| Filename | /Users/ap13/perl5/lib/perl5/Bio/Location/SplitLocationI.pm |
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| 1 | 1 | 1 | 14µs | 38µs | Bio::Location::SplitLocationI::BEGIN@80 |
| 1 | 1 | 1 | 10µs | 58µs | Bio::Location::SplitLocationI::BEGIN@82 |
| 1 | 1 | 1 | 8µs | 71µs | Bio::Location::SplitLocationI::BEGIN@84 |
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| 0 | 0 | 0 | 0s | 0s | Bio::Location::SplitLocationI::splittype |
| 0 | 0 | 0 | 0s | 0s | Bio::Location::SplitLocationI::sub_Location |
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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 |