| Filename | /Users/ap13/perl5/lib/perl5/Bio/Factory/LocationFactoryI.pm |
| Statements | Executed 7 statements in 118µs |
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| 1 | 1 | 1 | 13µs | 25µs | Bio::Factory::LocationFactoryI::BEGIN@91 |
| 1 | 1 | 1 | 9µs | 57µs | Bio::Factory::LocationFactoryI::BEGIN@92 |
| 1 | 1 | 1 | 9µs | 69µs | Bio::Factory::LocationFactoryI::BEGIN@94 |
| 0 | 0 | 0 | 0s | 0s | Bio::Factory::LocationFactoryI::from_string |
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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; |