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.\" ========================================================================
.\"
.IX Title "Bio::AlignIO::selex 3pm"
.TH Bio::AlignIO::selex 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::AlignIO::selex \- selex sequence input/output stream
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  # Do not use this module directly.  Use it via the L<Bio::AlignIO> class.
\&
\&  use Bio::AlignIO;
\&  use strict;
\&
\&  my $in = Bio::AlignIO\->new(\-format => \*(Aqselex\*(Aq,
\&                             \-file   => \*(Aqt/data/testaln.selex\*(Aq);
\&  while( my $aln = $in\->next_aln ) {
\&
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This object can transform Bio::Align::AlignI objects to and from selex flat
file databases.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.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
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 "AUTHORS \- Peter Schattner"
.IX Header "AUTHORS - Peter Schattner"
Email: schattner@alum.mit.edu
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Jason Stajich, jason\-at\-bioperl.org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "next_aln"
.IX Subsection "next_aln"
.Vb 8
\& Title   : next_aln
\& Usage   : $aln = $stream\->next_aln()
\& Function: returns the next alignment in the stream. Tries to read *all* selex
\&          It reads all non whitespace characters in the alignment
\&          area. For selexs with weird gaps (eg ~~~) map them by using
\&          $al\->map_chars(\*(Aq~\*(Aq,\*(Aq\-\*(Aq)
\& Returns : L<Bio::Align::AlignI> object
\& Args    : NONE
.Ve
.SS "write_aln"
.IX Subsection "write_aln"
.Vb 5
\& Title   : write_aln
\& Usage   : $stream\->write_aln(@aln)
\& Function: writes the $aln object into the stream in selex format
\& Returns : 1 for success and 0 for error
\& Args    : L<Bio::Align::AlignI> object
.Ve