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For bin/pan_genome_post_analysis
  Run on Fri Mar 27 11:43:32 2015
Reported on Fri Mar 27 11:45:28 2015

Filename/Users/ap13/perl5/lib/perl5/Bio/DB/RandomAccessI.pm
StatementsExecuted 7 statements in 162µs
Subroutines
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11116µs28µsBio::DB::RandomAccessI::::BEGIN@64Bio::DB::RandomAccessI::BEGIN@64
1118µs60µsBio::DB::RandomAccessI::::BEGIN@68Bio::DB::RandomAccessI::BEGIN@68
1117µs7µsBio::DB::RandomAccessI::::BEGIN@66Bio::DB::RandomAccessI::BEGIN@66
0000s0sBio::DB::RandomAccessI::::get_Seq_by_accBio::DB::RandomAccessI::get_Seq_by_acc
0000s0sBio::DB::RandomAccessI::::get_Seq_by_idBio::DB::RandomAccessI::get_Seq_by_id
0000s0sBio::DB::RandomAccessI::::get_Seq_by_versionBio::DB::RandomAccessI::get_Seq_by_version
Call graph for these subroutines as a Graphviz dot language file.
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1# POD documentation - main docs before the code
2#
3#
4
5=head1 NAME
6
7Bio::DB::RandomAccessI - Abstract interface for a sequence database
8
9=head1 SYNOPSIS
10
11 #
12 # get a database object somehow using a concrete class
13 #
14
15 $seq = $db->get_Seq_by_id('ROA1_HUMAN');
16
17 #
18 # $seq is a Bio::Seq object
19 #
20
21=head1 DESCRIPTION
22
23This is a pure interface class - in other words, all this does is define
24methods which other (concrete) classes will actually implement.
25
26The Bio::DB::RandomAccessI class defines what methods a generic database class
27should have. At the moment it is just the ability to make Bio::Seq objects
28from a name (id) or an accession number.
29
30=head1 CONTACT
31
32Ewan Birney E<lt>birney@ebi.ac.ukE<gt> originally wrote this class.
33
34=head2 Support
35
36Please direct usage questions or support issues to the mailing list:
37
38I<bioperl-l@bioperl.org>
39
40rather than to the module maintainer directly. Many experienced and
41reponsive experts will be able look at the problem and quickly
42address it. Please include a thorough description of the problem
43with code and data examples if at all possible.
44
45=head2 Reporting Bugs
46
47Report bugs to the Bioperl bug tracking system to help us keep track
48the bugs and their resolution. Bug reports can be submitted via the web:
49
50 https://github.com/bioperl/bioperl-live/issues
51
52=head1 APPENDIX
53
54The rest of the documentation details each of the object
55methods. Internal methods are usually preceded with a _
56
57=cut
58
59
60# Let the code begin...
61
62package Bio::DB::RandomAccessI;
63
64224µs240µs
# spent 28µs (16+12) within Bio::DB::RandomAccessI::BEGIN@64 which was called: # once (16µs+12µs) by base::import at line 64
use strict;
# spent 28µs making 1 call to Bio::DB::RandomAccessI::BEGIN@64 # spent 12µs making 1 call to strict::import
65
66225µs17µs
# spent 7µs within Bio::DB::RandomAccessI::BEGIN@66 which was called: # once (7µs+0s) by base::import at line 66
use Bio::Root::RootI;
# spent 7µs making 1 call to Bio::DB::RandomAccessI::BEGIN@66
67
682111µs260µs
# spent 60µs (8+53) within Bio::DB::RandomAccessI::BEGIN@68 which was called: # once (8µs+53µs) by base::import at line 68
use base qw(Bio::Root::Root);
# spent 60µs making 1 call to Bio::DB::RandomAccessI::BEGIN@68 # spent 53µs making 1 call to base::import, recursion: max depth 3, sum of overlapping time 53µs
69
70=head2 get_Seq_by_id
71
72 Title : get_Seq_by_id
73 Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
74 Function: Gets a Bio::Seq object by its name
75 Returns : a Bio::Seq object or undef if not found
76 Args : the id (as a string) of a sequence,
77
78=cut
79
80sub get_Seq_by_id{
81 my ($self,@args) = @_;
82 $self->throw_not_implemented();
83}
84
85=head2 get_Seq_by_acc
86
87 Title : get_Seq_by_acc
88 Usage : $seq = $db->get_Seq_by_acc('X77802');
89 $seq = $db->get_Seq_by_acc(Locus => 'X77802');
90 Function: Gets a Bio::Seq object by accession number
91 Returns : A Bio::Seq object or undef if not found
92 Args : accession number (as a string), or a two
93 element list consisting of namespace=>accession
94 Throws : "more than one sequences correspond to this accession"
95 if the accession maps to multiple primary ids and
96 method is called in a scalar context
97
98NOTE: The two-element form allows you to choose the namespace for the
99accession number.
100
101=cut
102
103sub get_Seq_by_acc{
104 my ($self,@args) = @_;
105 $self->throw_not_implemented();
106}
107
108
109=head2 get_Seq_by_version
110
111 Title : get_Seq_by_version
112 Usage : $seq = $db->get_Seq_by_version('X77802.1');
113 Function: Gets a Bio::Seq object by sequence version
114 Returns : A Bio::Seq object
115 Args : accession.version (as a string)
116 Throws : "acc.version does not exist" exception
117
118=cut
119
120
121sub get_Seq_by_version{
122 my ($self,@args) = @_;
123 $self->throw_not_implemented();
124}
125
126## End of Package
127
12812µs1;
129