Filename | /Users/ap13/perl5/lib/perl5/Bio/Factory/LocationFactoryI.pm |
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1 | # | ||||
2 | # BioPerl module for Bio::Factory::LocationFactoryI | ||||
3 | # | ||||
4 | # Please direct questions and support issues to <bioperl-l@bioperl.org> | ||||
5 | # | ||||
6 | # Cared for by Hilmar Lapp <hlapp at gmx.net> | ||||
7 | # | ||||
8 | # Copyright Hilmar Lapp | ||||
9 | # | ||||
10 | # You may distribute this module under the same terms as perl itself | ||||
11 | |||||
12 | # | ||||
13 | # (c) Hilmar Lapp, hlapp at gnf.org, 2002. | ||||
14 | # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002. | ||||
15 | # | ||||
16 | # You may distribute this module under the same terms as perl itself. | ||||
17 | # Refer to the Perl Artistic License (see the license accompanying this | ||||
18 | # software package, or see http://www.perl.com/language/misc/Artistic.html) | ||||
19 | # for the terms under which you may use, modify, and redistribute this module. | ||||
20 | # | ||||
21 | # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED | ||||
22 | # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF | ||||
23 | # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. | ||||
24 | # | ||||
25 | |||||
26 | # POD documentation - main docs before the code | ||||
27 | |||||
28 | =head1 NAME | ||||
29 | |||||
30 | Bio::Factory::LocationFactoryI - A factory interface for generating locations from a string | ||||
31 | |||||
32 | =head1 SYNOPSIS | ||||
33 | |||||
34 | # Do not use directly, see Bio::Factory::LocationFactory for example | ||||
35 | use Bio::Factory::FTLocationFactory; | ||||
36 | my $locfact = Bio::Factory::FTLocationFactory->new(); | ||||
37 | my $location = $locfact->from_string("1..200"); | ||||
38 | print $location->start(), " ", $location->end(), " ", $location->strand,"\n"; | ||||
39 | |||||
40 | =head1 DESCRIPTION | ||||
41 | |||||
42 | An interface for Location Factories which generate Bio::LocationI | ||||
43 | objects from a string. | ||||
44 | |||||
45 | =head1 FEEDBACK | ||||
46 | |||||
47 | =head2 Mailing Lists | ||||
48 | |||||
49 | User feedback is an integral part of the evolution of this and other | ||||
50 | Bioperl modules. Send your comments and suggestions preferably to | ||||
51 | the Bioperl mailing list. Your participation is much appreciated. | ||||
52 | |||||
53 | bioperl-l@bioperl.org - General discussion | ||||
54 | http://bioperl.org/wiki/Mailing_lists - About the mailing lists | ||||
55 | |||||
56 | =head2 Support | ||||
57 | |||||
58 | Please direct usage questions or support issues to the mailing list: | ||||
59 | |||||
60 | I<bioperl-l@bioperl.org> | ||||
61 | |||||
62 | rather than to the module maintainer directly. Many experienced and | ||||
63 | reponsive experts will be able look at the problem and quickly | ||||
64 | address it. Please include a thorough description of the problem | ||||
65 | with code and data examples if at all possible. | ||||
66 | |||||
67 | =head2 Reporting Bugs | ||||
68 | |||||
69 | Report bugs to the Bioperl bug tracking system to help us keep track | ||||
70 | of the bugs and their resolution. Bug reports can be submitted via the | ||||
71 | web: | ||||
72 | |||||
73 | https://github.com/bioperl/bioperl-live/issues | ||||
74 | |||||
75 | =head1 AUTHOR - Hilmar Lapp | ||||
76 | |||||
77 | Email hlapp at gmx.net | ||||
78 | |||||
79 | =head1 APPENDIX | ||||
80 | |||||
81 | The rest of the documentation details each of the object methods. | ||||
82 | Internal methods are usually preceded with a _ | ||||
83 | |||||
84 | =cut | ||||
85 | |||||
86 | |||||
87 | # Let the code begin... | ||||
88 | |||||
89 | |||||
90 | package Bio::Factory::LocationFactoryI; | ||||
91 | 2 | 21µs | 2 | 37µs | # spent 25µs (13+12) within Bio::Factory::LocationFactoryI::BEGIN@91 which was called:
# once (13µs+12µs) by base::import at line 91 # spent 25µs making 1 call to Bio::Factory::LocationFactoryI::BEGIN@91
# spent 12µs making 1 call to strict::import |
92 | 2 | 29µs | 2 | 105µs | # spent 57µs (9+48) within Bio::Factory::LocationFactoryI::BEGIN@92 which was called:
# once (9µs+48µs) by base::import at line 92 # spent 57µs making 1 call to Bio::Factory::LocationFactoryI::BEGIN@92
# spent 48µs making 1 call to Exporter::import |
93 | |||||
94 | 2 | 66µs | 2 | 69µs | # spent 69µs (9+60) within Bio::Factory::LocationFactoryI::BEGIN@94 which was called:
# once (9µs+60µs) by base::import at line 94 # spent 69µs making 1 call to Bio::Factory::LocationFactoryI::BEGIN@94
# spent 60µs making 1 call to base::import, recursion: max depth 1, sum of overlapping time 60µs |
95 | |||||
96 | =head2 from_string | ||||
97 | |||||
98 | Title : from_string | ||||
99 | Usage : $loc = $locfactory->from_string("100..200"); | ||||
100 | Function: Parses the given string and returns a Bio::LocationI implementing | ||||
101 | object representing the location encoded by the string. | ||||
102 | |||||
103 | Different implementations may support different encodings. An | ||||
104 | example of a commonly used encoding is the Genbank feature table | ||||
105 | encoding of locations. | ||||
106 | Example : | ||||
107 | Returns : A Bio::LocationI implementing object. | ||||
108 | Args : A string. | ||||
109 | |||||
110 | |||||
111 | =cut | ||||
112 | |||||
113 | sub from_string{ | ||||
114 | my ($self,@args) = @_; | ||||
115 | |||||
116 | $self->throw_not_implemented(); | ||||
117 | } | ||||
118 | |||||
119 | 1 | 2µs | 1; |