| Filename | /Users/ap13/perl5/lib/perl5/Bio/Location/WidestCoordPolicy.pm |
| Statements | Executed 8 statements in 182µs |
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| 1 | 1 | 1 | 28µs | 42µs | Bio::Location::WidestCoordPolicy::new |
| 1 | 1 | 1 | 12µs | 23µs | Bio::Location::WidestCoordPolicy::BEGIN@77 |
| 1 | 1 | 1 | 8µs | 425µs | Bio::Location::WidestCoordPolicy::BEGIN@80 |
| 0 | 0 | 0 | 0s | 0s | Bio::Location::WidestCoordPolicy::end |
| 0 | 0 | 0 | 0s | 0s | Bio::Location::WidestCoordPolicy::start |
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| 1 | # | ||||
| 2 | # BioPerl module for Bio::Location::WidestCoordPolicy | ||||
| 3 | # | ||||
| 4 | # Please direct questions and support issues to <bioperl-l@bioperl.org> | ||||
| 5 | # | ||||
| 6 | # Cared for by Hilmar Lapp <hlapp@gmx.net> | ||||
| 7 | # and Jason Stajich <jason@bioperl.org> | ||||
| 8 | # | ||||
| 9 | # Copyright Hilmar Lapp, Jason Stajich | ||||
| 10 | # | ||||
| 11 | # You may distribute this module under the same terms as perl itself | ||||
| 12 | # POD documentation - main docs before the code | ||||
| 13 | |||||
| 14 | =head1 NAME | ||||
| 15 | |||||
| 16 | Bio::Location::WidestCoordPolicy - class implementing | ||||
| 17 | Bio::Location::CoordinatePolicy as the widest possible and reasonable range | ||||
| 18 | |||||
| 19 | =head1 SYNOPSIS | ||||
| 20 | |||||
| 21 | See Bio::Location::CoordinatePolicyI | ||||
| 22 | |||||
| 23 | =head1 DESCRIPTION | ||||
| 24 | |||||
| 25 | CoordinatePolicyI implementing objects are used by Bio::LocationI | ||||
| 26 | implementing objects to determine integer-valued coordinates when | ||||
| 27 | asked for it. | ||||
| 28 | |||||
| 29 | This class will compute the coordinates such that always the widest possible | ||||
| 30 | range is returned, but by using some common sense. This means that e.g. | ||||
| 31 | locations like "E<lt>5..100" (start before position 5) will return 5 as start | ||||
| 32 | (returned values have to be positive integers). | ||||
| 33 | |||||
| 34 | =head1 FEEDBACK | ||||
| 35 | |||||
| 36 | User feedback is an integral part of the evolution of this and other | ||||
| 37 | Bioperl modules. Send your comments and suggestions preferably to one | ||||
| 38 | of the Bioperl mailing lists. Your participation is much appreciated. | ||||
| 39 | |||||
| 40 | bioperl-l@bioperl.org - General discussion | ||||
| 41 | http://bioperl.org/wiki/Mailing_lists - About the mailing lists | ||||
| 42 | |||||
| 43 | =head2 Support | ||||
| 44 | |||||
| 45 | Please direct usage questions or support issues to the mailing list: | ||||
| 46 | |||||
| 47 | I<bioperl-l@bioperl.org> | ||||
| 48 | |||||
| 49 | rather than to the module maintainer directly. Many experienced and | ||||
| 50 | reponsive experts will be able look at the problem and quickly | ||||
| 51 | address it. Please include a thorough description of the problem | ||||
| 52 | with code and data examples if at all possible. | ||||
| 53 | |||||
| 54 | =head2 Reporting Bugs | ||||
| 55 | |||||
| 56 | Report bugs to the Bioperl bug tracking system to help us keep track | ||||
| 57 | the bugs and their resolution. Bug reports can be submitted via the | ||||
| 58 | web: | ||||
| 59 | |||||
| 60 | https://github.com/bioperl/bioperl-live/issues | ||||
| 61 | |||||
| 62 | =head1 AUTHOR - Hilmar Lapp, Jason Stajich | ||||
| 63 | |||||
| 64 | Email E<lt>hlapp-at-gmx-dot-netE<gt>, E<lt>jason-at-bioperl-dot-orgE<gt> | ||||
| 65 | |||||
| 66 | =head1 APPENDIX | ||||
| 67 | |||||
| 68 | The rest of the documentation details each of the object | ||||
| 69 | methods. Internal methods are usually preceded with a _ | ||||
| 70 | |||||
| 71 | =cut | ||||
| 72 | |||||
| 73 | # Let the code begin... | ||||
| 74 | |||||
| 75 | |||||
| 76 | package Bio::Location::WidestCoordPolicy; | ||||
| 77 | 2 | 27µs | 2 | 34µs | # spent 23µs (12+11) within Bio::Location::WidestCoordPolicy::BEGIN@77 which was called:
# once (12µs+11µs) by Bio::Location::Atomic::BEGIN@79 at line 77 # spent 23µs making 1 call to Bio::Location::WidestCoordPolicy::BEGIN@77
# spent 11µs making 1 call to strict::import |
| 78 | |||||
| 79 | |||||
| 80 | 2 | 127µs | 2 | 425µs | # spent 425µs (8+418) within Bio::Location::WidestCoordPolicy::BEGIN@80 which was called:
# once (8µs+418µs) by Bio::Location::Atomic::BEGIN@79 at line 80 # spent 425µs making 1 call to Bio::Location::WidestCoordPolicy::BEGIN@80
# spent 418µs making 1 call to base::import, recursion: max depth 1, sum of overlapping time 418µs |
| 81 | |||||
| 82 | # spent 42µs (28+14) within Bio::Location::WidestCoordPolicy::new which was called:
# once (28µs+14µs) by base::import at line 83 of Bio/Location/Atomic.pm | ||||
| 83 | 1 | 2µs | my ($class, @args) = @_; | ||
| 84 | 1 | 20µs | 1 | 14µs | my $self = $class->SUPER::new(@args); # spent 14µs making 1 call to Bio::Root::Root::new |
| 85 | |||||
| 86 | 1 | 4µs | return $self; | ||
| 87 | } | ||||
| 88 | |||||
| - - | |||||
| 91 | =head2 start | ||||
| 92 | |||||
| 93 | Title : start | ||||
| 94 | Usage : $start = $policy->start($location); | ||||
| 95 | Function: Get the integer-valued start coordinate of the given location as | ||||
| 96 | computed by this computation policy. | ||||
| 97 | Returns : A positive integer number. | ||||
| 98 | Args : A Bio::LocationI implementing object. | ||||
| 99 | |||||
| 100 | =cut | ||||
| 101 | |||||
| 102 | sub start { | ||||
| 103 | my ($self,$loc) = @_; | ||||
| 104 | |||||
| 105 | # For performance reasons we don't check that it's indeed a Bio::LocationI | ||||
| 106 | # object. Hopefully, Location-object programmers are smart enough. | ||||
| 107 | my $pos = $loc->min_start(); | ||||
| 108 | # if min is not defined or equals 0 we resort to max | ||||
| 109 | $pos = $loc->max_start() if(! $pos); | ||||
| 110 | return $pos; | ||||
| 111 | } | ||||
| 112 | |||||
| 113 | =head2 end | ||||
| 114 | |||||
| 115 | Title : end | ||||
| 116 | Usage : $end = $policy->end($location); | ||||
| 117 | Function: Get the integer-valued end coordinate of the given location as | ||||
| 118 | computed by this computation policy. | ||||
| 119 | Returns : A positive integer number. | ||||
| 120 | Args : A Bio::LocationI implementing object. | ||||
| 121 | |||||
| 122 | =cut | ||||
| 123 | |||||
| 124 | sub end { | ||||
| 125 | my ($self,$loc) = @_; | ||||
| 126 | |||||
| 127 | # For performance reasons we don't check that it's indeed a Bio::LocationI | ||||
| 128 | # object. Hopefully, Location-object programmers are smart enough. | ||||
| 129 | my $pos = $loc->max_end(); | ||||
| 130 | # if max is not defined or equals 0 we resort to min | ||||
| 131 | $pos = $loc->min_end() if(! $pos); | ||||
| 132 | return $pos; | ||||
| 133 | } | ||||
| 134 | |||||
| 135 | 1 | 2µs | 1; | ||
| 136 |