Filename | /Users/ap13/perl5/lib/perl5/Bio/Seq/SeqFactory.pm |
Statements | Executed 5 statements in 252µs |
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1 | 1 | 1 | 16µs | 32µs | BEGIN@80 | Bio::Seq::SeqFactory::
1 | 1 | 1 | 10µs | 37.0ms | BEGIN@83 | Bio::Seq::SeqFactory::
0 | 0 | 0 | 0s | 0s | create | Bio::Seq::SeqFactory::
0 | 0 | 0 | 0s | 0s | new | Bio::Seq::SeqFactory::
0 | 0 | 0 | 0s | 0s | type | Bio::Seq::SeqFactory::
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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; |