Bio::AlignIO::clustalw - clustalw sequence input/output stream Do not use this module directly. Use it via the Bio::AlignIO class. This object can transform Bio::Align::AlignI objects to and from clustalw flat file databases.

Mailing Lists
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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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email: schattner@alum.mit.edu The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : $alignio = new Bio::AlignIO(-format => 'clustalw', -file => 'filename'); Function: returns a new Bio::AlignIO object to handle clustalw files Returns : Bio::AlignIO::clustalw object Args : -verbose => verbosity setting (-1,0,1,2) -file => name of file to read in or with ">" - writeout -fh => alternative to -file param - provide a filehandle to read from/write to -format => type of Alignment Format to process or produce -percentages => (clustalw only) display a percentage of identity in each line of the alignment. -linelength=> Set the 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 clustalw-format object (.aln) into the stream Returns : 1 for success and 0 for error Args : L<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)