Bio/Map/PositionWithSequence.pm

   1 # $Id: PositionWithSequence.pm,v 1.19 2006/09/20 10:20:01 sendu Exp $
   2 #
   3 # BioPerl module for Bio::Map::PositionWithSequence
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Sendu Bala <bix@sendu.me.uk>
   8 #
   9 # Copyright Sendu Bala
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::Map::PositionWithSequence - A position with a sequence.
  18
  19 =head1 SYNOPSIS
  20
  21     use Bio::Map::PositionWithSequence;
  22
  23     my $pos = Bio::Map::PositionWithSequence->new(-map => $map,
  24                                 -element => $element,
  25                                 -start => 0,
  26                                 -seq => 'ATGC');
  27
  28
  29 =head1 DESCRIPTION
  30
  31 Have a position with a sequence, eg. define what the binding site sequence of
  32 a certain transcription factor binding site is by modelling it as one of these
  33 objects with the -element assigned to a Bio::Map::TranscriptionFactor instance.
  34
  35 =head1 FEEDBACK
  36
  37 =head2 Mailing Lists
  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
  41 the Bioperl mailing list.  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 of 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 - Sendu Bala
  66
  67 Email bix@sendu.me.uk
  68
  69 =head1 APPENDIX
  70
  71 The rest of the documentation details each of the object methods.
  72 Internal methods are usually preceded with a _
  73
  74 =cut
  75
  76 # Let the code begin...
  77
  78 package Bio::Map::PositionWithSequence;
  79 use strict;
  80
  81 use base qw(Bio::Map::Position Bio::LocatableSeq);
  82
  83 =head2 new
  84
  85  Title   : new
  86  Usage   : my $obj = Bio::Map::PositionWithSequence->new();
  87  Function: Builds a new Bio::Map::PositionWithSequence object
  88  Returns : Bio::Map::PositionWithSequence
  89  Args    : -map      => Bio::Map::GeneMap object
  90            -element  => Bio::Map::Gene object
  91            -relative => Bio::Map::GeneRelative object
  92            -seq      => string, length of this string will set the length
  93                         of this position's range
  94
  95            * If this position has no range, or if a single value can describe
  96              the range *
  97            -value => scalar             : something that describes the single
  98                                           point position or range of this
  99                                           Position, most likely an int
 100
 101            * Or if this position has a range, at least two of *
 102            -start => int                : value of the start co-ordinate
 103            -end => int                  : value of the end co-ordinate
 104            -length => int               : length of the range
 105
 106 =cut
 107
 108 sub new {
 109     my ($class, @args) = @_;
 110     my $self = $class->SUPER::new(@args);
 111
 112     my ($seq) = $self->_rearrange([qw( SEQ )], @args);
 113
 114     $self->seq($seq) if $seq;
 115
 116     return $self;
 117 }
 118
 119 =head2 seq
 120
 121  Title   : seq
 122  Usage   : my $string = $obj->seq();
 123  Function: Get/set the sequence as a string of letters.
 124  Returns : scalar
 125  Args    : Optionally on set the new value (a string). An optional second
 126            argument presets the alphabet (otherwise it will be guessed).
 127
 128 =cut
 129
 130 sub seq {
 131     my ($self, $str, $alpha) = @_;
 132
 133     # done like this because SUPER will set seq to undef if undef supplied,
 134     # but GeneMap wants to send undef, undef, 1 to decendants of this method
 135
 136     my $seq;
 137     if ($str) {
 138         $alpha ? ($seq = $self->SUPER::seq($str, $alpha)) : ($seq = $self->SUPER::seq($str));
 139     }
 140     else {
 141         $seq = $self->SUPER::seq;
 142     }
 143
 144     if ($seq) {
 145         $self->length(length($seq));
 146         return $seq;
 147     }
 148     return;
 149 }
 150
 151 1;