| Filename | /Users/ap13/perl5/lib/perl5/Bio/DB/InMemoryCache.pm |
| Statements | Executed 7 statements in 967µs |
| Calls | P | F | Exclusive Time |
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| 1 | 1 | 1 | 1.61ms | 3.29ms | Bio::DB::InMemoryCache::BEGIN@75 |
| 1 | 1 | 1 | 13µs | 25µs | Bio::DB::InMemoryCache::BEGIN@73 |
| 1 | 1 | 1 | 10µs | 763µs | Bio::DB::InMemoryCache::BEGIN@77 |
| 0 | 0 | 0 | 0s | 0s | Bio::DB::InMemoryCache::_load_Seq |
| 0 | 0 | 0 | 0s | 0s | Bio::DB::InMemoryCache::_number_free |
| 0 | 0 | 0 | 0s | 0s | Bio::DB::InMemoryCache::agr |
| 0 | 0 | 0 | 0s | 0s | Bio::DB::InMemoryCache::get_Seq_by_acc |
| 0 | 0 | 0 | 0s | 0s | Bio::DB::InMemoryCache::get_Seq_by_id |
| 0 | 0 | 0 | 0s | 0s | Bio::DB::InMemoryCache::get_Seq_by_version |
| 0 | 0 | 0 | 0s | 0s | Bio::DB::InMemoryCache::new |
| 0 | 0 | 0 | 0s | 0s | Bio::DB::InMemoryCache::number |
| 0 | 0 | 0 | 0s | 0s | Bio::DB::InMemoryCache::seqdb |
| Line | State ments |
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| 1 | # | ||||
| 2 | # BioPerl module for Bio::DB::InMemoryCache | ||||
| 3 | # | ||||
| 4 | # Please direct questions and support issues to <bioperl-l@bioperl.org> | ||||
| 5 | # | ||||
| 6 | # Cared for by Ewan Birney <birney@sanger.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::DB::InMemoryCache - Abstract interface for a sequence database | ||||
| 17 | |||||
| 18 | =head1 SYNOPSIS | ||||
| 19 | |||||
| 20 | $cachedb = Bio::DB::InMemoryCache->new( -seqdb => $real_db, | ||||
| 21 | -number => 1000); | ||||
| 22 | # | ||||
| 23 | # get a database object somehow using a concrete class | ||||
| 24 | # | ||||
| 25 | |||||
| 26 | $seq = $cachedb->get_Seq_by_id('ROA1_HUMAN'); | ||||
| 27 | |||||
| 28 | # | ||||
| 29 | # $seq is a Bio::Seq object | ||||
| 30 | # | ||||
| 31 | |||||
| 32 | =head1 DESCRIPTION | ||||
| 33 | |||||
| 34 | This is a memory cache system which saves the objects returned by | ||||
| 35 | Bio::DB::RandomAccessI in memory to a hard limit of sequences. | ||||
| 36 | |||||
| 37 | =head1 CONTACT | ||||
| 38 | |||||
| 39 | Ewan Birney E<lt>birney@ebi.ac.ukE<gt> | ||||
| 40 | |||||
| 41 | =head2 Support | ||||
| 42 | |||||
| 43 | Please direct usage questions or support issues to the mailing list: | ||||
| 44 | |||||
| 45 | I<bioperl-l@bioperl.org> | ||||
| 46 | |||||
| 47 | rather than to the module maintainer directly. Many experienced and | ||||
| 48 | reponsive experts will be able look at the problem and quickly | ||||
| 49 | address it. Please include a thorough description of the problem | ||||
| 50 | with code and data examples if at all possible. | ||||
| 51 | |||||
| 52 | =head2 Reporting Bugs | ||||
| 53 | |||||
| 54 | Report bugs to the Bioperl bug tracking system to help us keep track | ||||
| 55 | the bugs and their resolution. Bug reports can be submitted via the | ||||
| 56 | web: | ||||
| 57 | |||||
| 58 | https://github.com/bioperl/bioperl-live/issues | ||||
| 59 | |||||
| 60 | =head1 APPENDIX | ||||
| 61 | |||||
| 62 | The rest of the documentation details each of the object | ||||
| 63 | methods. Internal methods are usually preceded with a _ | ||||
| 64 | |||||
| 65 | =cut | ||||
| 66 | |||||
| 67 | |||||
| 68 | # Let the code begin... | ||||
| 69 | |||||
| 70 | package Bio::DB::InMemoryCache; | ||||
| 71 | |||||
| 72 | |||||
| 73 | 2 | 23µs | 2 | 37µs | # spent 25µs (13+12) within Bio::DB::InMemoryCache::BEGIN@73 which was called:
# once (13µs+12µs) by Bio::SeqFeatureI::BEGIN@99 at line 73 # spent 25µs making 1 call to Bio::DB::InMemoryCache::BEGIN@73
# spent 12µs making 1 call to strict::import |
| 74 | |||||
| 75 | 2 | 257µs | 1 | 3.29ms | # spent 3.29ms (1.61+1.69) within Bio::DB::InMemoryCache::BEGIN@75 which was called:
# once (1.61ms+1.69ms) by Bio::SeqFeatureI::BEGIN@99 at line 75 # spent 3.29ms making 1 call to Bio::DB::InMemoryCache::BEGIN@75 |
| 76 | |||||
| 77 | 2 | 684µs | 2 | 763µs | # spent 763µs (10+752) within Bio::DB::InMemoryCache::BEGIN@77 which was called:
# once (10µs+752µs) by Bio::SeqFeatureI::BEGIN@99 at line 77 # spent 763µs making 1 call to Bio::DB::InMemoryCache::BEGIN@77
# spent 752µs making 1 call to base::import, recursion: max depth 1, sum of overlapping time 752µs |
| 78 | |||||
| 79 | sub new { | ||||
| 80 | my ($class,@args) = @_; | ||||
| 81 | |||||
| 82 | my $self = Bio::Root::Root->new(); | ||||
| 83 | bless $self,$class; | ||||
| 84 | |||||
| 85 | my ($seqdb,$number,$agr) = | ||||
| 86 | $self->_rearrange([qw(SEQDB NUMBER AGRESSION)],@args); | ||||
| 87 | |||||
| 88 | if( !defined $seqdb || !ref $seqdb || | ||||
| 89 | !$seqdb->isa('Bio::DB::RandomAccessI') ) { | ||||
| 90 | $self->throw("Must be a RandomAccess database not a [$seqdb]"); | ||||
| 91 | } | ||||
| 92 | |||||
| 93 | if( !defined $number ) { | ||||
| 94 | $number = 1000; | ||||
| 95 | } | ||||
| 96 | |||||
| 97 | $self->seqdb($seqdb); | ||||
| 98 | $self->number($number); | ||||
| 99 | $self->agr($agr); | ||||
| 100 | |||||
| 101 | # we consider acc as the primary id here | ||||
| 102 | $self->{'_cache_number_hash'} = {}; | ||||
| 103 | $self->{'_cache_id_hash'} = {}; | ||||
| 104 | $self->{'_cache_acc_hash'} = {}; | ||||
| 105 | $self->{'_cache_number'} = 1; | ||||
| 106 | |||||
| 107 | return $self; | ||||
| 108 | } | ||||
| 109 | |||||
| 110 | =head2 get_Seq_by_id | ||||
| 111 | |||||
| 112 | Title : get_Seq_by_id | ||||
| 113 | Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN') | ||||
| 114 | Function: Gets a Bio::Seq object by its name | ||||
| 115 | Returns : a Bio::Seq object | ||||
| 116 | Args : the id (as a string) of a sequence | ||||
| 117 | Throws : "id does not exist" exception | ||||
| 118 | |||||
| 119 | =cut | ||||
| 120 | |||||
| 121 | sub get_Seq_by_id{ | ||||
| 122 | my ($self,$id) = @_; | ||||
| 123 | |||||
| 124 | if( defined $self->{'_cache_id_hash'}->{$id} ) { | ||||
| 125 | my $acc = $self->{'_cache_id_hash'}->{$id}; | ||||
| 126 | my $seq = $self->{'_cache_acc_hash'}->{$acc}; | ||||
| 127 | $self->{'_cache_number_hash'}->{$seq->accession} = | ||||
| 128 | $self->{'_cache_number'}++; | ||||
| 129 | return $seq; | ||||
| 130 | } else { | ||||
| 131 | return $self->_load_Seq('id',$id); | ||||
| 132 | } | ||||
| 133 | } | ||||
| 134 | |||||
| 135 | =head2 get_Seq_by_acc | ||||
| 136 | |||||
| 137 | Title : get_Seq_by_acc | ||||
| 138 | Usage : $seq = $db->get_Seq_by_acc('X77802'); | ||||
| 139 | Function: Gets a Bio::Seq object by accession number | ||||
| 140 | Returns : A Bio::Seq object | ||||
| 141 | Args : accession number (as a string) | ||||
| 142 | Throws : "acc does not exist" exception | ||||
| 143 | |||||
| 144 | =cut | ||||
| 145 | |||||
| 146 | sub get_Seq_by_acc{ | ||||
| 147 | my ($self,$acc) = @_; | ||||
| 148 | |||||
| 149 | #print STDERR "In cache get for $acc\n"; | ||||
| 150 | if( defined $self->{'_cache_acc_hash'}->{$acc} ) { | ||||
| 151 | #print STDERR "Returning cached $acc\n"; | ||||
| 152 | my $seq = $self->{'_cache_acc_hash'}->{$acc}; | ||||
| 153 | $self->{'_cache_number_hash'}->{$seq->accession} = | ||||
| 154 | $self->{'_cache_number'}++; | ||||
| 155 | return $seq; | ||||
| 156 | } else { | ||||
| 157 | return $self->_load_Seq('acc',$acc); | ||||
| 158 | } | ||||
| 159 | } | ||||
| 160 | |||||
| - - | |||||
| 163 | sub number { | ||||
| 164 | my ($self, $number) = @_; | ||||
| 165 | if ($number) { | ||||
| 166 | $self->{'number'} = $number; | ||||
| 167 | } else { | ||||
| 168 | return $self->{'number'}; | ||||
| 169 | } | ||||
| 170 | } | ||||
| 171 | |||||
| 172 | sub seqdb { | ||||
| 173 | my ($self, $seqdb) = @_; | ||||
| 174 | if ($seqdb) { | ||||
| 175 | $self->{'seqdb'} = $seqdb; | ||||
| 176 | } else { | ||||
| 177 | return $self->{'seqdb'}; | ||||
| 178 | } | ||||
| 179 | } | ||||
| 180 | |||||
| 181 | sub agr { | ||||
| 182 | my ($self, $agr) = @_; | ||||
| 183 | if ($agr) { | ||||
| 184 | $self->{'agr'} = $agr; | ||||
| 185 | } else { | ||||
| 186 | return $self->{'agr'}; | ||||
| 187 | } | ||||
| 188 | } | ||||
| 189 | |||||
| 190 | |||||
| 191 | sub _load_Seq { | ||||
| 192 | my ($self,$type,$id) = @_; | ||||
| 193 | |||||
| 194 | my $seq; | ||||
| 195 | |||||
| 196 | if( $type eq 'id') { | ||||
| 197 | $seq = $self->seqdb->get_Seq_by_id($id); | ||||
| 198 | }elsif ( $type eq 'acc' ) { | ||||
| 199 | $seq = $self->seqdb->get_Seq_by_acc($id); | ||||
| 200 | } else { | ||||
| 201 | $self->throw("Bad internal error. Don't understand $type"); | ||||
| 202 | } | ||||
| 203 | if( ! $seq ) { | ||||
| 204 | # warding off bug #1628 | ||||
| 205 | $self->debug("could not find seq $id in seqdb\n"); | ||||
| 206 | return; | ||||
| 207 | } | ||||
| 208 | |||||
| 209 | if( $self->agr() ) { | ||||
| 210 | #print STDERR "Pulling out into memory\n"; | ||||
| 211 | my $newseq = Bio::Seq->new( -display_id => $seq->display_id, | ||||
| 212 | -accession_number => $seq->accession, | ||||
| 213 | -seq => $seq->seq, | ||||
| 214 | -desc => $seq->desc, | ||||
| 215 | ); | ||||
| 216 | if( $self->agr() == 1 ) { | ||||
| 217 | foreach my $sf ( $seq->top_SeqFeatures() ) { | ||||
| 218 | $newseq->add_SeqFeature($sf); | ||||
| 219 | } | ||||
| 220 | |||||
| 221 | $newseq->annotation($seq->annotation); | ||||
| 222 | } | ||||
| 223 | $seq = $newseq; | ||||
| 224 | } | ||||
| 225 | |||||
| 226 | if( $self->_number_free < 1 ) { | ||||
| 227 | # remove the latest thing from the hash | ||||
| 228 | my @accs = sort { $self->{'_cache_number_hash'}->{$a} <=> | ||||
| 229 | $self->{'_cache_number_hash'}->{$b} } | ||||
| 230 | keys %{$self->{'_cache_number_hash'}}; | ||||
| 231 | |||||
| 232 | my $acc = shift @accs; | ||||
| 233 | # remove this guy | ||||
| 234 | my $seq = $self->{'_cache_acc_hash'}->{$acc}; | ||||
| 235 | |||||
| 236 | delete $self->{'_cache_number_hash'}->{$acc}; | ||||
| 237 | delete $self->{'_cache_id_hash'}->{$seq->id}; | ||||
| 238 | delete $self->{'_cache_acc_hash'}->{$acc}; | ||||
| 239 | } | ||||
| 240 | |||||
| 241 | # up the number, register this sequence into the hash. | ||||
| 242 | $self->{'_cache_id_hash'}->{$seq->id} = $seq->accession; | ||||
| 243 | $self->{'_cache_acc_hash'}->{$seq->accession} = $seq; | ||||
| 244 | $self->{'_cache_number_hash'}->{$seq->accession} = $self->{'_cache_number'}++; | ||||
| 245 | |||||
| 246 | return $seq; | ||||
| 247 | } | ||||
| 248 | |||||
| 249 | |||||
| 250 | sub _number_free { | ||||
| 251 | my $self = shift; | ||||
| 252 | |||||
| 253 | return $self->number - scalar(keys %{$self->{'_cache_number_hash'}}); | ||||
| 254 | } | ||||
| 255 | |||||
| 256 | =head2 get_Seq_by_version | ||||
| 257 | |||||
| 258 | Title : get_Seq_by_version | ||||
| 259 | Usage : $seq = $db->get_Seq_by_version('X77802.1'); | ||||
| 260 | Function: Gets a Bio::Seq object by sequence version | ||||
| 261 | Returns : A Bio::Seq object | ||||
| 262 | Args : accession.version (as a string) | ||||
| 263 | Throws : "acc.version does not exist" exception | ||||
| 264 | |||||
| 265 | =cut | ||||
| 266 | |||||
| 267 | sub get_Seq_by_version{ | ||||
| 268 | my ($self,@args) = @_; | ||||
| 269 | $self->throw("Not implemented it"); | ||||
| 270 | } | ||||
| 271 | |||||
| 272 | ## End of Package | ||||
| 273 | |||||
| 274 | 1 | 2µs | 1; |