Bio::Tools::Run::PiseApplication::prettyplot # Bio::Tools::Run::PiseApplication::prettyplot Bioperl class for: PRETTYPLOT Displays aligned sequences, with colouring and boxing (EMBOSS) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/prettyplot.html for available values): prettyplot (String) init (String) msf (Sequence) Sequences file to be read in (-msf) pipe: seqsfile residuesperline (Integer) Number of residues to be displayed on each line (-residuesperline) resbreak (Integer) Residues before a space (-resbreak) ccolours (Switch) Colour residues by their consensus value. (-ccolours) cidentity (String) Colour to display identical residues (RED) (-cidentity) csimilarity (String) Colour to display similar residues (GREEN) (-csimilarity) cother (String) Colour to display other residues (BLACK) (-cother) docolour (Switch) Colour residues by table oily, amide etc. (-docolour) title (Switch) Do not display the title (-title) shade (String) shading (-shade) pair (String) Values to represent identical similar related (-pair) identity (Integer) Only match those which are identical in all sequences. (-identity) box (Switch) Display prettyboxes (-box) boxcol (Switch) Colour the background in the boxes (-boxcol) boxcolval (String) Colour to be used for background. (GREY) (-boxcolval) name (Switch) Display the sequence names (-name) maxnamelen (Integer) Margin size for the sequence name. (-maxnamelen) number (Switch) Display the residue number (-number) listoptions (Switch) Display the date and options used (-listoptions) plurality (Float) Plurality check value (totweight/2) (-plurality) consensus (Switch) Display the consensus (-consensus) collision (Switch) Allow collisions in calculating consensus (-collision) alternative (Integer) Use alternative collisions routine (-alternative) matrixfile (Excl) Matrix file (-matrixfile) showscore (Integer) Print residue scores (-showscore) portrait (Switch) Set page to Portrait (-portrait) data (Switch) data (-data) graph (Excl) graph [device to be displayed on] (-graph) auto (String) psouput (String)

Mailing Lists
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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.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/prettyplot.html Bio::Tools::Run::PiseApplication Bio::Tools::Run::AnalysisFactory::Pise Bio::Tools::Run::PiseJob

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