| Filename | /Users/ap13/perl5/lib/perl5/Bio/Seq/SeqFactory.pm |
| Statements | Executed 5 statements in 252µs |
| Calls | P | F | Exclusive Time |
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| 1 | 1 | 1 | 16µs | 32µs | Bio::Seq::SeqFactory::BEGIN@80 |
| 1 | 1 | 1 | 10µs | 37.0ms | Bio::Seq::SeqFactory::BEGIN@83 |
| 0 | 0 | 0 | 0s | 0s | Bio::Seq::SeqFactory::create |
| 0 | 0 | 0 | 0s | 0s | Bio::Seq::SeqFactory::new |
| 0 | 0 | 0 | 0s | 0s | Bio::Seq::SeqFactory::type |
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| 1 | # | ||||
| 2 | # BioPerl module for Bio::Seq::SeqFactory | ||||
| 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::Seq::SeqFactory - Instantiation of generic Bio::PrimarySeqI (or derived) objects through a factory | ||||
| 17 | |||||
| 18 | =head1 SYNOPSIS | ||||
| 19 | |||||
| 20 | use Bio::Seq::SeqFactory; | ||||
| 21 | my $factory = Bio::Seq::SeqFactory->new(); | ||||
| 22 | my $primaryseq = $factory->create( -seq => 'WYRAVLC', | ||||
| 23 | -id => 'name' ); | ||||
| 24 | |||||
| 25 | # Create Bio::Seq instead of Bio::PrimarySeq objects: | ||||
| 26 | my $factory = Bio::Seq::SeqFactory->new( -type => 'Bio::Seq' ); | ||||
| 27 | |||||
| 28 | |||||
| 29 | =head1 DESCRIPTION | ||||
| 30 | |||||
| 31 | This object will build L<Bio::PrimarySeqI> and L<Bio::SeqI> objects | ||||
| 32 | generically. | ||||
| 33 | |||||
| 34 | =head1 FEEDBACK | ||||
| 35 | |||||
| 36 | =head2 Mailing Lists | ||||
| 37 | |||||
| 38 | User feedback is an integral part of the evolution of this and other | ||||
| 39 | Bioperl modules. Send your comments and suggestions preferably to | ||||
| 40 | the Bioperl mailing list. Your participation is much appreciated. | ||||
| 41 | |||||
| 42 | bioperl-l@bioperl.org - General discussion | ||||
| 43 | http://bioperl.org/wiki/Mailing_lists - About the mailing lists | ||||
| 44 | |||||
| 45 | =head2 Support | ||||
| 46 | |||||
| 47 | Please direct usage questions or support issues to the mailing list: | ||||
| 48 | |||||
| 49 | I<bioperl-l@bioperl.org> | ||||
| 50 | |||||
| 51 | rather than to the module maintainer directly. Many experienced and | ||||
| 52 | reponsive experts will be able look at the problem and quickly | ||||
| 53 | address it. Please include a thorough description of the problem | ||||
| 54 | with code and data examples if at all possible. | ||||
| 55 | |||||
| 56 | =head2 Reporting Bugs | ||||
| 57 | |||||
| 58 | Report bugs to the Bioperl bug tracking system to help us keep track | ||||
| 59 | of the bugs and their resolution. Bug reports can be submitted via the | ||||
| 60 | web: | ||||
| 61 | |||||
| 62 | https://github.com/bioperl/bioperl-live/issues | ||||
| 63 | |||||
| 64 | =head1 AUTHOR - Jason Stajich | ||||
| 65 | |||||
| 66 | Email jason@bioperl.org | ||||
| 67 | |||||
| 68 | =head1 APPENDIX | ||||
| 69 | |||||
| 70 | The rest of the documentation details each of the object methods. | ||||
| 71 | Internal methods are usually preceded with a _ | ||||
| 72 | |||||
| 73 | =cut | ||||
| 74 | |||||
| 75 | |||||
| 76 | # Let the code begin... | ||||
| 77 | |||||
| 78 | |||||
| 79 | package Bio::Seq::SeqFactory; | ||||
| 80 | 2 | 38µs | 2 | 47µs | # spent 32µs (16+16) within Bio::Seq::SeqFactory::BEGIN@80 which was called:
# once (16µs+16µs) by Bio::Tools::GFF::BEGIN@150 at line 80 # spent 32µs making 1 call to Bio::Seq::SeqFactory::BEGIN@80
# spent 16µs making 1 call to strict::import |
| 81 | |||||
| 82 | |||||
| 83 | 2 | 212µs | 2 | 74.1ms | # spent 37.0ms (10µs+37.0) within Bio::Seq::SeqFactory::BEGIN@83 which was called:
# once (10µs+37.0ms) by Bio::Tools::GFF::BEGIN@150 at line 83 # spent 37.0ms making 1 call to Bio::Seq::SeqFactory::BEGIN@83
# spent 37.0ms making 1 call to base::import |
| 84 | |||||
| 85 | =head2 new | ||||
| 86 | |||||
| 87 | Title : new | ||||
| 88 | Usage : my $obj = Bio::Seq::SeqFactory->new(); | ||||
| 89 | Function: Builds a new Bio::Seq::SeqFactory object | ||||
| 90 | Returns : Bio::Seq::SeqFactory | ||||
| 91 | Args : -type => string, name of a PrimarySeqI derived class | ||||
| 92 | This is optional. Default=Bio::PrimarySeq. | ||||
| 93 | |||||
| 94 | =cut | ||||
| 95 | |||||
| 96 | sub new { | ||||
| 97 | my($class,@args) = @_; | ||||
| 98 | my $self = $class->SUPER::new(@args); | ||||
| 99 | my ($type) = $self->_rearrange([qw(TYPE)], @args); | ||||
| 100 | if( ! defined $type ) { | ||||
| 101 | $type = 'Bio::PrimarySeq'; | ||||
| 102 | } | ||||
| 103 | $self->type($type); | ||||
| 104 | return $self; | ||||
| 105 | } | ||||
| 106 | |||||
| 107 | |||||
| 108 | =head2 create | ||||
| 109 | |||||
| 110 | Title : create | ||||
| 111 | Usage : my $seq = $seqbuilder->create(-seq => 'CAGT', -id => 'name'); | ||||
| 112 | Function: Instantiates new Bio::SeqI (or one of its child classes) | ||||
| 113 | This object allows us to genericize the instantiation of sequence | ||||
| 114 | objects. | ||||
| 115 | Returns : Bio::PrimarySeq object (default) | ||||
| 116 | The return type is configurable using new(-type =>"..."). | ||||
| 117 | Args : initialization parameters specific to the type of sequence | ||||
| 118 | object we want. Typically | ||||
| 119 | -seq => $str, | ||||
| 120 | -display_id => $name | ||||
| 121 | |||||
| 122 | =cut | ||||
| 123 | |||||
| 124 | sub create { | ||||
| 125 | my ($self,@args) = @_; | ||||
| 126 | return $self->type->new(-verbose => $self->verbose, @args); | ||||
| 127 | } | ||||
| 128 | |||||
| 129 | =head2 type | ||||
| 130 | |||||
| 131 | Title : type | ||||
| 132 | Usage : $obj->type($newval) | ||||
| 133 | Function: | ||||
| 134 | Returns : value of type | ||||
| 135 | Args : newvalue (optional) | ||||
| 136 | |||||
| 137 | |||||
| 138 | =cut | ||||
| 139 | |||||
| 140 | sub type { | ||||
| 141 | my ($self, $value) = @_; | ||||
| 142 | if (defined $value) { | ||||
| 143 | eval "require $value"; | ||||
| 144 | if( $@ ) { $self->throw("$@: Unrecognized Sequence type for SeqFactory '$value'");} | ||||
| 145 | |||||
| 146 | my $a = bless {},$value; | ||||
| 147 | unless( $a->isa('Bio::PrimarySeqI') || | ||||
| 148 | $a->isa('Bio::Seq::QualI' ) ) { | ||||
| 149 | $self->throw("Must provide a valid Bio::PrimarySeqI or Bio::Seq::QualI or child class to SeqFactory Not $value"); | ||||
| 150 | } | ||||
| 151 | $self->{'type'} = $value; | ||||
| 152 | } | ||||
| 153 | return $self->{'type'}; | ||||
| 154 | } | ||||
| 155 | |||||
| 156 | 1 | 2µs | 1; |