Provided by: libbio-perl-perl_1.7.6-3_all
Bio::AlignIO::proda - proda sequence input/output stream This provides the basic capabilities to parse the output alignments from the ProDA multiple sequence alignment program (http://proda.stanford.edu)
Do not use this module directly. Use it via the Bio::AlignIO class.
This object can transform Bio::Align::AlignI objects to and from proda files.
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AUTHORS - Albert Vilella
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new Usage : $alignio = Bio::AlignIO->new(-format => 'proda', -file => 'filename'); Function: returns a new Bio::AlignIO object to handle proda files Returns : Bio::AlignIO::proda object Args : -verbose => verbosity setting (-1, 0, 1, 2) -file => name of file to read in or to write, with ">" -fh => alternative to -file param - provide a filehandle to read from or write to -format => alignment format to process or produce -percentages => display a percentage of identity in each line of the alignment (proda only) -linelength=> alignment output line length (default 60) next_aln Title : next_aln Usage : $aln = $stream->next_aln() Function: returns the next alignment in the stream Returns : Bio::Align::AlignI object Args : NONE See Bio::Align::AlignI for details write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the proda-format object (.aln) into the stream Returns : 1 for success and 0 for error Args : Bio::Align::AlignI object percentages Title : percentages Usage : $obj->percentages($newval) Function: Set the percentages flag - whether or not to show percentages in each output line Returns : value of percentages Args : newvalue (optional) line_length Title : line_length Usage : $obj->line_length($newval) Function: Set the alignment output line length Returns : value of line_length Args : newvalue (optional) no_header Title : no_header Usage : $obj->no_header($newval) Function: Set if the alignment input has a CLUSTAL header or not Returns : value of no_header Args : newvalue (optional)