Bio/Location/FuzzyLocationI.pm

   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
  14 Bio::Location::FuzzyLocationI - Abstract interface of a Location on a Sequence
  15 which 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
  25 This interface encapsulates the necessary methods for representing a
  26 Fuzzy Location, one that does not have clear start and/or end points.
  27 This will initially serve to handle features from Genbank/EMBL feature
  28 tables that are written as 1^100 meaning between bases 1 and 100 or
  29 E<lt>100..300 meaning it starts somewhere before 100.  Advanced
  30 implementations of this interface may be able to handle the necessary
  31 logic of overlaps/intersection/contains/union.  It was constructed to
  32 handle fuzzy locations that can be represented in Genbank/EMBL.
  33
  34 =head1 FEEDBACK
  35
  36 User feedback is an integral part of the evolution of this and other
  37 Bioperl modules. Send your comments and suggestions preferably to one
  38 of 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
  45 Please direct usage questions or support issues to the mailing list:
  46
  47 I<bioperl-l@bioperl.org>
  48
  49 rather than to the module maintainer directly. Many experienced and
  50 reponsive experts will be able look at the problem and quickly
  51 address it. Please include a thorough description of the problem
  52 with code and data examples if at all possible.
  53
  54 =head2 Reporting Bugs
  55
  56 Report bugs to the Bioperl bug tracking system to help us keep track
  57 the 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
  63 Email jason-at-bioperl-dot-org
  64
  65 =head1 APPENDIX
  66
  67 The rest of the documentation details each of the object
  68 methods. Internal methods are usually preceded with a _
  69
  70 =cut
  71
  72 # Let the code begin...
  73
  74
  75 package Bio::Location::FuzzyLocationI;
  76 use strict;
  77
  78 use base qw(Bio::LocationI);
  79
  80 =head1 LocationI methods
  81
  82 =head2 location_type
  83
  84   Title   : loc_type
  85   Usage   : my $location_type = $location->location_type();
  86   Function: Get location type encoded as text
  87   Returns : string ('EXACT', 'WITHIN', 'IN-BETWEEN')
  88   Args    : none
  89
  90 =cut
  91
  92 sub location_type {
  93     my ($self) = @_;
  94     $self->throw_not_implemented();
  95 }
  96
  97 =head1 Bio::LocationI methods
  98
  99 Bio::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
 210 1;