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For bin/pan_genome_post_analysis
  Run on Fri Mar 27 11:43:32 2015
Reported on Fri Mar 27 11:45:47 2015

Filename/Users/ap13/perl5/lib/perl5/Bio/AnnotationI.pm
StatementsExecuted 5 statements in 142µs
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11113µs26µsBio::AnnotationI::::BEGIN@116Bio::AnnotationI::BEGIN@116
1119µs77µsBio::AnnotationI::::BEGIN@120Bio::AnnotationI::BEGIN@120
0000s0sBio::AnnotationI::::as_textBio::AnnotationI::as_text
0000s0sBio::AnnotationI::::display_textBio::AnnotationI::display_text
0000s0sBio::AnnotationI::::hash_treeBio::AnnotationI::hash_tree
0000s0sBio::AnnotationI::::tagnameBio::AnnotationI::tagname
Call graph for these subroutines as a Graphviz dot language file.
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1#
2# BioPerl module for Bio::AnnotationI
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
16Bio::AnnotationI - Annotation interface
17
18=head1 SYNOPSIS
19
20 # generally you get AnnotationI's from AnnotationCollectionI's
21
22 foreach $key ( $ac->get_all_annotation_keys() ) {
23 @values = $ac->get_Annotations($key);
24 foreach $value ( @values ) {
25 # value is an Bio::AnnotationI, and defines a "as_text" method
26 print "Annotation ",$key," stringified value ",$value->as_text,"\n";
27 # you can also use a generic hash_tree method for getting
28 # stuff out say into XML format
29 $hash_tree = $value->hash_tree();
30 }
31 }
32
33=head1 DESCRIPTION
34
35Interface all annotations must support. There are two things that each
36annotation has to support.
37
38 $annotation->as_text()
39
40Annotations have to support an "as_text" method. This should be a
41single text string, without newlines representing the annotation,
42mainly for human readability. It is not aimed at being able to
43store/represent the annotation.
44
45The second method allows annotations to at least attempt to represent
46themselves as pure data for storage/display/whatever. The method
47hash_tree should return an anonymous hash with "XML-like" formatting:
48
49 $hash = $annotation->hash_tree();
50
51The formatting is as follows.
52
53 (1) For each key in the hash, if the value is a reference'd array -
54
55 (2) For each element of the array if the value is a object -
56 Assume the object has the method "hash_tree";
57 (3) else if the value is a reference to a hash
58 Recurse again from point (1)
59 (4) else
60 Assume the value is a scalar, and handle it directly as text
61 (5) else (if not an array) apply rules 2,3 and 4 to value
62
63The XML path in tags is represented by the keys taken in the
64hashes. When arrays are encountered they are all present in the path
65level of this tag
66
67This is a pretty "natural" representation of an object tree in an XML
68style, without forcing everything to inherit off some super-generic
69interface for representing things in the hash.
70
71=head1 FEEDBACK
72
73=head2 Mailing Lists
74
75User feedback is an integral part of the evolution of this
76and other Bioperl modules. Send your comments and suggestions preferably
77 to one of the Bioperl mailing lists.
78Your participation is much appreciated.
79
80 bioperl-l@bioperl.org
81
82=head2 Support
83
84Please direct usage questions or support issues to the mailing list:
85
86I<bioperl-l@bioperl.org>
87
88rather than to the module maintainer directly. Many experienced and
89reponsive experts will be able look at the problem and quickly
90address it. Please include a thorough description of the problem
91with code and data examples if at all possible.
92
93=head2 Reporting Bugs
94
95Report bugs to the Bioperl bug tracking system to help us keep track
96the bugs and their resolution. Bug reports can be submitted via the
97web:
98
99 https://github.com/bioperl/bioperl-live/issues
100
101=head1 AUTHOR - Ewan Birney
102
103Email birney@ebi.ac.uk
104
105=head1 APPENDIX
106
107The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
108
109=cut
110
111#'
112# Let the code begin...
113
114
115package Bio::AnnotationI;
116227µs239µs
# spent 26µs (13+13) within Bio::AnnotationI::BEGIN@116 which was called: # once (13µs+13µs) by base::import at line 116
use strict;
# spent 26µs making 1 call to Bio::AnnotationI::BEGIN@116 # spent 13µs making 1 call to strict::import
117
118# Object preamble - inherits from Bio::Root::Root
119
1202113µs277µs
# spent 77µs (9+67) within Bio::AnnotationI::BEGIN@120 which was called: # once (9µs+67µs) by base::import at line 120
use base qw(Bio::Root::RootI);
# spent 77µs making 1 call to Bio::AnnotationI::BEGIN@120 # spent 68µs making 1 call to base::import, recursion: max depth 1, sum of overlapping time 68µs
121
122=head2 as_text
123
124 Title : as_text
125 Usage :
126 Function: single text string, without newlines representing the
127 annotation, mainly for human readability. It is not aimed
128 at being able to store/represent the annotation.
129 Example :
130 Returns : a string
131 Args : none
132
133
134=cut
135
136sub as_text{
137 shift->throw_not_implemented();
138}
139
140=head2 display_text
141
142 Title : display_text
143 Usage : my $str = $ann->display_text();
144 Function: returns a string. Unlike as_text(), this method returns a string
145 formatted as would be expected for the specific implementation.
146
147 Implementations should allow passing a callback as an argument which
148 allows custom text generation; the callback will be passed the
149 current implementation.
150
151 Note that this is meant to be used as a simple representation
152 of the annotation data but probably shouldn't be used in cases
153 where more complex comparisons are needed or where data is
154 stored.
155 Example :
156 Returns : a string
157 Args : [optional] callback
158
159=cut
160
161sub display_text {
162 shift->throw_not_implemented();
163}
164
165=head2 hash_tree
166
167 Title : hash_tree
168 Usage :
169 Function: should return an anonymous hash with "XML-like" formatting
170 Example :
171 Returns : a hash reference
172 Args : none
173
174=cut
175
176sub hash_tree{
177 shift->throw_not_implemented();
178}
179
180=head2 tagname
181
182 Title : tagname
183 Usage : $obj->tagname($newval)
184 Function: Get/set the tagname for this annotation value.
185
186 Setting this is optional. If set, it obviates the need to
187 provide a tag to Bio::AnnotationCollectionI when adding
188 this object. When obtaining an AnnotationI object from the
189 collection, the collection will set the value to the tag
190 under which it was stored unless the object has a tag
191 stored already.
192
193 Example :
194 Returns : value of tagname (a scalar)
195 Args : new value (a scalar, optional)
196
197
198=cut
199
200sub tagname{
201 shift->throw_not_implemented();
202}
203
20412µs1;