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1 # $Id: AnnotationFactory.pm,v 1.1 2002/10/31 09:45:39 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Annotation::AnnotationFactory
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4 #
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5 # Cared for by Hilmar Lapp <hlapp at gmx.net>
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6 #
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7 # Copyright Hilmar Lapp
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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 #
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12 # (c) Hilmar Lapp, hlapp at gmx.net, 2002.
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13 # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
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14 #
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15 # You may distribute this module under the same terms as perl itself.
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16 # Refer to the Perl Artistic License (see the license accompanying this
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17 # software package, or see http://www.perl.com/language/misc/Artistic.html)
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18 # for the terms under which you may use, modify, and redistribute this module.
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19 #
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20 # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
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21 # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
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22 # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
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23 #
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24
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25 # POD documentation - main docs before the code
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26
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27 =head1 NAME
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28
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29 Bio::Annotation::AnnotationFactory - Instantiates a new Bio::AnnotationI (or derived class) through a factory
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30
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31 =head1 SYNOPSIS
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32
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33 use Bio::Annotation::AnnotationFactory;
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34 #
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35 my $factory = new Bio::Annotation::AnnotationFactory(-type => 'Bio::Annotation::SimpleValue');
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36 my $ann = $factory->create_object(-value => 'peroxisome',
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37 -tagname => 'cellular component');
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38
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39
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40 =head1 DESCRIPTION
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41
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42 This object will build L<Bio::AnnotationI> objects generically.
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43
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44 =head1 FEEDBACK
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45
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46 =head2 Mailing Lists
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47
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48 User feedback is an integral part of the evolution of this and other
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49 Bioperl modules. Send your comments and suggestions preferably to
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50 the Bioperl mailing list. Your participation is much appreciated.
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51
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52 bioperl-l@bioperl.org - General discussion
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53 http://bioperl.org/MailList.shtml - About the mailing lists
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54
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55 =head2 Reporting Bugs
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56
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57 Report bugs to the Bioperl bug tracking system to help us keep track
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58 of the bugs and their resolution. Bug reports can be submitted via
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59 email or the web:
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60
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61 bioperl-bugs@bioperl.org
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62 http://bugzilla.bioperl.org/
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63
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64 =head1 AUTHOR - Hilmar Lapp
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65
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66 Email hlapp at gmx.net
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67
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68
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69 =head1 CONTRIBUTORS
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70
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71 This is mostly copy-and-paste with subsequent adaptation from
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72 Bio::Seq::SeqFactory by Jason Stajich. Most credits should in fact go
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73 to him.
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74
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75 =head1 APPENDIX
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76
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77 The rest of the documentation details each of the object methods.
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78 Internal methods are usually preceded with a _
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79
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80 =cut
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81
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82
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83 # Let the code begin...
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84
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85
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86 package Bio::Annotation::AnnotationFactory;
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87 use vars qw(@ISA);
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88 use strict;
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89
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90 use Bio::Root::Root;
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91 use Bio::Factory::ObjectFactoryI;
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92
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93 @ISA = qw(Bio::Root::Root Bio::Factory::ObjectFactoryI);
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94
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95 =head2 new
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96
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97 Title : new
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98 Usage : my $obj = new Bio::Annotation::AnnotationFactory();
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99 Function: Builds a new Bio::Annotation::AnnotationFactory object
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100 Returns : Bio::Annotation::AnnotationFactory
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101 Args : -type => string, name of a L<Bio::AnnotationI> derived class.
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102 The default is L<Bio::Ontology::Term>.
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103
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104 =cut
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105
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106 sub new {
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107 my($class,@args) = @_;
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108
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109 my $self = $class->SUPER::new(@args);
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110
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111 my ($type) = $self->_rearrange([qw(TYPE)], @args);
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112
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113 $self->{'_loaded_types'} = {};
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114 $self->type($type) if $type;
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115
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116 return $self;
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117 }
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118
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119
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120 =head2 create_object
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121
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122 Title : create_object
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123 Usage : my $seq = $factory->create_object(<named parameters>);
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124 Function: Instantiates new Bio::AnnotationI (or one of its child classes)
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125
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126 This object allows us to genericize the instantiation of
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127 cluster objects.
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128
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129 Returns : L<Bio::AnnotationI> compliant object
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130 The return type is configurable using new(-type =>"...").
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131 Args : initialization parameters specific to the type of annotation
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132 object we want.
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133
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134 =cut
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135
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136 sub create_object {
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137 my ($self,@args) = @_;
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138
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139 my $type = $self->type();
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140 if(! $type) {
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141 # we need to guess this
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142 $type = $self->_guess_type(@args);
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143 if(! $type) {
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144 $self->throw("No annotation type set and unable to guess.");
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145 }
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146 # load dynamically if it hasn't been loaded yet
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147 if(! $self->{'_loaded_types'}->{$type}) {
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148 eval {
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149 $self->_load_module($type);
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150 $self->{'_loaded_types'}->{$type} = 1;
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151 };
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152 if($@) {
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153 $self->throw("Bio::AnnotationI implementation $type ".
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154 "failed to load: ".$@);
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155 }
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156 }
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157 }
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158 return $type->new(-verbose => $self->verbose, @args);
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159 }
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160
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161 =head2 type
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162
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163 Title : type
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164 Usage : $obj->type($newval)
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165 Function: Get/set the type of L<Bio::AnnotationI> object to be created.
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166
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167 This may be changed at any time during the lifetime of this
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168 factory.
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169
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170 Returns : value of type
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171 Args : newvalue (optional)
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172
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173
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174 =cut
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175
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176 sub type{
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177 my $self = shift;
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178
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179 if(@_) {
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180 my $type = shift;
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181 if($type && (! $self->{'_loaded_types'}->{$type})) {
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182 eval {
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183 $self->_load_module($type);
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184 };
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185 if( $@ ) {
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186 $self->throw("Annotation class '$type' failed to load: ".
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187 $@);
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188 }
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189 my $a = bless {},$type;
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190 if( ! $a->isa('Bio::AnnotationI') ) {
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191 $self->throw("'$type' does not implement Bio::AnnotationI. ".
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192 "Too bad.");
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193 }
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194 $self->{'_loaded_types'}->{$type} = 1;
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195 }
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196 return $self->{'type'} = $type;
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197 }
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198 return $self->{'type'};
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199 }
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200
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201 =head2 _guess_type
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202
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203 Title : _guess_type
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204 Usage :
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205 Function: Guesses the right type of L<Bio::AnnotationI> implementation
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206 based on initialization parameters for the prospective
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207 object.
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208 Example :
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209 Returns : the type (a string, the module name)
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210 Args : initialization parameters to be passed to the prospective
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211 cluster object
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212
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213
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214 =cut
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215
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216 sub _guess_type{
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217 my ($self,@args) = @_;
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218 my $type;
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219
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220 # we can only guess from a certain number of arguments
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221 my ($val,$db,$text,$name,$authors) =
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222 $self->_rearrange([qw(VALUE
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223 DATABASE
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224 TEXT
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225 NAME
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226 AUTHORS
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227 )], @args);
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228 SWITCH: {
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229 $val && do { $type = "SimpleValue"; last SWITCH; };
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230 $authors && do { $type = "Reference"; last SWITCH; };
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231 $db && do { $type = "DBLink"; last SWITCH; };
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232 $text && do { $type = "Comment"; last SWITCH; };
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233 $name && do { $type = "OntologyTerm"; last SWITCH; };
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234 # what else could we look for?
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235 }
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236 $type = "Bio::Annotation::".$type;
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237
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238 return $type;
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239 }
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240
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241 #####################################################################
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242 # aliases for naming consistency or other reasons #
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243 #####################################################################
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244
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245 *create = \&create_object;
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246
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247 1;
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