/ 
bioperl-1.2.2
/ Bio::AlignIO::clustalw

NAME

Bio::AlignIO::clustalw - clustalw sequence input/output stream

SYNOPSIS

Do not use this module directly. Use it via the Bio::AlignIO class.

DESCRIPTION

This object can transform Bio::Align::AlignI objects to and from clustalw flat file databases.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

bioperl-l@bioperl.org               - General discussion
http://bio.perl.org/MailList.html   - About the mailing lists

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/

AUTHORS - Peter Schattner

Email: schattner@alum.mit.edu

APPENDIX

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)