NAME

Bio::Tools::Run::PiseApplication::prettyplot

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::prettyplot

      Bioperl class for:

	PRETTYPLOT	Displays aligned sequences, with colouring and boxing (EMBOSS)


      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/prettyplot.html 
         for available values):


		prettyplot (String)

		init (String)

		msf (Sequence)
			Sequences file to be read in (-msf)
			pipe: seqsfile

		residuesperline (Integer)
			Number of residues to be displayed on each line (-residuesperline)

		resbreak (Integer)
			Residues before a space (-resbreak)

		ccolours (Switch)
			Colour residues by their consensus value. (-ccolours)

		cidentity (String)
			Colour to display identical residues (RED) (-cidentity)

		csimilarity (String)
			Colour to display similar residues (GREEN) (-csimilarity)

		cother (String)
			Colour to display other residues (BLACK) (-cother)

		docolour (Switch)
			Colour residues by table oily, amide etc. (-docolour)

		title (Switch)
			Do not display the title (-title)

		shade (String)
			shading (-shade)

		pair (String)
			Values to represent identical similar related (-pair)

		identity (Integer)
			Only match those which are identical in all sequences. (-identity)

		box (Switch)
			Display prettyboxes (-box)

		boxcol (Switch)
			Colour the background in the boxes (-boxcol)

		boxcolval (String)
			Colour to be used for background. (GREY) (-boxcolval)

		name (Switch)
			Display the sequence names (-name)

		maxnamelen (Integer)
			Margin size for the sequence name. (-maxnamelen)

		number (Switch)
			Display the residue number (-number)

		listoptions (Switch)
			Display the date and options used (-listoptions)

		plurality (Float)
			Plurality check value (totweight/2) (-plurality)

		consensus (Switch)
			Display the consensus (-consensus)

		collision (Switch)
			Allow collisions in calculating consensus (-collision)

		alternative (Integer)
			Use alternative collisions routine (-alternative)

		matrixfile (Excl)
			Matrix file (-matrixfile)

		showscore (Integer)
			Print residue scores (-showscore)

		portrait (Switch)
			Set page to Portrait (-portrait)

		data (Switch)
			data (-data)

		graph (Excl)
			graph [device to be displayed on] (-graph)

		auto (String)

		psouput (String)

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 the Bioperl mailing list. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

http://bugzilla.open-bio.org/

AUTHOR

Catherine Letondal (letondal@pasteur.fr)

COPYRIGHT

Copyright (C) 2003 Institut Pasteur & Catherine Letondal. All Rights Reserved.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

DISCLAIMER

This software is provided "as is" without warranty of any kind.

SEE ALSO

• http://bioweb.pasteur.fr/seqanal/interfaces/prettyplot.html

• Bio::Tools::Run::PiseApplication

• Bio::Tools::Run::AnalysisFactory::Pise

• Bio::Tools::Run::PiseJob

new

Title   : new()
Usage   : my $prettyplot = Bio::Tools::Run::PiseApplication::prettyplot->new($location, $email, @params);
Function: Creates a Bio::Tools::Run::PiseApplication::prettyplot object.
          This method should not be used directly, but rather by 
          a Bio::Tools::Run::AnalysisFactory::Pise instance.
          my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new();
          my $prettyplot = $factory->program('prettyplot');
Example : -
Returns : An instance of Bio::Tools::Run::PiseApplication::prettyplot.