Bio/Coordinate/MapperI.pm

   1 #
   2 # bioperl module for Bio::Coordinate::MapperI
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>
   7 #
   8 # Copyright Heikki Lehvaslaiho
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::Coordinate::MapperI - Interface describing coordinate mappers
  17
  18 =head1 SYNOPSIS
  19
  20   # not to be used directly
  21
  22 =head1 DESCRIPTION
  23
  24 MapperI defines methods for classes capable for mapping locations
  25 between coordinate systems.
  26
  27 =head1 FEEDBACK
  28
  29 =head2 Mailing Lists
  30
  31 User feedback is an integral part of the evolution of this and other
  32 Bioperl modules. Send your comments and suggestions preferably to the
  33 Bioperl mailing lists  Your participation is much appreciated.
  34
  35   bioperl-l@bioperl.org                  - General discussion
  36   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  37
  38 =head2 Support
  39
  40 Please direct usage questions or support issues to the mailing list:
  41
  42 I<bioperl-l@bioperl.org>
  43
  44 rather than to the module maintainer directly. Many experienced and
  45 reponsive experts will be able look at the problem and quickly
  46 address it. Please include a thorough description of the problem
  47 with code and data examples if at all possible.
  48
  49 =head2 Reporting Bugs
  50
  51 report bugs to the Bioperl bug tracking system to help us keep track
  52 the bugs and their resolution.  Bug reports can be submitted via the
  53 web:
  54
  55   https://redmine.open-bio.org/projects/bioperl/
  56
  57 =head1 AUTHOR - Heikki Lehvaslaiho
  58
  59 Email:  heikki-at-bioperl-dot-org
  60
  61 =head1 APPENDIX
  62
  63 The rest of the documentation details each of the object
  64 methods. Internal methods are usually preceded with a _
  65
  66 =cut
  67
  68
  69 # Let the code begin...
  70
  71 package Bio::Coordinate::MapperI;
  72 use strict;
  73
  74 # Object preamble - inherits from Bio::Root::RootI
  75
  76 use base qw(Bio::Root::RootI);
  77
  78
  79
  80 =head2 in
  81
  82  Title   : in
  83  Usage   : $obj->in('peptide');
  84  Function: Set and read the input coordinate system.
  85  Example :
  86  Returns : value of input system
  87  Args    : new value (optional), Bio::LocationI
  88
  89 =cut
  90
  91 sub in {
  92    my ($self,$value) = @_;
  93
  94    $self->throw_not_implemented();
  95
  96 }
  97
  98
  99 =head2 out
 100
 101  Title   : out
 102  Usage   : $obj->out('peptide');
 103  Function: Set and read the output coordinate system.
 104  Example :
 105  Returns : value of output system
 106  Args    : new value (optional), Bio::LocationI
 107
 108 =cut
 109
 110 sub out {
 111    my ($self,$value) = @_;
 112
 113    $self->throw_not_implemented();
 114 }
 115
 116 =head2 swap
 117
 118  Title   : swap
 119  Usage   : $obj->swap;
 120  Function: Swap the direction of mapping: input <-> output)
 121  Example :
 122  Returns : 1
 123  Args    :
 124
 125 =cut
 126
 127 sub swap {
 128    my ($self) = @_;
 129
 130    $self->throw_not_implemented();
 131
 132 }
 133
 134 =head2 test
 135
 136  Title   : test
 137  Usage   : $obj->test;
 138  Function: test that both components are of same length
 139  Example :
 140  Returns : ( 1 | undef )
 141  Args    :
 142
 143 =cut
 144
 145 sub test {
 146    my ($self) = @_;
 147
 148    $self->throw_not_implemented();
 149 }
 150
 151
 152 =head2 map
 153
 154  Title   : map
 155  Usage   : $newpos = $obj->map($loc);
 156  Function: Map the location from the input coordinate system
 157            to a new value in the output coordinate system.
 158  Example :
 159  Returns : new value in the output coordiante system
 160  Args    : Bio::LocationI
 161
 162 =cut
 163
 164 sub map {
 165    my ($self,$value) = @_;
 166
 167    $self->throw_not_implemented();
 168
 169 }
 170
 171 =head2 return_match
 172
 173  Title   : return_match
 174  Usage   : $obj->return_match(1);
 175  Function: A flag to turn on the simplified mode of
 176            returning only one joined Match object or undef
 177  Example :
 178  Returns : boolean
 179  Args    : boolean (optional)
 180
 181 =cut
 182
 183 sub return_match {
 184    my ($self,$value) = @_;
 185    if( defined $value) {
 186        $value ? ( $self->{'_return_match'} = 1 ) :
 187                 ( $self->{'_return_match'} = 0 );
 188    }
 189    return $self->{'_return_match'} || 0 ;
 190 }
 191
 192 1;
 193