diff variant_effect_predictor/Bio/LiveSeq/ChainI.pm @ 0:2bc9b66ada89 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/LiveSeq/ChainI.pm	Thu Apr 11 06:29:17 2013 -0400
@@ -0,0 +1,288 @@
+# $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;