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For bin/pan_genome_post_analysis
  Run on Fri Mar 27 11:43:32 2015
Reported on Fri Mar 27 11:45:43 2015

Filename/Users/ap13/perl5/lib/perl5/Bio/Seq/SeqFactory.pm
StatementsExecuted 5 statements in 252µs
Subroutines
Calls P F Exclusive
Time
Inclusive
Time
Subroutine
11116µs32µsBio::Seq::SeqFactory::::BEGIN@80Bio::Seq::SeqFactory::BEGIN@80
11110µs37.0msBio::Seq::SeqFactory::::BEGIN@83Bio::Seq::SeqFactory::BEGIN@83
0000s0sBio::Seq::SeqFactory::::createBio::Seq::SeqFactory::create
0000s0sBio::Seq::SeqFactory::::newBio::Seq::SeqFactory::new
0000s0sBio::Seq::SeqFactory::::typeBio::Seq::SeqFactory::type
Call graph for these subroutines as a Graphviz dot language file.
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Code
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
16Bio::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
31This object will build L<Bio::PrimarySeqI> and L<Bio::SeqI> objects
32generically.
33
34=head1 FEEDBACK
35
36=head2 Mailing Lists
37
38User feedback is an integral part of the evolution of this and other
39Bioperl modules. Send your comments and suggestions preferably to
40the 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
47Please direct usage questions or support issues to the mailing list:
48
49I<bioperl-l@bioperl.org>
50
51rather than to the module maintainer directly. Many experienced and
52reponsive experts will be able look at the problem and quickly
53address it. Please include a thorough description of the problem
54with code and data examples if at all possible.
55
56=head2 Reporting Bugs
57
58Report bugs to the Bioperl bug tracking system to help us keep track
59of the bugs and their resolution. Bug reports can be submitted via the
60web:
61
62 https://github.com/bioperl/bioperl-live/issues
63
64=head1 AUTHOR - Jason Stajich
65
66Email jason@bioperl.org
67
68=head1 APPENDIX
69
70The rest of the documentation details each of the object methods.
71Internal methods are usually preceded with a _
72
73=cut
74
75
76# Let the code begin...
77
78
79package Bio::Seq::SeqFactory;
80238µs247µs
# 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
use strict;
# spent 32µs making 1 call to Bio::Seq::SeqFactory::BEGIN@80 # spent 16µs making 1 call to strict::import
81
82
832212µs274.1ms
# 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
use base qw(Bio::Root::Root Bio::Factory::SequenceFactoryI);
# 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 $obj = Bio::Seq::SeqFactory->new();
89 Function: Builds a new Bio::Seq::SeqFactory object
90 Returns : Bio::Seq::SeqFactory
91 Args : -type => string, name of a PrimarySeqI derived class
92 This is optional. Default=Bio::PrimarySeq.
93
94=cut
95
96sub new {
97 my($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 => $name
121
122=cut
123
124sub create {
125 my ($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
140sub 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
15612µs1;