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 # Cared for by Sendu Bala <bix@sendu.me.uk>
   6 #
   7 # Copyright Sendu Bala
   8 #
   9 # You may distribute this module under the same terms as perl itself
  10
  11 # POD documentation - main docs before the code
  12
  13 =head1 NAME
  14
  15 Bio::Map::PositionWithSequence - A position with a sequence.
  16
  17 =head1 SYNOPSIS
  18
  19     use Bio::Map::PositionWithSequence;
  20
  21     my $pos = Bio::Map::PositionWithSequence->new(-map => $map,
  22                                 -element => $element,
  23                                 -start => 0,
  24                                 -seq => 'ATGC');
  25
  26
  27 =head1 DESCRIPTION
  28
  29 Have a position with a sequence, eg. define what the binding site sequence of
  30 a certain transcription factor binding site is by modelling it as one of these
  31 objects with the -element assigned to a Bio::Map::TranscriptionFactor instance.
  32
  33 =head1 FEEDBACK
  34
  35 =head2 Mailing Lists
  36
  37 User feedback is an integral part of the evolution of this and other
  38 Bioperl modules. Send your comments and suggestions preferably to
  39 the Bioperl mailing list.  Your participation is much appreciated.
  40
  41   bioperl-l@bioperl.org                  - General discussion
  42   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  43
  44 =head2 Reporting Bugs
  45
  46 Report bugs to the Bioperl bug tracking system to help us keep track
  47 of the bugs and their resolution. Bug reports can be submitted via the
  48 web:
  49
  50   http://bugzilla.open-bio.org/
  51
  52 =head1 AUTHOR - Sendu Bala
  53
  54 Email bix@sendu.me.uk
  55
  56 =head1 APPENDIX
  57
  58 The rest of the documentation details each of the object methods.
  59 Internal methods are usually preceded with a _
  60
  61 =cut
  62
  63 # Let the code begin...
  64
  65 package Bio::Map::PositionWithSequence;
  66 use strict;
  67
  68 use base qw(Bio::Map::Position Bio::LocatableSeq);
  69
  70 =head2 new
  71
  72  Title   : new
  73  Usage   : my $obj = Bio::Map::PositionWithSequence->new();
  74  Function: Builds a new Bio::Map::PositionWithSequence object
  75  Returns : Bio::Map::PositionWithSequence
  76  Args    : -map      => Bio::Map::GeneMap object
  77            -element  => Bio::Map::Gene object
  78            -relative => Bio::Map::GeneRelative object
  79            -seq      => string, length of this string will set the length
  80                         of this position's range
  81
  82            * If this position has no range, or if a single value can describe
  83              the range *
  84            -value => scalar             : something that describes the single
  85                                           point position or range of this
  86                                           Position, most likely an int
  87
  88            * Or if this position has a range, at least two of *
  89            -start => int                : value of the start co-ordinate
  90            -end => int                  : value of the end co-ordinate
  91            -length => int               : length of the range
  92
  93 =cut
  94
  95 sub new {
  96     my ($class, @args) = @_;
  97     my $self = $class->SUPER::new(@args);
  98
  99     my ($seq) = $self->_rearrange([qw( SEQ )], @args);
 100
 101     $self->seq($seq) if $seq;
 102
 103     return $self;
 104 }
 105
 106 =head2 seq
 107
 108  Title   : seq
 109  Usage   : my $string = $obj->seq();
 110  Function: Get/set the sequence as a string of letters.
 111  Returns : scalar
 112  Args    : Optionally on set the new value (a string). An optional second
 113            argument presets the alphabet (otherwise it will be guessed).
 114
 115 =cut
 116
 117 sub seq {
 118     my ($self, $str, $alpha) = @_;
 119
 120     # done like this because SUPER will set seq to undef if undef supplied,
 121     # but GeneMap wants to send undef, undef, 1 to decendants of this method
 122
 123     my $seq;
 124     if ($str) {
 125         $alpha ? ($seq = $self->SUPER::seq($str, $alpha)) : ($seq = $self->SUPER::seq($str));
 126     }
 127     else {
 128         $seq = $self->SUPER::seq;
 129     }
 130
 131     if ($seq) {
 132         $self->length(length($seq));
 133         return $seq;
 134     }
 135     return;
 136 }
 137
 138 1;