Bio::Tools::Run::PiseApplication njdist
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Bio::Tools::Run::PiseApplication::njdist
Package variables
No package variables defined.
Included modules
Bio::Tools::Run::PiseApplication
Inherit
Bio::Tools::Run::PiseApplication
Synopsis
  #
Description
Bio::Tools::Run::PiseApplication::njdist
      Bioperl class for:
Njdist NJDist Neighbor Joining Phylogeny from Distance Matrix (J. Adachi & M. Hasegawa) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/njdist.html
for available values):
njdist (String) distances (InFile) Distance Matrix File pipe: phylip_dist UPGMA (Switch) UPGMA (-u) branch (Switch) Branch Length (-w) leastsq (Switch) Least squares (-l) sequential (Switch) sequential input form (PHYLIP) (-S) outgroup (Integer) Branch number of Out group (-o) treefile (Switch) Output Tree (.tre) file? (-T) Topo_file (Switch) Output Topology (.tpl) file? (-t)
Methods
newDescriptionCode
Methods description
newcode    nextTop
 Title   : new()
Usage : my $njdist = Bio::Tools::Run::PiseApplication::njdist->new($location, $email, @params);
Function: Creates a Bio::Tools::Run::PiseApplication::njdist 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 $njdist = $factory->program('njdist');
Example : -
Returns : An instance of Bio::Tools::Run::PiseApplication::njdist.
Methods code
newdescriptionprevnextTop
sub new {
    my ($class, $location, $email, @params) = @_;
    my $self = $class->SUPER::new($location, $email);

# -- begin of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/njdist.pm
$self->{COMMAND} = "njdist"; $self->{VERSION} = "5.a"; $self->{TITLE} = "Njdist"; $self->{DESCRIPTION} = "NJDist Neighbor Joining Phylogeny from Distance Matrix "; $self->{OPT_EMAIL} = 0; $self->{AUTHORS} = "J. Adachi & M. Hasegawa"; $self->{_INTERFACE_STANDOUT} = undef; $self->{_STANDOUT_FILE} = undef; $self->{TOP_PARAMETERS} = [ "njdist", "distances", "distopt", ]; $self->{PARAMETERS_ORDER} = [ "njdist", "distances", # Distance Matrix File
"distopt", # NJDist Parameters
"UPGMA", # UPGMA (-u)
"branch", # Branch Length (-w)
"leastsq", # Least squares (-l)
"sequential", # sequential input form (PHYLIP) (-S)
"outgroup", # Branch number of Out group (-o)
"treefile", # Output Tree (.tre) file? (-T)
"Topo_file", # Output Topology (.tpl) file? (-t)
"tre_file", "tpl_file", "eps_file", ]; $self->{TYPE} = { "njdist" => 'String', "distances" => 'InFile', "distopt" => 'Paragraph', "UPGMA" => 'Switch', "branch" => 'Switch', "leastsq" => 'Switch', "sequential" => 'Switch', "outgroup" => 'Integer', "treefile" => 'Switch', "Topo_file" => 'Switch', "tre_file" => 'Results', "tpl_file" => 'Results', "eps_file" => 'Results', }; $self->{FORMAT} = { "distances" => { "perl" => '" $value"', }, "distopt" => { }, "UPGMA" => { "perl" => '($value)? " -u":""', }, "branch" => { "perl" => '($value)? " -w":""', }, "leastsq" => { "perl" => '($value)? " -l":""', }, "sequential" => { "perl" => '($value)? " -S":""', }, "outgroup" => { "perl" => '(defined $value)? " -o $value":""', }, "treefile" => { "perl" => '($value)? " -T $distances":""', }, "Topo_file" => { "perl" => '($value)? " -t $distances":""', }, "tre_file" => { }, "tpl_file" => { }, "eps_file" => { }, "njdist" => { "perl" => '"njdist"', } }; $self->{FILENAMES} = { "tre_file" => '*.tre', "tpl_file" => '*.tpl', "eps_file" => '*.eps', }; $self->{SEQFMT} = { }; $self->{GROUP} = { "distances" => 3, "UPGMA" => 1, "branch" => 1, "leastsq" => 1, "sequential" => 1, "outgroup" => 1, "treefile" => 1, "Topo_file" => 1, "njdist" => 0 }; $self->{BY_GROUP_PARAMETERS} = [ "tre_file", "distopt", "tpl_file", "eps_file", "njdist", "sequential", "outgroup", "treefile", "Topo_file", "UPGMA", "branch", "leastsq", "distances", ]; $self->{SIZE} = { }; $self->{ISHIDDEN} = { "distances" => 0, "distopt" => 0, "UPGMA" => 0, "branch" => 0, "leastsq" => 0, "sequential" => 0, "outgroup" => 0, "treefile" => 0, "Topo_file" => 0, "tre_file" => 0, "tpl_file" => 0, "eps_file" => 0, "njdist" => 1 }; $self->{ISCOMMAND} = { "distances" => 0, "distopt" => 0, "UPGMA" => 0, "branch" => 0, "leastsq" => 0, "sequential" => 0, "outgroup" => 0, "treefile" => 0, "Topo_file" => 0, "tre_file" => 0, "tpl_file" => 0, "eps_file" => 0, }; $self->{ISMANDATORY} = { "distances" => 1, "distopt" => 0, "UPGMA" => 0, "branch" => 0, "leastsq" => 0, "sequential" => 0, "outgroup" => 0, "treefile" => 0, "Topo_file" => 0, "tre_file" => 0, "tpl_file" => 0, "eps_file" => 0, }; $self->{PROMPT} = { "distances" => "Distance Matrix File", "distopt" => "NJDist Parameters", "UPGMA" => "UPGMA (-u)", "branch" => "Branch Length (-w)", "leastsq" => "Least squares (-l)", "sequential" => "sequential input form (PHYLIP) (-S)", "outgroup" => "Branch number of Out group (-o)", "treefile" => "Output Tree (.tre) file? (-T)", "Topo_file" => "Output Topology (.tpl) file? (-t)", "tre_file" => "", "tpl_file" => "", "eps_file" => "", }; $self->{ISSTANDOUT} = { "distances" => 0, "distopt" => 0, "UPGMA" => 0, "branch" => 0, "leastsq" => 0, "sequential" => 0, "outgroup" => 0, "treefile" => 0, "Topo_file" => 0, "tre_file" => 0, "tpl_file" => 0, "eps_file" => 0, }; $self->{VLIST} = { "distopt" => ['UPGMA','branch','leastsq','sequential','outgroup','treefile','Topo_file','tre_file','tpl_file','eps_file',], }; $self->{FLIST} = { }; $self->{SEPARATOR} = { }; $self->{VDEF} = { }; $self->{PRECOND} = { "distances" => { "perl" => '1' }, "distopt" => { "perl" => '1' }, "UPGMA" => { "perl" => '1' }, "branch" => { "perl" => '1' }, "leastsq" => { "perl" => '1' }, "sequential" => { "perl" => '1' }, "outgroup" => { "perl" => '1' }, "treefile" => { "perl" => '1' }, "Topo_file" => { "perl" => '1' }, "tre_file" => { "perl" => '$treefile', }, "tpl_file" => { "perl" => '$Topo_file', }, "eps_file" => { "perl" => '$Topo_file || $treefile', }, }; $self->{CTRL} = { }; $self->{PIPEOUT} = { }; $self->{WITHPIPEOUT} = { }; $self->{PIPEIN} = { "distances" => { "phylip_dist" => '1', }, }; $self->{WITHPIPEIN} = { }; $self->{ISCLEAN} = { "distances" => 0, "distopt" => 0, "UPGMA" => 0, "branch" => 0, "leastsq" => 0, "sequential" => 0, "outgroup" => 0, "treefile" => 0, "Topo_file" => 0, "tre_file" => 0, "tpl_file" => 0, "eps_file" => 0, }; $self->{ISSIMPLE} = { "distances" => 1, "distopt" => 0, "UPGMA" => 0, "branch" => 0, "leastsq" => 0, "sequential" => 0, "outgroup" => 0, "treefile" => 0, "Topo_file" => 0, "tre_file" => 0, "tpl_file" => 0, "eps_file" => 0, }; $self->{PARAMFILE} = { }; $self->{COMMENT} = { }; $self->{SCALEMIN} = { }; $self->{SCALEMAX} = { }; $self->{SCALEINC} = { }; $self->{INFO} = { }; # -- end of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/njdist.pm
$self->_init_params(@params); return $self; } 1; # Needed to keep compiler happy
}
General documentation
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AUTHORTop
Catherine Letondal (letondal@pasteur.fr)
COPYRIGHTTop
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.
DISCLAIMERTop
This software is provided "as is" without warranty of any kind.
SEE ALSOTop
    *(1)
http://bioweb.pasteur.fr/seqanal/interfaces/njdist.html
    *(2)
    Bio::Tools::Run::PiseApplication
    *(3)
    Bio::Tools::Run::AnalysisFactory::Pise
    *(4)
    Bio::Tools::Run::PiseJob