| Filename | /Users/ap13/perl5/lib/perl5/Bio/Factory/SequenceStreamI.pm |
| Statements | Executed 5 statements in 198µs |
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| 1 | 1 | 1 | 24µs | 38µs | Bio::Factory::SequenceStreamI::BEGIN@78 |
| 1 | 1 | 1 | 12µs | 113µs | Bio::Factory::SequenceStreamI::BEGIN@80 |
| 0 | 0 | 0 | 0s | 0s | Bio::Factory::SequenceStreamI::next_seq |
| 0 | 0 | 0 | 0s | 0s | Bio::Factory::SequenceStreamI::sequence_factory |
| 0 | 0 | 0 | 0s | 0s | Bio::Factory::SequenceStreamI::write_seq |
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| 1 | # | ||||
| 2 | # BioPerl module for Bio::Factory::SequenceStreamI | ||||
| 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::SequenceStreamI - Interface describing the basics of a Sequence Stream. | ||||
| 17 | |||||
| 18 | =head1 SYNOPSIS | ||||
| 19 | |||||
| 20 | # get a SequenceStreamI object somehow like with SeqIO | ||||
| 21 | use Bio::SeqIO; | ||||
| 22 | my $in = Bio::SeqIO->new(-file => '< fastafile'); | ||||
| 23 | while( my $seq = $in->next_seq ) { | ||||
| 24 | } | ||||
| 25 | |||||
| 26 | =head1 DESCRIPTION | ||||
| 27 | |||||
| 28 | This interface is for describing objects which produces | ||||
| 29 | Bio::PrimarySeqI objects or processes Bio::PrimarySeqI objects to a | ||||
| 30 | data stream. | ||||
| 31 | |||||
| 32 | =head1 FEEDBACK | ||||
| 33 | |||||
| 34 | =head2 Mailing Lists | ||||
| 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 | ||||
| 38 | the Bioperl mailing list. 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 | of 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 - Jason Stajich | ||||
| 63 | |||||
| 64 | Email jason@bioperl.org | ||||
| 65 | |||||
| 66 | =head1 APPENDIX | ||||
| 67 | |||||
| 68 | The rest of the documentation details each of the object methods. | ||||
| 69 | Internal methods are usually preceded with a _ | ||||
| 70 | |||||
| 71 | =cut | ||||
| 72 | |||||
| 73 | |||||
| 74 | # Let the code begin... | ||||
| 75 | |||||
| 76 | |||||
| 77 | package Bio::Factory::SequenceStreamI; | ||||
| 78 | 2 | 49µs | 2 | 52µs | # spent 38µs (24+14) within Bio::Factory::SequenceStreamI::BEGIN@78 which was called:
# once (24µs+14µs) by parent::import at line 78 # spent 38µs making 1 call to Bio::Factory::SequenceStreamI::BEGIN@78
# spent 14µs making 1 call to strict::import |
| 79 | |||||
| 80 | 2 | 147µs | 2 | 213µs | # spent 113µs (12+101) within Bio::Factory::SequenceStreamI::BEGIN@80 which was called:
# once (12µs+101µs) by parent::import at line 80 # spent 113µs making 1 call to Bio::Factory::SequenceStreamI::BEGIN@80
# spent 101µs making 1 call to base::import |
| 81 | |||||
| 82 | =head2 next_seq | ||||
| 83 | |||||
| 84 | Title : next_seq | ||||
| 85 | Usage : $seq = stream->next_seq | ||||
| 86 | Function: Reads the next sequence object from the stream and returns it. | ||||
| 87 | |||||
| 88 | Certain driver modules may encounter entries in the stream that | ||||
| 89 | are either misformatted or that use syntax not yet understood | ||||
| 90 | by the driver. If such an incident is recoverable, e.g., by | ||||
| 91 | dismissing a feature of a feature table or some other non-mandatory | ||||
| 92 | part of an entry, the driver will issue a warning. In the case | ||||
| 93 | of a non-recoverable situation an exception will be thrown. | ||||
| 94 | Do not assume that you can resume parsing the same stream after | ||||
| 95 | catching the exception. Note that you can always turn recoverable | ||||
| 96 | errors into exceptions by calling $stream->verbose(2). | ||||
| 97 | Returns : a Bio::Seq sequence object | ||||
| 98 | Args : none | ||||
| 99 | |||||
| 100 | See L<Bio::Root::RootI> | ||||
| 101 | |||||
| 102 | =cut | ||||
| 103 | |||||
| 104 | sub next_seq { | ||||
| 105 | shift->throw_not_implemented(); | ||||
| 106 | } | ||||
| 107 | |||||
| 108 | =head2 write_seq | ||||
| 109 | |||||
| 110 | Title : write_seq | ||||
| 111 | Usage : $stream->write_seq($seq) | ||||
| 112 | Function: writes the $seq object into the stream | ||||
| 113 | Returns : 1 for success and 0 for error | ||||
| 114 | Args : Bio::Seq object | ||||
| 115 | |||||
| 116 | =cut | ||||
| 117 | |||||
| 118 | sub write_seq { | ||||
| 119 | shift->throw_not_implemented(); | ||||
| 120 | } | ||||
| 121 | |||||
| 122 | =head2 sequence_factory | ||||
| 123 | |||||
| 124 | Title : sequence_factory | ||||
| 125 | Usage : $seqio->sequence_factory($seqfactory) | ||||
| 126 | Function: Get the Bio::Factory::SequenceFactoryI | ||||
| 127 | Returns : Bio::Factory::SequenceFactoryI | ||||
| 128 | Args : none | ||||
| 129 | |||||
| 130 | |||||
| 131 | =cut | ||||
| 132 | |||||
| 133 | sub sequence_factory{ | ||||
| 134 | shift->throw_not_implemented(); | ||||
| 135 | } | ||||
| 136 | |||||
| 137 | 1 | 2µs | 1; |