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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The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
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)
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
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
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)
Title : line_length
Usage : $obj->line_length($newval)
Function: Set the alignment output line length
Returns : value of line_length
Args : newvalue (optional)
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)