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Bio::Tools::Run::PiseApplication::boxshade.3pm
Langue: en
Version: 2008-11-10 (debian - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Tools::Run::PiseApplication::boxshadeSYNOPSIS
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DESCRIPTION
Bio::Tools::Run::PiseApplication::boxshadeBioperl 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
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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
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- http://bioweb.pasteur.fr/seqanal/interfaces/boxshade.html
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- Bio::Tools::Run::PiseApplication
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- Bio::Tools::Run::AnalysisFactory::Pise
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- 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.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre