Ewan Birney


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.


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AUTHORS - Peter Schattner

Email: schattner@alum.mit.edu


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


 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
           -percentages => (clustalw only) display a percentage of identity
                           in each line of the alignment.


 Title   : next_aln
 Usage   : $aln = $stream->next_aln()
 Function: returns the next alignment in the stream
 Returns : L<Bio::Align::AlignI> object
 Args    : NONE


 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


 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)