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For bin/pan_genome_post_analysis
  Run on Fri Mar 27 11:43:32 2015
Reported on Fri Mar 27 11:46:11 2015

Filename/Users/ap13/perl5/lib/perl5/Bio/DB/InMemoryCache.pm
StatementsExecuted 7 statements in 967µs
Subroutines
Calls P F Exclusive
Time
Inclusive
Time
Subroutine
1111.61ms3.29msBio::DB::InMemoryCache::::BEGIN@75Bio::DB::InMemoryCache::BEGIN@75
11113µs25µsBio::DB::InMemoryCache::::BEGIN@73Bio::DB::InMemoryCache::BEGIN@73
11110µs763µsBio::DB::InMemoryCache::::BEGIN@77Bio::DB::InMemoryCache::BEGIN@77
0000s0sBio::DB::InMemoryCache::::_load_SeqBio::DB::InMemoryCache::_load_Seq
0000s0sBio::DB::InMemoryCache::::_number_freeBio::DB::InMemoryCache::_number_free
0000s0sBio::DB::InMemoryCache::::agrBio::DB::InMemoryCache::agr
0000s0sBio::DB::InMemoryCache::::get_Seq_by_accBio::DB::InMemoryCache::get_Seq_by_acc
0000s0sBio::DB::InMemoryCache::::get_Seq_by_idBio::DB::InMemoryCache::get_Seq_by_id
0000s0sBio::DB::InMemoryCache::::get_Seq_by_versionBio::DB::InMemoryCache::get_Seq_by_version
0000s0sBio::DB::InMemoryCache::::newBio::DB::InMemoryCache::new
0000s0sBio::DB::InMemoryCache::::numberBio::DB::InMemoryCache::number
0000s0sBio::DB::InMemoryCache::::seqdbBio::DB::InMemoryCache::seqdb
Call graph for these subroutines as a Graphviz dot language file.
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Code
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
16Bio::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 # $seq is a Bio::Seq object
30 #
31
32=head1 DESCRIPTION
33
34This is a memory cache system which saves the objects returned by
35Bio::DB::RandomAccessI in memory to a hard limit of sequences.
36
37=head1 CONTACT
38
39Ewan Birney E<lt>birney@ebi.ac.ukE<gt>
40
41=head2 Support
42
43Please direct usage questions or support issues to the mailing list:
44
45I<bioperl-l@bioperl.org>
46
47rather than to the module maintainer directly. Many experienced and
48reponsive experts will be able look at the problem and quickly
49address it. Please include a thorough description of the problem
50with code and data examples if at all possible.
51
52=head2 Reporting Bugs
53
54Report bugs to the Bioperl bug tracking system to help us keep track
55the bugs and their resolution. Bug reports can be submitted via the
56web:
57
58 https://github.com/bioperl/bioperl-live/issues
59
60=head1 APPENDIX
61
62The rest of the documentation details each of the object
63methods. Internal methods are usually preceded with a _
64
65=cut
66
67
68# Let the code begin...
69
70package Bio::DB::InMemoryCache;
71
72
73223µs237µs
# spent 25µs (13+12) within Bio::DB::InMemoryCache::BEGIN@73 which was called: # once (13µs+12µs) by Bio::SeqFeatureI::BEGIN@99 at line 73
use strict;
# spent 25µs making 1 call to Bio::DB::InMemoryCache::BEGIN@73 # spent 12µs making 1 call to strict::import
74
752257µs13.29ms
# spent 3.29ms (1.61+1.69) within Bio::DB::InMemoryCache::BEGIN@75 which was called: # once (1.61ms+1.69ms) by Bio::SeqFeatureI::BEGIN@99 at line 75
use Bio::Seq;
# spent 3.29ms making 1 call to Bio::DB::InMemoryCache::BEGIN@75
76
772684µs2763µs
# spent 763µs (10+752) within Bio::DB::InMemoryCache::BEGIN@77 which was called: # once (10µs+752µs) by Bio::SeqFeatureI::BEGIN@99 at line 77
use base qw(Bio::Root::Root Bio::DB::SeqI);
# spent 763µs making 1 call to Bio::DB::InMemoryCache::BEGIN@77 # spent 752µs making 1 call to base::import, recursion: max depth 1, sum of overlapping time 752µs
78
79sub new {
80 my ($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 = $db->get_Seq_by_id('ROA1_HUMAN')
114 Function: Gets a Bio::Seq object by its name
115 Returns : a Bio::Seq object
116 Args : the id (as a string) of a sequence
117 Throws : "id does not exist" exception
118
119=cut
120
121sub get_Seq_by_id{
122 my ($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 = $db->get_Seq_by_acc('X77802');
139 Function: Gets a Bio::Seq object by accession number
140 Returns : A Bio::Seq object
141 Args : accession number (as a string)
142 Throws : "acc does not exist" exception
143
144=cut
145
146sub get_Seq_by_acc{
147 my ($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
- -
163sub number {
164 my ($self, $number) = @_;
165 if ($number) {
166 $self->{'number'} = $number;
167 } else {
168 return $self->{'number'};
169 }
170}
171
172sub seqdb {
173 my ($self, $seqdb) = @_;
174 if ($seqdb) {
175 $self->{'seqdb'} = $seqdb;
176 } else {
177 return $self->{'seqdb'};
178 }
179}
180
181sub agr {
182 my ($self, $agr) = @_;
183 if ($agr) {
184 $self->{'agr'} = $agr;
185 } else {
186 return $self->{'agr'};
187 }
188}
189
190
191sub _load_Seq {
192 my ($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
250sub _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 = $db->get_Seq_by_version('X77802.1');
260 Function: Gets a Bio::Seq object by sequence version
261 Returns : A Bio::Seq object
262 Args : accession.version (as a string)
263 Throws : "acc.version does not exist" exception
264
265=cut
266
267sub get_Seq_by_version{
268 my ($self,@args) = @_;
269 $self->throw("Not implemented it");
270}
271
272## End of Package
273
27412µs1;