Bio::Tools::Run::PiseApplication::boxshade.3pm

Langue: en

Autres versions - même langue

Version: 2008-11-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

Sommaire

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 (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.