lib/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
  77 use strict;
  78
  79 use base qw(Bio::LocationI);
  80
  81 =head1 LocationI methods
  82
  83 =head2 location_type
  84
  85   Title   : loc_type
  86   Usage   : my $location_type = $location->location_type();
  87   Function: Get location type encoded as text
  88   Returns : string ('EXACT', 'WITHIN', 'IN-BETWEEN')
  89   Args    : none
  90
  91 =cut
  92
  93 sub location_type {
  94     my ($self) = @_;
  95     $self->throw_not_implemented();
  96 }
  97
  98 =head1 Bio::LocationI methods
  99
 100 Bio::LocationI methods follow
 101
 102 =head2 min_start
 103
 104   Title   : min_start
 105   Usage   : my $minstart = $location->min_start();
 106   Function: Get minimum starting location of feature startpoint
 107   Returns : integer or undef if no maximum starting point.
 108   Args    : none
 109
 110 =cut
 111
 112 =head2 max_start
 113
 114   Title   : max_start
 115   Usage   : my $maxstart = $location->max_start();
 116   Function: Get maximum starting location of feature startpoint
 117   Returns : integer or undef if no maximum starting point.
 118   Args    : none
 119
 120 =cut
 121
 122 =head2 start_pos_type
 123
 124   Title   : start_pos_type
 125   Usage   : my $start_pos_type = $location->start_pos_type();
 126   Function: Get start position type (ie <,>, ^)
 127   Returns : type of position coded as text
 128             ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
 129   Args    : none
 130
 131 =cut
 132
 133 =head2 min_end
 134
 135   Title   : min_end
 136   Usage   : my $minend = $location->min_end();
 137   Function: Get minimum ending location of feature endpoint
 138   Returns : integer or undef if no minimum ending point.
 139   Args    : none
 140
 141 =cut
 142
 143 =head2 max_end
 144
 145   Title   : max_end
 146   Usage   : my $maxend = $location->max_end();
 147   Function: Get maximum ending location of feature endpoint
 148   Returns : integer or undef if no maximum ending point.
 149   Args    : none
 150
 151 =cut
 152
 153 =head2 end_pos_type
 154
 155   Title   : end_pos_type
 156   Usage   : my $end_pos_type = $location->end_pos_type();
 157   Function: Get end position type (ie <,>, ^)
 158   Returns : type of position coded as text
 159             ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
 160   Args    : none
 161
 162 =cut
 163
 164 =head2 seq_id
 165
 166   Title   : seq_id
 167   Usage   : my $seqid = $location->seq_id();
 168   Function: Get/Set seq_id that location refers to
 169   Returns : seq_id
 170   Args    : [optional] seq_id value to set
 171
 172 =cut
 173
 174 =head2 coordinate_policy
 175
 176   Title   : coordinate_policy
 177   Usage   : $policy = $location->coordinate_policy();
 178             $location->coordinate_policy($mypolicy); # set may not be possible
 179   Function: Get the coordinate computing policy employed by this object.
 180
 181             See Bio::Location::CoordinatePolicyI for documentation about
 182             the policy object and its use.
 183
 184             The interface *does not* require implementing classes to accept
 185             setting of a different policy. The implementation provided here
 186             does, however, allow one to do so.
 187
 188             Implementors of this interface are expected to initialize every
 189             new instance with a CoordinatePolicyI object. The implementation
 190             provided here will return a default policy object if none has
 191             been set yet. To change this default policy object call this
 192             method as a class method with an appropriate argument. Note that
 193             in this case only subsequently created Location objects will be
 194             affected.
 195
 196   Returns : A Bio::Location::CoordinatePolicyI implementing object.
 197   Args    : On set, a Bio::Location::CoordinatePolicyI implementing object.
 198
 199 =cut
 200
 201 =head2 to_FTstring
 202
 203   Title   : to_FTstring
 204   Usage   : my $locstr = $location->to_FTstring()
 205   Function: returns the FeatureTable string of this location
 206   Returns : string
 207   Args    : none
 208
 209 =cut
 210
 211 1;