Filename | /Users/ap13/perl5/lib/perl5/Bio/Location/SplitLocationI.pm |
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1 | 1 | 1 | 14µs | 38µs | BEGIN@80 | Bio::Location::SplitLocationI::
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1 | 1 | 1 | 8µs | 71µs | BEGIN@84 | Bio::Location::SplitLocationI::
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1 | # | ||||
2 | # BioPerl module for Bio::Location::SplitLocationI | ||||
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 | |||||
14 | Bio::Location::SplitLocationI - Abstract interface of a Location on a Sequence | ||||
15 | which has multiple locations (start/end points) | ||||
16 | |||||
17 | =head1 SYNOPSIS | ||||
18 | |||||
19 | # get a SplitLocationI somehow | ||||
20 | print $splitlocation->start, "..", $splitlocation->end, "\n"; | ||||
21 | my @sublocs = $splitlocation->sub_Location(); | ||||
22 | |||||
23 | my $count = 1; | ||||
24 | # print the start/end points of the sub locations | ||||
25 | foreach my $location ( sort { $a->start <=> $b->start } @sublocs ) { | ||||
26 | printf "sub feature %d [%d..%d]\n", $location->start,$location->end; | ||||
27 | $count++; | ||||
28 | } | ||||
29 | |||||
30 | =head1 DESCRIPTION | ||||
31 | |||||
32 | This interface encapsulates the necessary methods for representing the | ||||
33 | location of a sequence feature that has more that just a single | ||||
34 | start/end pair. Some examples of this are the annotated exons in a | ||||
35 | gene or the annotated CDS in a sequence file. | ||||
36 | |||||
37 | =head1 FEEDBACK | ||||
38 | |||||
39 | User feedback is an integral part of the evolution of this and other | ||||
40 | Bioperl modules. Send your comments and suggestions preferably to one | ||||
41 | of the Bioperl mailing lists. Your participation is much appreciated. | ||||
42 | |||||
43 | bioperl-l@bioperl.org - General discussion | ||||
44 | http://bioperl.org/wiki/Mailing_lists - About the mailing lists | ||||
45 | |||||
46 | =head2 Support | ||||
47 | |||||
48 | Please direct usage questions or support issues to the mailing list: | ||||
49 | |||||
50 | I<bioperl-l@bioperl.org> | ||||
51 | |||||
52 | rather than to the module maintainer directly. Many experienced and | ||||
53 | reponsive experts will be able look at the problem and quickly | ||||
54 | address it. Please include a thorough description of the problem | ||||
55 | with code and data examples if at all possible. | ||||
56 | |||||
57 | =head2 Reporting Bugs | ||||
58 | |||||
59 | Report bugs to the Bioperl bug tracking system to help us keep track | ||||
60 | the bugs and their resolution. Bug reports can be submitted via the | ||||
61 | web: | ||||
62 | |||||
63 | https://github.com/bioperl/bioperl-live/issues | ||||
64 | |||||
65 | =head1 AUTHOR - Jason Stajich | ||||
66 | |||||
67 | Email jason-at-bioperl-dot-org | ||||
68 | |||||
69 | =head1 APPENDIX | ||||
70 | |||||
71 | The rest of the documentation details each of the object | ||||
72 | methods. Internal methods are usually preceded with a _ | ||||
73 | |||||
74 | =cut | ||||
75 | |||||
76 | # Let the code begin... | ||||
77 | |||||
78 | |||||
79 | package Bio::Location::SplitLocationI; | ||||
80 | 2 | 24µs | 2 | 61µs | # spent 38µs (14+24) within Bio::Location::SplitLocationI::BEGIN@80 which was called:
# once (14µs+24µs) by base::import at line 80 # spent 38µs making 1 call to Bio::Location::SplitLocationI::BEGIN@80
# spent 24µs making 1 call to strict::import |
81 | |||||
82 | 2 | 26µs | 2 | 107µs | # spent 58µs (10+48) within Bio::Location::SplitLocationI::BEGIN@82 which was called:
# once (10µs+48µs) by base::import at line 82 # spent 58µs making 1 call to Bio::Location::SplitLocationI::BEGIN@82
# spent 48µs making 1 call to Exporter::import |
83 | |||||
84 | 2 | 136µs | 2 | 71µs | # spent 71µs (8+62) within Bio::Location::SplitLocationI::BEGIN@84 which was called:
# once (8µs+62µs) by base::import at line 84 # spent 71µs making 1 call to Bio::Location::SplitLocationI::BEGIN@84
# spent 62µs making 1 call to base::import, recursion: max depth 1, sum of overlapping time 62µs |
85 | |||||
86 | |||||
87 | =head2 sub_Location | ||||
88 | |||||
89 | Title : sub_Location | ||||
90 | Usage : @locations = $feat->sub_Location(); | ||||
91 | Function: Returns an array of LocationI objects | ||||
92 | Returns : An array | ||||
93 | Args : none | ||||
94 | |||||
95 | =cut | ||||
96 | |||||
97 | sub sub_Location { | ||||
98 | my ($self,@args) = @_; | ||||
99 | $self->throw_not_implemented(); | ||||
100 | } | ||||
101 | |||||
102 | =head2 splittype | ||||
103 | |||||
104 | Title : splittype | ||||
105 | Usage : $splittype = $fuzzy->splittype(); | ||||
106 | Function: get/set the split splittype | ||||
107 | Returns : the splittype of split feature (join, order) | ||||
108 | Args : splittype to set | ||||
109 | |||||
110 | =cut | ||||
111 | |||||
112 | sub splittype { | ||||
113 | my($self) = @_; | ||||
114 | $self->throw_not_implemented(); | ||||
115 | } | ||||
116 | |||||
117 | |||||
118 | =head2 is_single_sequence | ||||
119 | |||||
120 | Title : is_single_sequence | ||||
121 | Usage : if($splitloc->is_single_sequence()) { | ||||
122 | print "Location object $splitloc is split ". | ||||
123 | "but only across a single sequence\n"; | ||||
124 | } | ||||
125 | Function: Determine whether this location is split across a single or | ||||
126 | multiple sequences. | ||||
127 | Returns : TRUE if all sublocations lie on the same sequence as the root | ||||
128 | location (feature), and FALSE otherwise. | ||||
129 | Args : none | ||||
130 | |||||
131 | =cut | ||||
132 | |||||
133 | sub is_single_sequence { | ||||
134 | my ($self) = @_; | ||||
135 | $self->throw_not_implemented(); | ||||
136 | } | ||||
137 | |||||
138 | =head1 Bio::LocationI methods | ||||
139 | |||||
140 | Bio::LocationI inherited methods follow | ||||
141 | |||||
142 | =head2 min_start | ||||
143 | |||||
144 | Title : min_start | ||||
145 | Usage : my $minstart = $location->min_start(); | ||||
146 | Function: Get minimum starting location of feature startpoint | ||||
147 | Returns : integer or undef if no maximum starting point. | ||||
148 | Args : none | ||||
149 | |||||
150 | =cut | ||||
151 | |||||
152 | =head2 max_start | ||||
153 | |||||
154 | Title : max_start | ||||
155 | Usage : my $maxstart = $location->max_start(); | ||||
156 | Function: Get maximum starting location of feature startpoint | ||||
157 | Returns : integer or undef if no maximum starting point. | ||||
158 | Args : none | ||||
159 | |||||
160 | =cut | ||||
161 | |||||
162 | =head2 start_pos_type | ||||
163 | |||||
164 | Title : start_pos_type | ||||
165 | Usage : my $start_pos_type = $location->start_pos_type(); | ||||
166 | Function: Get start position type (ie <,>, ^) | ||||
167 | Returns : type of position coded as text | ||||
168 | ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') | ||||
169 | Args : none | ||||
170 | |||||
171 | =cut | ||||
172 | |||||
173 | =head2 min_end | ||||
174 | |||||
175 | Title : min_end | ||||
176 | Usage : my $minend = $location->min_end(); | ||||
177 | Function: Get minimum ending location of feature endpoint | ||||
178 | Returns : integer or undef if no minimum ending point. | ||||
179 | Args : none | ||||
180 | |||||
181 | =cut | ||||
182 | |||||
183 | =head2 max_end | ||||
184 | |||||
185 | Title : max_end | ||||
186 | Usage : my $maxend = $location->max_end(); | ||||
187 | Function: Get maximum ending location of feature endpoint | ||||
188 | Returns : integer or undef if no maximum ending point. | ||||
189 | Args : none | ||||
190 | |||||
191 | =cut | ||||
192 | |||||
193 | =head2 end_pos_type | ||||
194 | |||||
195 | Title : end_pos_type | ||||
196 | Usage : my $end_pos_type = $location->end_pos_type(); | ||||
197 | Function: Get end position type (ie <,>, ^) | ||||
198 | Returns : type of position coded as text | ||||
199 | ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') | ||||
200 | Args : none | ||||
201 | |||||
202 | =cut | ||||
203 | |||||
204 | =head2 seq_id | ||||
205 | |||||
206 | Title : seq_id | ||||
207 | Usage : my $seqid = $location->seq_id(); | ||||
208 | Function: Get/Set seq_id that location refers to | ||||
209 | Returns : seq_id | ||||
210 | Args : [optional] seq_id value to set | ||||
211 | |||||
212 | =cut | ||||
213 | |||||
214 | =head2 coordinate_policy | ||||
215 | |||||
216 | Title : coordinate_policy | ||||
217 | Usage : $policy = $location->coordinate_policy(); | ||||
218 | $location->coordinate_policy($mypolicy); # set may not be possible | ||||
219 | Function: Get the coordinate computing policy employed by this object. | ||||
220 | |||||
221 | See Bio::Location::CoordinatePolicyI for documentation about | ||||
222 | the policy object and its use. | ||||
223 | |||||
224 | The interface *does not* require implementing classes to accept | ||||
225 | setting of a different policy. The implementation provided here | ||||
226 | does, however, allow to do so. | ||||
227 | |||||
228 | Implementors of this interface are expected to initialize every | ||||
229 | new instance with a CoordinatePolicyI object. The implementation | ||||
230 | provided here will return a default policy object if none has | ||||
231 | been set yet. To change this default policy object call this | ||||
232 | method as a class method with an appropriate argument. Note that | ||||
233 | in this case only subsequently created Location objects will be | ||||
234 | affected. | ||||
235 | |||||
236 | Returns : A Bio::Location::CoordinatePolicyI implementing object. | ||||
237 | Args : On set, a Bio::Location::CoordinatePolicyI implementing object. | ||||
238 | |||||
239 | =cut | ||||
240 | |||||
241 | =head2 to_FTstring | ||||
242 | |||||
243 | Title : to_FTstring | ||||
244 | Usage : my $locstr = $location->to_FTstring() | ||||
245 | Function: returns the FeatureTable string of this location | ||||
246 | Returns : string | ||||
247 | Args : none | ||||
248 | |||||
249 | =cut | ||||
250 | |||||
251 | 1 | 2µs | 1; | ||
252 |