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Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" Bio::AlignIO::arp \- ARP MSA Sequence input/output stream .SH "SYNOPSIS" .IX Header "SYNOPSIS" Do not use this module directly. Use it via the Bio::AlignIO class. .SH "DESCRIPTION" .IX Header "DESCRIPTION" This object can create Bio::SimpleAlign objects from \&\s-1ARP\s0 flat files. These are typically configuration-like data files for the program Arlequin. For more information, see: .PP .Vb 1 \& http://lgb.unige.ch/arlequin/ .Ve .PP For the moment, this retains the allele sequence data in the \s-1DATA\s0 section and inserts them into SimpleAlign objects. \s-1ARP\s0 files that contain other data (\s-1RFLP,\s0 etc.) are not expected to parse properly. Also, if the \s-1DNA\s0 data is actually \s-1SNP\s0 data, then the LocatableSeq object instantiation will throw an error. .PP 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: .PP .Vb 6 \& 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 .Ve .PP 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: .PP .Vb 3 \& ($samples) = $aln\->annotation\->get_Annotations(\*(AqSamples\*(Aq); \& say $samples\->display_text; \& # or use other relevant TagTree methods to retrieve data .Ve .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" .IX Header "AUTHORS" Chris Fields (cjfields) .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 7 \& 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) .Ve .PP See Bio::Align::AlignI .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 xmfa format \& Returns : 1 for success and 0 for error \& Args : L object .Ve .PP See Bio::Align::AlignI