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/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/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.