

  if ($args{-string}) {
    $obj = $thing->string2chain($args{-string}, $args{-offset});
  } elsif ($args{-array}) {
    $obj = $thing->array2chain($args{-array}, $args{-offset});
  } else {
    croak "$class not initialized properly";
  }

  $obj = bless $obj, $class;
  return $obj;
}

# added as of 1.9
sub string2chain {
  shift @_; # so that it doesn't pass the object reference
  return Bio::LiveSeq::Chain::string2chain(@_);
}
sub array2chain {
  shift @_; # so that it doesn't pass the object reference
  return Bio::LiveSeq::Chain::array2chain(@_);
}
#
sub chain2string {
  croak "ambiguous method call. Explicit down_ or up_";
}
sub down_chain2string {
  return Bio::LiveSeq::Chain::down_chain2string(@_);
}
sub up_chain2string {
  return Bio::LiveSeq::Chain::up_chain2string(@_);
}
sub chain2string_verbose {
  croak "ambiguous method call. Explicit down_ or up_";
}
sub down_chain2string_verbose {
  return Bio::LiveSeq::Chain::down_chain2string_verbose(@_);
}
sub up_chain2string_verbose {
  return Bio::LiveSeq::Chain::up_chain2string_verbose(@_);
}
sub invert_chain {
  return Bio::LiveSeq::Chain::invert_chain(@_);
}
sub mutate_element {
  croak "Old method name, please update code to: set_value_at_label";
}

# new as of version 2.33 of Chain.pm
sub down_labels {
  return Bio::LiveSeq::Chain::down_labels(@_);
}
sub up_labels {
  return Bio::LiveSeq::Chain::up_labels(@_);
}

sub start {
  return Bio::LiveSeq::Chain::start(@_);
}
sub end {
  return Bio::LiveSeq::Chain::end(@_);
}
sub label_exists {
  return Bio::LiveSeq::Chain::label_exists(@_);
}

sub get_value_at_pos {
  croak "ambiguous method call. Explicit down_ or up_";
}
sub down_get_value_at_pos {
  return Bio::LiveSeq::Chain::down_get_value_at_pos(@_);
}
sub up_get_value_at_pos {
  return Bio::LiveSeq::Chain::up_get_value_at_pos(@_);
}
sub set_value_at_pos {
  croak "ambiguous method call. Explicit down_ or up_";
}
sub down_set_value_at_pos {
  return Bio::LiveSeq::Chain::down_set_value_at_pos(@_);
}
sub up_set_value_at_pos {
  return Bio::LiveSeq::Chain::up_set_value_at_pos(@_);
}
sub get_value_at_label {
  return Bio::LiveSeq::Chain::get_value_at_label(@_);
}
sub set_value_at_label {
  return Bio::LiveSeq::Chain::set_value_at_label(@_);
}
sub get_label_at_pos {
  croak "ambiguous method call. Explicit down_ or up_";
}
sub up_get_label_at_pos {
  return Bio::LiveSeq::Chain::up_get_label_at_pos(@_);
}
sub down_get_label_at_pos {
  return Bio::LiveSeq::Chain::down_get_label_at_pos(@_);
}
sub get_pos_of_label {
  croak "ambiguous method call. Explicit down_ or up_";
}
sub up_get_pos_of_label {
  return Bio::LiveSeq::Chain::up_get_pos_of_label(@_);
}
sub down_get_pos_of_label {
  return Bio::LiveSeq::Chain::down_get_pos_of_label(@_);
}
#

sub preinsert_string {
  return Bio::LiveSeq::Chain::praeinsert_string(@_);
}
sub preinsert_array {
  return Bio::LiveSeq::Chain::praeinsert_array(@_);
}
sub praeinsert_string {
  return Bio::LiveSeq::Chain::praeinsert_string(@_);
}
sub postinsert_string {
  return Bio::LiveSeq::Chain::postinsert_string(@_);
}
sub praeinsert_array {
  return Bio::LiveSeq::Chain::praeinsert_array(@_);
}
sub postinsert_array {
  return Bio::LiveSeq::Chain::postinsert_array(@_);
}
sub down_element{
  return Bio::LiveSeq::Chain::down_element(@_);
}
sub up_element {
  return Bio::LiveSeq::Chain::up_element(@_);
}
sub is_downstream {
  return Bio::LiveSeq::Chain::is_downstream(@_);
}
sub is_upstream {
  return Bio::LiveSeq::Chain::is_upstream(@_);
}
sub check_chain {
  return Bio::LiveSeq::Chain::check_chain(@_);
}
sub chain_length {
  return Bio::LiveSeq::Chain::chain_length(@_);
}
sub splice_chain {
  return Bio::LiveSeq::Chain::splice_chain(@_);
}
sub pos_of_element {
  croak "ambiguous and old method name. use: down_pos_of_label";
}
sub up_pos_of_element {
  croak "old method name. use: down_pos_of_label";
  return Bio::LiveSeq::Chain::up_pos_of_element(@_);
}
sub down_pos_of_element {
  croak "old method name. use: up_pos_of_label";
  return Bio::LiveSeq::Chain::down_pos_of_element(@_);
}
sub subchain_length {
  croak "ambiguous method call. Explicit down_ or up_";
}
sub down_subchain_length {
  return Bio::LiveSeq::Chain::down_subchain_length(@_);
}
sub up_subchain_length {
  return Bio::LiveSeq::Chain::up_subchain_length(@_);
}

# these have to be deleted and changed names to conform to terminology
sub elements {
  return Bio::LiveSeq::Chain::down_elements(@_);
}
sub up_elements {
  return Bio::LiveSeq::Chain::up_elements(@_);
}
sub down_elements {
  return Bio::LiveSeq::Chain::down_elements(@_);
}

1;