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1 # $Id: ClusterFactory.pm,v 1.2 2002/10/31 09:45:39 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Cluster::ClusterFactory
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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::Cluster::ClusterFactory - Instantiates a new Bio::ClusterI (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::Cluster::ClusterFactory;
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34 # if you don't provide a default type, the factory will try
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35 # some guesswork based on display_id and namespace
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36 my $factory = new Bio::Cluster::ClusterFactory(-type => 'Bio::Cluster::UniGene');
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37 my $clu = $factory->create_object(-description => 'NAT',
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38 -display_id => 'Hs.2');
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39
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40
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41 =head1 DESCRIPTION
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42
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43 This object will build L<Bio::ClusterI> objects generically.
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44
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45 =head1 FEEDBACK
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46
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47 =head2 Mailing Lists
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48
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49 User feedback is an integral part of the evolution of this and other
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50 Bioperl modules. Send your comments and suggestions preferably to
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51 the Bioperl mailing list. Your participation is much appreciated.
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52
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53 bioperl-l@bioperl.org - General discussion
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54 http://bioperl.org/MailList.shtml - About the mailing lists
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55
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56 =head2 Reporting Bugs
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57
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58 Report bugs to the Bioperl bug tracking system to help us keep track
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59 of the bugs and their resolution. Bug reports can be submitted via
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60 email or the web:
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61
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62 bioperl-bugs@bioperl.org
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63 http://bugzilla.bioperl.org/
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64
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65 =head1 AUTHOR - Hilmar Lapp
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66
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67 Email hlapp at gmx.net
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68
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69
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70 =head1 CONTRIBUTORS
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71
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72 This is mostly copy-and-paste with subsequent adaptation from
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73 Bio::Seq::SeqFactory by Jason Stajich. Most credits should in fact go
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74 to him.
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75
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76 =head1 APPENDIX
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77
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78 The rest of the documentation details each of the object methods.
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79 Internal methods are usually preceded with a _
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80
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81 =cut
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82
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83
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84 # Let the code begin...
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85
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86
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87 package Bio::Cluster::ClusterFactory;
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88 use vars qw(@ISA);
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89 use strict;
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90
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91 use Bio::Root::Root;
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92 use Bio::Factory::ObjectFactoryI;
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93
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94 @ISA = qw(Bio::Root::Root Bio::Factory::ObjectFactoryI);
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95
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96 =head2 new
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97
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98 Title : new
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99 Usage : my $obj = new Bio::Cluster::ClusterFactory();
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100 Function: Builds a new Bio::Cluster::ClusterFactory object
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101 Returns : Bio::Cluster::ClusterFactory
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102 Args : -type => string, name of a ClusterI derived class.
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103 If not provided, the factory will have to guess
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104 from ID and namespace, which may or may not be
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105 successful.
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106
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107 =cut
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108
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109 sub new {
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110 my($class,@args) = @_;
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111
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112 my $self = $class->SUPER::new(@args);
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113
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114 my ($type) = $self->_rearrange([qw(TYPE)], @args);
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115
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116 $self->{'_loaded_types'} = {};
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117 $self->type($type) if $type;
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118
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119 return $self;
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120 }
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121
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122
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123 =head2 create_object
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124
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125 Title : create_object
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126 Usage : my $seq = $factory->create_object(<named parameters>);
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127 Function: Instantiates new Bio::ClusterI (or one of its child classes)
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128
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129 This object allows us to genericize the instantiation of
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130 cluster objects.
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131
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132 Returns : L<Bio::ClusterI> compliant object
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133 The return type is configurable using new(-type =>"...").
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134 Args : initialization parameters specific to the type of cluster
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135 object we want. Typically
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136 -display_id => $name
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137 -description => description of the cluster
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138 -members => arrayref, members of the cluster
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139
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140 =cut
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141
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142 sub create_object {
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143 my ($self,@args) = @_;
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144
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145 my $type = $self->type();
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146 if(! $type) {
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147 # we need to guess this
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148 $type = $self->_guess_type(@args);
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149 if(! $type) {
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150 $self->throw("No cluster type set and unable to guess.");
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151 }
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152 # load dynamically if it hasn't been loaded yet
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153 if(! $self->{'_loaded_types'}->{$type}) {
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154 eval {
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155 $self->_load_module($type);
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156 $self->{'_loaded_types'}->{$type} = 1;
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157 };
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158 if($@) {
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159 $self->throw("Bio::ClusterI implementation $type ".
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160 "failed to load: ".$@);
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161 }
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162 }
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163 }
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164 return $type->new(-verbose => $self->verbose, @args);
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165 }
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166
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167 =head2 type
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168
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169 Title : type
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170 Usage : $obj->type($newval)
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171 Function: Get/set the type of L<Bio::ClusterI> object to be created.
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172
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173 This may be changed at any time during the lifetime of this
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174 factory.
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175
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176 Returns : value of type
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177 Args : newvalue (optional)
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178
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179
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180 =cut
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181
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182 sub type{
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183 my $self = shift;
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184
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185 if(@_) {
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186 my $type = shift;
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187 if($type && (! $self->{'_loaded_types'}->{$type})) {
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188 eval {
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189 $self->_load_module($type);
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190 };
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191 if( $@ ) {
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192 $self->throw("Cluster implementation '$type' failed to load: ".
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193 $@);
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194 }
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195 my $a = bless {},$type;
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196 if( ! $a->isa('Bio::ClusterI') ) {
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197 $self->throw("'$type' does not implement Bio::ClusterI. ".
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198 "Too bad.");
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199 }
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200 $self->{'_loaded_types'}->{$type} = 1;
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201 }
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202 return $self->{'type'} = $type;
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203 }
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204 return $self->{'type'};
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205 }
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206
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207 =head2 _guess_type
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208
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209 Title : _guess_type
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210 Usage :
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211 Function: Guesses the right type of L<Bio::ClusterI> implementation
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212 based on initialization parameters for the prospective
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213 object.
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214 Example :
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215 Returns : the type (a string, the module name)
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216 Args : initialization parameters to be passed to the prospective
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217 cluster object
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218
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219
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220 =cut
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221
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222 sub _guess_type{
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223 my ($self,@args) = @_;
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224 my $type;
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225
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226 # we can only guess from a certain number of arguments
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227 my ($dispid, $ns, $members) =
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228 $self->_rearrange([qw(DISPLAY_ID
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229 NAMESPACE
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230 MEMBERS
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231 )], @args);
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232 # Unigene namespace or ID?
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233 if($ns && (lc($ns) eq "unigene")) {
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234 $type = 'Bio::Cluster::UniGene';
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235 } elsif($dispid && ($dispid =~ /^Hs\.[0-9]/)) {
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236 $type = 'Bio::Cluster::UniGene';
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237 }
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238 # what else could we look for?
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239 return $type;
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240 }
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241
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242 #####################################################################
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243 # aliases for naming consistency or other reasons #
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244 #####################################################################
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245
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246 *create = \&create_object;
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247
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248 1;
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