NAME

Bio::Tools::Run::PiseApplication::boxshade

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::boxshade

      Bioperl class for:

	BOXSHADE	printouts from multiple-aligned protein or DNA sequences (Hofmann, Baron)


      Parameters: 

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


		boxshade (String)

		alignment (Sequence)
			Alignment File
			pipe: readseq_ok_alig

		input_format (String)

		output_format (Excl)
			Output format

		print_name (Switch)
			Should sequence name be printed

		ruler (Switch)
			Display ruler line

		space_between_name_sequence (Integer)
			How many spaces between name and sequence

		ignored_gaps (Integer)
			Number of gaps to be ignored when shading (-1: none)

		sequence_characters (Integer)
			How many sequence characters per line

		lines (Integer)
			How many lines between two sequence blocks

		character_size (Integer)
			Character size in Points (except for HTML and ASCII output formats)

		save_shading (Excl)
			Save Shading/Text

		rotate (Switch)
			Rotate plot

		label_similar (Switch)
			Special label for similar residues

		label_identical (Switch)
			Special label for identical residues in all sequences

		consensus (Switch)
			Display consensus line

		threshold (Float)
			Identity threshold

		different_background (Excl)
			Background for different residues

		different_foreground (Excl)
			Foreground for different residues (lowercase choices mean lowercase letters in the sequence)

		identical_background (Excl)
			Background for identical residues

		identical_foreground (Excl)
			Foreground for identical residues (lowercase choices mean lowercase letters in the sequence)

		similar_background (Excl)
			Background for similar residues

		similar_foreground (Excl)
			Foreground for similar residues (lowercase choices mean lowercase letters in the sequence)

		conserved_background (Excl)
			Background for conserved residues (if special label for identical residues)

		conserved_foreground (Excl)
			Foreground for conserved residues (lowercase choices mean lowercase letters in the sequence)

		single (Switch)
			Similarity to a single sequence

		seq_no (Integer)
			Which sequence (give its number)

		hide (Switch)
			Hide this sequence

		show_normal (Switch)
			Show this sequence in all-normal rendition

		matrix (Switch)
			Create identity / similarity matrix

		print_position (Excl)

		outfile (OutFile)

		psfile (OutFile)

		htmlfile (OutFile)

		pictfile (OutFile)

		matrixfile (OutFile)

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/MailList.shtml  - 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 email or the web:

bioperl-bugs@bioperl.org
http://bioperl.org/bioperl-bugs/

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/boxshade.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

Title   : new()
Usage   : my $boxshade = Bio::Tools::Run::PiseApplication::boxshade->new($location, $email, @params);
Function: Creates a Bio::Tools::Run::PiseApplication::boxshade 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 $boxshade = $factory->program('boxshade');
Example : -
Returns : An instance of Bio::Tools::Run::PiseApplication::boxshade.