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.\" ========================================================================
.\"
.IX Title "Bio::Map::PositionWithSequence 3pm"
.TH Bio::Map::PositionWithSequence 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Map::PositionWithSequence \- A position with a sequence.
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&    use Bio::Map::PositionWithSequence;
\&    
\&    my $pos = Bio::Map::PositionWithSequence\->new(\-map => $map, 
\&                                \-element => $element,
\&                                \-start => 0,
\&                                \-seq => \*(AqATGC\*(Aq);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Have a position with a sequence, eg. define what the binding site sequence of
a certain transcription factor binding site is by modelling it as one of these
objects with the \-element assigned to a Bio::Map::TranscriptionFactor instance.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "Mailing Lists"
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
rather than to the module maintainer directly. Many experienced and 
reponsive experts will be able look at the problem and quickly 
address it. Please include a thorough description of the problem 
with code and data examples if at all possible.
.SS "Reporting Bugs"
.IX Subsection "Reporting Bugs"
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Sendu Bala"
.IX Header "AUTHOR - Sendu Bala"
Email bix@sendu.me.uk
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 9
\& Title   : new
\& Usage   : my $obj = Bio::Map::PositionWithSequence\->new();
\& Function: Builds a new Bio::Map::PositionWithSequence object 
\& Returns : Bio::Map::PositionWithSequence
\& Args    : \-map      => Bio::Map::GeneMap object
\&           \-element  => Bio::Map::Gene object
\&           \-relative => Bio::Map::GeneRelative object
\&           \-seq      => string, length of this string will set the length
\&                        of this position\*(Aqs range
\&
\&           * If this position has no range, or if a single value can describe
\&             the range *
\&           \-value => scalar             : something that describes the single
\&                                          point position or range of this
\&                                          Position, most likely an int
\&
\&           * Or if this position has a range, at least two of *
\&           \-start => int                : value of the start co\-ordinate
\&           \-end => int                  : value of the end co\-ordinate
\&           \-length => int               : length of the range
.Ve
.SS "seq"
.IX Subsection "seq"
.Vb 6
\& Title   : seq
\& Usage   : my $string = $obj\->seq();
\& Function: Get/set the sequence as a string of letters.
\& Returns : scalar
\& Args    : Optionally on set the new value (a string). An optional second
\&           argument presets the alphabet (otherwise it will be guessed).
.Ve