NAME

Bio::Tools::Run::PiseApplication::cirdna

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::cirdna

      Bioperl class for:

        CIRDNA  Draws circular maps of DNA constructs (EMBOSS)


      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/cirdna.html 
         for available values):


                cirdna (String)

                init (String)

                graphout (Excl)
                        graphout [device to be displayed on] (-graphout)

                inputfile (InFile)
                        input file containing mapping data (-inputfile)

                ruler (Switch)
                        do you want a ruler (-ruler)

                blocktype (Excl)
                        type of blocks (-blocktype)

                originangle (Float)
                        position of the molecule's origin on the circle (enter a number in the range 0 - 360) (-originangle)

                posticks (Excl)
                        ticks inside or outside the circle (enter In or Out) (-posticks)

                posblocks (Excl)
                        text inside or outside the blocks (enter In or Out) (-posblocks)

                intersymbol (Switch)
                        do you want horizontal junctions between blocks (-intersymbol)

                intercolour (Integer)
                        colour of junctions between blocks (enter a colour number) (-intercolour)

                interticks (Switch)
                        do you want horizontal junctions between ticks (-interticks)

                gapsize (Integer)
                        interval between ticks in the ruler (enter an integer) (-gapsize)

                ticklines (Switch)
                        do you want vertical lines at the ruler's ticks (-ticklines)

                textheight (Float)
                        height of text (enter a number to multiply the default height) (-textheight)

                textlength (Float)
                        length of text (enter a number to multiply the default length) (-textlength)

                tickheight (Float)
                        height of ticks (enter a number to multiply the default height) (-tickheight)

                blockheight (Float)
                        height of blocks (enter a number to multiply the default height) (-blockheight)

                rangeheight (Float)
                        height of range ends (enter a number to multiply the default height) (-rangeheight)

                gapgroup (Float)
                        space between groups (enter a number to multiply the default space) (-gapgroup)

                postext (Float)
                        space between text and ticks, blocks, and ranges (enter a number to multiply the default space) (-postext)

                auto (String)

                psouput (String)

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/cirdna.html

• Bio::Tools::Run::PiseApplication

• Bio::Tools::Run::AnalysisFactory::Pise

• Bio::Tools::Run::PiseJob

new

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