Bio/LiveSeq/ChainI.pm

   1 #
   2 # bioperl module for Bio::LiveSeq::ChainI
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Joseph Insana <insana@ebi.ac.uk> <jinsana@gmx.net>
   7 #
   8 # Copyright Joseph Insana
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11 #
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::LiveSeq::ChainI - Double linked chain data structure
  17
  18 =head1 SYNOPSIS
  19
  20   #documentation needed
  21
  22 =head1 DESCRIPTION
  23
  24 This class generates and manipulates generic double linked list, chain,
  25 that can be used to manage biological sequences.
  26
  27 The advantages over strings or plain arrays is the ease of tracking
  28 changes (mutations) in the elements (sequence). The other side of the
  29 coin is that these structures need consideraly more memory, but that
  30 is cheap and constantly inceasing resource in computers.
  31
  32 =head1 FEEDBACK
  33
  34 =head2 Mailing Lists
  35
  36 User feedback is an integral part of the evolution of this and other
  37 Bioperl modules. Send your comments and suggestions preferably to one
  38 of the Bioperl mailing lists.  Your participation is much appreciated.
  39
  40   bioperl-l@bioperl.org                  - General discussion
  41   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  42
  43 =head2 Support
  44
  45 Please direct usage questions or support issues to the mailing list:
  46
  47 I<bioperl-l@bioperl.org>
  48
  49 rather than to the module maintainer directly. Many experienced and
  50 reponsive experts will be able look at the problem and quickly
  51 address it. Please include a thorough description of the problem
  52 with code and data examples if at all possible.
  53
  54 =head2 Reporting Bugs
  55
  56 Report bugs to the Bioperl bug tracking system to help us keep track
  57 the bugs and their resolution.  Bug reports can be submitted via the
  58 web:
  59
  60   https://github.com/bioperl/bioperl-live/issues
  61
  62 =head1 AUTHOR - Joseph A.L. Insana
  63
  64 Email:  Insana@ebi.ac.uk, jinsana@gmx.net
  65
  66 =head1 APPENDIX
  67
  68 The rest of the documentation details each of the object
  69 methods. Internal methods are usually preceded with a _
  70
  71 =cut
  72
  73 # Let the code begin...
  74
  75 package Bio::LiveSeq::ChainI;
  76
  77 use Carp qw(croak);
  78 use strict; # this will be moved before when strict enforced in Chain.pm
  79
  80 use Bio::LiveSeq::Chain; # package where all the subroutines are defined
  81
  82
  83 =head2 new
  84
  85   Title   : new
  86   Usage   : $chain = Bio::LiveSeq::ChainI->new(-string => "thequickbrownfoxjumpsoverthelazydog",
  87                                              -offset => 3 );
  88          OR $chain = Bio::LiveSeq::ChainI->new(-array => \@array,
  89                                              -offset => 3 );
  90   Function: generates a new Bio::LiveSeq:ChainI
  91   Returns : a new Chain
  92   Args    : string
  93          OR arrayreference
  94         AND optional offset to create element labels
  95
  96 =cut
  97
  98 sub new {
  99   my ($thing, %args) = @_;
 100   my $class = ref($thing) || $thing;
 101   my $obj;
 102
 103   if ($args{-string}) {
 104     $obj = $thing->string2chain($args{-string}, $args{-offset});
 105   } elsif ($args{-array}) {
 106     $obj = $thing->array2chain($args{-array}, $args{-offset});
 107   } else {
 108     croak "$class not initialized properly";
 109   }
 110
 111   $obj = bless $obj, $class;
 112   return $obj;
 113 }
 114
 115 # added as of 1.9
 116 sub string2chain {
 117   shift @_; # so that it doesn't pass the object reference
 118   return Bio::LiveSeq::Chain::string2chain(@_);
 119 }
 120 sub array2chain {
 121   shift @_; # so that it doesn't pass the object reference
 122   return Bio::LiveSeq::Chain::array2chain(@_);
 123 }
 124 #
 125 sub chain2string {
 126   croak "ambiguous method call. Explicit down_ or up_";
 127 }
 128 sub down_chain2string {
 129   return Bio::LiveSeq::Chain::down_chain2string(@_);
 130 }
 131 sub up_chain2string {
 132   return Bio::LiveSeq::Chain::up_chain2string(@_);
 133 }
 134 sub chain2string_verbose {
 135   croak "ambiguous method call. Explicit down_ or up_";
 136 }
 137 sub down_chain2string_verbose {
 138   return Bio::LiveSeq::Chain::down_chain2string_verbose(@_);
 139 }
 140 sub up_chain2string_verbose {
 141   return Bio::LiveSeq::Chain::up_chain2string_verbose(@_);
 142 }
 143 sub invert_chain {
 144   return Bio::LiveSeq::Chain::invert_chain(@_);
 145 }
 146 sub mutate_element {
 147   croak "Old method name, please update code to: set_value_at_label";
 148 }
 149
 150 # new as of version 2.33 of Chain.pm
 151 sub down_labels {
 152   return Bio::LiveSeq::Chain::down_labels(@_);
 153 }
 154 sub up_labels {
 155   return Bio::LiveSeq::Chain::up_labels(@_);
 156 }
 157
 158 sub start {
 159   return Bio::LiveSeq::Chain::start(@_);
 160 }
 161 sub end {
 162   return Bio::LiveSeq::Chain::end(@_);
 163 }
 164 sub label_exists {
 165   return Bio::LiveSeq::Chain::label_exists(@_);
 166 }
 167
 168 sub get_value_at_pos {
 169   croak "ambiguous method call. Explicit down_ or up_";
 170 }
 171 sub down_get_value_at_pos {
 172   return Bio::LiveSeq::Chain::down_get_value_at_pos(@_);
 173 }
 174 sub up_get_value_at_pos {
 175   return Bio::LiveSeq::Chain::up_get_value_at_pos(@_);
 176 }
 177 sub set_value_at_pos {
 178   croak "ambiguous method call. Explicit down_ or up_";
 179 }
 180 sub down_set_value_at_pos {
 181   return Bio::LiveSeq::Chain::down_set_value_at_pos(@_);
 182 }
 183 sub up_set_value_at_pos {
 184   return Bio::LiveSeq::Chain::up_set_value_at_pos(@_);
 185 }
 186 sub get_value_at_label {
 187   return Bio::LiveSeq::Chain::get_value_at_label(@_);
 188 }
 189 sub set_value_at_label {
 190   return Bio::LiveSeq::Chain::set_value_at_label(@_);
 191 }
 192 sub get_label_at_pos {
 193   croak "ambiguous method call. Explicit down_ or up_";
 194 }
 195 sub up_get_label_at_pos {
 196   return Bio::LiveSeq::Chain::up_get_label_at_pos(@_);
 197 }
 198 sub down_get_label_at_pos {
 199   return Bio::LiveSeq::Chain::down_get_label_at_pos(@_);
 200 }
 201 sub get_pos_of_label {
 202   croak "ambiguous method call. Explicit down_ or up_";
 203 }
 204 sub up_get_pos_of_label {
 205   return Bio::LiveSeq::Chain::up_get_pos_of_label(@_);
 206 }
 207 sub down_get_pos_of_label {
 208   return Bio::LiveSeq::Chain::down_get_pos_of_label(@_);
 209 }
 210 #
 211
 212 sub preinsert_string {
 213   return Bio::LiveSeq::Chain::praeinsert_string(@_);
 214 }
 215 sub preinsert_array {
 216   return Bio::LiveSeq::Chain::praeinsert_array(@_);
 217 }
 218 sub praeinsert_string {
 219   return Bio::LiveSeq::Chain::praeinsert_string(@_);
 220 }
 221 sub postinsert_string {
 222   return Bio::LiveSeq::Chain::postinsert_string(@_);
 223 }
 224 sub praeinsert_array {
 225   return Bio::LiveSeq::Chain::praeinsert_array(@_);
 226 }
 227 sub postinsert_array {
 228   return Bio::LiveSeq::Chain::postinsert_array(@_);
 229 }
 230 sub down_element{
 231   return Bio::LiveSeq::Chain::down_element(@_);
 232 }
 233 sub up_element {
 234   return Bio::LiveSeq::Chain::up_element(@_);
 235 }
 236 sub is_downstream {
 237   return Bio::LiveSeq::Chain::is_downstream(@_);
 238 }
 239 sub is_upstream {
 240   return Bio::LiveSeq::Chain::is_upstream(@_);
 241 }
 242 sub check_chain {
 243   return Bio::LiveSeq::Chain::check_chain(@_);
 244 }
 245 sub chain_length {
 246   return Bio::LiveSeq::Chain::chain_length(@_);
 247 }
 248 sub splice_chain {
 249   return Bio::LiveSeq::Chain::splice_chain(@_);
 250 }
 251 sub pos_of_element {
 252   croak "ambiguous and old method name. use: down_pos_of_label";
 253 }
 254 sub up_pos_of_element {
 255   croak "old method name. use: down_pos_of_label";
 256   return Bio::LiveSeq::Chain::up_pos_of_element(@_);
 257 }
 258 sub down_pos_of_element {
 259   croak "old method name. use: up_pos_of_label";
 260   return Bio::LiveSeq::Chain::down_pos_of_element(@_);
 261 }
 262 sub subchain_length {
 263   croak "ambiguous method call. Explicit down_ or up_";
 264 }
 265 sub down_subchain_length {
 266   return Bio::LiveSeq::Chain::down_subchain_length(@_);
 267 }
 268 sub up_subchain_length {
 269   return Bio::LiveSeq::Chain::up_subchain_length(@_);
 270 }
 271
 272 # these have to be deleted and changed names to conform to terminology
 273 sub elements {
 274   return Bio::LiveSeq::Chain::down_elements(@_);
 275 }
 276 sub up_elements {
 277   return Bio::LiveSeq::Chain::up_elements(@_);
 278 }
 279 sub down_elements {
 280   return Bio::LiveSeq::Chain::down_elements(@_);
 281 }
 282
 283 1;