| Filename | /Users/ap13/perl5/lib/perl5/Bio/Factory/SequenceFactoryI.pm |
| Statements | Executed 5 statements in 60µs |
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| 1 | 1 | 1 | 15µs | 28µs | Bio::Factory::SequenceFactoryI::BEGIN@86 |
| 1 | 1 | 1 | 9µs | 424µs | Bio::Factory::SequenceFactoryI::BEGIN@88 |
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| 1 | # | ||||
| 2 | # BioPerl module for Bio::Factory::SequenceFactoryI | ||||
| 3 | # | ||||
| 4 | # Please direct questions and support issues to <bioperl-l@bioperl.org> | ||||
| 5 | # | ||||
| 6 | # Cared for by Jason Stajich <jason@bioperl.org> | ||||
| 7 | # | ||||
| 8 | # Copyright Jason Stajich | ||||
| 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 | |||||
| 16 | Bio::Factory::SequenceFactoryI - This interface allows for generic building of sequences in factories which create sequences (like SeqIO) | ||||
| 17 | |||||
| 18 | =head1 SYNOPSIS | ||||
| 19 | |||||
| 20 | # do not use this object directly it is an interface | ||||
| 21 | # get a Bio::Factory::SequenceFactoryI object like | ||||
| 22 | |||||
| 23 | use Bio::Seq::SeqFactory; | ||||
| 24 | my $seqbuilder = Bio::Seq::SeqFactory->new('-type' => 'Bio::PrimarySeq'); | ||||
| 25 | |||||
| 26 | my $seq = $seqbuilder->create(-seq => 'ACTGAT', | ||||
| 27 | -display_id => 'exampleseq'); | ||||
| 28 | |||||
| 29 | print "seq is a ", ref($seq), "\n"; | ||||
| 30 | |||||
| 31 | =head1 DESCRIPTION | ||||
| 32 | |||||
| 33 | A generic way to build Sequence objects via a pluggable factory. This | ||||
| 34 | reduces the amount of code that looks like | ||||
| 35 | |||||
| 36 | if( $type eq 'Bio::PrimarySeq' ) { ... } | ||||
| 37 | elsif( $type eq 'Bio::Seq::RichSeq' ) { ... } | ||||
| 38 | |||||
| 39 | =head1 FEEDBACK | ||||
| 40 | |||||
| 41 | =head2 Mailing Lists | ||||
| 42 | |||||
| 43 | User feedback is an integral part of the evolution of this and other | ||||
| 44 | Bioperl modules. Send your comments and suggestions preferably to | ||||
| 45 | the Bioperl mailing list. Your participation is much appreciated. | ||||
| 46 | |||||
| 47 | bioperl-l@bioperl.org - General discussion | ||||
| 48 | http://bioperl.org/wiki/Mailing_lists - About the mailing lists | ||||
| 49 | |||||
| 50 | =head2 Support | ||||
| 51 | |||||
| 52 | Please direct usage questions or support issues to the mailing list: | ||||
| 53 | |||||
| 54 | I<bioperl-l@bioperl.org> | ||||
| 55 | |||||
| 56 | rather than to the module maintainer directly. Many experienced and | ||||
| 57 | reponsive experts will be able look at the problem and quickly | ||||
| 58 | address it. Please include a thorough description of the problem | ||||
| 59 | with code and data examples if at all possible. | ||||
| 60 | |||||
| 61 | =head2 Reporting Bugs | ||||
| 62 | |||||
| 63 | Report bugs to the Bioperl bug tracking system to help us keep track | ||||
| 64 | of the bugs and their resolution. Bug reports can be submitted via the | ||||
| 65 | web: | ||||
| 66 | |||||
| 67 | https://github.com/bioperl/bioperl-live/issues | ||||
| 68 | |||||
| 69 | =head1 AUTHOR - Jason Stajich | ||||
| 70 | |||||
| 71 | Email jason-at-bioperl.org | ||||
| 72 | |||||
| 73 | =head1 APPENDIX | ||||
| 74 | |||||
| 75 | The rest of the documentation details each of the object methods. | ||||
| 76 | Internal methods are usually preceded with a _ | ||||
| 77 | |||||
| 78 | =cut | ||||
| 79 | |||||
| 80 | |||||
| 81 | # Let the code begin... | ||||
| 82 | |||||
| 83 | |||||
| 84 | package Bio::Factory::SequenceFactoryI; | ||||
| 85 | |||||
| 86 | 2 | 31µs | 2 | 42µs | # spent 28µs (15+13) within Bio::Factory::SequenceFactoryI::BEGIN@86 which was called:
# once (15µs+13µs) by base::import at line 86 # spent 28µs making 1 call to Bio::Factory::SequenceFactoryI::BEGIN@86
# spent 13µs making 1 call to strict::import |
| 87 | |||||
| 88 | 2 | 27µs | 2 | 424µs | # spent 424µs (9+415) within Bio::Factory::SequenceFactoryI::BEGIN@88 which was called:
# once (9µs+415µs) by base::import at line 88 # spent 424µs making 1 call to Bio::Factory::SequenceFactoryI::BEGIN@88
# spent 415µs making 1 call to base::import, recursion: max depth 1, sum of overlapping time 415µs |
| 89 | |||||
| 90 | =head2 create | ||||
| 91 | |||||
| 92 | Title : create | ||||
| 93 | Usage : my $seq = $seqbuilder->create(-seq => 'CAGT', | ||||
| 94 | -id => 'name'); | ||||
| 95 | Function: Instantiates new Bio::PrimarySeqI (or one of its child classes) | ||||
| 96 | This object allows us to genericize the instantiation of sequence | ||||
| 97 | objects. | ||||
| 98 | Returns : Bio::PrimarySeqI | ||||
| 99 | Args : initialization parameters specific to the type of sequence | ||||
| 100 | object we want. Typically | ||||
| 101 | -seq => $str, | ||||
| 102 | -display_id => $name | ||||
| 103 | |||||
| 104 | =cut | ||||
| 105 | |||||
| 106 | 1 | 2µs | 1; |