| Filename | /Users/ap13/perl5/lib/perl5/Bio/Annotation/TypeManager.pm |
| Statements | Executed 5 statements in 304µs |
| Calls | P | F | Exclusive Time |
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| 1 | 1 | 1 | 15µs | 28µs | Bio::Annotation::TypeManager::BEGIN@80 |
| 1 | 1 | 1 | 9µs | 82µs | Bio::Annotation::TypeManager::BEGIN@86 |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::TypeManager::_add_type_map |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::TypeManager::is_valid |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::TypeManager::new |
| 0 | 0 | 0 | 0s | 0s | Bio::Annotation::TypeManager::type_for_key |
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| 1 | # | ||||
| 2 | # BioPerl module for Bio::Annotation::TypeManager | ||||
| 3 | # | ||||
| 4 | # Please direct questions and support issues to <bioperl-l@bioperl.org> | ||||
| 5 | # | ||||
| 6 | # Cared for by Ewan Birney <birney@ebi.ac.uk> | ||||
| 7 | # | ||||
| 8 | # Copyright Ewan Birney | ||||
| 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::Annotation::TypeManager - Manages types for annotation collections | ||||
| 17 | |||||
| 18 | =head1 SYNOPSIS | ||||
| 19 | |||||
| 20 | # default type manager | ||||
| 21 | |||||
| 22 | $tm = Bio::Annotation::TypeManager->new(); | ||||
| 23 | |||||
| 24 | # $key is a string or a Bio::Ontology::TermI compliant object | ||||
| 25 | print "The type for $key is ",$tm->type_for_key($key),"\n"; | ||||
| 26 | |||||
| 27 | if( !$tm->is_valid($key,$object) ) { | ||||
| 28 | $self->throw("Invalid object for key $key"); | ||||
| 29 | } | ||||
| 30 | |||||
| 31 | =head1 DESCRIPTION | ||||
| 32 | |||||
| 33 | Manages types for annotation collections. | ||||
| 34 | |||||
| 35 | =head1 FEEDBACK | ||||
| 36 | |||||
| 37 | =head2 Mailing Lists | ||||
| 38 | |||||
| 39 | User feedback is an integral part of the evolution of this | ||||
| 40 | and other Bioperl modules. Send your comments and suggestions preferably | ||||
| 41 | to one of the Bioperl mailing lists. | ||||
| 42 | Your participation is much appreciated. | ||||
| 43 | |||||
| 44 | bioperl-l@bioperl.org | ||||
| 45 | |||||
| 46 | =head2 Support | ||||
| 47 | |||||
| 48 | Please direct usage questions or support issues to the mailing list: | ||||
| 49 | |||||
| 50 | I<bioperl-l@bioperl.org> | ||||
| 51 | |||||
| 52 | rather than to the module maintainer directly. Many experienced and | ||||
| 53 | reponsive experts will be able look at the problem and quickly | ||||
| 54 | address it. Please include a thorough description of the problem | ||||
| 55 | with code and data examples if at all possible. | ||||
| 56 | |||||
| 57 | =head2 Reporting Bugs | ||||
| 58 | |||||
| 59 | Report bugs to the Bioperl bug tracking system to help us keep track | ||||
| 60 | the bugs and their resolution. | ||||
| 61 | Bug reports can be submitted via the web: | ||||
| 62 | |||||
| 63 | https://github.com/bioperl/bioperl-live/issues | ||||
| 64 | |||||
| 65 | =head1 AUTHOR - Ewan Birney | ||||
| 66 | |||||
| 67 | Email birney@ebi.ac.uk | ||||
| 68 | |||||
| 69 | =head1 APPENDIX | ||||
| 70 | |||||
| 71 | The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ | ||||
| 72 | |||||
| 73 | =cut | ||||
| 74 | |||||
| 75 | |||||
| 76 | # Let the code begin... | ||||
| 77 | |||||
| 78 | |||||
| 79 | package Bio::Annotation::TypeManager; | ||||
| 80 | 2 | 28µs | 2 | 41µs | # spent 28µs (15+13) within Bio::Annotation::TypeManager::BEGIN@80 which was called:
# once (15µs+13µs) by Bio::Annotation::Collection::BEGIN@92 at line 80 # spent 28µs making 1 call to Bio::Annotation::TypeManager::BEGIN@80
# spent 13µs making 1 call to strict::import |
| 81 | |||||
| 82 | # Object preamble - inherits from Bio::Root::Root | ||||
| 83 | |||||
| - - | |||||
| 86 | 2 | 273µs | 2 | 154µs | # spent 82µs (9+72) within Bio::Annotation::TypeManager::BEGIN@86 which was called:
# once (9µs+72µs) by Bio::Annotation::Collection::BEGIN@92 at line 86 # spent 82µs making 1 call to Bio::Annotation::TypeManager::BEGIN@86
# spent 72µs making 1 call to base::import |
| 87 | # new() can be inherited from Bio::Root::Root | ||||
| 88 | |||||
| 89 | =head2 new | ||||
| 90 | |||||
| 91 | Title : new | ||||
| 92 | Usage : | ||||
| 93 | Function: | ||||
| 94 | Example : | ||||
| 95 | Returns : | ||||
| 96 | Args : | ||||
| 97 | |||||
| 98 | |||||
| 99 | =cut | ||||
| 100 | |||||
| 101 | sub new{ | ||||
| 102 | my ($class,@args) = @_; | ||||
| 103 | |||||
| 104 | my $self = $class->SUPER::new(@args); | ||||
| 105 | |||||
| 106 | $self->{'_type'} = {}; | ||||
| 107 | |||||
| 108 | $self->_add_type_map('reference',"Bio::Annotation::Reference"); | ||||
| 109 | $self->_add_type_map('comment',"Bio::Annotation::Comment"); | ||||
| 110 | $self->_add_type_map('dblink',"Bio::Annotation::DBLink"); | ||||
| 111 | |||||
| 112 | return $self; | ||||
| 113 | } | ||||
| 114 | |||||
| 115 | |||||
| 116 | =head2 type_for_key | ||||
| 117 | |||||
| 118 | Title : type_for_key | ||||
| 119 | Usage : | ||||
| 120 | Function: | ||||
| 121 | Example : | ||||
| 122 | Returns : | ||||
| 123 | Args : | ||||
| 124 | |||||
| 125 | |||||
| 126 | =cut | ||||
| 127 | |||||
| 128 | sub type_for_key{ | ||||
| 129 | my ($self,$key) = @_; | ||||
| 130 | |||||
| 131 | $key = $key->name() if ref($key) && $key->isa("Bio::Ontology::TermI"); | ||||
| 132 | return $self->{'_type'}->{$key}; | ||||
| 133 | } | ||||
| 134 | |||||
| 135 | |||||
| 136 | =head2 is_valid | ||||
| 137 | |||||
| 138 | Title : is_valid | ||||
| 139 | Usage : | ||||
| 140 | Function: | ||||
| 141 | Example : | ||||
| 142 | Returns : | ||||
| 143 | Args : | ||||
| 144 | |||||
| 145 | |||||
| 146 | =cut | ||||
| 147 | |||||
| 148 | sub is_valid{ | ||||
| 149 | my ($self,$key,$object) = @_; | ||||
| 150 | |||||
| 151 | if( !defined $object || !ref $object ) { | ||||
| 152 | $self->throw("Cannot type an object [$object]!"); | ||||
| 153 | } | ||||
| 154 | |||||
| 155 | if( !$object->isa($self->type_for_key($key)) ) { | ||||
| 156 | return 0; | ||||
| 157 | } else { | ||||
| 158 | return 1; | ||||
| 159 | } | ||||
| 160 | } | ||||
| 161 | |||||
| 162 | |||||
| 163 | =head2 _add_type_map | ||||
| 164 | |||||
| 165 | Title : _add_type_map | ||||
| 166 | Usage : | ||||
| 167 | Function: | ||||
| 168 | Example : | ||||
| 169 | Returns : | ||||
| 170 | Args : | ||||
| 171 | |||||
| 172 | |||||
| 173 | =cut | ||||
| 174 | |||||
| 175 | sub _add_type_map{ | ||||
| 176 | my ($self,$key,$type) = @_; | ||||
| 177 | |||||
| 178 | $key = $key->name() if ref($key) && $key->isa("Bio::Ontology::TermI"); | ||||
| 179 | $self->{'_type'}->{$key} = $type; | ||||
| 180 | } | ||||
| 181 | |||||
| 182 | 1 | 3µs | 1; |