NAME

       Bio::AlignIO::arp - ARP MSA Sequence input/output stream

SYNOPSIS

       Do not use this module directly.  Use it via the Bio::AlignIO class.

DESCRIPTION

       This object can create Bio::SimpleAlign objects from ARP flat files.  These are typically
       configuration-like data files for the program Arlequin.  For more information, see:

         http://lgb.unige.ch/arlequin/

       For the moment, this retains the allele sequence data in the DATA section and inserts them
       into SimpleAlign objects. ARP files that contain other data (RFLP, etc.) are not expected
       to parse properly.  Also, if the DNA data is actually SNP data, then the LocatableSeq
       object instantiation will throw an error.

       This is now set up as a generic parser (i.e. it parses everything) and collects as much
       data as possible into the SimpleAlign object.  The following in a general mapping of where
       data can be found:

           Tag        SimpleAlign
                      Method
           ----------------------------------------------------------------------
           Title      description
           SampleName id
           ----------------------------------------------------------------------

           Tag        Bio::Annotation   TagName                    Bio::Annotation
                      Class                                        Parameters
           ----------------------------------------------------------------------
            NE        SimpleValue       pfam_family_accession      value
            NL        SimpleValue       sequence_start_stop        value
            SS        SimpleValue       sec_structure_source       value
            BM        SimpleValue       build_model                value
            RN        Reference         reference                  *
           ----------------------------------------------------------------------
         * RN is generated based on the number of Bio::Annotation::Reference objects

       In addition, the number of samples found in the alignment is retained in a
       Bio::Annotation::TagTree object in the annotation collection and is accessible via:

         ($samples) = $aln->annotation->get_Annotations('Samples');
         say $samples->display_text;
         # or use other relevant TagTree methods to retrieve data

FEEDBACK

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       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.

   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:

         https://redmine.open-bio.org/projects/bioperl/

AUTHORS

       Chris Fields (cjfields)

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

   next_aln
        Title   : next_aln
        Usage   : $aln = $stream->next_aln
        Function: returns the next alignment in the stream.
        Returns : Bio::Align::AlignI object - returns 0 on end of file
                   or on error
        Args    : -width => optional argument to specify the width sequence
                  will be written (60 chars by default)

       See Bio::Align::AlignI

   write_aln
        Title   : write_aln
        Usage   : $stream->write_aln(@aln)
        Function: writes the $aln object into the stream in xmfa format
        Returns : 1 for success and 0 for error
        Args    : L<Bio::Align::AlignI> object

       See Bio::Align::AlignI