Bio::Tools::Run::PiseApplication::boxshade # 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)

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 the web: http://bugzilla.bioperl.org/ 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. This software is provided "as is" without warranty of any kind. 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.