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1 #-----------------------------------------------------------------------------
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2 # PACKAGE : Bio::Root::Xref.pm
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3 # AUTHOR : Steve Chervitz (sac@bioperl.org)
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4 # CREATED : 8 May 1997
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5 # REVISION: $Id: Xref.pm,v 1.9 2002/10/22 07:38:37 lapp Exp $
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6 # STATUS : Pre-Alpha
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7 #
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8 # WARNING: This is considered an experimental module.
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9 #
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10 # Copyright (c) 1997-8 Steve Chervitz. All Rights Reserved.
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11 # This module is free software; you can redistribute it and/or
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12 # modify it under the same terms as Perl itself.
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13 #-----------------------------------------------------------------------------
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14
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15 package Bio::Root::Xref;
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16
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17 use Bio::Root::Global;
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18 use Bio::Root::Object ();
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19 use Bio::Root::Vector ();
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20
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21 @Bio::Root::Xref::ISA = qw( Bio::Root::Vector Bio::Root::Object );
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22
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23 use vars qw($ID $VERSION);
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24 $ID = 'Bio::Root::Xref';
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25 $VERSION = 0.01;
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26
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27 ## POD Documentation:
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28
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29 =head1 NAME
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30
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31 Bio::Root::Xref - A generic cross-reference object.
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32
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33 B<WARNING: This module is still in the experimental phase and has not been tested.>
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34
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35 =head1 SYNOPSIS
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36
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37 =head2 Object Creation
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38
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39 use Bio::Root::Object;
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40
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41 $myObj->xref($object_ref);
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42
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43 =head2 Object Manipulation
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44
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45 Accessors
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46 ---------------------------------------------------------------------
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47 obj() - Get the cross-referenced object.
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48 desc() - Description of the nature of the cross-reference.
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49 set_desc() - Set description.
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50 type() - Symmetric or assymetric.
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51
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52 Methods
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53 ---------------------------------------------------------------------
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54 clear() - remove all cross-references within the Xref object (not implemented).
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55
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56 =head1 DESCRIPTION
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57
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58 An instance of B<Bio::Root::Xref.pm> manages sets of objects not
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59 necessarily related by inheritance or composition, but by an arbitrary
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60 criterion defined by the client. Currently, Bio::Root::Xref inherits
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61 from both B<Bio::Root::Object.pm> and B<Bio::Root::Vector.pm>. An Xref
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62 object is an example of a heterogeneous Vector object since different
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63 objects in the vector need not all derive from the same base class.
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64
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65 The two objects involved in the cross-reference typically involve a
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66 symmetrical relationship in which each will have a Xref object relating it
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67 to the other object. This relationship is not necessarily transitive,
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68 however: if A is an xref of B and B is an xref of C, A is not
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69 necessarily an xref of C. Assymetric Xrefs are also possible.
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70
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71 The establishment of cross-references is managed by B<Bio::Root::Object.pm>.
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72 See the xref() method in that module.
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73
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74 B<The API for this module is not complete since the module is under development. Caveat emptor.>
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75
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76
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77 =head1 SEE ALSO
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78
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79 Bio::Root::Object.pm - Core object
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80 Bio::Root::Global.pm - Manages global variables/constants
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81
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82 http://bio.perl.org/Projects/modules.html - Online module documentation
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83 http://bio.perl.org/ - Bioperl Project Homepage
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84
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85 =head1 FEEDBACK
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86
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87 =head2 Mailing Lists
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88
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89 User feedback is an integral part of the evolution of this and other Bioperl modules.
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90 Send your comments and suggestions preferably to one of the Bioperl mailing lists.
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91 Your participation is much appreciated.
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92
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93 bioperl-l@bioperl.org - General discussion
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94 http://bioperl.org/MailList.shtml - About the mailing lists
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95
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96 =head2 Reporting Bugs
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97
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98 Report bugs to the Bioperl bug tracking system to help us keep track the bugs and
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99 their resolution. Bug reports can be submitted via email or the web:
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100
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101 bioperl-bugs@bio.perl.org
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102 http://bugzilla.bioperl.org/
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103
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104 =head1 AUTHOR
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105
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106 Steve Chervitz E<lt>sac@bioperl.orgE<gt>
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107
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108 See L<the FEEDBACK section | FEEDBACK> for where to send bug reports and comments.
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109
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110 =head1 VERSION
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111
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112 Bio::Root::Xref.pm, 0.01 pre-alpha
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113
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114 =head1 COPYRIGHT
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115
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116 Copyright (c) 1997-8 Steve Chervitz. All Rights Reserved.
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117 This module is free software; you can redistribute it and/or
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118 modify it under the same terms as Perl itself.
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119
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120
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121 =head1 TODO
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122
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123 Update documentation to work with pod2html from Perl 5.004.
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124
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125 =cut
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126
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127 #
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128 ##
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129 ###
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130 #### END of main POD documentation.
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131 ###
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132 ##
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133 #
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134
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135
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136
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137 #####################################################################################
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138 ## CONSTRUCTOR ##
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139 #####################################################################################
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140
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141 sub _initialize {
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142 my( $self, %param ) = @_;
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143
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144 $self->SUPER::_initialize(%param);
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145
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146 $self->{'_obj'} = ($param{-OBJ} || undef);
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147
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148 ## By default, all Xrefs are symmetric.
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149 ## Create symmetric cross-reference in obj.
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150 if(!$param{-ASYM}) {
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151 $self->{'_obj'}->xref(-OBJ=>$param{-PARENT});
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152 $self->{'_type'} = 'sym';
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153 } else {
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154 $self->{'_type'} = 'asym';
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155 }
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156 }
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157
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158
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159 #####################################################################################
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160 ## ACCESSORS ##
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161 #####################################################################################
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162
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163 sub obj {my ($self) = shift; return $self->{'_obj'}; }
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164 sub desc {my ($self) = shift; return $self->{'_desc'}; }
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165 sub type {my ($self) = shift; return $self->{'_type'}; }
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166
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167 sub set_desc {my ($self,$desc) = @_;
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168 $self->{'_desc'} = $desc;
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169 }
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170
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171 sub clear {
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172 ## Not implemented. Need to do this carefully.
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173 ## Not sure if this method is needed.
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174 my ($self) = @_;
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175 }
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176
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177 1;
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178 __END__
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179
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180 #####################################################################################
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181 # END OF CLASS #
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182 #####################################################################################
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183
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184 =head1 DATA MEMBERS
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185
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186 _obj : The object being cross-referenced to the parent.
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187 _type : Symmetric or asymmetric
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188 _desc : Description associated with the cross-reference
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189
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190 INHERITED DATA MEMBERS (from Bio::Root::Object)
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191
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192 _parent : The object receiving the cross-reference.
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193 _name : Descriptive nature of the cross-reference.
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194
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195 =cut
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196
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197
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