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1 # $Id: ChainI.pm,v 1.9 2002/10/22 07:38:34 lapp Exp $
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2 #
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3 # bioperl module for Bio::LiveSeq::ChainI
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4 #
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5 # Cared for by Joseph Insana <insana@ebi.ac.uk> <jinsana@gmx.net>
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6 #
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7 # Copyright Joseph Insana
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8 #
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9 # You may distribute this module under the same terms as perl itself
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10 #
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11 # POD documentation - main docs before the code
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12
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13 =head1 NAME
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14
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15 Bio::LiveSeq::ChainI - Double linked chain data structure
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16
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17 =head1 SYNOPSIS
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18
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19 #documentation needed
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20
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21 =head1 DESCRIPTION
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22
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23 This class generates and manipulates generic double linked list, chain,
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24 that can be used to manage biological sequences.
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25
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26 The advantages over strings or plain arrays is the ease of tracking
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27 changes (mutations) in the elements (sequence). The other side of the
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28 coin is that these structures need consideraly more memory, but that
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29 is cheap and constantly inceasing resource in computers.
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30
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31 =head1 FEEDBACK
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32
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33 =head2 Mailing Lists
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34
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35 User feedback is an integral part of the evolution of this and other
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36 Bioperl modules. Send your comments and suggestions preferably to one
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37 of the Bioperl mailing lists. Your participation is much appreciated.
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38
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39 bioperl-l@bioperl.org - General discussion
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40 http://bio.perl.org/MailList.html - About the mailing lists
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41
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42 =head2 Reporting Bugs
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43
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44 Report bugs to the Bioperl bug tracking system to help us keep track
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45 the bugs and their resolution. Bug reports can be submitted via email
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46 or the web:
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47
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48 bioperl-bugs@bio.perl.org
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49 http://bugzilla.bioperl.org/
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50
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51 =head1 AUTHOR - Joseph A.L. Insana
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52
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53 Email: Insana@ebi.ac.uk, jinsana@gmx.net
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54 Address:
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55
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56 EMBL Outstation, European Bioinformatics Institute
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57 Wellcome Trust Genome Campus, Hinxton
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58 Cambs. CB10 1SD, United Kingdom
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59
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60 =head1 APPENDIX
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61
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62 The rest of the documentation details each of the object
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63 methods. Internal methods are usually preceded with a _
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64
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65 =cut
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66
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67 # Let the code begin...
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68
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69 package Bio::LiveSeq::ChainI;
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70 $VERSION=1.9;
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71 # Version history:
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72 # Thu Mar 16 01:38:25 GMT 2000 v.1.4 1st wraparound of methods complete
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73 # tested with chainseq_asobj_test.pl
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74 # Thu Mar 16 19:03:56 GMT 2000 v.1.5 decided to stick with same names as Chain
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75 # Fri Mar 17 05:08:15 GMT 2000 v.1.6 in sync with Chain 2.4
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76 # Fri Mar 17 15:47:23 GMT 2000 v.1.7 added pos_of_label, enforced down_ or up_
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77 # Fri Mar 17 20:12:27 GMT 2000 v.1.8 NAMING change: index->label everywhere
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78 # Mon Mar 20 19:20:17 GMT 2000 v.1.81 minor addings, Chain 2.52
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79 # Mon Mar 20 23:15:09 GMT 2000 v.1.82 in sync with Chain 2.6
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80 # Tue Mar 21 01:36:29 GMT 2000 v.1.83 added default strand if new(DNA)
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81 # Tue Mar 21 14:19:17 GMT 2000 v.1.9 moved new(DNA) to DNA, added chain2string()
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82
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83 use Carp qw(croak);
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84 use strict; # this will be moved before when strict enforced in Chain.pm
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85
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86 use Bio::LiveSeq::Chain 2.6; # package where all the subroutines are defined
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87
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88
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89 =head2 new
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90
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91 Title : new
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92 Usage : $chain = Bio::LiveSeq::ChainI->new(-string => "thequickbrownfoxjumpsoverthelazydog",
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93 -offset => 3 );
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94 OR $chain = Bio::LiveSeq::ChainI->new(-array => \@array,
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95 -offset => 3 );
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96 Function: generates a new Bio::LiveSeq:ChainI
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97 Returns : a new Chain
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98 Args : string
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99 OR arrayreference
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100 AND optional offset to create element labels
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101 =cut
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102
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103 sub new {
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104 my ($thing, %args) = @_;
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105 my $class = ref($thing) || $thing;
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106 my $obj;
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107
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108 if ($args{-string}) {
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109 $obj = $thing->string2chain($args{-string}, $args{-offset});
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110 } elsif ($args{-array}) {
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111 $obj = $thing->array2chain($args{-array}, $args{-offset});
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112 } else {
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113 croak "$class not initialized properly";
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114 }
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115
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116 $obj = bless $obj, $class;
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117 return $obj;
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118 }
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119
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120 # added as of 1.9
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121 sub string2chain {
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122 shift @_; # so that it doesn't pass the object reference
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123 return Bio::LiveSeq::Chain::string2chain(@_);
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124 }
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125 sub array2chain {
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126 shift @_; # so that it doesn't pass the object reference
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127 return Bio::LiveSeq::Chain::array2chain(@_);
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128 }
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129 #
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130 sub chain2string {
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131 croak "ambiguous method call. Explicit down_ or up_";
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132 }
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133 sub down_chain2string {
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134 return Bio::LiveSeq::Chain::down_chain2string(@_);
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135 }
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136 sub up_chain2string {
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137 return Bio::LiveSeq::Chain::up_chain2string(@_);
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138 }
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139 sub chain2string_verbose {
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140 croak "ambiguous method call. Explicit down_ or up_";
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141 }
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142 sub down_chain2string_verbose {
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143 return Bio::LiveSeq::Chain::down_chain2string_verbose(@_);
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144 }
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145 sub up_chain2string_verbose {
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146 return Bio::LiveSeq::Chain::up_chain2string_verbose(@_);
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147 }
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148 sub invert_chain {
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149 return Bio::LiveSeq::Chain::invert_chain(@_);
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150 }
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151 sub mutate_element {
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152 croak "Old method name, please update code to: set_value_at_label";
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153 }
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154
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155 # new as of version 2.33 of Chain.pm
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156 sub down_labels {
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157 return Bio::LiveSeq::Chain::down_labels(@_);
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158 }
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159 sub up_labels {
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160 return Bio::LiveSeq::Chain::up_labels(@_);
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161 }
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162
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163 sub start {
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164 return Bio::LiveSeq::Chain::start(@_);
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165 }
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166 sub end {
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167 return Bio::LiveSeq::Chain::end(@_);
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168 }
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169 sub label_exists {
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170 return Bio::LiveSeq::Chain::label_exists(@_);
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171 }
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172
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173 sub get_value_at_pos {
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174 croak "ambiguous method call. Explicit down_ or up_";
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175 }
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176 sub down_get_value_at_pos {
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177 return Bio::LiveSeq::Chain::down_get_value_at_pos(@_);
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178 }
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179 sub up_get_value_at_pos {
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180 return Bio::LiveSeq::Chain::up_get_value_at_pos(@_);
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181 }
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182 sub set_value_at_pos {
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183 croak "ambiguous method call. Explicit down_ or up_";
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184 }
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185 sub down_set_value_at_pos {
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186 return Bio::LiveSeq::Chain::down_set_value_at_pos(@_);
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187 }
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188 sub up_set_value_at_pos {
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189 return Bio::LiveSeq::Chain::up_set_value_at_pos(@_);
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190 }
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191 sub get_value_at_label {
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192 return Bio::LiveSeq::Chain::get_value_at_label(@_);
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193 }
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194 sub set_value_at_label {
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195 return Bio::LiveSeq::Chain::set_value_at_label(@_);
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196 }
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197 sub get_label_at_pos {
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198 croak "ambiguous method call. Explicit down_ or up_";
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199 }
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200 sub up_get_label_at_pos {
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201 return Bio::LiveSeq::Chain::up_get_label_at_pos(@_);
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202 }
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203 sub down_get_label_at_pos {
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204 return Bio::LiveSeq::Chain::down_get_label_at_pos(@_);
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205 }
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206 sub get_pos_of_label {
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207 croak "ambiguous method call. Explicit down_ or up_";
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208 }
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209 sub up_get_pos_of_label {
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210 return Bio::LiveSeq::Chain::up_get_pos_of_label(@_);
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211 }
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212 sub down_get_pos_of_label {
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213 return Bio::LiveSeq::Chain::down_get_pos_of_label(@_);
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214 }
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215 #
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216
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217 sub preinsert_string {
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218 return Bio::LiveSeq::Chain::praeinsert_string(@_);
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219 }
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220 sub preinsert_array {
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221 return Bio::LiveSeq::Chain::praeinsert_array(@_);
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222 }
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223 sub praeinsert_string {
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224 return Bio::LiveSeq::Chain::praeinsert_string(@_);
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225 }
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226 sub postinsert_string {
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227 return Bio::LiveSeq::Chain::postinsert_string(@_);
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228 }
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229 sub praeinsert_array {
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230 return Bio::LiveSeq::Chain::praeinsert_array(@_);
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231 }
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232 sub postinsert_array {
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233 return Bio::LiveSeq::Chain::postinsert_array(@_);
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234 }
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235 sub down_element{
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236 return Bio::LiveSeq::Chain::down_element(@_);
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237 }
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238 sub up_element {
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239 return Bio::LiveSeq::Chain::up_element(@_);
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240 }
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241 sub is_downstream {
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242 return Bio::LiveSeq::Chain::is_downstream(@_);
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243 }
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244 sub is_upstream {
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245 return Bio::LiveSeq::Chain::is_upstream(@_);
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246 }
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247 sub check_chain {
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248 return Bio::LiveSeq::Chain::check_chain(@_);
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249 }
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250 sub chain_length {
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251 return Bio::LiveSeq::Chain::chain_length(@_);
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252 }
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253 sub splice_chain {
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254 return Bio::LiveSeq::Chain::splice_chain(@_);
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255 }
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256 sub pos_of_element {
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257 croak "ambiguous and old method name. use: down_pos_of_label";
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258 }
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259 sub up_pos_of_element {
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260 croak "old method name. use: down_pos_of_label";
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261 return Bio::LiveSeq::Chain::up_pos_of_element(@_);
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262 }
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263 sub down_pos_of_element {
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264 croak "old method name. use: up_pos_of_label";
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265 return Bio::LiveSeq::Chain::down_pos_of_element(@_);
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266 }
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267 sub subchain_length {
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268 croak "ambiguous method call. Explicit down_ or up_";
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269 }
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270 sub down_subchain_length {
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271 return Bio::LiveSeq::Chain::down_subchain_length(@_);
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272 }
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273 sub up_subchain_length {
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274 return Bio::LiveSeq::Chain::up_subchain_length(@_);
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275 }
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276
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277 # these have to be deleted and changed names to conform to terminology
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278 sub elements {
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279 return Bio::LiveSeq::Chain::down_elements(@_);
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280 }
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281 sub up_elements {
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282 return Bio::LiveSeq::Chain::up_elements(@_);
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283 }
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284 sub down_elements {
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285 return Bio::LiveSeq::Chain::down_elements(@_);
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286 }
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287
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288 1;
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