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

Filename/Users/ap13/perl5/lib/perl5/Bio/Location/FuzzyLocationI.pm
StatementsExecuted 5 statements in 162µs
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11120µs39µsBio::Location::FuzzyLocationI::::BEGIN@76Bio::Location::FuzzyLocationI::BEGIN@76
11112µs84µsBio::Location::FuzzyLocationI::::BEGIN@78Bio::Location::FuzzyLocationI::BEGIN@78
0000s0sBio::Location::FuzzyLocationI::::location_typeBio::Location::FuzzyLocationI::location_type
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1#
2# BioPerl module for Bio::Location::FuzzyLocationI
3# Please direct questions and support issues to <bioperl-l@bioperl.org>
4#
5# Cared for by Jason Stajich <jason@bioperl.org>
6#
7# Copyright Jason Stajich
8#
9# You may distribute this module under the same terms as perl itself
10# POD documentation - main docs before the code
11
12=head1 NAME
13
14Bio::Location::FuzzyLocationI - Abstract interface of a Location on a Sequence
15which has unclear start/end location
16
17=head1 SYNOPSIS
18
19 # Get a FuzzyLocationI object somehow
20 print "Fuzzy FT location string is ", $location->to_FTstring();
21 print "location is of the type ", $location->loc_type, "\n";
22
23=head1 DESCRIPTION
24
25This interface encapsulates the necessary methods for representing a
26Fuzzy Location, one that does not have clear start and/or end points.
27This will initially serve to handle features from Genbank/EMBL feature
28tables that are written as 1^100 meaning between bases 1 and 100 or
29E<lt>100..300 meaning it starts somewhere before 100. Advanced
30implementations of this interface may be able to handle the necessary
31logic of overlaps/intersection/contains/union. It was constructed to
32handle fuzzy locations that can be represented in Genbank/EMBL.
33
34=head1 FEEDBACK
35
36User feedback is an integral part of the evolution of this and other
37Bioperl modules. Send your comments and suggestions preferably to one
38of the Bioperl mailing lists. 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
45Please direct usage questions or support issues to the mailing list:
46
47I<bioperl-l@bioperl.org>
48
49rather than to the module maintainer directly. Many experienced and
50reponsive experts will be able look at the problem and quickly
51address it. Please include a thorough description of the problem
52with code and data examples if at all possible.
53
54=head2 Reporting Bugs
55
56Report bugs to the Bioperl bug tracking system to help us keep track
57the bugs and their resolution. Bug reports can be submitted via the web:
58
59 https://github.com/bioperl/bioperl-live/issues
60
61=head1 AUTHOR - Jason Stajich
62
63Email jason-at-bioperl-dot-org
64
65=head1 APPENDIX
66
67The rest of the documentation details each of the object
68methods. Internal methods are usually preceded with a _
69
70=cut
71
72# Let the code begin...
73
74
75package Bio::Location::FuzzyLocationI;
76249µs259µs
# spent 39µs (20+20) within Bio::Location::FuzzyLocationI::BEGIN@76 which was called: # once (20µs+20µs) by base::import at line 76
use strict;
# spent 39µs making 1 call to Bio::Location::FuzzyLocationI::BEGIN@76 # spent 20µs making 1 call to strict::import
77
782110µs284µs
# spent 84µs (12+72) within Bio::Location::FuzzyLocationI::BEGIN@78 which was called: # once (12µs+72µs) by base::import at line 78
use base qw(Bio::LocationI);
# spent 84µs making 1 call to Bio::Location::FuzzyLocationI::BEGIN@78 # spent 72µs making 1 call to base::import, recursion: max depth 1, sum of overlapping time 72µs
79
80=head1 LocationI methods
81
82=head2 location_type
83
84 Title : loc_type
85 Usage : my $location_type = $location->location_type();
86 Function: Get location type encoded as text
87 Returns : string ('EXACT', 'WITHIN', 'IN-BETWEEN')
88 Args : none
89
90=cut
91
92sub location_type {
93 my ($self) = @_;
94 $self->throw_not_implemented();
95}
96
97=head1 Bio::LocationI methods
98
99Bio::LocationI methods follow
100
101=head2 min_start
102
103 Title : min_start
104 Usage : my $minstart = $location->min_start();
105 Function: Get minimum starting location of feature startpoint
106 Returns : integer or undef if no maximum starting point.
107 Args : none
108
109=cut
110
111=head2 max_start
112
113 Title : max_start
114 Usage : my $maxstart = $location->max_start();
115 Function: Get maximum starting location of feature startpoint
116 Returns : integer or undef if no maximum starting point.
117 Args : none
118
119=cut
120
121=head2 start_pos_type
122
123 Title : start_pos_type
124 Usage : my $start_pos_type = $location->start_pos_type();
125 Function: Get start position type (ie <,>, ^)
126 Returns : type of position coded as text
127 ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
128 Args : none
129
130=cut
131
132=head2 min_end
133
134 Title : min_end
135 Usage : my $minend = $location->min_end();
136 Function: Get minimum ending location of feature endpoint
137 Returns : integer or undef if no minimum ending point.
138 Args : none
139
140=cut
141
142=head2 max_end
143
144 Title : max_end
145 Usage : my $maxend = $location->max_end();
146 Function: Get maximum ending location of feature endpoint
147 Returns : integer or undef if no maximum ending point.
148 Args : none
149
150=cut
151
152=head2 end_pos_type
153
154 Title : end_pos_type
155 Usage : my $end_pos_type = $location->end_pos_type();
156 Function: Get end position type (ie <,>, ^)
157 Returns : type of position coded as text
158 ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
159 Args : none
160
161=cut
162
163=head2 seq_id
164
165 Title : seq_id
166 Usage : my $seqid = $location->seq_id();
167 Function: Get/Set seq_id that location refers to
168 Returns : seq_id
169 Args : [optional] seq_id value to set
170
171=cut
172
173=head2 coordinate_policy
174
175 Title : coordinate_policy
176 Usage : $policy = $location->coordinate_policy();
177 $location->coordinate_policy($mypolicy); # set may not be possible
178 Function: Get the coordinate computing policy employed by this object.
179
180 See Bio::Location::CoordinatePolicyI for documentation about
181 the policy object and its use.
182
183 The interface *does not* require implementing classes to accept
184 setting of a different policy. The implementation provided here
185 does, however, allow to do so.
186
187 Implementors of this interface are expected to initialize every
188 new instance with a CoordinatePolicyI object. The implementation
189 provided here will return a default policy object if none has
190 been set yet. To change this default policy object call this
191 method as a class method with an appropriate argument. Note that
192 in this case only subsequently created Location objects will be
193 affected.
194
195 Returns : A Bio::Location::CoordinatePolicyI implementing object.
196 Args : On set, a Bio::Location::CoordinatePolicyI implementing object.
197
198=cut
199
200=head2 to_FTstring
201
202 Title : to_FTstring
203 Usage : my $locstr = $location->to_FTstring()
204 Function: returns the FeatureTable string of this location
205 Returns : string
206 Args : none
207
208=cut
209
21012µs1;